Aquatic Environment and Biodiversity Annual Review 2012

Aquatic Environment and Biodiversity 

Annual Review 2012 

A summary of environmental interactions between 

fisheries and the aquatic environment

AEBAR 2012: Preface 

MINISTRY FOR PRIMARY 

INDUSTRIES 

AQUATIC ENVIRONMENT AND 

BIODIVERSITY ANNUAL REVIEW 

(2012) 

Fisheries Management Science Team

AEBAR 2012 

Acknowledgements 

In addition to the thanks due to members of AEWG and BRAG working groups, special 

acknowledgement is due to Owen Anderson (NIWA) for his contribution to the new chapter on Nonprotected 

Bycatch; Igor Debski (DOC) on the new seabirds chapter, and Ian Tuck (NIWA) on the 

benthic chapter. Notwithstanding these contributions, any errors or omissions are the Ministry’s. 

Image on cover 

Chatham-Challenger Ocean Survey 20/20 

Disclaimer 

This document is published by the Ministry Primary Industries which was formed from the merger of 

the Ministry of Fisheries, the Ministry of Agriculture and Forestry and the New Zealand Food Safety 

Authority in 2010 and 2011. All references to the Ministry of Fisheries in this document should, 

therefore, be taken to refer also to the legal entity, the Ministry for Primary Industries. The 

information in this publication is not government policy. While every effort has been made to ensure 

the information is accurate, the Ministry for Primary Industries does not accept any responsibility or 

liability for error of fact, omission, interpretation or opinion that may be present, nor for the 

consequences of any decisions based on this information. Any view or opinion expressed does not 

necessarily represent the view of the Ministry for Primary Industries. 

Publisher 

Fisheries Management Science Team 

Ministry for Primary Industries 

Pastoral House, 25 The Terrace 

PO Box 2526, Wellington 6140 

New Zealand 

www.mpi.govt.nz 

Telephone: 0800 00 83 33 

Facsimile: +64 4 894 0300 

ISBN 978-0-478-40503-3 (print) 

ISBN 978-0-478-40504-0 (online) 

© Crown Copyright March 2013 – Ministry for Primary Industries 

Preferred citation 

Ministry for Primary Industries (2012). Aquatic Environment and Biodiversity Annual Review 2012. 

Compiled by the Fisheries Management Science Team, Ministry for Primary Industries, Wellington, 

New Zealand. 387 p. 

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PREFACE 

This, the 2012 edition of the Aquatic Environment and Biodiversity Review, expands and updates the first 

edition published in 2011. It summarises information on a range of issues related to the environmental effects of 

fishing and aspects of marine biodiversity and productivity relevant to fish and fisheries. This review is a 

conceptual analogue of the Ministry’s annual Reports from the Fisheries Assessment Plenary. It summarises the 

most recent data and analyses on particular aquatic environment issues and, where appropriate, assesses current 

status against any specified targets or limits. Whereas the Reports from the Fisheries Assessment Plenary are 

organised by fishstock, however, the Aquatic Environment and Biodiversity Review is organised by issue (for 

example, protected species bycatch, benthic impacts), and almost all issues involve more than one fishstock or 

fishery. 

Several Fisheries Assessment Working Groups (FAWGs) contribute to the Fisheries Assessment Plenary, but 

only two generally contribute to the Aquatic Environment and Biodiversity Review. These are the Aquatic 

Environment Working Group (AEWG) and the Biodiversity Research Advisory Group (BRAG). However, a 

wider variety of research is summarised in the Aquatic Environment and Biodiversity Review than in the 

Reports from the Fisheries Assessment Plenary, and some of this is peer-reviewed through processes other than 

the Ministry’s science working groups. In particular, the Department of Conservation funds and reviews research 

on protected species, and the Ministry of Business Innovation and Employment funds a wide variety of research, 

some of which is relevant to fisheries. Where such research is relevant to fisheries it will be considered for 

inclusion in the review. 

As has happened with the Reports from the Fisheries Assessment Plenary, continual future expansion and 

improvement of the Aquatic Environment and Biodiversity Review is anticipated and additional chapters will be 

developed to provide increasingly comprehensive coverage of the issues. New chapters are included this year for 

seabirds (Chapter 5) and the bycatch and discards of fish and invertebrates (Chapter 6), and a new appendix 

summarising aquatic environment and marine biodiversity research since 1998 has now been developed 

(Appendix 12.9). A chapter on Hector’s/Maui’s dolphins has been identified as a priority for development in 

2013. Data acquisition, modelling, and assessment techniques will also progressively improve, and it is expected 

that reference points to guide fisheries management decisions will be developed. Both will lead to changes to the 

current chapters. We hope the condensation in this review of the information from previously scattered reports 

will assist fisheries managers, stakeholders and other interested parties to understand the issues, locate relevant 

documents, track research progress and make informed decisions. 

This revision has been led by the Science Team within the Directorate of Fisheries Management of the Ministry 

for Primary Industries (primarily Martin Cryer, Rohan Currey, Rich Ford, and Mary Livingston) but has relied 

critically on the input of members of the Ministry’s Aquatic Environment Working Group (AEWG) and 

Biodiversity Research Advisory Group (BRAG) and the Department of Conservation’s Conservation Services 

Technical Working Group (DOC-CSTWG). I would especially like to recognise and thank the large number of 

research providers and scientists from research organisations, academia, the seafood industry, environmental 

NGOs, Māori customary, DOC, and MPI, along with all other technical and non-technical participants in present 

and past AEWG and BRAG meetings for their substantial contributions to this review. My sincere thanks to each 

and all who have contributed. 

I am pleased to endorse this document as representing the best available scientific information relevant to the 

aspects of the environmental effects of fishing and marine biodiversity covered as at December 2012. 

Pamela Mace 

Principal Adviser Fisheries Science 


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Contents 

PREFACE ............................................................................................................................................... 3 

1. INTRODUCTION .......................................................................................................................... 6 

1.1. Context and purpose ................................................................................................................ 6 

1.2. Legislation ............................................................................................................................... 6 

1.3. Policy Setting .......................................................................................................................... 9 

1.4. Science processes .................................................................................................................. 11 

1.5. References ............................................................................................................................. 12 

2. Research themes covered in this document .................................................................................. 13 

THEME 1: PROTECTED SPECIES .................................................................................................... 16 

3. New Zealand sea lions (Phocarctos hookeri) ............................................................................... 17 

3.1. Context .................................................................................................................................. 17 

3.2. Biology .................................................................................................................................. 19 

3.3. Global understanding of fisheries interactions ...................................................................... 25 

3.4. State of knowledge in New Zealand ...................................................................................... 25 

3.5. Indicators and trends ............................................................................................................. 39 

3.6. References ............................................................................................................................. 41 

4. New Zealand fur seal (Arctocephalus forsteri)............................................................................. 44 

4.1. Context .................................................................................................................................. 44 

4.2. Biology .................................................................................................................................. 45 



4.5. Indicators and trends ............................................................................................................. 59 

4.6. References ............................................................................................................................. 60 

5. New Zealand seabirds ................................................................................................................... 63 

5.1. Context .................................................................................................................................. 64 

5.2. Biology .................................................................................................................................. 68 



5.5. Indicators and trends ........................................................................................................... 113 

5.6. References ........................................................................................................................... 115 

THEME 2: NON-PROTECTED BYCATCH ..................................................................................... 120 

6. Non-protected species (fish and invertebrates) bycatch ............................................................. 121 

6.1. Context ................................................................................................................................ 122 

6.2. Global understanding .......................................................................................................... 123 

6.3. State of knowledge in New Zealand .................................................................................... 124 


6.5. References ........................................................................................................................... 157 

THEME 3: BENTHIC IMPACTS ...................................................................................................... 159 

7. Benthic (seabed) impacts ............................................................................................................ 160 

7.1. Context ................................................................................................................................ 161 




7.5. References ........................................................................................................................... 184 

THEME 4: ECOSYSTEM EFFECTS ................................................................................................. 187 

8. New Zealand Climate and Oceanic Setting ................................................................................ 188 

8.1. Context ................................................................................................................................ 189 


8.3. Ocean climate trends and New Zealand fisheries ................................................................ 201 

8.4. References ........................................................................................................................... 203 

9. Habitats of particular significance for fisheries management..................................................... 205 

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9.1. Context ................................................................................................................................ 205 




9.5. References ........................................................................................................................... 213 

10. Land-based effects on fisheries, aquaculture and supporting biodiversity .............................. 216 

10.1. Context ............................................................................................................................ 216 

10.2. Global understanding ...................................................................................................... 218 

10.3. State of knowledge in New Zealand ................................................................................ 220 

10.4. Indicators and trends ....................................................................................................... 224 

10.5. References ....................................................................................................................... 225 

THEME 5: MARINE BIODIVERSITY ............................................................................................. 228 

11. Biodiversity ............................................................................................................................. 229 

11.1. Introduction ..................................................................................................................... 231 

11.2. Global understanding and developments ......................................................................... 235 

11.3. State of knowledge in New Zealand ................................................................................ 243 

11.4. Progress and re-alignment ............................................................................................... 281 

11.5. References ....................................................................................................................... 286 

11.6. Appendix ......................................................................................................................... 295 

12. Appendices .............................................................................................................................. 298 

12.1. Terms of Reference for the Aquatic Environment Working Group in 2012 ................... 298 

12.2. AEWG Membership 2012 ............................................................................................... 303 

12.3. Terms of Reference for the Biodiversity Research Advisory Group (BRAG) 2012 ....... 304 

12.4. BRAG attendance 2011-2012.......................................................................................... 310 

12.5. Generic Terms of Reference for Research Advisory Groups (Sept 2010) .................... 310 

12.6. Fisheries 2030 .................................................................................................................. 314 

12.7. OUR STRATEGY 2030: Growing and protecting New Zealand ................................... 316 

12.8. Other strategic policy documents .................................................................................... 317 

12.9. Appendix of Aquatic Environment and Biodiversity funded and related projects .......... 323 

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1. INTRODUCTION 

1.1. Context and purpose 

AEBAR 2012: Introduction 

This document contains a summary of information and research on aquatic environment issues 

relevant to the management of New Zealand fisheries and expands and updates the first version 

published in 2011 (MAF 2011). It is designed to complement the Ministry’s annual Reports from 

Fisheries Assessment Plenaries (e.g., MPI 2012a & b) and emulate those documents’ dual role in 

providing an authoritative summary of current understanding and an assessment of status relative to 

any overall targets and limits. However, whereas the Reports from Fisheries Assessment Plenaries 

have a focus on individual fishstocks, this report has a focus on aquatic environment fisheries 

management issues and biodiversity responsibilities that often cut across many fishstocks, fisheries, or 

activities, and sometimes across the responsibilities of multiple agencies. 

This update has been developed by the Science Team within the Fisheries Management Directorate of 

the Resource Management and Programmes branch, Ministry for Primary Industries (MPI). It does not 

cover all issues but, as anticipated, includes more chapters than the first edition in 2011. As with the 

Reports from Fisheries Assessment Plenaries, it is expected to change and grow as new information 

becomes available, more issues are considered, and as feedback and ideas are received. This synopsis 

has a broad, national focus on each issue and the general approach has been to avoid too much detail at 

a fishery or fishstock level. For instance, the benthic (seabed) effects of mobile bottom-fishing 

methods are dealt with at the level of all bottom trawl and dredge fisheries combined rather than at the 

level of a target fishery that might contribute only a small proportion of the total impact. The details of 

benthic impacts by individual fisheries will be documented in the respective chapters in the May or 

November Report from the Fisheries Assessment Plenary, and linked there to the fine detail and 

analysis in Aquatic Environment and Biodiversity Reports (AEBRs), Fisheries Assessment Reports 

(FARs), and Final Research Reports (FRRs). Such sections have already been developed for several 

species in both 2012 Fishery Assessment Plenary Reports, and others will follow. 

The first part of this document describes the legislative and broad policy context for aquatic 

environment and biodiversity research commissioned by MPI, and the science processes used to 

generate and review that research. The second, and main, part of the document contains chapters 

focused on various aquatic environment issues for fisheries management. Those chapters are divided 

into five broad themes: protected species; non-QMS fish bycatch; benthic effects; ecosystem issues 

(including New Zealand’s oceanic setting); and marine biodiversity. A third part of the review 

includes a number of appendices for reference. This review is not comprehensive in its coverage of all 

issues or of all research within each issue, but attempts to summarise the best available information on 

the issues covered. Each chapter has been considered by the appropriate working group at least once. 

1.2. Legislation 

The primary legislation for the management of fisheries, including effects on the aquatic environment, 

is the Fisheries Act 1996. The main sections setting out the obligation to avoid, remedy, or mitigate 

any adverse effect of fishing on the aquatic environment are sections 8, 9, and 15, although sections 

10, 11, and 13 are also relevant to decision-making under this Act (Table 1.1). The Ministry also 

administers the residual parts of the Fisheries Act 1983, the Treaty of Waitangi (Fisheries Claims) 

Settlement Act 1992, the Fisheries (Quota Operations Validation) Act 1997, the Maori Fisheries Act 

2004, the Maori Commercial Aquaculture Claims Settlement Act 2004, the Aquaculture Reform 

(Repeals and Transitional Provisions) Act 2004, the Driftnet Prohibition Act 1991, and the Antarctic 

Marine Living Resources Act 1981. Other Acts are relevant in specific circumstances: the Wildlife 

Act 1953 and the Marine Mammals Protection Act 1978 for protected species; the Marine Reserves 

Act 1971 for “no take” marine reserves; the Conservation Act 1987; the Hauraki Gulf Marine Park Act 

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2000; the Resource Management Act 1991 for issues in coastal marine areas that could affect fisheries 

interests or be the subject of sustainability measures under section 11 of the Fisheries Act; and the 

Exclusive Economic Zone and Continental Shelf (Environmental Effects) Act 2012 for issues outside 

the Territorial Sea. These Acts are administered by other agencies and this leads to a requirement for 

the Ministry for Primary Industries to work with other government departments (especially the 

Department of Conservation and through the Natural Resource Sector 1 ) and with various territorial 

authorities (especially Regional Councils) to a greater extent than is required for most fisheries stock 

assessment issues. 

Table 1.1: Sections of the Fisheries Act 1996 relevant to the management of the effects of fishing on the aquatic 

environment. 

Fisheries Act 1996 

s8 Purpose – 

(1) The purpose of this Act is to provide for the utilisation of fisheries resources while ensuring sustainability, where 

(2) “Ensuring sustainability” means – 

(a) Maintaining the potential of fisheries resources to meet the reasonably foreseeable needs of future generations: and 

(b) Avoiding, remedying, or mitigating any adverse effects of fishing on the aquatic environment: 

“Utilisation” means conserving, using, enhancing, and developing fisheries resources to enable people to provide for their 

social, economic, and cultural well-being. 

s9 Environmental Principles. 

associated or dependent species should be maintained above a level that ensures their long-term viability; 

biological diversity of the aquatic environment should be maintained: 

habitat of particular significance for fisheries management should be protected. 

s11 Sustainability Measures. The Minister may take into account, in setting any sustainability measure, (a) any effects of 

fishing on any stock and the aquatic environment; 

s15 Fishing-related mortality of marine mammals or other wildlife. A range of management considerations are set out in 

the Fisheries Act 1996, which empower the Minister to take measures to avoid, remedy or mitigate any adverse 

effects of fishing on associated or dependent species and any effect of fishing-related mortality on any protected 

species. These measures include the setting of catch limits or the prohibition of fishing methods or all fishing in an 

area, to ensure that such catch limits are not exceeded. 

Under the primary legislation lie various layers of Regulations and Orders in Council (see 

http://www.legislation.govt.nz/). It is beyond the scope of this document to summarise these. 

In addition to its domestic legislation, the New Zealand government is a signatory to a wide variety of 

International Instruments and Agreements that bring with them various International Obligations 

(Table 1.2). Section 5 of the Fisheries Act requires that the Act be interpreted in a manner that is 

consistent with international obligations and with the Treaty of Waitangi (Fisheries Claims) Settlement 

Act 1992. 

1 The Natural Resources Sector is a network of government agencies established to enhance collaboration. Its 

main purpose is to ensure a strategic, integrated and aligned approach is taken to natural resources development 

and management across government agencies. The network is chaired by MfE’s Chief Executive. The Sector 

aims to provide high-quality advice to government and provide effective implementation and execution of major 

government policies through coordination and integration across agencies, management of relationships, and 

alignment of the policies and practices of individual agencies. 

7


Table 1.2: International agreements and regional agreements to which New Zealand is a signatory, that are relevant 

to the management of the effects of fishing on the aquatic environment. 

International Instruments Regional Fisheries Agreements 

• Convention on the Conservation of Migratory Species of Wild 

Animals (CMS). Aims to conserve terrestrial, marine and avian 

migratory species throughout their range. 

• Agreement on the Conservation of Albatrosses and Petrels 

(ACAP). Aims to introduce a number of conservation measures to 

reduce the threat of extinction to the Albatross and Petrel species. 

• Convention on Biological Diversity (CBD) Provides for 

conservation of biological diversity and sustainable use of 

components. States accorded the right to exploit resources 

pursuant to environmental policies. 

• United Nations Convention on the Law of the Sea (UNCLOS) 

Acknowledges the right to explore and exploit, conserve and 

manage natural resources in the State’s EEZ…with regard to the 

protection and preservation of the marine environment including 

associated and dependent species, pursuant to the State’s 

environmental policies. 

• Convention on the International Trade in Endangered Species 

of Wild Fauna and Flora (CITES). Aims to ensure that 

international trade in wild animals and plants does not threaten 

their survival. 

• United Nations Fishstocks Agreements. Aims to lay down a 

comprehensive regime for the conservation and management of 

straddling and highly migratory fish stocks. 

• International Whaling Commission (IWC) Aims to provide for 

the proper conservation of whale stocks and thus make possible 

the orderly development of the whaling industry. 

• Wellington Convention Aims to prohibit drift net fishing activity 

in the convention area. 

• Food and Agriculture Organisation – International Plan of 

Action for Seabirds (FAO-IPOA Seabirds) Voluntary 

framework for reducing the incidental catch of seabirds in longline 

fisheries. 

• Food and Agriculture Organisation – International Plan of 

Action for Sharks (FAO –IPOA Sharks) Voluntary framework 

for the conservation and management of sharks. 

• Noumea Convention. Promotes protection and management of 

natural resources. Parties to regulate or prohibit activity likely to 

have adverse effects on species, ecosystems and biological 

processes. 

• Food and Agriculture Organisation - Code of Conduct for 

Responsible Fisheries Provides principles and standards 

applicable to the conservation, management and development of 

all fisheries, to be interpreted and applied to conform to the rights, 

jurisdiction and duties of Sates contained in UNCLOS. 

8 

• Convention for the Conservation of 

Southern Bluefin Tuna (CCSBT) Aims to 

ensure, through appropriate management, the 

conservation and optimum utilisation of the 

global Southern Bluefin Tuna fishery. The 

Convention specifically provides for the 

exchange of data on ecologically related 

species to aid in the conservation of these 

species when fishing for southern bluefin 

tuna. 

• Convention for the Conservation of 

Antarctic Marine Living Resources 

(CCAMLR). Aims to conserve, including 

rational use of Antarctic marine living 

resources. This includes supporting research 

to understand the effects of CCAMLR 

fishing on associated and dependent species, 

and monitoring levels of incidental take of 

these species on New Zealand vessels fishing 

in CCAMLR waters. 

• Convention on the Conservation and 

Management of Highly Migratory Fish 

Stocks in the Western and Central Pacific 

Ocean (WCPFC). The objective is to 

ensure, through effective management, the 

long-term conservation and sustainable use 

of highly migratory fish stocks in accordance 

with UNCLOS. 

• South Tasman Rise Orange Roughy 

Arrangement. The arrangement puts in 

place the requirement for New Zealand and 

Australian fishers to have approval from the 

appropriate authorities to trawl or carry out 

other demersal fishing for any species in the 

STR area 

• Convention on the Conservation and 

Management of High Seas Fishery 

Resources in the South Pacific Ocean (a 

Regional Fisheries Management 

Organisation, colloquially SPRFMO) has 

recently been negotiated to facilitate 

management of non-highly migratory species 

in the South Pacific.

1.3. Policy Setting 


1.3.1. Our Strategy 2030 and MPI’s Statement of Intent 

2012/15 

The Ministry for Primary Industries’ Statement of Intent, SOI, is an important guiding document for 

the short to medium term. That for 2012–15 is available on the Ministry’s website at: 

http://www.mpi.govt.nz/Default.aspx?TabId=126&id=1341 

The SOI sets out the Ministry’s strategic direction for the coming three years, primarily through 

implementation of Our Strategy 2030 (Appendix 12.7). This strategy was agreed by Cabinet in August 

2011and sets out MPI’s vision of “growing and protecting New Zealand” and defines the focus and 

approach of the organisation. The strategy includes four focus areas and outcomes: maximising export 

opportunities; improving sector productivity; increasing sustainable resource use; and protecting from 

biological risk. 

MPI is the single key adviser to the Government across all aspects of the primary industries, food 

production and related trade issues. MPI is the principal adviser to the Government on agriculture, 

horticulture, aquaculture, fisheries, forestry, and food industries, animal welfare, and the protection of 

New Zealand’s primary industries from biological risk. Aspects of the role specific to fisheries 

itemized in the SOI include supporting the development of sustainable limits to natural resource use. 

To that end, MPI contracts the following types of research (relevant to this document): 

• aquatic environment research to assess the effects of fishing on marine habitats, protected 

species, trophic linkages, and to understand habitats of special significance for fisheries; 

• biodiversity research to increase our understanding of the systems that support resilient 

ecosystems and productive fisheries. 

1.3.2. Fisheries 2030 

New Zealand’s Quota Management System (QMS) forms the overall framework for management of 

domestic fisheries (see http://www.fish.govt.nz/en-nz/Commercial/Quota+Management+System/default.htm). Within 

that framework, Fisheries 2030 provides a long-term goal for the New Zealand fisheries sector. After 

endorsement by Cabinet, it was released by the Minister of Fisheries in September 2009. It can be 

found on the MPI website at: 

http://www.fish.govt.nz/en-nz/Fisheries+2030/default.htm?wbc_purpose=bas 

(noting that the Ministry of Fisheries merged with the Ministry of Agriculture and Forestry on 1 July 2011 and 

became the Ministry for Primary Industries on 30 April 2012. This URL and subsequent links in this document 

will eventually change as the new Ministry’s systems are progressively merged). 

Fisheries 2030 sets out a goal to have New Zealanders maximising benefits from the use of fisheries 

within environmental limits. To support this goal, major outcomes for Use (of fisheries) and 

Environment are specified. The Environment outcome is the main driver for aquatic environment 

research: The capacity and integrity of the aquatic environment, habitats and species are sustained at 

levels that provide for current and future use. Fisheries 2030 states that this means: 

• Biodiversity and the function of ecological systems, including trophic linkages, are conserved 

• Habitats of special significance to fisheries are protected 

• Adverse effects on protected species are reduced or avoided 

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• Impacts, including cumulative impacts, of activities on land, air or water on aquatic 

ecosystems are addressed. 

1.3.3. Fisheries Plans 

Fisheries planning processes for deepwater, highly migratory species, inshore finfish, inshore shellfish 

and freshwater fisheries use objective-based management to drive the delivery of services, as 

described in Fisheries 2030 and affirmed in the 2012/15 SOI and Our Strategy 2030. The planning 

processes are guided by five National Fisheries Plans, which recognise the distinctive characteristics 

of these fisheries. Plans for Deepwater and Highly Migratory species have been approved by the 

Minister and a suite of three plans for inshore species has been released in prototype form. These plans 

establish management objectives for each fishery, including those related to the environmental effects 

of fishing. All are available on the Ministry’s websites. 

Deepwater and middle depth fisheries: 

http://www.fish.govt.nz/ennz/Consultations/Archive/2010/National+Fisheries+Plan+for+Deepwater+and+Middle- 

Depth+Fisheries/default.htm 

Highly migratory species (HMS) fisheries: 

http://www.fish.govt.nz/ennz/Consultations/Archive/2010/National+Fisheries+Plan+for+Highly+Migratory+Species/default.htm 

Inshore fisheries (comprising finfish, shellfish, and freshwater fisheries): 

http://www.fish.govt.nz/en-nz/Fisheries+Planning/default.htm 

Certain research areas (aquatic environment, recreational and biodiversity) are not entirely covered by 

fish plans, as many of these issues span multiple fisheries and plans. Antarctic research is also 

excluded from fish plans as it is beyond their spatial scope. These areas are administered by the 

science team and subject to the drivers in Tables 1.1, 1.2 and Fisheries 2030. 

1.3.4. Other strategic documents 

A number of strategies or reviews have been published that potentially affect fisheries values and 

research. These include: the New Zealand Biodiversity Strategy (2000); the Biosecurity Strategy 

(2003, followed by its science strategy 2007); the MPA Policy and Implementation Plan (2005); 

MfE’s discussion paper on Management of Activities in the EEZ (2007); MRST’s Roadmap for 

Environment Research (2007); the Revised Coastal Policy Statement (2010); the National Plan of 

Action to Reduce the Incidental Catch of Seabirds in New Zealand Fisheries (2004, soon to be 

revised); and the New Zealand National Plan of Action for the Conservation and Management of 

Sharks (2008). Links to these documents are provided in Appendix 12.8 because they provide some of 

the broad policy setting for aquatic environment issues and research across multiple organisations and 

agencies. 

In 2012, the Natural Resource Sector cluster formed a Marine Director’s Group to improve data 

sharing and information exchange across key agencies with marine environmental responsibilities, 

particularly MPI, DOC, MfE, EPA, LINZ, MBIE. The Marine Director’s Group is chaired by MPI and 

DOC and a substantial amount of cross-agency work has been initiated to: summarise relevant marine 

information held by different agencies and current marine research investment; identify knowledge 

and funding gaps; and to develop a long-term Marine Research Strategy for New Zealand. 

10

1.4. Science processes 


1.4.1. Research Planning 

Until 2010 the Ministry of Fisheries ran an iterative planning process to determine, in conjunction with 

stakeholders and subject to government policy, the future directions and priorities for fisheries 

research. Subsequently, the Ministry has adopted an overall approach of specifying objectives for 

fisheries in Fisheries Plans and using these plans to develop associated implementation strategies and 

required services, including research. These services are identified in Annual Operational Plans that 

are updated each year. 

For deepwater fisheries and highly migratory stocks (HMS), the transition to the new research 

planning approach is well advanced because fisheries plans for these areas have been approved by the 

Minister. Research for these fisheries are already being developed using Fisheries Plan and Annual 

Operating Plan processes as primary drivers, and, as necessary, Research Advisory Groups (RAGs) to 

develop the technical detail of particular projects. The Ministry’s website contains more information 

on this approach, developed during the Research Services Strategy Review, at: 

http://www.fish.govt.nz/NR/rdonlyres/04D579E5-6DCC-42A6-BF68- 

9CAB800D6392/0/Research_Services_Strategy_Review_Report.pdf (see Section 5.2, pages 14 to 21) and in 

summary at: http://www.fish.govt.nz/NR/rdonlyres/432EA3A0-AEA7-41DD-8E5C-D0DCA9A3B96B/0/RSS_letter.pdf. 

Generic terms of reference for Research Advisory Groups are in Appendix 12.5. For inshore fisheries, 

the three Fisheries Plans (inshore finfish, shellfish, and freshwater) are still under development, so a 

transitional research planning process was established for 2010 and developed slightly in 2011. This 

included the following steps: 

• Identification of the main management information needs using: 

o Fisheries Plans or Fisheries Operational Plans where available 

o Any relevant Medium Term Research Plan 

o Fishery managers’ understanding of decisions likely to require research information in the 

next 1–3 years. 

• Technical discussions as required (i.e., tailored to the needs of the different research areas) to 

consider: 

o The feasibility and utility of each project 

o The likely cost of each project 

o Any synergies or overlaps with work being conducted by other providers (including 

industry, CRIs, MBIE, Universities, etc.) 

• Stakeholder meetings as required to discuss relative priorities for particular projects 

The process for aquatic environment research for 2011/12 and 2012/13 (other than aspects driven by 

deepwater and HMS plans or the specific needs of inshore fishery managers) followed essentially 

these same steps. 

The Ministry runs a separate planning group to design and prioritise its research programme on marine 

biodiversity. Given its much broader and more strategic focus, the Biodiversity Research Advisory 

Group (BRAG) has both peer review and planning roles and therefore differs slightly in constitution 

from the Ministry’s other working and planning groups. 

1.4.2. Contributing Working Groups 

The main contributing working groups for this document are the Ministry’s Aquatic Environment 

Working Group (AEWG) and Biodiversity Research Advisory Group (BRAG). The Department of 

Conservation’s Conservation Services Programme and National Plan of Action Seabirds Technical 

Working Group (CSP/NPOA-TWG, see http://www.doc.govt.nz/conservation/marine-and- 

11


coastal/commercial-fishing/marine-conservation-services/meetings-and-project-updates/) also considers a 

wide range of DOC-funded projects related to protected species, sometimes in joint meetings with the 

AEWG. The Ministry’s Fishery Assessment Working Groups occasionally consider research relevant 

to this synopsis. Terms of reference for AEWG and BRAG are periodically revised and updated (see 

Appendix 12.1 and 12.3 for the 2012 Terms of Reference for AEWG and BRAG, respectively). 

AEWG is convened for the Ministry’s peer review purposes with an overall purpose of assessing, 

based on scientific information, the effects of fishing, aquaculture, and enhancement on the aquatic 

environment for all New Zealand fisheries. The purview of AEWG includes: bycatch and unobserved 

mortality of protected species, fish, and other marine life; effects of bottom fisheries on benthic 

biodiversity, species, and habitat; effects of fishing on biodiversity, including genetic diversity; 

changes to ecosystem structure and function as a result of fishing, including trophic effects; and effects 

of aquaculture and fishery enhancement on the environment and on fishing. Where possible, AEWG 

may explore the implications of any effects, including with respect to any standards, reference points, 

and relevant indicators. The AEWG is a technical forum to assess the effects of fishing or 

environmental status and make projections. It has no mandate to make management recommendations 

or decisions. Membership of AEWG is open (attendees for 2012 are listed in Appendix 12.2). 

The two main responsibilities of BRAG are: to review, discuss, and convey views on the results of 

marine biodiversity research projects contracted by the Ministry; and to discuss, evaluate, make 

recommendations and convey views on Medium Term Biodiversity Research Plans and constituent 

individual projects. Both tasks have hitherto been undertaken in the context the strategic goals in the 

New Zealand Biodiversity Strategy (2000) and the Strategy for New Zealand Science in Antarctica 

and the Southern Ocean (2010), but the focus of the programme is currently being reviewed to align it 

with more recent strategic documents. BRAG also administers some large cross-government projects 

such as NORFANZ, BIOROSS, Fisheries and Biodiversity Ocean Survey 20/20; and International 

Polar Year (IPY) Census of Antarctic Marine Life (IPY-CAML). Membership of BRAG is also open 

(attendees for 2011 and 2012 are listed in Appendix 12.4). 

Following consideration at one or more meetings of appropriate working groups, reports from 

individual projects are also technically reviewed by the Ministry before they are finalised for use in 

management and/or for public release. Fisheries Assessment Reports, FARs, and Aquatic Environment 

and Biodiversity reports, AEBRs, are also subject to editorial review whereas Final Research Reports, 

FRRs, and Research Progress Reports, RPRs, are not. Finalised FARs, AEBRs, historical FARDs 

(Fisheries Assessment Research Documents) and MMBRs (Marine Biodiversity and Biosecurity 

Reports), and some FRRs can be found at: 

http://fs.fish.govt.nz/Page.aspx?pk=61&tk=209. 

Increasingly, reports will be available from the MPI website at: http://www.mpi.govt.nz/newsresources/publications. 

1.5. References 

Ministry of Agriculture and Forestry (2011). Aquatic Environment and Biodiversity Annual Review 2011: a summary of 

environmental interactions between fisheries and the aquatic environment. Compiled by the Fisheries Science 

Group, Ministry of Agriculture and Forestry, Wellington, New Zealand. 199 p. 

Ministry for Primary Industries (2012a). Report from the Fisheries Assessment Plenary, May 2012: stock assessments and 

yield estimates. Compiled by the Fisheries Science Group, Ministry for Primary Industries, Wellington, New 

Zealand. 1194 p. 

Ministry for Primary Industries (2012b). Fisheries Assessment Plenary, November 2012: stock assessments and yield 

estimates. Compiled by the Fisheries Science Group, Ministry for Primary Industries, Wellington, New Zealand. 

531 p. 

12

AEBAR 2012: Research themes 

2. Research themes covered in this document 

The Ministry has identified four broad categories of research on the environmental effects of fishing 

(Figure 2.1): bycatch and fishing-related mortality of protected species; bycatch of non-protected 

species, primarily non-QMS fish; modification of benthic habitats (including seamounts); and various 

ecosystem effects (including fishing and non-fishing effects on habitats of particular significance for 

fisheries management and trophic relationships). Other emerging issues (such as the genetic 

consequences of selective fishing and the impacts of aquaculture) are not dealt with in detail in this 

synopsis but it is anticipated that those that turn out to be important will be dealt with in future 

iterations. A fifth theme for this document is MPI research on marine biodiversity. The research has 

been driven largely by the Biodiversity Strategy but has strategic importance for fisheries in that it 

provides for better understanding of the ecosystems that support fisheries productivity. 

Our understanding is not uniform across these themes and, for example, our knowledge of the 

quantum and consequences of fishing-related mortality of protected species is much better developed 

than our knowledge of the consequences of mortalities of non-target fish, bottom trawl impacts, or 

land management choices for ecosystem processes or fisheries productivity. Ultimately, the goal of 

research described in this synopsis is to complement information on fishstocks to ensure that the 

Ministry has the information required to underpin the ecosystem approach to fisheries management 

envisaged in Fisheries 2030. Stock assessment results have been published for many years in Fisheries 

Assessment Reports, and Final Research Reports, and the Annual Report from the Fishery Assessment 

Plenary. Collectively, these provide a rich and well-understood resource for fisheries managers and 

stakeholders. In 2005, an environmental section was included in the hoki plenary report as part of the 

characterisation of that fishery and to highlight any particular environmental issues associated with the 

fishery. Similar, fishery-specific sections have since been developed for other working group reports 

and the plenary, including many fisheries for highly migratory species and the trawl fisheries for 

scampi and squid, but work on environmental issues has otherwise been more difficult to access for 

fisheries managers and stakeholders. The Ministry is, therefore, looking at improving ways to 

document, review, publicise, and integrate information from environmental assessments with 

traditional fishery assessments. This will rely heavily on studies that are published in Aquatic 

Environment and Biodiversity Reports and Final Research Reports but, given the overlapping 

mandates and broader scope of work in this area, also on results published by other organisations. The 

integration of all this work into a single source document analogous to the Report from the Fishery 

Assessment Plenary will take time and not all issues will be covered for some years. 

13


THEME RESEARCH QUESTIONS CURRENT WORK 

1.PROTECTED 

SPECIES 

• Marine mammals 

• Seabirds 

• Turtles 

• Protected fish 

• Corals 

• How many of each NZ-breeding protected 

species are caught and killed in our fisheries 

(and out of zone)? 

• How many unobserved deaths are caused? 

• What is the likely effect of fishing-related 

mortality on protected species populations? 

• Which species or populations are most at 

risk? 

• Which fisheries cause the most risk and 

where are the most cost-effective gains to 

be made? 

• What mitigation approaches are most 

successful and in what circumstances? 

• What levels of bycatch would lead to 

14 

• Estimation of annual bycatch of 

protected species by fishery 

• Abundance and productivity of 

key seabird populations 

• Abundance and productivity of 

Hector’s & Maui’s dolphins 

• Semi-quantitative risk assessment 

for all seabirds 

• Semi-quantitative risk assessment 

for other protected species 

• Full quantitative risk assessment 

for selected seabird populations 

• Modelling to assess robust links 

between observed ycatch and 

different population outcomes? 

population outcomes 

2. OTHER • How much non-target fish is caught and • Continued monitoring cycle for 

BYCATCH 

discarded in our fisheries? 

deepwater and highly migratory 

• Non-QMS fish & • What is the effect of that bycatch? • Risk assessment for tier 3 

invertebrates • What do trends in bycatch show? 

deepwater bycatch species 

3. BENTHIC • What seabed habitats occur where in our • Testing of habitat classifications 

EFFECTS 

TS/EEZ and how much of each is affected • Assessment of recovery rate of 

• Distribution of by trawling or shellfish dredging? 

some key inshore habitats 

habitats & trawling • How sensitive is each habitat to disturbance • Assessment of relative sensitivity 

• Effects of trawling and what do we lose when each is 

of habitats 

on each 

disturbed? 

• Mapping of sensitive biogenic 

• What are the consequences of different habitats, and deepwater and 

management approaches? 

inshore trawl footprints 

4. ECOSYSTEM • How do the ecosystems that support our • Habitat of significance: Kaipara 

EFFECTS 

fisheries function? 

Harbour fish habitats (SNA) 

• Trophic studies • What are the key predator-prey or • Habitat of significance: review of 

• Habitats of 

synergistic relationships in these systems? information for inshore finfish 

significance • Are our fisheries affecting food webs or • Habitat of significance: coastal 

• Ecosystem 

ecosystem services? 

shark nursery areas (starting with 

indicators • What changes are occurring in the 

rig) 

• Land-use effects ecosystems that support our fisheries? • Multi-impact risk assessment 

• Climate variability • What is “habitat of particular significance • Monitoring and indicators of 

• Climate Change for fisheries management”? 

environmental change for 

• System productivity • How do fisheries and/or land management deepwater fisheries 

affect fish habitat and fisheries production? • Ecotrophic factors affecting 

• What are the major risks and opportunities 

from ocean-climate variability and trends? 

highly migratory species 

5. MARINE • What are the key drivers of pattern in New • Mapping key biogenic habitats 

BIODIVERSITY Zealand’s marine biodiversity? 

• SPRFMO benthic habitats 

• Characterising NZ • How does biodiversity contribute to the • Modelling seabed response and 

biodiversity resilience of ecosystems to perturbation and recovery from disturbance 

• Functional ecology climate change? 

• Ocean acidification in fish habitat 

• Genetic diversity • What drives genetic connectivity within • Experimental response of shellfish 

• Ocean climate species? 

to warming and acidification 

• Metrics & indicators • What do we need to measure and monitor to • Monitoring surface plankton 

• Threats & impacts assess risks and change? 

• Implications of ocean acidification 

• Ross Sea & IPY • How are biota adapted to polar conditions for plankton productivity 

and what is their sensitivity to perturbation? • Marine environmental monitoirng 

Figure 2.1: Summary of themes in the Aquatic Environment and Biodiversity Annual Review 2011.


CURRENT STATE OF KNOWLEDGE 

• Aggregate “on deck” bycatch of seabirds (and approximate species composition), marine mammals, and 

large sharks known reasonably well for offshore trawl and longline fisheries, but less well for inshore 

fisheries (where observer coverage has historically been low). 

• Incidental, cryptic, or unobserved mortality very poorly known (and difficult to assess). 

• Factors affecting fishing related mortality are well known for most seabirds and marine mammals. 

• Knowledge of population abundance is increasing for some key seabird species and well known for sea 

lions, but poorly known or dated for other seabirds, some species of dolphins, fur seals, and most sharks. 

• Qualitative or semi-quantitative risk assessments have been completed for almost all seabirds and marine 

mammals. 

• Fully quantitative risk assessments have been completed for two seabird populations, Hector’s / Maui’s 

dolphins, and sea lions. 

• Impact of fishing-related mortality on most protected species remains uncertain because of some key 

knowledge gaps. 

• Some methods of mitigating bycatch have been formally tested. 

• Bycatch and discards are monitored and reported using observer records for the main deepwater and 

highly migratory fisheries. 

• Bycatch and discards for inshore vessels remain poorly known. 

• Some mitigation approaches have been assessed (e.g., for scampi trawl). 

• Modelled predictions (that have been tested in deepwater) are available of the distribution of seabed 

habitats at a broad scale using classifications (BOMEC) and at finer scale for seamounts and some 

biogenic habitats. 

• Excellent understanding of the distribution of bottom trawling in offshore waters (but not in coastal 

waters, especially for most shellfish dredge fisheries). 

• Good understanding of the effects of trawling on some nearshore habitats. 

• General understanding of the effects of trawling on biogeochemical processes. 

• General understanding of the relative sensitivity of different habitats. 

• Variability in the diets of key commercial species in the Chatham Rise ecosystem have been described as 

part of a wider biodiversity and MSI programme. 

• A preliminary trophic model of the Subantarctic ecosystem suggests a low productivity system 

supporting a simple food chain with high transfer efficiencies. 

• Atlases have been developed showing the distribution of spawning, pupping, egg-laying, and juveniles of 

key species (this needs finalising for inshore species). 

• A review of land-based effects on fish habitat and coastal biodiversity has been completed. 

• A start has been made on assessing ecosystem change over time (through fish-based indicators calculated 

from trawl survey data and acoustic time series of mesopelagic biomass) 

• A summary of ocean climate variability and change has been produced. 

• Broad reviews have been completed of the impacts of climate variability on fisheries (especially 

recruitment), but the likely impacts of ocean climate change or acidification remain poorly known. 

• This theme has links and synergies with MBIE, DOC, universities and the MPI biodiversity programme.s 

• Taxonomy and ID Guides have been produced and specimens recorded in National Collections. 

• Biodiversity surveys completed on local scale (Fiordland, Spirits Bay, seamounts) and larger fishery 

scale (Norfolk ridge, Chatham Rise, Challenger Plateau, BOI). 

• Measures and indicators for marine biodiversity measures and ecosystem have been developed. 

• Predictive modelling techniques have been applied and habitat classification methods improved 

• Productivity in benthic communities has been measured. 

• Specimens from New Zealand have been genetically assessed and entered into the barcode of life. 

• Seamount connectivity, land-sea connectivity, and endemism have been studied. 

• A plan for monitoring the marine environment for long-term change is under development. 

• Demersal fish trophic studies on the Chatham Rise have been completed. 

• A review of NZ data from deep-sea and abyssal habitats has been completed. 

• A multidisciplinary study of longterm (1000 years) changes to NZ marine ecosystem is ongoing. 

• Latitudinal gradient project, ICECUBE and 2 large scale surveys in the Ross Sea have been conducted. 

• This theme has links and synergies with MBIE, DOC, universities and the MPI AEWG programmes 

Figure 2.1 continued: Summary of Themes in the Aquatic Environment & Biodiversity Review 2011 

15

AEBAR 2012: Protected species: 

THEME 1: PROTECTED SPECIES 

16

AE&B Review: Protected species: Sea lions 

3. New Zealand sea lions (Phocarctos hookeri) 

Scope of chapter This chapter outlines the biology of New Zealand (or Hooker’s) sea 

lions (Phocarctos hookeri), the nature of fishing interactions, the 

management approach, trends in key indicators of fishing effects and 

major sources of uncertainty. 

Area Southern parts of the New Zealand EEZ and Territorial Sea. 

Focal localities Areas with significant fisheries interactions include the Auckland 

Islands Shelf, the Stewart/Snares Shelf and Campbell Plateau. 

Key issues Improving estimates of incidental bycatch in some trawl fisheries (e.g. 

scampi), improving estimates of SLED post-exit survival, improving 

understanding of interaction rate and improving understanding of the 

demographic processes underlying recent population trends. 

Emerging issues Assessing potential impacts of resource competition and/or resource 

limitation through ecosystem effects on NZ sea lion population viability. 

The role of fisheries impacts in light of ongoing declines in population 

MPI Research 

(current) 

Other Govt 

Research (current) 

Links to 2030 

objectives 

Related 

issues/chapters 

3.1. Context 

size. Estimation of interactions given low numbers of observed captures. 

PRO2010-01 Estimating the nature & extent of incidental captures of 

seabirds, marine mammals & turtles in New Zealand commercial 

fisheries; PRO2012-02 Assess the risk posed to marine mammal 

populations from New Zealand fisheries; External review of the Breen- 

Fu-Gilbert model (SRP2011-04). 

DOC Marine Conservation Services Programme (CSP): INT2012-01 To 

understand the nature and extent of protected species interactions with 

New Zealand commercial fishing activities; POP2012-01 To provide 

information on the population level and dynamics of the New Zealand 

sea lion at the Auckland Islands relevant to assessing the impacts of 

commercial fishing impacts on this population; POP2012-02 To 

determine the key demographic factors driving the observed population 

decline of New Zealand sea lions at the Auckland Islands. 

NIWA Research: SA123098 Multispecies modelling to evaluate the 

potential drivers of decline in New Zealand sea lions; TMMA103 

Conservation of New Zealand's threatened iconic marine megafauna. 

Objective 6: Manage impacts of fishing and aquaculture. 

Strategic Action 6.2: Set and monitor environmental standards, 

including for threatened and protected species and seabed impacts. 

See the New Zealand fur seal chapter. 

Management of fisheries impacts on New Zealand (NZ) sea lions is legislated under the Marine 

Mammals Protection Act (MMPA) 1978 and the Fisheries Act (FA) 1996. Under s.3E of the MMPA, 

the Minister of Conservation, with the concurrence of the Minister for Primary Industries (formerly 

the Minister of Fisheries), may approve a population management plan (PMP). Although a NZ sea 

lion PMP was proposed by the Department of Conservation (DOC) in 2007 (DOC 2007), following 

consultation DOC decided not to proceed with the PMP. 

All marine mammal species are designated as protected species under s.2(1) of the FA. In 2005, the 

Minister of Conservation approved the Conservation General Policy, which specifies in Policy 4.4 (f) 

that “Protected marine species should be managed for their long-term viability and recovery 

17


throughout their natural range.” DOC’s Regional Conservation Management Strategies outline 

specific policies and objectives for protected marine species at a regional level. New Zealand’s sub- 

Antarctic islands, including Auckland and Campbell islands, were inscribed as a World Heritage area 

in 1998. 

The Minister of Conservation gazetted the NZ sea lion as a threatened species in 1997. In 2009, DOC 

approved the New Zealand sea lion species management plan 2 : 2009–2014 (DOC 2009). It aims: “To 

make significant progress in facilitating an increase in the New Zealand sea lion population size and 

distribution.” The plan specifies a number of goals, of which the following are most relevant for 

fisheries interactions: 

“To avoid or minimise adverse human interactions on the population and individuals. 

To ensure comprehensive protection provisions are in place and enforced. 

To ensure widespread stakeholder understanding, support and involvement in 

management measures.” 

In the absence of a PMP, the Ministry for Primary Industries (MPI, formerly the Ministry of Fisheries, 

MFish) manages fishing-related mortality of NZ sea lions under s.15(2) of the FA. Under that section, 

the Minister “may take such measures as he or she considers are necessary to avoid, remedy, or 

mitigate the effect of fishing-related mortality on any protected species, and such measures may 

include setting a limit on fishing-related mortality.” 

Management of NZ sea lion bycatch aligns with Fisheries 2030 Objective 6: Manage impacts of 

fishing and aquaculture. Further, the management actions follow Strategic Action 6.2: Set and 

monitor environmental standards, including for threatened and protected species and seabed impacts. 

The relevant National Fisheries Plan for the management of NZ sea lion bycatch is the National 

Fisheries Plan for Deepwater and Middle-depth Fisheries (the National Deepwater Plan). Under the 

National Deepwater Plan, the objective most relevant for management of NZ sea lions is Management 

Objective 2.5: Manage deepwater and middle-depth fisheries to avoid or minimise adverse effects on 

the long-term viability of endangered, threatened and protected species. 

Specific objectives for the management of NZ sea lion bycatch will be outlined in the fishery-specific 

chapters of the National Deepwater Plan for the fisheries with which NZ sea lions are most likely to 

interact. These fisheries include trawl fisheries for arrow squid (SQU1T and SQU6T), southern blue 

whiting (SBW) and scampi (SCI). The SBW chapter of the National Deepwater Plan is complete and 

includes Operational Objective 2.2: Ensure that incidental New Zealand sea lion mortalities, in the 

southern blue whiting fishery at the Campbell Islands (SBW6I), do not impact the long term viability 

of the sea lion population and captures are minimised through good operational practices. Chapters 

in the National Deepwater Plan for arrow squid and scampi are under development. 

Currently, MPI limits the actual or estimated bycatch of sea lions in the SQU6T trawl fishery based 

on tests of the likely performance of candidate bycatch control rules (and, hence, bycatch limits) using 

an integrated population and fishery model (Breen et al. 2010). Candidate rules are assessed against 

the following two criteria: 

a. A rule should provide for an increase in the sea lion population to more than 90% of carrying 

capacity 3 , or to within 10% of the population size that would have been attained in the 

2 The species management plan differs from the draft Population Management Plan in that it is quite broad in 

scope; providing a framework to guide the Department of Conservation in its management of the NZ sea lion 

over the next 5 years. The draft population management plan focused on options for managing the extent of 

incidental mortality of NZ sea lions from fishing through establishing a maximum allowable level of fishingrelated 

mortality (MALFiRM) for all New Zealand fisheries waters. 

3 Carrying capacity in this instance applies to the current range. For managing the SQU6T fishery, carrying 

capacity refers to the maximum number of NZ sea lions that could be sustained on the Auckland Islands. 

18


absence of fishing, and that these levels must be attained with 90% certainty, over 20-year 

and 100-year projections. 

b. A rule should attain a mean number of mature mammals that exceeded 90% of carrying 

capacity in the second 50 years of 100-year projection runs. 

These management criteria were developed and approved in 2003 by a Technical Working Group 

comprised of MFish, DOC, squid industry representatives, and environmental groups. 

Likely performance is also assessed against two additional criteria proposed by DOC: 

a) A rule should maintain numbers above 90% of the carrying capacity in at least 18 of the first 

20 years. 

b) A rule should lead to at least a 50% chance of an increase in the number of mature animals 

over the first 20 years of the model projections. 

3.2. Biology 

3.2.1. Taxonomy 

The NZ sea lion (Phocarctos hookeri, Gray, 1844) is one of only two species of otariid (eared seals, 

including fur seals and sea lions) native to New Zealand, the other being the NZ fur seal 

(Arctocephalus forsteri, Lesson, 1828). The NZ sea lion is also New Zealand’s only endemic 

pinniped. 

3.2.2. Distribution 

Before human habitation, NZ sea lions ranged around the North and South Islands of New Zealand. 

Pre-European remains of NZ sea lions have been identified from at least 47 archaeological sites, 

ranging from Stewart Island to North Cape, with most occurring in the southern half of the South 

Island (Smith 1989, 2011, Childerhouse and Gales 1998, Gill 1998). Subsistence hunting on the 

mainland and subsequent commercial harvest from outlying islands of NZ sea lions for skins and oil 

resulted in population decline and contraction of the species’ range (Gales 1995, Childerhouse and 

Gales 1998, Nagaoka 2001, 2006). Currently, most NZ sea lions are found in the New Zealand Sub- 

Antarctic, with individuals ranging to the NZ mainland and Macquarie Island. 

NZ sea lion breeding colonies 4 are highly localized, with most pups being born at two main breeding 

areas, the Auckland Islands and Campbell Island (Wilkinson et al. 2003, Chilvers 2008). At the 

Auckland Islands, there are three breeding colonies: Enderby Island (mainly at Sandy Bay and South 

East Point); Dundas Island; and Figure of Eight Island. On Campbell Island there is one breeding 

colony at Davis Point, another colony at Paradise Point, plus a small number of non-colonial breeders 

(Wilkinson et al. 2003, Chilvers 2008, Maloney et al. 2009, Maloney et al. 2012). Twenty-five sea 

lion pups were captured and tagged around Stewart Island during a DOC recreational hut and track 

maintance trip in March 2012. Breeding on the Auckland Islands represents 71–87% of the pup 

production for the species, with the remaining 13–29% occurring on Campbell Island (based on 

concurrent pup counts in 2003, 2008 and 2010; see section 3.2.5). 

4 DOC (2009) defines colonies as “haul-out sites where 35 pups or more are born each year for a period of 5 

years or more.” Haul-out sites are defined as “terrestrial sites where NZ sea lions occur but where pups are not 

born, or where less than 35 pups are born per year over 5 consecutive years.” 

19


Although breeding is concentrated on the Auckland Islands and Campbell Island, occasional births 

have been reported from the Snares and Stewart Islands (Wilkinson et al. 2003, Chilvers et al. 2007). 

Breeding is also taking place on the New Zealand mainland at the Otago peninsula, mainly the result 

of a single female arriving in 1992 and giving birth in 1993 (McConkey et al., 2002). 

On land, NZ sea lions are able to travel long distances and climb high hills, and are found in a variety 

of habitats including sandy beaches, grass fields, bedrock, and dense bush and forest (Gales 1995, 

Augé et al. 2012). Following the end of the females’ oestrus cycle in late January, adult and sub-adult 

males disperse throughout the species’ range, whereas dispersal of females (both breeding and nonbreeding) 

appears more restricted (Marlow 1975, Robertson et al. 2006, Chilvers and Wilkinson 

2008). 

3.2.3. Foraging ecology 

Most foraging studies have been conducted on lactating female NZ sea lions from Enderby Island 

(Chilvers et al. 2005a, 2006, Chilvers and Wilkinson 2009, although work is underway at Campbell 

Island under NIWA project TMMA103, Conservation of New Zealand's threatened iconic marine 

megafauna). These show that females from this place forage primarily within the Auckland Islands 

continental shelf and its northern edge, and that individuals show strong foraging site fidelity both 

within and across years. Satellite tagging data from lactating females showed that the mean return 

distance travelled per foraging trip is 423 ± 43 km (n = 26), which is greater than that recorded for any 

other sea lion species (Chilvers et al. 2005a). While foraging, about half of the time is spent 

submerged, with a mean dive depth of 130 ± 5 m (max. 597 m) and a mean dive duration of 4 ± 

1 minutes (max. 14.5 minutes; Chilvers et al. 2006). NZ sea lions, like most pinnipeds, may use their 

whiskers to help them capture prey at depths where light does not penetrate (Marshall 2008, Hanke et 

al. 2010). 

Studies conducted on female NZ sea lions suggest that the foraging behaviour of each individual falls 

into one of two distinct categories, benthic or meso-pelagic (Chilvers and Wilkinson 2009). Benthic 

divers have fairly consistent dive profiles, reaching similar depths (120 m on average) on consecutive 

dives in relatively shallow water to presumably feed on benthic prey. Meso-pelagic divers, by 

contrast, exhibit more varied dive profiles, undertaking both deep (> 200 m) and shallow (< 50 m) 

dives over deeper water. Benthic divers tend to forage further from their breeding colonies, making 

their way to the north-eastern limits of Auckland Islands’ shelf, whereas meso-pelagic divers tend to 

forage along the north-western edge of the shelf over depths of approximately 3000 m (Chilvers and 

Wilkinson 2009). 

The differences in dive profiles have further implications for the animals’ estimated aerobic dive 

limits (ADL; Chilvers et al. 2006), defined as the maximum amount of time that can be spent 

underwater without increasing blood lactate concentrations (a by-product of anaerobic metabolism). If 

animals exceed their ADL and accumulate lactate, they must surface and go through a recovery period 

in order to aerobically metabolize the lactate before they can undertake subsequent dives. Chilvers et 

al. (2006) estimated that lactating female NZ sea lions exceed their ADL on 69% of all dives, a much 

higher proportion than most other otariids (which exceed their ADL for only 4–10% of dives; 

Chilvers et al. 2006). NZ sea lions that exhibit benthic diving profiles are estimated to exceed their 

ADL on 82% of dives, compared with 51% for meso-pelagic divers (Chilvers 2008). 

Chilvers et al. (2006) and Chilvers and Wilkinson (2009) suggested that the long, deep diving 

behaviour, the propensity to exceed their estimated ADL, and differences in physical condition and 

age at first reproduction from animals at Otago together indicate that females from the Auckland 

Islands may be foraging at or near their physiological limits. However, Bowen (2012) suggested a 

lack of relationship between surface time and anaerobic diving would seem to indicate that ADL has 

been underestimated. Further, given a number of studies of diving behaviour were conducted during 

20


early lactation when the demands of offspring are less than they would be later in lactation, Bowen 

(2012) considered it unlikely that females are operating at or near a physiological limit. 

Adult females at Otago are generally heavier for a given age, breed earlier, undertake shorter foraging 

trips, and have shallower dive profiles compared with females from the Auckland Islands (Table 3.1). 

Any observed differences may reflect differences in environment between the Auckland Islands and 

the Otago peninsula, a founder effect, or a combination of these or other factors. 

Table 3.1: Comparison of select characteristics between adult female NZ sea lions from the Auckland Islands and 

those from the Otago peninsula (Chilvers et al. 2006, Augé et al. 2011a, 2011b, 2011c). Data are means ± SE (where 

available). 

Characteristic Auckland Islands Otago 

Reproduction at age 4 < 5% of females > 85% of females 

Average mass at 8-13 years of 

age 

112 kg 152 kg 

Foraging distance from shore 102.0 ± 7.7 km (max = 175 km) 4.7 ± 1.6 km (max = 25 km) 

Time spent foraging at sea 66.2 ± 4.2 hrs 11.8 ± 1.5 hrs 

Dive depth 129.4 ± 5.3 m (max = 597 m) 20.2 ± 24.5 m (max = 389 m) 

Dives estimated to exceed ADL 68.7 ± 4.4 percent 7.1 ± 8.1 percent 

NZ sea lions are generalist predators with a varied diet that includes fish (rattail, red cod, opalfish, 

hoki), cephalopods (octopus, squid), crustaceans (lobster krill, scampi), and salps (Cawthorn et al. 

1985; Childerhouse et al. 2001; Meynier et al. 2009). The three main methods used to assess NZ sea 

lion diets involve analyses of stomach contents, scats and regurgitate, and the fatty acid composition 

of blubber (Meynier et al. 2008). Stomach contents of by-caught animals tend to be biased towards 

the target species of the fishery concerned (e.g. squid in the SQU6T fishery), whereas scats and 

regurgitates are biased towards less digestible prey (Meynier et al. 2008). Stomach, scat and 

regurgitate approaches tend to reflect only recent prey (Meynier et al. 2008). By contrast, analysis of 

the fatty acid composition of blubber provides a longer-term perspective on diets ranging from weeks 

to months (although individual prey species are not identifiable). This approach suggests that the diet 

of female NZ sea lions tends to include proportionally more arrow squid (Nototodarus sloanii) and 

proportionally less red cod (Pseudophycis bachus) and scampi (Metanephrops challengeri) than for 

male NZ sea lions, while lactating and non-lactating females do not differ in their diet (Meynier et al. 

2008; Meynier 2010). 

3.2.4. Reproductive biology 

NZ sea lions exhibit marked sexual dimorphism, with adult males being larger and darker in colour 

than adult females (Walker and Ling 1981, Cawthorn et al. 1985). Cawthorn et al. (1985) and Dickie 

(1999) estimated the maximum age of males and females to be 21 and 23 years, respectively, but 

Childerhouse et al. (2010a) recently reported a maximum estimated age for females of 28 years 

(although the AEWG had some concerns about the methods used and this estimate may not be 

reliable). Although females can become sexually mature as early as age 2 and give birth the following 

year, most do not breed until they are 6 years old (Childerhouse et al. 2010a). Males generally reach 

sexual maturity at 4 years of age, but because of their polygynous colonial breeding strategy (i.e., 

males actively defend territories and mate with multiple females within a harem) they are only able to 

successfully breed at 7–9 years old, once they have attained sufficient physical size (Marlow 1975, 

Cawthorn et al. 1985). Reproductive rate in females increases rapidly between the ages of 3 and 7, 

reaching a plateau until the age of approximately 15 and declining rapidly thereafter, with the 

maximum recorded age at reproduction being 26 years (Breen et al. 2010, Childerhouse et al. 2010b, 

Chilvers et al. 2010). Chilvers et al. (2010) estimated from tagged sea lions that the median lifetime 

21


reproductive output of a female NZ sea lion was 4.4 pups, and 27% of all females that survive to age 

3 never breed. Analysis of tag-resight data from female New Zealand sea lions on Enderby Island 

indicates average annual breeding probability is approximately 0.30-0.35 for prime-age females that 

did not breed in the previous year (ranges reflect variation relating to the definition of breeders) and 

0.65-0.68 for prime-age females that did breed in the previous year (MacKenzie 2011). 

NZ sea lions are philopatric (i.e., they return to breed at the same location where they were born, 

although more so for females than males). Breeding is highly synchronised and starts in late 

November when adult males establish territories for their harems (Robertson et al. 2006, Chilvers and 

Wilkinson 2008). Pregnant and non-pregnant females appear at the breeding colonies in December 

and early January, with pregnant females giving birth to a single pup in late December before entering 

oestrus 7–10 days later and mating again (Marlow 1975). Twin births and the fostering of pups in NZ 

sea lions are rare (Childerhouse and Gales 2001). Shortly after the breeding season ends in mid- 

January, the harems break up with the males dispersing offshore and females often moving away from 

the rookeries with their pups (Marlow 1975, Cawthorn et al. 1985). 

Pups at birth weigh 8–12 kg with parental care restricted to females (Walker and Ling 1981, 

Cawthorn et al. 1985, Chilvers et al. 2006). Females remain ashore for about 10 days after giving 

birth before alternating between foraging trips lasting approximately two days out at sea and returning 

for about one day to suckle their pups (Gales and Mattlin 1997, Chilvers et al. 2005). New Zealand 

pup growth rates are lower than those reported for other sea lion species, and may be linked to a 

relatively low concentration of lipids in the females’ milk during early lactation (Riet-Sapriza et al. 

2012, Chilvers 2008). Pups are weaned after about 10–12 months (Marlow 1975, Gales and Mattlin 

1997). 

3.2.5. Population biology 

For NZ sea lions, the overall size of the population is indexed using estimates of the number of pups 

that are born each year (Chilvers et al. 2007). Since 1995, the Department of Conservation (DOC) has 

conducted mark-recapture counts at each of the main breeding colonies at the Auckland Islands to 

estimate annual pup production (i.e., the total number of pups born each year, including dead and live 

animals; Robertson and Chilvers 2011). The data show a decline in pup production from a peak of 

3021 in 1997/98 to a low of 1501 ± 16 pups in 2008/09 (Chilvers and Wilkinson 2011, Robertson and 

Chilvers 2011; Table 3.2), with the largest single-year decline (31%) occurring between the 2007/08 

and 2008/09 counts. The most recent estimate of pup production for the Auckland Islands population 

was 1683 ± 16 pups in 2011/12 (Chilvers 2012a) and a project is underway to obtain a comparable 

estimate for 2012/13 (POP2012-01). 

Total NZ sea lion abundance (including pups) at the Auckland Islands has been estimated using 

Bayesian population models (Breen et al. 2003, Breen and Kim 2006a, Breen and Kim 2006b, Breen 

et al. 2010). Although other abundance estimates are available (e.g. Gales and Fletcher 1999), the 

integrated models are preferred because they take into account a variety of age-specific factors 

(breeding, survival, maturity, vulnerability to fishing, and the proportion incidentally captured by 

fishing), as well as data on the re-sighting of tagged animals and pup production estimates, to generate 

estimates of the overall size of the NZ sea lion population inhabiting the Auckland Islands (Table 

3.2). The most recent estimate of NZ sea lion abundance for the Auckland Islands population was 

12 065 animals (90% CI: 11 160–13 061) in 2009. The integrated model suggested a net decline at the 

Auckland Islands of 23% between 1995 and 2009, or 29% between the maximum estimated 

population size in 1998 and 2009. 

22


Table 3.2: Pup production and population estimates of NZ sea lions from the Auckland Islands from 1995 to 2010. 

Pup production data are direct counts or mark-recapture estimates from Chilvers et al. (2007), Robertson and 

Chilvers (2011) and Chilvers (2012a). Standard errors only apply to the portion of pup production estimated using 

mark-recapture methods. Population estimates from P. Breen, estimated in the model by Breen et al. 2010. Year 

refers to the second year of a breeding season (e.g., 2010 refers to the 2009-10 season). 

Year Pup production estimate Population size estimate 

Mean Standard error (for mark Median 90% confidence 

recapture estimates) 

interval 

1995 2 518 21 15 675 14 732–16 757 

1996 2 685 22 16 226 15 238–17 318 

1997 2 975 26 16 693 15 656–17 829 

1998 3 021 94 16 911 15 786–18 128 

1999 2 867 33 15 091 13 932–16 456 

2000 2 856 43 15 248 14 078–16 586 

2001 2 859 24 15 005 13 870–16 282 

2002 2 282 34 13 890 12 856–15 079 

2003 2 518 38 14 141 13 107–15 295 

2004 2 515 40 14 096 13 057–15 278 

2005 2 148 34 13 369 12 383–14 518 

2006 2 089 30 13 110 12 150–14 156 

2007 2 224 38 13 199 12 231–14 215 

2008 2 175 44 12 733 11 786–13 757 

2009 1 501 16 12 065 11 160–13 061 

2010 1 814 36 

2011 1 550 5 41 

2012 1 683 16 

For the Campbell Island population, pup production was estimated at 681–726 pups in 2010 

(Robertson and Chilvers 2011, Maloney et al. 2012). Pup production estimates at Campbell Island are 

increasing over time, although there have been changes to the methodology (Maloney et al. 2009). 

Previous estimates of total pup production were: 150 in 1992/93; 385 in 2003; and 583 in 2007-08 

(Cawthorn 1993, Childerhouse et al. 2005, Maloney et al. 2009). There were also minimum pup 

counts of 51 in 1987/88, 122 in 1991/92 and 78 (from a partial count) in 1997/98 (Moore and Moffat 

1990, McNally et al. 2001, M. Fraser, unpubl. data cited in Maloney et al. 2009). 

For the Otago sub-population, annual pup production has ranged from 0 to 7 pups since the 1994/95 

breeding season, with five pups recorded in 2010/11 (McConkey et al. 2002, Augé 2011). A 

modelling exercise suggested that this population can expand to 9–22 adult females by 2018 (Lalas 

and Bradshaw 2003). The sub-population at Otago is of special interest because it highlights the 

potential for establishing new breeding colonies, in this case from a single pregnant female 

(McConkey et al. 2002). 

Established anthropogenic sources of mortality in NZ sea lion include: historic subsistence hunting 

and commercial harvest (Gales 1995, Childerhouse and Gales 1998); pup entrapment in rabbit 

burrows prior to rabbit eradication from Enderby Island in 1993 (Gales and Fletcher 1999); human 

disturbance, including attacks by dogs, vehicle strikes and deliberate shooting on mainland New 

Zealand (Gales 1995); and fisheries bycatch (see below). 

In addition to the established effects, there are a number of other anthropogenic effects that may also 

influence NZ sea lion mortality. However their role, if any, is presently unclear. These include: 

possible competition for resources between NZ sea lions and the various fisheries (Robertson and 

5 Due to extreme weather conditions there was some delay in making the 2010/11 pup count which may affect 

comparability with previous years. However DOC’s analysis suggests any such effect is unlikely to be large 

(Chilvers and Wilkinson 2011). 

23


Chilvers 2011, Bowen 2012); effects of organic and inorganic pollutants, including polychlorinated 

biphenyls (PCBs), dichlorodiphenyltrichloroethane (DDT) and heavy metals such as mercury and 

cadmium (Baker 1999, Robertson and Chilvers 2011); and impacts of eco-tourism. 

Other sources of mortality include epizootics, particularly Campylobacter which killed 1600 pups 

(53% of pup production) and at least 74 adult females on the Auckland Islands in 1997/98 (Wilkinson 

et al. 2003, Robertson and Chilvers 2011) and Klebsiella pneumoniae which killed 33% and 21% of 

pups on the Auckland Islands in 2001/02 and 2002/03 respectively (Wilkinson et al. 2006). The 1998 

epizootic event may have affected the fecundity of the surviving pups; reducing their breeding rate 

relative to other cohorts (Gilbert and Chilvers 2008). There are also occurrences of predation by 

sharks (Cawthorn et al. 1985, Robertson and Chilvers 2011), starvation of pups if they become 

separated from their mothers (Walker and Ling 1981, Castinel et al. 2007), drowning in wallows and 

male aggression towards females and pups (Wilkinson et al. 2000, Chilvers et al. 2005b). 

Analysis of tag-resight data on Enderby Island yielded estimates of average annual survival for primeage 

females of 0.90 for females that did not breed and 0.95 for females that did breed, with no 

indication of a systematic change in survival during the period 1997/98 to 2010/11 (MacKenzie 

2011). Further analysis of tag-resight data is planned under DOC project POP2012-02 to determine 

the key demographic factors driving the observed population decline of New Zealand sea lions at the 

Auckland Islands. 

Despite a historic reduction in population size as a result of subsistence hunting and commercial 

harvest, the NZ sea lion population does not display low genetic diversity at microsatellite loci and 

thus does not appear to have suffered effects of genetic drift and inbreeding depression (Robertson 

and Chilvers 2011). 

3.2.6. Conservation biology and threat classification 

Threat classification is an established approach for identifying species at risk of extinction (IUCN 

2010). The risk of extinction for NZ sea lions has been assessed under two threat classification 

systems, the International Union for the Conservation of Nature (IUCN) Red List of Threatened 

Species (IUCN 2010) and the New Zealand Threat Classification System (Townsend et al. 2008). 

In 2008, the IUCN updated the Red List status of NZ sea lions, listing them as Vulnerable, A3b 6 on 

the basis of a marked (30%) decline in pup production in the last 10 years, at some of the major 

rookeries (Gales 2008). The IUCN further recommended that the species should be reviewed within a 

decade in light of what they considered to be the current status of NZ sea lions (i.e., declining pup 

production, reducing population size, severe disease outbreaks). 

In 2010, DOC updated the New Zealand Threat Classification status of all NZ marine mammals 

(Baker et al. 2010). In the revised list, NZ sea lions had their threat classification increased from At 

Risk, Range Restricted 7 to Nationally Critical under criterion C 8 with a Range Restricted qualifier 

based on the recent rate of decline (Baker et al. 2010). 

6 A taxon is listed as ‘Vulnerable’ if it is considered to be facing a high risk of extinction in the wild. A3b refers 

to a reduction in population size (A), based on a reduction of ≥ 30% over the last 10 years or three generations 

(whichever is longer up to a maximum of 100 years (3); and when considering an index of abundance that is 

appropriate to the taxon (b; IUCN 2010). 

7 A taxon is listed as ‘Range Restricted’ if it is confined to specific substrates, habitats or geographic areas of 

less than 1000 km 2 (100 000 ha); this is assessed by taking into account the area of occupied habitat of all subpopulations 

(Townsend et al. 2008). 

8 A taxon is listed as ‘Nationally Critical’ under criterion C if the population (irrespective of size or number of 

sub-populations) has a very high (rate of) ongoing or predicted decline; greater than 70% over 10 years or three 

generations, whichever is longer (Townsend et al. 2008). 

24


3.3. Global understanding of fisheries interactions 

Reviews of fisheries interactions among pinnipeds globally can be found in Read et al. 2006, 

Woodley and Lavigne (1991), Katsanevakis (2008) and Moore et al. (2009). Because NZ sea lions are 

endemic to New Zealand, the global understanding of fisheries interactions for this species is outlined 

under state of knowledge in New Zealand. For related information on fishing interactions for NZ fur 

seals, both within New Zealand and overseas, see the NZ fur seal chapter. 

3.4. State of knowledge in New Zealand 

NZ sea lions interact with trawl fisheries resulting in incidental bycatch, specifically from animals 

being caught and drowned in the trawl nets. These interactions are largely confined to trawl fisheries 

in Sub-Antarctic waters (Figure 3.1); particularly the Auckland Islands arrow squid fishery (SQU6T), 

but also the Auckland Islands scampi fishery (SCI6A), other Auckland Islands trawl fisheries, the 

Campbell Island southern blue whiting (Micromesistius australis) fishery (SBW6I) and the Stewart- 

Snares shelf fisheries targeting mainly arrow squid (SQU1T; Thompson and Abraham 2010, 

Thompson et al. 2011, Thompson et al. 2012). 9 

NZ sea lions forage to depths of up to 600 m (Table 3.1), within the habitat where depth ranges for 

prey species range from 0–500 m for arrow squid, 250–600 m for spawning southern blue whiting and 

350–550 m for scampi (Tuck 2009, Ministry of Fisheries 2011). There is seasonal variation in the 

distribution overlap between NZ sea lions and the target species fisheries (Table 3.3). Breeding male 

sea lions, breeding ashore between November and January with occasional trips to sea, then migrate 

away from the Auckland island area (Robertson et al. 2006). Breeding females are in the Auckland 

island area year round, ashore to give birth for up to 10 days during December and January and then 

dividing their time between foraging at sea (~2days) and suckling their pup ashore (~1.5 days; 

Chilvers et al. 2005a).The SQU6T fishery currently operates between February and July, peaking 

between February and May, whereas the SQU1T fishery operates between December and May, 

peaking between January and April, before the squid spawn. The SBW6I fishery operates in August 

and September, peaking in the latter month, when the fish aggregate to spawn. The SCI6A fishery 

may operate at any time of the year but does not operate continuously. 

3.4.1. Quantifying fisheries interactions 

Since 1988, the level of NZ sea lion bycatch has been monitored by government observers aboard a 

proportion of the fishing fleet in the SQU6T fishery (Wilkinson et al. 2003), generally amounting to 

around 20–40% observer coverage between 1995 and 2010 but reaching almost 100% during the 

2001/02 season (see Table 3.4). Over the same period, there has also been 1–15% observer coverage 

for non-squid trawl fisheries operating around the Auckland Islands (primarily targeting scampi, but 

also jack mackerel, orange roughy and hoki), 20–60% observer coverage in the Campbell Island 

southern blue whiting fishery, and 8–43% observer coverage for the Stewart-Snares shelf trawl 

fisheries (primarily targeting squid, but also hoki, jack mackerel and barracouta; Table 3.4). 

Unobserved trips have tended to report NZ sea lion captures at a lower rate than observed trips across 

all observed fisheries. Fishers reported 177 NZ sea lion captures between 1998–99 and 2008–09, 

while observers reported 196 captures over the same period (Abraham and Thompson 2011). 

Observers observed an overall average of 4.7–11.2% of trawl tows each year over this time period, 

but fisheries where most sea lions are caught had higher observer coverage. 

9 See the Report from the Fisheries Assessment Plenary, May 2011 (Ministry of Fisheries 2011) for further 

information regarding the biology and stock assessments for these species. 

25


Table 3.3: Monthly distribution of NZ sea lion activity and the main trawl fisheries with observed reports of NZ sea 

lion incidental captures (see text for details). 

NZ sea lions Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug 

Breeding males 

Breeding 

females 

Dispersed at sea 

or at haulouts 

At sea 

At breeding colony Dispersed at sea or at haulouts 

At breeding 

colony 

26 

At breeding colony and at-sea foraging and suckling 

Pups At sea At breeding colony 

Non-breeders Dispersed at sea, at haulouts, or breeding colony periphery 

Major fisheries Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug 

Squid Stewart- 

Snares Shelf 

Southern blue 

whiting 

Pukaki Rise and 

Campbell Rise 

Auckland Islands and 

Stewart-Snares Shelf 

Scampi Auckland Islands 

Auckland 

Islands 

Bounty 


The number of NZ sea lion captures reported by observers has been incorporated in increasingly 

sophisticated models to estimate the total number of captures across the entire fishing fleet in each 

fishing year (Smith and Baird 2007b, Thompson and Abraham 2010, Abraham and Thompson 2011). 

This approach is currently applied using information collected under DOC project INT2012-01 and 

analysed under MPI project PRO2010-01 (Thompson et al. 2011, Thompson et al. 2012). Estimates in 

Table 3.4 for the SQU6T and Campbell Island fisheries were generated using Bayesian models, 

whereas those for the Stewart-Snares and the Auckland Islands scampi and Auckland Islands other 

fisheries were generated using ratio estimates (Thompson et al. 2012). Captures comprise the number 

of NZ sea lions brought on deck (both dead and alive), and necessarily exclude the unknown fraction 

of animals that exit trawls through Sea Lion Exclusion Devices (SLEDs) as well as those that were 

decomposed upon capture or that climbed aboard vessels (Smith and Baird 2007b, Thompson and 

Abraham 2010 Thompson et al. 2011). Only 8 of the 248 captures from 1995/96 to 2008/09 were 

released alive (Thompson and Abraham 2010). Interactions are defined as the number of sea lion that 

would have been caught if no SLEDs were used (Thompson et al. 2012). 

In the years since SLEDs were introduced in the SQU6T fishery, both the observed and estimated 

numbers of NZ sea lion captures have declined overall, except for a slight increase in 2009/10 (Table 

3.4). Conversely, for those other fisheries where SLEDs are not deployed, observed and estimated 

numbers of NZ sea lion captures increased in the Campbell Island southern blue whiting fishery to a 

peak in 2010 (Table 3.4). For the Stewart-Snares and the Auckland Islands non-squid fisheries, the 

observed and estimated numbers of NZ sea lion captures have fluctuated without trend (Table 3.4). 

Capture rate is defined as the number of NZ sea lions caught per 100 tows. Strike rate is defined as the 

number of NZ sea lions that would be caught per 100 tows if no SLEDs were fitted. Models indicate 

that the interaction rate of female NZ sea lions (equivalent to the capture rate were no SLEDs fitted) is 

influenced by a number of factors including year, distance from rookery, tow duration, and change of 

tow direction (Smith and Baird 2005). Conversely, the interaction rate of male NZ sea lions is


influenced by year, the number of days into the fishery (males leave the rookeries soon after mating 

whereas females remain with the pups), and time of day (Smith and Baird 2005). 

Figure 3.1: Distribution of trawl fishing effort and observed NZ sea lion captures, 2002-03 to 2010-11 

(http://data.dragonfly.co.nz/psc/). Fishing effort is mapped into 0.2-degree cells, with the colour of each cell being 

related to the amount of effort. Observed fishing events are indicated by black dots, and observed captures are 

indicated by red dots. Fishing is only shown if the effort could be assigned a latitude and longitude, and if there were 

three or more vessels fishing within a cell. In this case, 96.0% of the effort is shown. 

27


Table 3.4a: Effort, observed and estimated NZ sea lion captures in trawl fisheries by fishing year in the New Zealand EEZ (http://data.dragonfly.co.nz/psc/). For each fishing year, 

the table gives the the total number of tows; the observer coverage (the percentage of tows that were observed); the number of observed captures (both dead and alive); the capture 

rate (captures per hundred tows); the estimation method used (model, ratio or both combined); the mean number of estimated total captures (with 95% confidence interval); the 

mean number of estimated total interactions (with 95% confidence interval), and the stike rate (interactions per hundred tows). For more information on the methods used to 

prepare the data, see Thompson et al. (2012). 

Fishing year Fishing effort 

Observed captures 

28 

Estimated captures 

Estimated interations 

Estimatedstrike rate 

All effort % obs Number Rate Method Mean 95% c.i. Mean 95% c.i. Mean 95% c.i. 

Trawl fisheries 

1995–96 10 081 10 

16 1.5 

Both 148 85–242 

148 85–243 

1.5 0.8–2.4 

1996–97 10 941 15 

28 1.7 

Both 155 104–221 

155 102–225 

1.4 0.9–2.1 

1997–98 9 964 14 

14 1.0 

Both 76 47–119 

76 45–121 

0.8 0.5–1.2 

1998–99 10 551 16 

6 0.4 

Both 33 20–49 

33 19–50 

0.3 0.2–0.5 

1999–00 9 043 22 

28 1.4 

Both 88 63–129 

89 59–130 

1.0 0.7–1.4 

2000–01 8 910 40 

46 1.3 

Both 61 52–72 

83 59–111 

0.9 0.7–1.2 

2001–02 9 945 19 

23 1.2 

Both 64 46–88 

94 61–139 

0.9 0.6–1.4 

2002–03 8 308 19 

11 0.7 

Both 34 22–48 

62 37–97 

0.7 0.4–1.2 

2003–04 10 033 23 

21 0.9 

Both 61 43–85 

214 120–376 

2.1 1.2–3.7 

2004–05 11 109 23 

14 0.5 

Both 53 36–77 

181 94–325 

1.6 0.8–2.9 

2005–06 9 316 21 

14 0.7 

Both 52 35–75 

174 86–334 

1.9 0.9–3.6 

2006–07 6 728 24 

15 0.9 

Both 47 32–66 

118 59–235 

1.8 0.9–3.5 

2007–08 6 545 33 

8 0.4 

Both 29 18–42 

118 35–418 

1.8 0.5–6.4 

2008–09 6 677 27 

3 0.2 

Both 22 12–36 

103 25–383 

1.5 0.4–5.7 

2009–10 5 541 34 

15 0.8 

Both 46 32–66 

141 51–439 

2.5 0.9–7.9 

2010–11 6 389 31 6 0.3 Both 29 17–43 

81 26–259 

1.3 0.4–4.1 

Auckland Islands squid 

1995–96 4 467 12 

13 2.4 

Model 131 69–226 

131 67–224 

2.9 1.6–5.0 

1996–97 3 716 19 

28 3.9 

Model 142 91–208 

142 89–210 

3.8 2.6–5.5 

1997–98 1 441 22 

13 4.2 

Model 60 33–102 

60 31–104 

4.2 2.5–6.9 

1998–99 402 38 

5 3.2 

Model 14 5–27 

15 5–29 

3.6 2.1–5.9 

1999–00 1 206 36 

25 5.7 

Model 69 45–107 

69 42–108 

5.8 4.0–8.6 

2000–01 583 99 

39 6.7 

Model 39 39–40 

61 39–87 

10.4 8.6–13.1 

2001–02* 1 648 34 

21 3.7 

Model 43 30–64 

73 43–116 

4.4 3.0–6.6 

2002–03 1 470 29 

11 2.6 

Model 19 13–29 

48 24–81 

3.2 2.0–5.1 

2003–04 2 594 30 

16 2.0 

Model 41 26–62 

194 100–356 

7.5 4.0–13.5 

2004–05^ 2 706 30 

9 1.1 

Model 31 17–51 

159 73–303 

5.9 2.7–11.1 

2005–06 2 462 28 

9 1.3 

Model 28 15–45 

149 62–308 

6.0 2.7–12.5 

2006–07 1 320 41 

7 1.3 

Model 16 9–27 

87 29–201 

6.6 2.3–14.8 

2007–08 1 265 46 

5 0.9 

Model 12 6–21 

101 19–396 

8.0 1.6–30.9 

2008–09 1 925 40 

2 0.3 

Model 8 3–17 

89 12–365 

4.6 0.7–18.4 

2009–10 1 190 25 

3 1.0 

Model 13 5–27 

107 18–402 

9.0 1.7–33.6 

2010–11 1 586 34 0 – Model 4 0–11 

56 4–233 

3.5 0.4–14.9 

* SLEDs introduced. ^ SLEDs standardised and in widespread use.

AEBAR 2012: Protected species: Sea lions 

Table 3.4b: Effort, observed and estimated NZ sea lion captures in trawl fisheries by fishing year in the New Zealand 

EEZ (http://data.dragonfly.co.nz/psc/). For each fishing year, the table gives the the total number of tows; the 

observer coverage (the percentage of tows that were observed); the number of observed captures (both dead and 

alive); the capture rate (captures per hundred tows or per thousand hooks); the estimation method used (model, ratio 

or both combined); and the mean number of estimated total captures (with 95% confidence interval). For more 

information on the methods used to prepare the data, see Thompson et al. (2012). 

Fishing year Fishing effort Observed captures Estimated captures 

All effort % obs Number Rate Method Mean 95% c.i. 

Auckland Islands scampi 

1995-96 1 303 5 

2 3.2 

Ratio 11 4–19 

1996-97 1 222 15 

0 - 

Ratio 7 2–15 

1997-98 1 107 11 

0 - 

Ratio 7 1–15 

1998-99 1 254 2 

0 - 

Ratio 9 2–18 

1999-00 1 383 5 

0 - 

Ratio 9 3–18 

2000-01 1 417 6 

4 4.8 

Ratio 14 7–23 

2001-02 1 604 9 

0 - 

Ratio 10 3–20 

2002-03 1 351 11 

0 - 

Ratio 9 2–17 

2003-04 1 363 12 

3 1.8 

Ratio 12 5–20 

2004-05 1 275 0 

NA NA 

Ratio 9 3–18 

2005-06 1 331 9 

1 0.9 

Ratio 10 3–18 

2006-07 1 328 7 

1 1.1 

Ratio 10 4–19 

2007-08 1 327 7 

0 - 

Ratio 9 2–18 

2008-09 1 457 4 

1 1.6 

Ratio 11 4–21 

2009-10 940 10 

0 - 

Ratio 6 1–13 

2010-11 

Auckland Islands other 

1 401 15 0 - Ratio 9 2–17 

1995-96 405 6 

1 4.0 

Ratio 3 1–6 

1996-97 296 4 

0 - 

Ratio 1 0–4 

1997-98 684 17 

1 0.9 

Ratio 3 1–8 

1998-99 525 10 

1 1.8 

Ratio 3 1–7 

1999-00 750 13 

0 - 

Ratio 3 0–8 

2000-01 577 7 

0 - 

Ratio 2 0–7 

2001-02 589 4 

0 - 

Ratio 2 0–7 

2002-03 543 13 

0 - 

Ratio 2 0–7 

2003-04 289 17 

0 - 

Ratio 1 0–4 

2004-05 170 7 

0 - 

Ratio 1 0–3 

2005-06 39 15 

0 - 

Ratio 0 0–1 

2006-07 38 5 

0 - 

Ratio 0 0–1 

2007-08 147 45 

0 - 

Ratio 0 0–2 

2008-09 121 50 

0 - 

Ratio 0 0–2 

2009-10 77 66 

0 - 

Ratio 0 0–1 

2010-11 131 37 0 - Ratio 0 0–2 

29


Table 3.4c: Effort, observed and estimated NZ sea lion captures in trawl fisheries by fishing year (calendar year for 

SBW) in the New Zealand EEZ (http://data.dragonfly.co.nz/psc/). For each fishing year, the table gives the the total 

number of tows; the observer coverage (the percentage of tows that were observed); the number of observed captures 

(both dead and alive); the capture rate (captures per hundred tows or per thousand hooks); the estimation method 

used (model, ratio or both combined); and the mean number of estimated total captures (with 95% confidence 

interval). For more information on the methods used to prepare the data, see Thompson et al. (2012). 


All effort % observed Number Rate Type Mean 95% c.i. 

Campbell Island SBW 

1996 474 27 

0 - Model 0 0–4 

1997 641 34 

0 - Model 1 0–3 

1998 963 28 

0 - Model 1 0–5 

1999 788 28 

0 - Model 1 0–5 

2000 447 52 

0 - Model 0 0–3 

2001 672 60 

0 - Model 0 0–2 

2002 980 28 

1 0.4 Model 4 1–11 

2003 599 43 

0 - Model 1 0–3 

2004 690 34 

1 0.4 Model 3 1–9 

2005 726 37 

2 0.7 Model 5 2–12 

2006 521 28 

3 2.1 Model 10 3–21 

2007 544 32 

6 3.5 Model 15 6–29 

2008 557 41 

2 0.9 Model 8 5–14 

2009 627 20 

0 - Model 1 0–7 

2010 550 43 

11 4.7 Model 24 15–36 

2011 815 40 6 1.8 Model 15 8–25 

Stewart-Snares (mainly squid) 

1995-96 3432 8 

0 - 

Ratio 3 0–7 

1996-97 5066 10 

0 - 

Ratio 4 0–9 

1997-98 5769 10 

0 - 

Ratio 5 1–10 

1998-99 7582 16 

0 - 

Ratio 6 1–13 

1999-00 5257 23 

3 0.3 

Ratio 7 3–12 

2000-01 5661 43 

3 0.1 

Ratio 6 3–10 

2001-02 5124 18 

1 0.1 

Ratio 5 1–10 

2002-03 4345 16 

0 - 

Ratio 3 0–8 

2003-04 5097 21 

1 0.1 

Ratio 5 1–10 

2004-05 6232 24 

3 0.2 

Ratio 7 4–13 

2005-06 4963 19 

1 0.1 

Ratio 5 1–10 

2006-07 3498 24 

1 0.1 

Ratio 4 1–7 

2007-08 3249 36 

1 0.1 

Ratio 3 1–7 

2008-09 2547 31 

0 - 

Ratio 2 0–5 

2009-10 2784 43 

1 0.1 

Ratio 3 1–6 

2010-11 2456 36 0 - Ratio 1 0–4 

3.4.2. Managing fisheries interactions 

For NZ sea lions, efforts to mitigate fisheries bycatch have focused on the SQU6T fishery. Spatial 

and/or temporal closures have been put in place, SLEDs were developed by industry, codes of 

practice were introduced, and mortality limits imposed. In 1982 the Minister of Fisheries established a 

12 nautical mile exclusion zone around the Auckland Islands from which all fishing activities were 

excluded (Wilkinson et al. 2003). In 1995, the exclusion zone was replaced with a Marine Mammal 

Sanctuary with the same controls on fishing (Chilvers 2008). The area was subsequently also 

designated as a Marine Reserve in 2003. In addition to these area-based measures, mitigation devices 

in the form of SLEDs were introduced in the SQU6T fishing fleet in 2001/02 (Figure 3.2), with 

widespread and standardised use by all the fleet since 2004/05. The use of SLEDs is not mandatory, 

but is required by the current industry body (the Deepwater Group), fleet wide in application and 

monitored by MPI observers. In 1992, the Ministry adopted a fisheries-related mortality limit (FRML; 

previously referred to as a maximum allowable level of fisheries-related mortality or MALFiRM) to 

set an upper limit on the number of NZ sea lions that could be incidentally drowned each year in the 

30


SQU6T trawl fishery (Chilvers 2008). If this limit is reached, the fishery may be mandatorily closed 

for the remainder of the season. This has happened seven times (1996 to1998, 2000, and 2002 to 

2004) since this plan was first adopted in 1993 (Table 3.5; Robertson and Chilvers 2011). 

Figure 3.2: Diagram of a NZ sea lion exclusion device (SLED) inside a trawl net. Image courtesy of the Deepwater 

Group. 

Before the widespread use of SLEDs, NZ sea lions incidentally caught during fishing were usually 

retained in trawl nets and hauled on board, allowing observers to gain an accurate assessment of the 

number of NZ sea lions being captured on observed tows in a given fishery. This enabled a relatively 

simple estimation of the total number of NZ sea lions killed. However, following the introduction of 

SLEDs, the number of NZ sea lions interacting with SLEDs and the proportion of those surviving are 

much more difficult to estimate. Since the introduction of SLEDs, therefore, it has become necessary 

to estimate the number of NZ sea lions interacting with trawls using a predetermined strike rate to 

monitor performance against any bycatch limits set. Using a predetermined strike rate enables the 

FRML to be converted into a number of tows for management purposes. The rate of 5.65% assumed 

by MPI for the SQU6T fishery is based on rates observed on vessels without SLEDs from 2003/04 to 

2005/06 and is also assumed as part of the fishery implementation within an integrated management 

procedure evaluation model (named the BFG model after its authors, see section 3.3.3). A strike rate 

of 5.89 will be assumed for the 2012-13 season, reflecting a slight increase in the long-term average. 

The most recent strike rates are given in Table 3.4 (Thompson et al. 2012). 

The current management regime for the SQU6T fishery provides for a “discounted” strike rate to 

apply to all tows when an approved SLED is used (because SLEDs allow some NZ sea lions to escape 

and survive their encounters with trawl nets; Thompson and Abraham 2010, see Table 3.5). The 

SLED discount rate is a fisheries management setting and should not be confused with the actual 

survival of NZ sea lions that encounter a trawl equipped with a SLED, but the discount mechanism is 

31


duplicated in the BFG simulations. The current discount rate of 82% means that the strike rate is 

reduced from 5.89% to 1.06% so that, for every 100 tows using an approved SLED, 1.06 NZ sea lions 

are presumed killed. Ideally, the discount rate would be equal to the survival rate of NZ sea lions that 

encounter a trawl in circumstances that would be fatal if no SLED were fitted. This survival rate is the 

product of the proportion of animals that exit a trawl with a SLED and their post-exit survival. 

Table 3.5: Maximum allowable level of fisheries-related mortality (MALFiRM) or fisheries-related mortality limit 

(FRML) from 1991 to 2013. Note, however, that direct comparisons among years of the limits in Table 3.5 are not 

possible because the assumptions underlying the MALFiRM or FRML changed over time. 

Year MALFiRM or Discount Management actions 

FRML rate 

1991/92 16 (female only) 

1992/93 63 

1993/94 63 

1994/95 69 

1995/96 73 Fishery closed by MFish (4 May) 

1996/97 79 Fishery closed by MFish (28 March) 


1998/99 64 


2000/01 75 Voluntary withdrawal by industry 

2001/02 79 Fishery closed by MFish (13April) 

2002/03 70 Fishery closed by MFish (29 March), overturned by High Court 

2003/04 62 (124) 20% Fishery closed by MFish (22 March), overturned by High Court FRML increased 

2004/05 115 20% Voluntary withdrawal by industry on reaching the FRML 

2005/06 97 (150) 20% FRML increased in mid-March due to abundance of squid 

2006/07 93 20% 

2007/08 81 35% 

2008/09 113 (95) 35% Lower interim limit agreed due to the decrease in pup numbers 

2009/10 76 35% 

2010/11 68 35% 

2011/12 68 35% 

2012/13 68 82% 

In 2004, the Minister of Fisheries requested that the squid fishery industry organisation (Squid Fishery 

Management Company), government agencies and other stakeholders with an interest in sea lion 

conservation work collaboratively to develop a plan of action to determine SLED efficacy. In 

response, an independently chaired working group (the SLED Working Group) was established to 

develop an action plan to determine the efficacy of SLEDs, with a particular focus on the survivability 

of NZ sea lions that exit the nets via the exit hole in the SLED. The group undertook a number of 

initiatives, most notably the standardisation of SLED specifications (including grid spacing) across 

the fleet (Clement and Associates Ltd. 2007) and the establishment of an underwater video monitoring 

programme to help understand what happens when a NZ sea lion exits a SLED. White light and infrared 

illuminators were tested. Sea lions were observed outside the net on a number of occasions, but 

only one fur seal and one NZ sea lion were observed exiting the net via the SLED (on tows when 

white light illumination was used). The footage contributed to understanding of SLED performance, 

but established that video monitoring was only suitable for tows using mid water gear, as the camera 

view was often obscured on tows where bottom gear was used. The SLED Working Group was 

disbanded in early 2010. 

The original “MALFiRM” was calculated using the potential biological removal approach (PBR; 

Wade 1998) and was used from 1992/93 to 2003/04 (Smith and Baird 2007a). Since 2003/04 the 

FRML has been translated into a maximum permitted number of tows after which the SQU6T fishing 

32


season may be halted by the Minister regardless of the observed NZ sea lion mortality. This approach 

has been taken because NZ sea lion mortality can no longer be monitored directly since the 

introduction of SLEDs. 

3.4.3. Modelling population-level impacts of fisheries interactions 

The population-level impact of fisheries interactions has been assessed for the Auckland Islands via a 

management procedure evaluation model for the SQU6T fishery (see below). The impact of fisheries 

interactions for all NZ sea lion populations (and other marine mammal populations) will be assessed 

as part of the marine mammal risk assessment project (PRO2012-02). The goal of this project is to 

assess the risk posed to marine mammal populations from New Zealand fisheries by applying a 

similar approach to the recent seabird risk assessment (Richard et al. 2011). In this approach, risk is 

defined as the ratio of total estimated annual fatalities due to bycatch in fisheries, to the level of PBR 

(Wade 1998). The results of this project should be available in 2014. 

Since 2000, an integrated Bayesian management procedure evaluation model having both population 

and fishery components has been used to assess the likely performance of a variety of management 

control rules, each of which can be used to determine the FRML for a given SQU6T season (Breen et 

al. 2003, Breen and Kim 2006a, Breen and Kim 2006b, and Breen, Fu and Gilbert 2010). The model 

underwent several iterations. An early version, developed in 2000/01, was a relatively simple 

deterministic, partially age-structured population model with density-dependence applied to pup 

production (Breen et al. 2003). An updated version called the Breen-Kim model was built in 2003 to 

render it fully age-structured and to incorporate various datasets supplied by DOC (Breen and Kim 

2006a, 2006b). This model was further revised in 2007/08 to incorporate the latest NZ sea lion 

population data and to address various model uncertainties and called the BFG model (after its 

authors, Breen, Fu and Gilbert 2010). In 2009, the model was again updated to incorporate the low 

NZ sea lion pup counts observed in 2008/09 (and thus better reflect the observed variability in pup 

survival and pupping rates), as well as NZ sea lion bycatch that occurs in fisheries other than SQU6T. 

The BFG model was re-run in 2011 using the same underlying data and structure as in 2009 to 

evaluate the effect of different model assumptions about the survival of NZ sea lions that exit trawl 

nets via SLEDs (see below). Additional details on the NZ sea lion population model can be found in 

Breen et al. (2010). 

The BFG model incorporates various population dynamics observations (tag re-sighting observations, 

pup births and mortality, age at maturity) as well as bycatch counts and catch-at-age data from the 

SQU6T trawl fishery. The model was projected into the future by applying the observed dynamics 

and a virtual fishery model that is managed in roughly the same way as the real SQU6T fishery. A 

large number of projections were run and used to assess the likely performance of a wide range of 

different management control rules against the four performance criteria described in Context (two 

MFish criteria and two DOC criteria). For each set of runs the population indicators were summarised 

and the rules compared in tables. The BFG model is sensitive to several key parameters (see Sources 

of uncertainty, below) and is scheduled to be reviewed in 2013. 

SLEDs are effective in allowing most NZ sea lions to exit a trawl but some are retained and drowned 

and others may not survive the encounter. An experimental approach to assessing non-retained fatality 

rate involved intentionally capturing animals as they exited the escape hole of a SLED between 

1999/2000 and 2002/03. Cover nets were added over the escape holes of some SLEDs and sea lions 

were restrained in these nets after they exited the SLED proper. An underwater video camera was 

deployed in 2001 to assess the behaviour and the likelihood of post-exit survival of those animals that 

were retained in the cover nets (Wilkinson et al. 2003, Mattlin 2004). The low number of captures 

filmed and the inability to assess longer term survival meant that this approach could not be used to 

determine likely survival rates (e.g., Roe 2010). 

33


Necropsies were conducted on animals recovered from the cover net trials and on those incidentally 

caught and recovered from vessels operating in the SQU6T, SQU1T and SBW6I fisheries. Although 

all of the NZ sea lions returned for necropsy died as a result of drowning rather than physical trauma 

(from interactions with the trawl gear including the SLED grid; Roe and Meynier 2010, Roe 2010), 

necropsies were designed to assess the nature and severity of trauma sustained during capture and to 

infer the survival prognosis had those animals been able to exit the net (Mattlin 2004). However, 

problems associated with this approach limited the usefulness of the results. For example, NZ sea 

lions were frozen on vessels and stored for periods of up to several months before being thawed for 3– 

5 days to allow necropsy. Roe and Meynier (2010) concluded that this freeze-thaw process created 

artefactual lesions that mimic trauma but, particularly in the case of brain trauma, could also obscure 

real lesions. Further, two reviews in 2011 concluded that the lesions in retained animals may not be 

representative of the injuries sustained by animals that exit a trawl via a SLED (Roe and Meynier 

2010, Roe 2010). As a result of these reviews, the use of necropsies to infer the survival of sea lions 

interacting with SLEDs was discontinued. 

Notwithstanding the limitations of the necropsy data in assessing trauma for previously frozen 

animals, it was possible to determine that none of the necropsied animals sustained sufficient injuries 

to the body (excluding the head) to compromise survival (Roe and Meynier 2010, Roe 2010). Head 

trauma, most likely due to impacts with the SLED grid, could not be ruled out as a potential 

contributing factor (Roe and Meynier 2010, Roe 2010). In order to quantify the likelihood of a NZ sea 

lion experiencing physical trauma sufficient to render the animal insensible (and therefore likely to 

drown) after a colliosion with a SLED grid, a number of factors need to be assessed. These include 

the likelihood of a head-first impact, the speed of impact, the angle of impact relative to individual 

grid bars and relative to the grid plane, the location of impact on the grid, head mass, and the risk of 

brain injury for a given impact speed and head mass. The effect of multiple impacts also needs to be 

considered. Estimates for each of these factors were derived from a number of sources, including 

necropsies (for head mass), video footage of Australian fur seals interacting with Seal Exclusion 

Devices (SEDs) (for impact speed, location and body orientation) and biomechanical modelling of 

impacts on the SLED grid (for the risk of brain injury). 

In the absence of sufficient video footage of NZ sea lion interacting with SLEDs, footage of fur seals 

(thought to be Australian fur seals) interacting with SEDs in the Tasmanian small pelagic mid-water 

trawl fishery has been used (Lyle 2011). The SEDs are similar, but not identical, to the New Zealand 

SLEDs in that both have sloping steel grids to separate the catch from pinnipeds and guide the latter 

toward an escape hole in the trawl. The angle of slope and the number of sections in the steel grids are 

variable (either two or three sections, depending on the vessel). Lyle and Willcox (2008) conducted a 

camera trial between January 2006 and February 2007 to assess the efficacy of the SED and 

documented 457 interactions for about 170 individual fur seals. Lyle (2011) reanalysed the footage to 

estimate impact speed, impact location across the SED grid and body orientation at the time of 

impact. The situation faced by NZ sea lions in a squid trawl is not identical to that faced by the fur 

seals studied by Lyle and co-workers, but these are closely related otariids of similar size and, in the 

absence of specific data, Australian fur seals are considered a reasonable proxy to estimate impact 

speed, impact location and body orientation. 

The risk of brain injury was assessed by biomechanical testing and modelling. Tests using an artificial 

“head form” (as used in vehicular “crash test” studies) were used to assess the likelihood of brain 

injury to NZ sea lions colliding with a SLED grid (Ponte et al. 2010, 2011). In an initial trial (Ponte et 

al. 2010), the head form (weighing 4.8 kg) was launched at three locations on the SLED grid at a 

speed of 10 m.s -1 (about 20 knots). This was considered a “worst feasible case” collision representing 

the combined velocities of a sea lion swimming with a burst speed of 8 m.s -1 (after Ray 1963, Fish 

2008) and a net being towed at 2 m.s -1 (about 4 knots). A head injury criterion (HIC, a predictor of the 

risk of brain injury) was calculated based on criteria validated against human-vehicle impact studies 

and translated into the probability of mild traumatic brain injury (MTBI) for a given collision, taking 

into account differences between human and sea lion head and brain masses. MTBI is assumed to 

have the potential to lead to insensibility or disorientation and subsequent death through drowning for 

34


a NZ sea lion experiencing such an injury at depth. Ponte et al. (2010) calculated that a collision at the 

stiffest part of the SLED grid at this highest feasible speed had a very high risk of MTBI, especially 

for smaller sea lions. This provides an upper bound for the assessment of risk but Ponte et al. (2010) 

also imputed risk at speeds below the maximum. 

In a follow-up study, after a research advisory group meeting with other experts, Ponte et al. (2011) 

tested a wider variety of impact locations on the grid and various angles of impact relative to the bars 

and to the plane of the grid and combined these to produce a HIC “map” for a SLED grid. This HIC 

map can be used to estimate the risk of MTBI for a collision by a sea lion at any given speed, location, 

and orientation. 

The data collected from the footage of Australian fur seal SED interactions (Lyle 2011) and the 

biomechanical modelling (Ponte et al. 2010, 2011) were combined in a simulation-based probabilistic 

model to estimate the risk of a sea lion suffering a mild traumatic brain injury when striking a SLED 

grid (Abraham 2011). The simulation involved selecting an impact location on the SLED grid (from 

the fur seal data), selecting a head mass (from NZ sea lion necropsy data) and an impact speed (from 

the fur seal data), calculating the head impact criterion (HIC) (from the HIC map), scaling the HIC to 

the head mass and impact speed and calculating the expected probability of mild traumatic brain 

injury, MTBI. Both 45° and 90° degree impacts were considered, with the former, reflecting the angle 

of a grid when deployed, adopted as the base case. The head masses used may be at the lower end of 

the range of head masses for NZ sea lions. Impact speeds were drawn from the distribution of speeds 

observed for fur seals colliding with SEDs (2–6 m.s -1 ) and these are broadly consistent with the 

combined tow speed and observed swimming speeds of NZ sea lions in the wild (Crocker et al. 2001). 

Different scaling of HIC values was assessed to gauge sensitivity. 

For the base case, the simulation results indicated there was a 3.3% chance of a single head-first 

collision resulting in MTBI with a 95 percentile of 15.7% risk of MTBI (Abraham 2011). Sensitivities 

modulating single parameters resulted in up to 6.2% probability of a single collision resulting in 

MTBI. One sensitivity trial involving changes in multiple parameters resulted in a 10.9% probability 

of MTBI. This scenario considered impact speeds 20% above those measured for fur seals, multiple 

collisions with the grid, and the least favourable values of scaling exponents used in scaling the test 

HIC values and calculating MTBI from the HIC (Abraham 2011). These results are probabilities of 

MTBI resulting from a single head first collision but, because each individual can have multiple 

interactions with the grid while in a trawl, and some of these will not be head-first, some additional 

assumptions were made based on the Australian observations. Using these data, Abraham (2011) 

estimated the number of head-first collisions per interaction as 0.74, leading to an estimated 

probability of MTBI for a NZ sea lion interacting with a trawl of 2.7%. Single parameter sensitivity 

runs increased this to up to 4.6% and the multiple parameter sensitivity using the scenario described 

above increased it to 8.2% (Abraham 2011). Assuming synergistic interaction between successive 

head-first strikes (each collision carrying 5 times more risk than previous ones) did not appreciably 

increase the overall risk because few fur seals had multiple head-first collisions. These results indicate 

that the risk of mortality for NZ sea lions interacting with the SLED grid is probably low, although 

some remaining areas of uncertainty were identified (see below). 

3.4.4. Sources of uncertainty 

There are several outstanding sources of uncertainty in modelling the effects of fisheries interactions 

on NZ sea lions at the Auckland Islands, including uncertainty relating to the Bayesian management 

procedure evaluation model (the BFG model, Breen et al. 2010), uncertainty in the modelling of stike 

rate (Thompson et al. 2011) and uncertainty relating to the biomechanical modelling (Ponte et al. 

2010, 2011, Abraham 2011, Lyle 2011). 

35


The BFG model is sensitive to several key parameters. Some relate mostly to uncertainty about the 

productivity of the NZ sea lion population (including maximum population growth rate, abundance 

relative to carrying capacity, maximum rate of pup production, and density dependence), whereas 

others relate to how the fishery works and is managed (including strike rates and the survival of NZ 

sea lions that interact with SLEDs but are not retained in the net). Conclusions drawn from the BFG 

model results are sensitive to prior assumptions about how fast this NZ sea lion population is able to 

grow. The maximum population growth rate (lambda, λ) for this population of NZ sea lions is not 

known. Fitting the model to the observed data with an uninformative prior led to an estimated 

maximum rate of less than 1% per year, potentially as a consequence of attempting to estimate λ for a 

declining population. This is a very low maximum growth rate for a pinniped (some suggest a default 

value of 12% per year, Wade 1998), so a prior of 8% was applied to the base model. In a sensitivity 

run, the model was fitted using a prior of 5% per year, and the results were more consistent with the 

observed data than when 8% was used. 

The estimated abundance of NZ sea lions relative to the carrying capacity of mature individuals at the 

Auckland Islands (K) is another source of uncertainty. When the model is run in the absence of 

fishing, the median numbers of mature animals after 100 years was only 94.4% of K as estimated 

from the model. Although the population is not presently near K, over this timescale, the population 

would normally be expected to approach K. This is thought to be an artefact of the parameterisation of 

survival rates in the model, which renders the model conservative when assessing performance 

against K (Breen et al. 2010). 

The density dependent response for this population of NZ sea lions is largely unknown, although there 

is presently no evidence of a density dependent response in life-history traits such as pup mass, pup 

survival or female fecundity (Chilvers 2012b). Ecological principles suggest that, as numbers in a 

population decline, individuals compete less with one another for resources. Less competition may 

result in NZ sea lions growing faster as well as having lower mortality rates and higher rates of pup 

production and survival. The effect of this type of response is that populations tend to recover from 

events that reduce their numbers, and populations with strong density dependence recover more 

strongly than those with weak density dependence. In the BFG model, the shape of the density 

dependent response was “hard wired” in the model and assumed to occur entirely in the mortality rate 

of pups. The strength of this response is unknown, and there was no information to support a strong 

preference for any of the assumed values used in sensitivity runs. This means the base model results 

may be either conservative or optimistic. 

The maximum rate of pup production for this population is not known but can be estimated in the 

population model. Other modelling conducted for DOC (albeit using different assumptions, Breen et 

al. 2010) suggests that the maximum rate of pup production is


Table 3.6: Tow duration in the SQU6T fishery (i.e. for trawl fishers targeting SQU in statistical areas 602, 603, 617 

and 618). Years are calendar years. Data from MPI databases. 

No. of Mean tow duration 

Percentage of tows 

Year 

tows 

(hours) Less than 4 hours Between 4 & 8 hours More than 8 hours 

1995 4 014 3.7 64.2 33.5 2.2 

1996 4 474 3.6 64.3 34.2 1.5 

1997 3 719 3.8 62.7 33.7 3.7 

1998 1 446 3.2 74.4 24.7 0.9 

1999 403 3.5 73.0 24.3 2.7 

2000 1 213 3.5 70.3 27.0 2.7 

2001 583 3.3 72.9 26.6 0.5 

2002 1 647 3.8 59.8 38.8 1.4 

2003 1 467 4.1 52.4 44.0 3.6 

2004 2 598 5.0 36.7 53.6 9.7 

2005 2 693 4.7 43.7 48.6 7.7 

2006 2 462 6.3 26.0 49.6 24.3 

2007 1 317 7.3 18.9 46.3 34.8 

2008 1 265 6.2 20.4 58.7 20.9 

2009 1 925 6.5 21.1 51.4 27.5 

2010 1 190 7.9 16.4 37.4 46.2 

2011 1 585 6.8 24.7 42.8 32.4 

2012* 1 283 6.6 23.5 49.3 27.3 

* Includes data up to November 30, 2012. 

There are a number of possible sources of uncertainty relating to the biomechanical modelling (Ponte 

et al. 2010, 2011, Abraham 2011, Lyle 2011). The use of linear acceleration, as opposed to rotational 

(angular) acceleration, in the biomechanical modelling may underestimate the risk of MTBI, although 

this was thought to be accounted for at least in part by sensitivity analysis of the scaling of HIC 

values. The testing used an artificial “head form” based on human anatomy, so the effect of NZ sea 

lion scalp thickness and skull morphology is unknown, although differences in head and brain masses 

are accounted for. Potential effects of differences in the angle of the head on impact (relative to the 

neck) were not tested. Impact speeds, locations and orientations of NZ sea lions may differ from those 

of Australian fur seals, although the fur seal data were considered to be a reasonable proxy by a 

Research Advisory Group. The head mass values used may be lower than average for NZ sea lions; 

this would mean risk is likely to be overestimated. This approach assesses risk associated with 

collisions with the grid of a SLED and cannot be used to assess other sources of mortality resulting, 

for example, from an animal being retained in a net long enough for them to exceed their dive limit 

before reaching the surface after escaping from either the SLED or the front of the net. Such sources 

of cryptic mortality have always existed, are presently unquantified and are not reflected in the 

estimated overall survival rate of encounters with trawls. 

3.4.5. Potential indirect threats 

In addition to sources of uncertainty associated with direct fisheries interactions, there is the 

possibility that indirect fisheries effects may have population-level consequences for NZ sea lions. 

Such indirect effects may include competition for food resources between various fisheries and NZ 

sea lions (Robertson and Chilvers 2011). In order to determine whether resource competition is 

present and is having a population-level effect on NZ sea lions, research must identify if there are 

resources in common for NZ sea lions and the various fisheries within the range of NZ sea lions, and 

if those resources are limiting. Diet studies have demonstrated overlap in the species consumed by NZ 

sea lions and those caught in fisheries within the range of NZ sea lions, particularly hoki and arrow 

squid (Cawthorn et al. 1985, Childerhouse et al. 2001, Meynier et al. 2009). A recent study focused 

on energy and amino acid content of prey determined that the selected prey species contained all 

37


essential amino acids and were of low to medium energy levels (Meynier 2010). This may indicate 

that the nutritional content of prey species is not limiting the metabolic activity of NZ sea lions, 

although vitamin and mineral content were not considered. Meynier (2010) also developed a bioenergetic 

model and used it to estimate the amount of prey consumed by NZ sea lions at 17 871 

tonnes (95% CI 17 738–18 000 t) per year. This is equivalent to ~30% of the tonnage of arrow squid, 

and ~15% of the hoki harvested annually by the fisheries in the Sub-Antarctic between 2000 and 2006 

(Meynier 2010). Comparison of the temporal and spatial distributions of sea lion prey, sea lion 

foraging and of historical fishing extractions may help to identify the mechanisms whereby resource 

competition might occur (Bowen 2012). The effects of fishing on sea lion prey species are likely to be 

complicated by food web interactions and multispecies models may help to assess the extent to which 

resource competition can impact on sea lion populations, such as those currently being developed by 

NIWA (Project SA123098). In addition, multispecies models may provide a means for simultaneously 

assessing multiple drivers of sea lion population change (a review of potential causes is given in 

Robertson & Chilvers 2011) which may be a more effective approach than focussing on single factor 

explanations for the recent observed decline in NZ sea lions (Bowen 2012). 

38

3.5. Indicators and trends 


Population size • 12 065 animals (including pups < 1 yr old) at the Auckland Islands (90% CI: 

11 160–13 061) in 2009 (most recent model estimate) 10 

• 1 683 pups at the Auckland Islands (SE = 16) in 2011/12 11 

• 681–726 pups at Campbell Island in 2010 12 

• 25 pups tagged at Stewart Island during a DOC recreational hut and track 

maintance trip in March 2012 

• 5 pups at the Otago Peninsula in 2011/12 13 

Population trend • Estimated abundance at the Auckland Islands: 

• Pup production at the Auckland Islands: 

• The population is probably increasing at Campbell Island based on substantial 

increases in pup counts (although methodology has changed over time). 

• The population is increasing at the Otago Peninsula through a combination of 

reproduction and immigration. 

10 Breen et al. (2010). 

11 Chilvers (2012). 

12 Robertson and Chilvers (2011), Maloney et al. (2012). 

13 For more information, see: http://www.sealiontrust.org.nz/otago-sea-lion-family-tree/. 

39


Threat status • NZ: Nationally Critical, Criterion C 14 , Range Restricted 15 , in 2010 16 

• IUCN: Vulnerable, A3b 17 , in 2008 18 

Number of 

interactions 19 

• 81 estimated interactions (95% CI: 26-259) in trawl fisheries in 2010-11 

• 29 estimated captures (95% CI: 17-43) in trawl fisheries in 2010-11 

• 6 observed captures in trawl fisheries in 2010-11 

Trend in interactions Trawl fisheries: 

14 A taxon is listed as ‘Nationally Critical’ under criterion C if the population (irrespective of size or number of 

sub-populations) has a very high (rate of) ongoing or predicted decline; greater than 70% over 10 years or three 

generations, whichever is longer (Townsend et al. 2008). 

15 A taxon is listed as ‘Range Restricted’ if it is confined to specific substrates, habitats or geographic areas of 

less than 1000 km 2 (100 000 ha); this is assessed by taking into account the area of occupied habitat of all subpopulations 

(Townsend et al. 2008). 

16 Baker et al. (2010). 

17 A taxon is listed as ‘Vulnerable’ if it is considered to be facing a high risk of extinction in the wild. A3b refers 

to a reduction in population size (A), based on a reduction of ≥ 30% over the last 10 years or three generations 

(whichever is longer up to a maximum of 100 years (3); and when considering an index of abundance that is 

appropriate to the taxon (b; IUCN 2010). 

18 Gales (2008). 

19 For more information, see: http://data.dragonfly.co.nz/psc/. 

40



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AEBAR 2012: Protected species: Fur seals 

4. New Zealand fur seal (Arctocephalus forsteri) 

Scope of chapter This chapter outlines the biology New Zealand fur seals (Arctocephalus 

forsteri), the nature of any fishing interactions, the management 

approach, trends in key indicators of fishing effects and major sources of 

uncertainty. 

Area All of the New Zealand EEZ and territorial sea. 

Focal localities Areas with significant fisheries interactions include waters over or close 

to the continental shelf surrounding the South Island and southern 

offshore islands, notably Cook Strait, West Coast South Island, Banks 

Peninsula and the Bounty Islands, plus offshore of Bay of Plenty-East 

Cape. 

Key issues Improving estimates of incidental bycatch in some fisheries, and 

assessing the potential for populations to sustain the present levels of 

bycatch. 

Emerging issues Improving data and information sources for future ecological risk 

MPI Research 

(current) 

Other Govt 


Links to 2030 

objectives 

Related 

issues/chapters 

assessments. 

4.1. Context 

PRO2010-01 Estimating the nature & extent of incidental captures of 

seabirds, marine mammals & turtles in New Zealand commercial 

fisheries; PRO2012-02 Assess the risk posed to marine mammal 

populations from New Zealand fisheries. 

DOC Marine Conservation Services Programme (CSP): INT2012-01 To 

understand the nature and extent of protected species interactions with 

New Zealand commercial fishing activities. 



including for threatened and protected species and seabed impacts 

See the New Zealand sea lion chapter. 

Management of fisheries impacts on New Zealand (NZ) fur seals is legislated under the Marine 

Mammals Protection Act (MMPA) 1978 and the Fisheries Act (FA) 1996. Under s.3E of the MMPA, 

the Minister of Conservation, with the concurrence of the Minister for Primary Industries (formerly 

the Minister of Fisheries), may approve a population management plan (PMP). There is no PMP in 

place for NZ fur seals. 

In the absence of a PMP, the Ministry for Primary Industries (MPI) manages fishing-related mortality 

of NZ fur seals under s.15(2) of the FA “to avoid, remedy, or mitigate the effect of fishing-related 

mortality on any protected species, and such measures may include setting a limit on fishing-related 

mortality.” 

All marine mammal species are designated as protected species under s.2(1) of the FA. In 2005, the 

Minister of Conservation approved the Conservation General Policy, which specifies in Policy 4.4 (f) 

that “Protected marine species should be managed for their long-term viability and recovery 

throughout their natural range.” DOC’s Regional Conservation Management Strategies outline 

specific policies and objectives for protected marine species at a regional level. 

44


In 2004, DOC approved the Department of Conservation Marine Mammal Action Plan for 2005– 

2010 20 (Suisted and Neale 2009). The plan specifies a number of species-specific key objectives for 

NZ fur seals, of which the following is most relevant for fisheries interactions: “To control/mitigate 

fishing-related mortality of NZ fur seals in trawl fisheries (including the WCSI hoki and Bounty Island 

southern blue whiting fisheries).” 

Management of NZ fur seal incidental captures aligns with Fisheries 2030 Objective 6: Manage 

impacts of fishing and aquaculture. Further, the management actions follow Strategic Action 6.2: Set 

and monitor environmental standards, including for threatened and protected species and seabed 

impacts. 

All National Fisheries Plans except those for inshore shellfish and freshwater fisheries are relevant to 

the management of fishing-related mortality of NZ fur seals. 

Under the National Deepwater Plan, the objective most relevant for management of NZ fur seals is 

Management Objective 2.5: Manage deepwater and middle-depth fisheries to avoid or minimise 

adverse effects on the long-term viability of endangered, threatened and protected species. 

Specific objectives for the management of NZ fur seals bycatch are to be outlined in the fisheryspecific 

chapters of the National Deepwater Plan for the fisheries with which NZ fur seals are most 

likely to interact. These fisheries include hoki (HOK), southern blue whiting (SBW), hake (HAK) and 

jack mackerel (JMA). The HOK chapter of the National Deepwater Plan is complete and includes 

Operational Objective 2.11: Ensure that incidental marine mammal captures in the hoki fishery are 

avoided and minimised to acceptable levels (which may include standards) by 2012. The SBW 

chapter is nearing completion while the timeframes for the HAK and JMA chapters are yet to be 

confirmed. 

Management Objective 7 of the National Fisheries Plan for Highly Migratory Species (HMS) is to 

“Implement an ecosystem approach to fisheries management, taking into account associated and 

dependent species.” This comprises four components: Avoid, remedy, or mitigate the adverse effects 

of fishing on associated and dependent species, including through maintaining foodchain 

relationships; Minimise unwanted bycatch and maximise survival of incidental catches of protected 

species in HMS fisheries, using a risk management approach; Increase the level and quality of 

information available on the capture of protected species; and Recognise the intrinsic values of HMS 

and their ecosystems, comprising predators, prey, and protected species. 

The Environment Objective is the same for all groups of fisheries in the draft National Fisheries Plan 

for Inshore Finfish, to “Minimise adverse effects of fishing on the aquatic environment, including on 

biological diversity”. The draft National Fisheries Plans for Inshore Shellfish and Freshwater have the 

same objective but are unlikely to be relevant to management of fishing-related mortality of NZ fur 

seals. 

4.2. Biology 

4.2.1. Taxonomy 

The NZ fur seal (Arctocephalus forsteri (Lesson, 1828)) is one of only two species of otariid (eared 

seals, includes fur seals and sea lions) native to New Zealand, the other being the New Zealand sea 

lion (Phocarctos hookeri (Gray, 1844)). 

20 

DOC has confirmed that the Marine Mammal Action Plan for 2005–2010 still reflects DOC’s priorities for 

marine mammal conservation. 

45

4.2.2. Distribution 


Pre-European archaeological evidence suggests that NZ fur seals were present along much of the east 

coasts of the North Island (except the less rocky coastline of Bay of Plenty and Hawke Bay) and the 

South Island, and, to a lesser extent, on the west coasts, where fewer areas of suitable habitat were 

available (Smith 1989, 2005, 2011). A combination of subsistence hunting and commercial harvest 

resulted contraction of the species’ range and in population decline almost to the point of extinction 

(Smith 1989, 2005, 2011, Ling 2002, Lalas 2008). NZ fur seals became fully protected in the 1890’s 

and, with the exception of one year of licenced harvest in the 1950’s, have remained protected since. 

Currently, NZ fur seals are dispersed throughout New Zealand waters, especially in waters south of 

about 40º S to Macquarie Island. On land, NZ fur seals are distributed around the New Zealand 

coastline, on offshore islands, and on sub-Antarctic islands (Crawley and Wilson 1976, Wilson 1981, 

Mattlin 1987). The recolonisation of the coastline by NZ fur seals has resulted in the northward 

expansion of the distribution of breeding colonies and haulouts (Lalas and Bradshaw 2001), and 

breeding colonies present on many exposed rocky areas (Baird 2011). The extent of breeding colony 

distribution in New Zealand waters is bounded to the north by a very small (space-limited) colony at 

Gannet Island off the North Island west coast (latitude 38° S), to the east by colonies of unknown 

sizes at the Chatham Islands group, to the west by colonies of unknown size on Fiordland offshore 

islands, and to the south by unknown numbers on Campbell Island. Outside New Zealand waters, 

breeding populations exist in South and Western Australia (Shaughnessy et al. 1994, Shaughnessy 

1999, Goldsworthy et al. 2003). 

The seasonal distribution of the NZ fur seals is determined by the sex and maturity of each animal. 

Males are generally at the breeding colonies from late October to late January then move to haulout 

areas around the New Zealand coastline (see Bradshaw et al. 1999), with peak density of males and 

sub-adult males at haulouts during July–August and lowest densities in September–October (Crawley 

and Wilson 1976). Females arrive at the breeding colony from November and lactating females 

remain at the colony (apart from short foraging trips) for about 10 months until the pups are weaned, 

usually during August–September (Crawley and Wilson 1976). 

4.2.3. Foraging ecology 

Most foraging research in New Zealand has focused on lactating NZ fur seals at Open Bay Islands off 

the South Island west coast (Mattlin et al. 1998), Otago Peninsula (Harcourt et al. 2002), and Ohau 

Point, Kaikoura (Boren 2005), using time-depth-recorders, satellite-tracking, or very-high-frequency 

transmitters. Individual females show distinct dive pattern behaviour and may be relatively shallow or 

deep divers, but most forage at night and in depths shallower than 200 m. At Open Bay Islands, dives 

were generally deeper and longer in duration during autumn and winter. Females can dive to at least 

274 m (for a 5.67 min dive in autumn) and remain near the bottom at over 237 m for up to 11.17 min 

in winter (Mattlin et al. 1998). Females in some locations undertook longer dive trips, with some to 

deeper waters, in autumn (in over 1000 m beyond the continental shelf; Harcourt et al. 2002). 

The relatively shallow dives and nocturnal feeding during summer suggested that seals fed on pelagic 

and vertical migrating prey species (for example, arrow squid, Nototodarus sloanii). Conversely, the 

deeper dives and increased number of dives in daylight during autumn and winter suggested that the 

prey species may include benthic, demersal, and pelagic species (Mattlin et al. 1998, Harcourt et al. 

2002). The deeper dives enabled seals to forage along or off the continental shelf (within 10 km) of 

the colony studied (at Open Bay Islands). These deeper dives may be to the benthos or to depths in the 

water column where spawning hoki are concentrated. 

46


Methods to analyse NZ fur seal diets have included investigation of freshly killed animals (Sorensen 

1969), scats, and regurgitates (e.g. Allum and Maddigan 2012). Fish prey items can be recognised by 

the presence of otoliths, bones, scales, and lenses, while cephalopods are indicated by beaks and pens. 

Foraging appears to be specific to individuals and different diets may be represented in the scats and 

regurgitations of males and females as well as juveniles from one colony. These analyses can be 

biased, however, particularly if only one collection method is used, and this limits fully quantitative 

assessment of prey species composition. 

Dietary studies of NZ fur seals have been conducted at colonies in Nelson-Marlborough, west coast 

South Island, Otago Peninsula, Kaikoura, Banks Peninsula, Snares Islands, and off Stewart Island, and 

summaries are provided by Carey (1992), Harcourt (2001), Boren (2010), and Baird (2011). 

NZ fur seals are opportunistic foragers and, depending on the time of year, method of analysis, and 

location, their diet includes at least 61 taxa (Holborow 1999) of mainly fish (particularly lanternfish 

(myctophids) in all studied colonies except Tonga Island (in Golden Bay, Willis et al. 2008), as well 

as anchovy (Engraulis australis), aruhu (Auchenoceros punctatus), barracouta (Thrysites atun), hoki 

(Macruronus novaezelandiae), jack mackerel (Trachurus spp.), pilchard (Sardinops sagax), red cod 

(Pseudophycis bachus), red gurnard (Chelidonichthys kumu), silverside (Argentina elongate), sprat 

(Sprattus spp.) and cephalopods (octopus (Macroctopus maorum), squid (Nototodarus sloanii, 

Sepioteuthis bilineata)). For example, myctophids were present in Otago scats throughout the year 

(representing offshore foraging), but aruhu, sprat, and juvenile red cod were present only during 

winter-spring (Fea et al. 1999). Medium-large arrow squid predominated in summer and autumn. Jack 

mackerel species, barracouta, and octopus were dominant in winter and spring. Prey such as 

lanternfish and arrow squid rise in the water column at night, the time when NZ fur seals exhibit 

shallow foraging (Harcourt et al. 1995, Mattlin et al. 1998, Fea et al. 1999). 

4.2.4. Reproductive biology 

NZ fur seals are sexually dimorphic and polygynous (Crawley and Wilson 1976); males may weigh 

up to 160 kg, whereas females weigh up to about 50 kg (Miller 1975; Mattlin 1978a, 1987; Troy et al. 

1999). Adult males are much larger around the neck and shoulders than females and breeding males 

are on average 3.5 times the weight of breeding females (Crawley and Wilson 1976). Females are 

philopatric and are sexually mature at 4–6 years, whereas males mature at 5–9 years (Mattlin 1987, 

Dickie and Dawson 2003). The maximum age recorded for NZ fur seals in New Zealand waters is 22 

years for females (Dickie and Dawson 2003) and 15 years for males (Mattlin 1978). 

NZ fur seals are annual breeders and generally produce one pup after a gestation period of about 10 

months (Crawley and Wilson 1976). Twinning can occur and females may foster a pup (Dowell et al. 

2008), although both are rare. Breeding animals come ashore to mate after a period of sustained 

feeding at sea. Breeding males arrive at the colonies to establish territories during October– 

November. Breeding females arrive at the colony from late November and give birth shortly after. 

Peak pupping occurs in mid December (Crawley and Wilson 1976). 

Females remain at the colony with their newborn pups for about 10 days, by which time they have 

usually mated. Females then leave the colony on short foraging trips of 3–5 days before returning to 

suckle pups for 2–4 days (Crawley and Wilson 1976). As the pups grow, these foraging trips are 

progressively longer in duration. Pups remain at the breeding colony from birth until weaning (at 8– 

12 months of age). 

Breeding males generally disperse after mating to feed and occupy haulout areas, often in more 

northern areas (Crawley and Wilson 1976). This movement of breeding adults away from the colony 

area during January allows for an influx of sub-adults from nearby areas. Little is described about the 

ratio of males to females on breeding colonies (Crawley and Wilson 1976), or the reproductive 

47


success. Boren (2005) reported a fecundity rate of 62% for a Kaikoura colony, based on two annual 

samples of between about 5 and 8% of the breeding female population. This rate is similar to the 67% 

estimated by Goldsworthy and Shaughnessy (1994) for a South Australian colony. 

Newborn pups are about 55 cm long and weigh about 3.5 kg (Crawley and Wilson 1976). Male pups 

are generally heavier than female pups at birth and throughout their growth (Crawley and Wilson 

1976, Mattlin 1981, Chilvers et al. 1995, Bradshaw et al. 2003b, Boren 2005). Pup growth rates may 

vary by colony (see Harcourt 2001). The proximity of a colony to easily accessible rich food sources 

will vary, and pup condition at a colony can vary markedly between years (Mattlin 1981, Bradshaw et 

al. 2000, Boren 2005). Food availability may be affected by climate variation, and pup growth rates 

probably represent variation in the ability of mothers to provision their pups from year to year. The 

sex ratio of pups at a colony may vary by season (Bradshaw et al. 2003a, 2003b, Boren 2005), and in 

years of high food resource availability, more mothers may produce males or more males may survive 

(Bradshaw et al. 2003a, 2003b). 

4.2.5. Population biology 

Historically, the population of NZ fur seals in New Zealand was thought to number above 1.25 

million animals (possibly as high as 1.5 to 2 million) before the extensive sealing of the early 19 th 

century (Richards 1994). Present day population estimates for NZ fur seals in New Zealand are few 

and highly localised. In the most comprehensive attempt to quantify the total NZ fur seal population, 

Wilson (1981) summarised population surveys of mainland New Zealand and offshore islands 

undertaken in the 1970s and estimated the population size within the New Zealand region at between 

30,000 and 50,000 animals. Since then, several authors have suggested a population size of ~100,000 

animals (Taylor 1990, see Harcourt 2001), but this estimate is very much an approximation and its 

accuracy is difficult to assess in the absence of comprehensive surveys. 

Fur seal colonies provide the best data for consistent estimates of population numbers, generally based 

on pup production in a season (see Shaughnessy et al. 1994). Data used to provide colony population 

estimates of NZ fur seals have been, and generally continue to be, collected in an ad hoc fashion. 

Regular pup counts are made at some discrete populations. A 20-year time series of Otago Peninsula 

colony data is updated, maintained, and published primarily by Chris Lalas (assisted by Sanford 

(South Island) Limited), and the most recent estimate is 20,000–30,000 animals (Lalas 2008). A 20year 

plus time series of pup counts exists for three west coast South Island colonies (Cape Foulwind, 

Wekekura Point, and Open Bay Islands; Best 2011). Recent Kaikoura work by Boren (2005) covered 

four seasons and unpublished data are available for the subsequent seasons. 

Other studies of breeding colonies generally provide estimates for one or two seasons, but many of 

these are more than 10 years old. Published estimates suggest that populations have stabilised at the 

Snares Islands after a period of growth in the 1950s and 1960s (Carey 1998) and increased at the 

Bounty Islands (Taylor 1996), Nelson-Marlborough region (Taylor et al. 1995), Kaikoura (Boren 

2005), Otago (Lalas and Harcourt 1995, Lalas and Murphy 1998, Lalas 2008), and near Wellington 

(Dix 1993). 

For many areas where colonies or haulouts exist, count data have been collected opportunistically 

(generally by Department of Conservation staff during their field activities) and thus data are not often 

comparable because counts may represent different life stages, different assessment methods, and 

different seasons (see Baird 2011). 

Baker et al. (2010a) conducted an aerial survey of the South Island west coast from Farewell Spit to 

Puysegur Point and Solander Island in 2009 but were their counts were quite different from ground 

counts collected at a similar time at the main colonies (Melina and Cawthorn 2009). This discrepancy 

was thought to be a result mainly of the survey design and the nature of the terrain. However, the 

48


aerial survey confirmed the localities shown by Wilson (1981) of potentially large numbers of pups at 

sites such as Cascade Point, Yates Point, Chalky Island, and Solander Island. 

Population numbers for some areas, especially more isolated ones, are not well known. The most 

recent counts for the Chatham Islands were collected in the 1970s (Wilson 1981), and the most recent 

for the Bounty Islands in 1993–94. Taylor (1996) reported an increase in pup production at the 

Bounty Islands since 1980, and estimated that the total population was at least 21 500, occupying over 

50% of the available area. Information is sparse for populations at Campbell Island, the Auckland 

Islands group and the Antipodes Islands 

Little is reported about the natural mortality of NZ fur seals, other than reports of sources and 

estimates of pup mortality for some breeding colonies. Estimates of pup mortality or pup survival 

vary in the manner in which they were determined and in the number of seasons they represent, and 

are not directly comparable. Each colony will be affected by different sources of mortality related to 

habitat, location, food availability, environment, and year, as well as the ability of observers to count 

all the dead pups (may be limited by terrain, weather, or time of day). 

Reported pup mortality rates vary: 8% for Otago Peninsula pups up to 30 days old and 23% for pups 

up to 66 days old (Lalas and Harcourt 1995); 20% from birth to 50 days and about 40% from birth to 

300 days for Taumaka Island, Open Bay Islands pups (Mattlin 1978b); and in one year, 3% of 

Kaikoura pups before the age of 50 days (Boren 2005). Starvation was the major cause of death, 

although stillbirth, suffocation, trampling, drowning, predation, and human disturbance also occur. 

Pup survival of at least 85% was estimated for a mean 47 day interval for three Otago colonies, 

incorporating data such as pup body mass (Bradshaw et al. 2003b), though pup mortality before the 

first capture effort was unknown. Other sources of natural mortality for NZ fur seals include predators 

such as sharks and NZ sea lions (Mattlin 1978b, Bradshaw et al. 1998). 

Human-induced sources of mortality include: fishing, for example, entanglement or capture in fishing 

gear; vehicle-related deaths (Lalas and Bradshaw 2001, Boren 2005, Boren et al. 2006, 2008); and 

mortality through shooting, bludgeoning, and dog attacks. NZ fur seals are vulnerable to certain 

bacterial diseases and parasites and environmental contaminants, though it is not clear how lifethreatening 

these are. The more obvious problems include tuberculosis infections, Salmonella, 

hookworm enteritis, phocine distemper, and septicaemia (associated with abortion) (Duignan 2003, 

Duignan and Jones 2007). Low food availability and persistent organohalogen compounds (which can 

affect the immune and the reproductive systems) may also affect NZ fur seal health. 

Various authors have investigated fur seals genetic differentiation among colonies and regions in New 

Zealand (Lento et al. 1994; Robertson and Gemmell (2005). Lento et al. (1994) described the 

geographic distribution of mitochondrial cytochrome b DNA haplotypes, whereas Robertson and 

Gemmell (2005) described low levels of genetic differentiation (consistent with homogenising gene 

flow between colonies and an expanding population) based on genetic material from NZ fur seal pups 

from seven colonies. One aim of the work is to determine the provenance of animals captured during 

fishing activities, through the identification and isolation of any colony genetic differences. 

4.2.6. Conservation biology and threat classification 

Threat classification is an established approach for identifying species at risk of extinction (IUCN 

2010). The risk of extinction for NZ fur seals has been assessed under two threat classification 

systems: the New Zealand Threat Classification System (Townsend et al. 2008) and the International 

Union for the Conservation of Nature (IUCN) Red List of Threatened Species (IUCN 2010). 

In 2008, the IUCN updated the Red List status of NZ fur seals, listing them as Least Concern on the 

basis of their large and apparently increasing population size (Goldsworthy and Gales 2008). In 2010, 

49


DOC updated the New Zealand Threat Classification status of all NZ marine mammals (Baker et al. 

2010b). In the revised list, NZ fur seals were classified as Not Threatened with the qualifiers 

increasing (Inc) and secure overseas (SO) (Baker et al. 2010b). 


NZ fur seals are found in both Australian and New Zealand waters. Overall abundance has been 

suggested to be as high as 200 000, with about half of the population in Australian waters 

(Goldsworthy and Gales 2008). However, this figure is very much an approximation, and its accuracy 

is difficult to assess in the absence of comprehensive surveys. 

Pinnipeds are caught incidentally in a variety of fisheries worldwide (Read et al. 2006), including: NZ 

fur seals, Australian fur seals, and Australian sea lions in Australian trawl and inshore fisheries (e.g., 

Shaughnessy 1999, Norman 2000); Cape fur seals in South African fisheries (Shaughessy and Payne 

1979); South Amercian sea lions in trawl fisheries off Patagonia (Dans et al. 2003); and seals and sea 

lions in United States waters (Moore et al. 2009). 


NZ fur seals are attracted to feeding opportunities in various fishing gears and anecdotal evidence 

suggests that the sound of winches as trawlers haul their gear acts as a ‘dinner gong’. The attraction of 

fish in a trawl net, on longline hooks, or caught in a setnet provide opportunities for NZ fur seals to 

interact with fishing gear, which can result in capture and, potentially, death via drowning or injury. 

Most captures occur in trawl fisheries and NZ fur seals are most at risk from capture during shooting 

and hauling (Shaughnessy and Payne 1979), when the net mouth is within diving depths. Once in the 

net some animals may have difficulty in finding their way out within their maximum breath-hold time 

(Shaughnessy and Davenport 1996). The operational aspects that are associated with NZ fur seal 

captures on trawlers include factors that attract the NZ fur seals, such as the presence of offal and 

discards, the sound of the winches, vessel lights, and the presence of ‘stickers’ in the net (Baird 2005). 

NZ fur seals are at particular risk of capture when a vessel partially hauls the net during a tow and 

executes a turn with the gear close to the surface. At the haul, NZ fur seals pften attempt to feed from 

the codend as it is hauled and dive after fish that come loose and escape from the net (Baird 2005). 

Factors identified as important influences on the potential capture of NZ fur seals in trawl gear 

include the year or season, the fishery area, gear type and fishing strategies (often specific to certain 

nationalities within the fleet), time of day, and distance to shore (Baird and Bradford 2000, Mormede 

et al. 2008, Smith and Baird 2009). These analyses did not include any information on NZ fur seal 

numbers or activity in the water at the stern of the vessel. Other influences on NZ fur seal capture rate 

(of Australian and NZ fur seals) may include inclement weather and sea state, vessel speed, increased 

numbers of vessels and trawl frequency, and potentially the weight of the fish catch and the presence 

of certain bycatch fish species (Hamer and Goldsworthy 2006). This Australian study found similar 

mortality rates for tows with and without Seal Exclusion Devices (see also Hooper et al. 2005). 

The spatial and temporal overlap of commercial fishing grounds and NZ fur seal foraging areas has 

resulted in NZ fur seal captures in fishing gear (Mattlin 1987, Rowe 2009). Most fisheries with 

observed captures occur in waters over or close to the continental shelf. Because the topography 

around much of the South Island and offshore islands slopes steeply to deeper waters, most captures 

occur close to colonies and haulouts (Figures 4.1 and 4.2). 

Observed NZ fur seal captures are mainly from trawls in defined seasons in areas where fishing 

occurs relatively close to NZ fur seal colonies or haulouts. Winter hoki fisheries attract NZ fur seals 

50


off the west coast South Island and in Cook Strait between late June and September (Table 4.1). In 

August–October, NZ fur seals are caught in southern blue whiting effort near the Bounty Islands and 

Campbell Island. In September–October captures may occur in hoki and ling fisheries off Puysegur 

Point on the southwestern coast of the South Island. Captures are also reported from the Stewart- 

Snares shelf fisheries that operate during summer months, mainly for hoki and other middle depths 

species and squid, and from fisheries throughout the year on the Chatham Rise though captures have 

not been observed east of longitude 180° on the Chatham Rise. 

Captures were reported from trawl fisheries for species such as hoki, hake (Merluccius australis), ling 

(Genypterus blacodes), squid, southern blue whiting, Jack mackerel, and barracouta (Baird and Smith 

2007, Abraham et al. 2010a). Between 1 and 3% of observed tows targeting middle depths fish 

species catch NZ fur seals compared with about 1% for squid tows, and under 1% of observed tows 

targeting deepwater species such as orange roughy (Hoplostethus atlanticus) and oreo species (for 

example, Allocyttus niger, Pseudocyttus maculatus) (Baird and Smith 2007). The main fishery areas 

that contribute to the estimated annual catch of NZ fur seals (modelled from observed captures) in 

middle depths and deepwater trawl fisheries are Cook Strait hoki, west coast South Island middle 

depths fisheries (mainly hoki), western Chatham Rise hoki, and the Bounty Islands southern blue 

whiting fishery (Baird and Smith 2007, Thompson and Abraham 2010). Captures on longlines occur 

when the NZ fur seals attempt to feed on the fish catch during hauling. Most NZ fur seals are released 

alive from surface and bottom longlines, typically with a hook and short snood or trace still attached. 

Table 4.1: Monthly distribution of NZ fur seal activity and the main trawl and longline fisheries with observed 

reports of NZ fur seal incidental captures. 

NZ fur seals Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep 

Breeding males At breeding colony Dispersed at sea or at haulouts 

Breeding 

females 

At sea 

At breeding 

colony 

At breeding colony and at-sea foraging and suckling At sea 

Pups At sea At breeding colony At sea 

Non-breeders Dispersed at sea, at haulouts, or breeding colony periphery 

Major fisheries Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep 

Hoki trawl Puysegur Chatham Rise Cook Strait, west coast South 

Island 

Squid trawl Stewart-Snares shelf, Auckland Is. Shelf, East Coast South 

Island 

Southern blue 

whiting trawl 

Southern bluefin 

tuna longline 

Campbell Rise Bounty Is., 

Pukaki Rise 

51 

Fiordland


Figure 4.1: Distribution of trawl fishing effort and observed NZ fur seal captures, 2002-03 to 2010-11 (for more 

information see http://data.dragonfly.co.nz/psc/). Fishing effort is mapped into 0.2-degree cells, with the colour of 

each cell being related to the amount of effort. Observed fishing events are indicated by black dots, and observed 

captures are indicated by red dots. Fishing is only shown if the effort could be assigned a latitude and longitude, and 

if there were three or more vessels fishing within a cell. In this case, 96.0% of the effort is shown. 

52


Figure 4.2: Distribution of surface longline fishing effort and observed NZ fur seal captures, 2002-03 to 2010-11 (for 

more information see http://data.dragonfly.co.nz/psc/). Fishing effort is mapped into 0.2-degree cells, with the colour 

of each cell being related to the amount of effort. Observed fishing events are indicated by black dots, and observed 

captures are indicated by red dots. Fishing is only shown if the effort could be assigned a latitude and longitude, and 

if there were three or more vessels fishing within a cell. In this case, 75.3% of the effort is shown. 

53



Observer data and commercial effort data have been used historically to characterise the incidental 

captures and estimate the total numbers caught (Baird and Smith 2007, Smith and Baird 2009, 

Thompson and Abraham 2010, Abraham and Thompson 2011). This approach is currently applied 

using information collected under DOC project INT2012-01 and analysed under MPI project 

PRO2010-01 (Thompson et al. 2011, Thompson et al. 2012). The analytical methods used to estimate 

capture numbers across the commercial fisheries have depended on the quantity and quality of the 

data, in terms of the numbers observed captured and the representativeness of the observer coverage. 

Initially, stratified ratio estimates were provided for the main trawl fisheries, starting in the late 1980s, 

after scientific observers reported 198 NZ fur seal deaths during the July to September west coast 

South Island spawning hoki fishery (Mattlin 1994a, 1994b). In the following years, ratio estimation 

was used to estimate NZ fur seal captures in the Taranaki Bight jack mackerel fisheries and Bounty 

Platform, Pukaki Rise, and Campbell Rise southern blue whiting fisheries, based on observed catches 

and stratified by area, season, and gear type (Baird 1994). 

In the last 10 years, model-based estimates of captures have been developed for all trawl fisheries in 

waters south of 40° S (Baird and Smith 2007, Smith and Baird 2009, Thompson and Abraham 2010, 

Abraham and Thompson 2011, Thompson et al. 2011, Thompson et al. 2012). These models use the 

observed and unobserved data in an hierarchical Bayesian approach that combines season and vesselseason 

random effects with covariates (for example, day of fishing year, time of day, tow duration, 

distance from shore, gear type, target) to model variation in capture rates among tows. This method 

compensates in part for the lack of representativeness of the observer coverage and includes the 

contribution from correlation in the capture rate among tows by the same vessel. The method is 

limited by the very large differences in the observed and non-observed proportions of data for the 

different vessel sizes; most observer coverage is on larger vessels that generally operate in waters 

deeper than 200 m. The operation of inshore vessels in terms of the location of effort, gear, and the 

fishing strategies used is also relatively unknown compared with the deeper water fisheries although 

changes to reporting requirements means that data is now improving and inshore trawl effort (not 

including flatfish trawl effort) is now able to be included in the modelling (Thompson et al. 2012, see 

also description of the Trawl Catch Effort Return, TCER, in use since 2007/08, in Chapter 7 on 

benthic effects). 

Since 2005, there has been a small downward trend in estimated capture rates, and annual estimated 

NZ fur seal captures (Smith and Baird 2009, Thompson and Abraham 2010, Abraham and Thompson 

2011, Thompson et al. 2011, Thompson et al. 2012, Figure 4.3). This probably reflects efforts to 

reduce bycatch combined with a reduction in fishing effort since the late 1990s. Similar modelling 

methods were used to produce the most recent set of estimated NZ fur seal captures in trawl fisheries 

(Thompson and Abraham 2010, Abraham and Thompson 2011, Thompson et al. 2011, Thompson et 

al. 2012). The overall downward trend in estimated annual captures for trawl fisheries has continued 

(see Table 4.2), as a result of the continued decrease in total tows made each year and a concurrent 

decrease in capture rate. Note these capture rates include animals that are released alive (7% of 

observed trawl capture in 2008-09, Thompson and Abraham 2010). 

Ratio estimation was used to calculate total captures in longline fisheries by target fishery fleet and 

area (Baird 2008) and by all fishing methods (Abraham et al. 2010a). NZ fur seal captures in surface 

longline fisheries have been generally observed in waters south and west of Fiordland, but also in the 

Bay of Plenty and off East Cape. Estimated numbers range from 127 (95% c.i. 121–133) in 1998–99 

to 25 (14–39) in 2007–08 during southern bluefin tuna fishing by chartered and domestic vessels 

(Abraham et al. 2010a). These capture rates include animals that are released alive (100% of observed 

surface longline capture in 2008-09, Thompson and Abraham 2010). Captures of NZ fur seals have 

also been recorded in other fisheries; 8 in setnets and 2 in bottom longline fisheries since 2002-03 

54


(Thompson et al. 2012). Captures associated with recreational fishing activities are poorly known 

(Abraham et al. 2010b). 

Table 4.2: Effort, observed and estimated NZ fur seal captures in trawl and surface longline fisheries by fishing year 

in the New Zealand EEZ (Abraham and Thompson 2011 and http://data.dragonfly.co.nz/psc/). For each fishing year, 

the table gives the the total number of tows or hooks; the observer coverage (the percentage of tows or hooks that 

were observed); the number of observed captures (both dead and alive); the capture rate (captures per hundred tows 

or per thousand hooks); the estimation method used (model or ratio); and the mean number of estimated total 

captures (with 95% confidence interval). For more information on the methods used to prepare the data, see 

Abraham and Thompson (2011). 


All effort % observed Number Rate Type Mean 95% c.i. 

Trawl fisheries 

1998–1999 153 412 4.7 

190 2.62 Ratio 1 591 1454–1744 

1999–2000 139 057 5.5 

203 2.65 Ratio 1 539 1400–1693 

2000–2001 134 243 6.8 

170 1.87 Ratio 1 490 1348–1649 

2001–2002 127 883 6.0 

157 2.03 Ratio 1 273 1164–1394 

2002–2003 130 344 5.2 

68 1.00 Model 841 503 – 1380 

2003–2004 121 494 5.4 

84 1.28 Model 1 052 635 – 1728 

2004–2005 120 590 6.4 

200 2.59 Model 1 471 914 – 2392 

2005–2006 110 230 5.9 

143 2.18 Model 917 577 – 1479 

2006–2007 103 529 7.7 

73 0.92 Model 533 324 – 871 

2007–2008 89 537 10.1 

141 1.56 Model 765 476 – 1348 

2008–2009 87 587 11.2 

72 0.73 Model 546 308 – 961 

2009–2010 92 886 9.7 

72 0.80 Model 472 269 – 914 

2010–2011 86 073 8.6 69 0.93 Model 376 221 – 668 

Surface longline fisheries 

1998–1999 6 855 124 18.9 

102 0.08 Ratio 138 120–160 

1999–2000 8 258 537 10.4 

42 0.05 Ratio 67 54–83 

2000–2001 9 698 805 10.8 

43 0.04 Ratio 64 51–83 

2001–2002 10 833 533 9.1 

44 0.04 Ratio 75 61–93 

2002–2003 10 764 588 20.4 

56 0.03 Ratio 73 63–87 

2003–2004 7 380 779 21.8 

40 0.02 Ratio 107 61–189 

2004–2005 3 676 365 21.3 

20 0.03 Ratio 46 26–71 

2005–2006 3 687 339 19.1 

12 0.02 Ratio 59 28–100 

2006–2007 3 738 362 27.8 

10 0.01 Ratio 31 18–49 

2007–2008 2 244 339 19.0 

10 0.02 Ratio 29 17–46 

2008–2009 3 115 633 30.1 

22 0.02 Ratio 48 29–75 

2009–2010 2 992 285 22.3 

19 0.03 Ratio 65 35–103 

2010–2011 3 164 159 21.3 17 0.03 Ratio 57 26–99 

55

a 

b 

c 

d 

e 

f 


Figure 4.3: Observed captures of NZ fur seals in trawl fisheries (both dead and alive), the capture rate (captures per 

hundred tows) and the mean number of estimated total captures (with 95% confidence interval) by fishing year for 

regions with more than 50 observed captures since 2002-03: (a) the New Zealand EEZ; (b) the Cook Strait area; (c) 

the East Coast South Island area; (d) the Stewart Snares Shelf area; (e) the Subantarctic area; and (f) the West Coast 

South Island area (Abraham and Thompson 2011 and http://data.dragonfly.co.nz/psc/). For more information on the 

methods used to prepare the data, see Abraham and Thompson (2011). 

56



The impact of fishing related captures on the NZ fur seal population is presently unknown. However, 

fishing interactions are considered unlikely to have adverse population-level consequences for NZ fur 

seals given: the scale of bycatch relative to overall NZ fur seal abundance; the apparently increasing 

population and range; and the NZ and IUCN threat status of the species. The consequences of fishing 

related mortality for some individual colonies may be more or less severe. 

Management has focused on encouraging vessel operators to alter fishing practices to reduce captures, 

and monitoring captures via the observer programme. A marine mammal operating procedure 

(MMOP) has been developed by the deepwater sector to reduce the risk of marine mammal captures 

and is currently applied to trawlers greater than 28 m LOA and is supported by annual training. It 

includes a number of mitigation measures, such as managing offal discharge and refraining from 

shooting and hauling the gear when NZ fur seals are congregating around the vessel. Its major focus is 

reducing the time gear is at or near the surface when it poses the greatest risk. MPI monitors and 

audits vessel performance against this procedure (see the MPI National Deepwater Plan for further 

details). 

Research into methods to minimise or mitigate NZ fur seal captures in commercial fisheries has 

focused on fisheries in which NZ fur seals are more likely to be captured (trawl fisheries, see Clement 

and Associates 2009). Finding ways to mitigate captures has proven difficult because the animals are 

free swimming, can easily dive to the depths of the net when it is being deployed, hauled, or brought 

to the surface during a turn, and are known to deliberately enter nets to feed. Further, any measures 

also need to ensure that the catch is not greatly compromised, either in terms of the amount of fish or 

their condition. This is one potential drawback of using seal exclusion devices (see Rowe 2007). 

Adhering to current risk mitigation methods (e.g. MMOP) will help to minimise the level of impacts, 

however rates may fluctuate depending on fleet deployment, NZ fur seal abundance and local feeding 

conditions. 

4.4.3. Modelling population-level impacts of fisheries interactions 

The uncertainty about the size of the NZ fur seal population has restricted the potential to investigate 

any effects that NZ fur seal deaths through fishing may have on the population as a whole or on the 

viability of colonies or groups of colonies. The provenance of NZ fur seals caught during fishing is 

presently unknown, although proposed genetic research potentially could identify which animals 

belonged to a specific colony (Robertson and Gemmell 2005). 

In response to the requirements for the Marine Stewardship Council certification of the hoki fishery 

(one target fishery contributing to NZ fur seal mortality), expert knowledge about NZ fur seals and 

their interactions with trawl gear (including some comparisons of annual capture estimates) have been 

used for an expert-based qualitative ecological risk assessment (ERAs). The results of this study have 

not been reviewed by the AEWG or DOC’s CSP-TWG. 

The impact of fisheries interactions on NZ fur seal populations (and other marine mammal 

populations) will be assessed in the marine mammal risk assessment project (PRO2012-02) due to be 

commissioned in 2013. The goal of this project is to assess the risk posed to marine mammal 

populations by New Zealand fisheries by applying a similar approach to the recent seabird risk 

assessment (Richard et al. 2011). In this approach, risk is defined as the ratio of total estimated annual 

fatalities due to bycatch in fisheries, to the level of Potential Biological Removal (PBR, Wade 1998). 

The results should be available in 2014. 

57

4.4.4. Sources of uncertainty 


Any measure of the effect of NZ fur seal mortality from commercial fisheries on NZ fur seal 

populations requires adequate information on the size of the populations at different colonies. 

Although there is reasonable information about where the main NZ fur seal breeding colonies exist, 

the size and dynamics of the overall populations are poorly understood. At present, the main sources 

of uncertainty are the lack of consistent data on: abundance by colony and in total; population 

demographic parameters; and at-sea distribution (which would ideally be available at the level of a 

colony or wider geographic area where several colonies are close together) (Baird 2011). Collation 

and analysis of existing data, such as that for the west coast South Island, would fill some of these 

gaps; there is a 20-year time series of pup production from three west coast South Island colonies, a 

reasonably long data series from the Otago Peninsula, and another from Kaikoura. Maximum benefit 

could be gained through the use of all available data, as shown by the monitoring of certain colonies 

of NZ fur seals in Australia to provide a measure of overall population stability (see Shaughnessy et 

al. 1994, Goldsworthy et al. 2003). 

Fur seals may forage in waters near a colony or haulout, or may range widely, depending on the sex, 

age, and individual preferences of the animal (Baird 2011). It is not known whether the NZ fur seals 

around a fishing vessel are from colonies nearby. Some genetic work is proposed to test the potential 

to differentiate between colonies so that in the future NZ fur seals drowned by fishing gear may be 

identified as being from a certain colony (Robertson and Gemmell 2005). 

The low to moderate levels of observer coverage in some fishery-area strata adds uncertainty to the 

total estimated captures. However, the main source of uncertainty in the level of bycatch is the paucity 

of information from the inshore fishing fleets using a variety of methods. Recent increases in observer 

coverage enabled fur seal capture estimates to include inshore fishing effort. Further increases in 

coverage, particularly for inshore fisheries, would provide better data on the life stage, sex, and size of 

captured animals, as well as samples for fatty acid or stable isotope analysis to assess diet and to 

determine provenance. Information on the aspects of fishing operations that lead to capture in inshore 

fisheries would also be useful to design mitigation. 

58



Population size Unknown, but potentially ~100 000 in the New Zealand EEZ 21 . 

Population trend Increasing at some mainland colonies but unknown for offshore island colonies. Range is 

thought to be increasing. 

Threat status NZ: Not Threatened, Increasing, Secure Overseas, in 2010 22 . 

Number of 

interactions 24 

Trends in 

interactions 

IUCN: Least Concern, in 2008 23 . 

376 estimated captures (95%CI: 221-668) in trawl fisheries in 2010-11 

57 estimated captures (95%CI: 26-99) in surface longline fisheries in 2010-11 

69 observed captures in trawl fisheries in 2010-11 

17 observed captures in surface longline fisheries in 2010-11 

Trawl fisheries: 

Surface longline fisheries: 

21 Taylor (1990), Harcourt (2001). 

22 Baker et al. (2010b). 

23 Goldsworthy and Gales (2008). 

24 For more information, see: http://data.dragonfly.co.nz/psc/. 

59



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5. New Zealand seabirds 

AEBAR 2012: Protected species: Seabirds 

Scope of chapter This chapter focuses on estimates of captures and risk assessments 

conducted for seabirds that breed in New Zealand waters. Also included 

are descriptions of the nature of fishing interactions, the management 

context and approach, trends in key indicators and major sources of 

uncertainty. It does not include detail on the biology or response of 

individual seabird species other than those four taxa for which 

quantitative population modelling has been conducted. 

Area New Zealand EEZ and Territorial Sea (noting that many seabirds are 

highly migratory and spend prolonged periods outside the NZ EEZ; on 

the high seas these effects are considered by CCSBT, WCPFC, 

CCAMLR, SPRFMO, etc. and New Zealand capture estimates are 

reported to those organisations). 

Focal localities Interactions with fisheries occur in many parts of the EEZ and TS. 

Key issues Quantitative and semi-quantitative risk assessments can be improved 

through better estimates of: incidental captures in fisheries that are 

poorly or un-observed; species identity, especially of birds released 

alive; cryptic mortality rates; survival of birds released alive; and the 

ability of seabird populations to sustain given levels of bycatch, 

especially given fisheries interactions and captures outside the New 

Zealand EEZ and in non-commercial fisheries. Consolidating qualitative 

and (semi) quantitative risk assessments is a key challenge. 

Emerging issues Assessing fisheries impacts in the context of other factors influencing 

seabird survival and reproduction, including other anthropogenic effects. 

MFish Research 

(current) 

Other Govt 


Links to 2030 

objectives 

Related 

chapters/issues 

Magnitude of “deck strike” mortality. 

PRO2006-01 Demographic, distributional and trophic information on 

selected seabird species; PRO2006-02 Modelling the effects of fishing 

on selected seabird species; PRO2010-01 Estimating incidental 

captures of protected species; PRO2010-02 Addressing key areas of 

uncertainty (including in risk assessments) for a revised NPOA- 

seabirds. 

DOC Conservation Services Programme (CSP) projects: INT2012-01, 

Observing commercial fisheries; INT2010-02, Identification of seabirds 

captured in New Zealand fisheries; POP2011-02, Flesh-footed 

shearwater population study trial and at-sea distribution; POP2012-03, 

Black petrel at-sea distribution and population estimate; POP2012-04, 

Campbell Island and grey-headed albatrosses population estimates; 

POP2012-05, White-capped albatross population estimate; POP2012- 

06, Salvin’s albatross population estimate and at-sea distribution; 

POP2012-07, Gibson’s albatross population estimate; POP2012-08, Pitt 

Island shags foraging ecology; MIT2012-01, Inshore bottom longline 

seabird mitigation design and analysis; MIT2012-02, Inshore trawl 

warp-strike mitigation analysis of effectiveness; MIT2012-03, Review of 

mitigation techniques in setnet fisheries; MIT2012-04, Surface longline 

seabird mitigation; MIT2012-05, Protected species bycatch newsletter 



including for threatened and protected species and seabed impacts. 

National Plan of Action to reduce the incidental catch of seabirds in 

New Zealand fisheries 

63

5.1. Context 


Seabird names and taxonomy in this document generally follow that adopted by the Ornithological 

Society of New Zealand (OSNZ 2010) except where a different classification has been agreed by the 

parties to the Agreement for the Conservation of Albatrosses and Petrels, ACAP, or the New Zealand 

Threat Classification Scheme (NZTCS) classifies multiple taxa within a single OSNZ species (Table 

5.1). The key exceptions to the OSNZ (2010) classification are for: white-capped albatross (OSNZ 

cites a subspecies Thalassarche cauta steadi whereas full species status is used here following 

ACAP); blue penguins (OSNZ cites a single species, little penguin Eudyptula minor, whereas multiple 

sub-species are used here to reflect NZTCS); and OSNZ (2010) and white-fronted tern (OSNZ cite a 

single species Sterna striata, whereas multiple sub-species are use here to reflect NZTCS). Southern 

and northern Buller’s albatrosses are treated as separate taxa here, although ACAP lists a single 

species “Buller’s albatross”. The taxonomy and common names adopted here will, therefore, differ in 

some instances from those used in legislation or other documents. 

There are about 140 000 bird species worldwide, but fewer than 400 are classified as seabirds (being 

specialised marine foragers). All but seven seabird taxa in New Zealand are absolutely protected 

under s.3 of the Wildlife Act 1953, meaning that it is an offence to hunt or kill them. Southern blackbacked 

gull, Larus dominicanus, is the only species that is not protected. Black shag, Phalacrocorax 

carbo, and sea hawk, Catharacta lonnbergi, are partially protected, and sooty shearwater, Puffinus 

griseus, grey-faced petrel, Pterodroma macroptera, little shag, Phalacrocorax melanoleucos 

brevirostris, and pied shag, Phalacrocorax varius, may be hunted or killed subject to Minister’s 

notification. Of the 85 seabird taxa that breed in New Zealand waters, 47 are considered threatened 

(by far the largest number on the world). For albatrosses and petrels, a key threat is injury or death in 

fishing operations, although the Wildlife Act provides defences if the death or injury took place as 

part of a fishing operation or if all reasonable steps to avoid the death or injury were taken, as long as 

the interaction is reported. Commercial fishers are required to complete a Non-Fish and Protected 

Species Catch Return (NFPSR, s11E of the Fisheries (Reporting) Regulations 2001). 

Relevant, high level guidance from the 2005 statement of General Policy under the Conservation Act 

1987 and Wildlife Act 1953 includes the following stated policies: 

4.4 (f) Marine protected species should be managed for their long-term viability and recovery 

throughout their natural range. 

4.4 (g) Where unprotected marine species are identified as threatened, consideration will be 

given to amending the Wildlife Act 1953 schedules to declare such species absolutely 

protected. 

4.4 (j) Human interactions with marine mammals and other marine protected species should be 

managed to avoid or minimise adverse effects on populations and individuals. 

4.4 (l) The Department should work with other agencies and interests to protect marine species. 

The Minister of Conservation may approve a Population Management Plan (PMP) for one or more 

species under s.14F of the Wildlife Act and a PMP can include a maximum allowable level of fishingrelated 

mortality for a species (MALFiRM). Such a limit would apply to New Zealand fisheries 

waters and would be for the purpose of enabling a threatened species to achieve a non-threatened 

status as soon as reasonably practicable or, in the case of non-threatened species, neither cause a net 

reduction in the size of the population nor seriously threaten the reproductive capacity of the species 

(s.14G). No PMPs are in place for seabirds but, in the absence of a PMP, the Minister of Fisheries 

(Primary Industries) may, after consultation with the Minister of Conservation, take such measures as 

they consider necessary to avoid, remedy, or mitigate the effect of fishing-related mortality on any 

protected species (s.15(2) of the Fisheries Act). 

64


New Zealand is a signatory to a number of international conventions and agreements to 

provide for the management of threats to seabirds, including: 

• the United Nations Convention on the Law of the Sea (UNCLOS); 

• the United Nations Fish Stocks Agreement (insofar as it relates to the conservation of 

non-target, associated and dependent species); 

• the Convention on Biological Diversity (CBD); 

• the Convention on Migratory Species (CMS); 

• the Food and Agriculture Organisation’s (FAO) International Plan of Action for 

Reducing the Incidental Catch of Seabirds in Longline Fisheries (IPOA); 

• the FAO Code of Conduct for Responsible Fisheries and the interpretive Best Practice 

Technical Guidelines; 

• the Agreement on the Conservation of Albatrosses and Petrels (ACAP) 

The ACAP agreement requires that parties achieve and maintain a favourable conservation 

status for a number of albatross and petrel taxa. Under the IPOA-seabirds, New Zealand 

developed a National Plan of Action (NPOA) to reduce the incidental catch of seabirds in 

New Zealand fisheries in 2004 (MFish and DOC 2004) and recently (2012) consulted on a 

revised NPOA-seabirds (http://www.fish.govt.nz/en-nz/Consultations/npoa+seabirds/default.htm). The 

scopes of the 2004 NPOA (and the 2012 draft) are broader than the original IPOA to facilitate 

a co-ordinated and long-term approach to reducing the impact of fishing activity on seabirds. 

Management of fishing-related mortality of seabirds is consistent with Fisheries 2030 Objective 6: 

Manage impacts of fishing and aquaculture. Further, the management actions follow Strategic Action 

6.2: Set and monitor environmental standards, including for threatened and protected species and 

seabed impacts. 

All National Fisheries Plans except that for freshwater fisheries are relevant to the management of 

fishing-related mortality of seabirds. 

Under the National Deepwater Plan, the objective most relevant for management of seabirds is 

Management Objective 2.5: Manage deepwater and middle-depth fisheries to avoid or minimise 

adverse effects on the long-term viability of endangered, threatened and protected species. 

Management objective 7 of the National Fisheries Plan for Highly Migratory Species (HMS) is to 

“Implement an ecosystem approach to fisheries management, taking into account associated and 

dependent species”. This comprises four components: Avoid, remedy, or mitigate the adverse effects 

of fishing on associated and dependent species, including through maintaining food-chain 

relationships; Minimise unwanted bycatch and maximise survival of incidental catches of protected 

species in HMS fisheries, using a risk management approach; Increase the level and quality of 

information available on the capture of protected species; and Recognise the intrinsic values of HMS 

and their ecosystems, comprising predators, prey, and protected species. 

The Environment Objective is the same for all groups of fisheries in the draft National Fisheries Plan 

for Inshore Finfish and the draft National Fisheries Plan for Inshore Shellfish, to “Minimise adverse 

effects of fishing on the aquatic environment, including on biological diversity”. The draft National 

Fisheries Plan for Freshwater has the same objective but is unlikely to be relevant to management of 

fishing-related mortality of seabirds. 

65


Table 5.1: List of New Zealand seabird taxa, excluding occasional visitors and vagrants, according to the 

Ornithological Society of New Zealand (OSNZ 2010) unless otherwise indicated (all taxa under the New 

Zealand Threat Classification System are listed and ACAP taxonomy generally takes precedence). Broad 

categories of threat status are listed, but comprehensive threat classifications are given by IUCN 

(http://www.iucnredlist.org/) and DOC (http://www.doc.govt.nz/publications/conservation/nz-threatclassification-system/nz-threat-classification-system-lists-2008-2011/, 

see also Miskelly et al. 2008, to be 

updated shortly). 

Common name Scientific name DOC category 

Wandering albatross Diomedea exulans – 

Antipodean albatross Diomedea antipodensis antipodensis Threatened 

Gibson's albatross Diomedea antipodensis gibsonii Threatened 

Southern royal albatross Diomedea epomophora At Risk 

Northern royal albatross Diomedea sanfordi At Risk 

Black-browed albatross Thalassarche melanophrys – 

Campbell black-browed albatross Thalassarche impavida At Risk 

Southern Buller's albatross Thalassarche bulleri At Risk 

Northern Buller's albatross Thalassarche bulleri platei. At Risk 

White-capped albatross Thalassarche steadi* Threatened 

Salvin's albatross Thalassarche salvini Threatened 

Chatham Island albatross Thalassarche eremita At Risk 

Indian yellow-nosed albatross Thalassarche carteri – 

Grey-headed albatross Thalassarche chrysostoma Threatened 

Light mantled sooty albatross Phoebetria palpebrata At Risk 

Flesh-footed shearwater Puffinus carneipes Threatened 

Wedge-tailed shearwater Puffinus pacificus At Risk 

Buller's shearwater Puffinus bulleri At Risk 

Sooty shearwater Puffinus griseus At Risk 

Short-tailed shearwater Puffinus tenuirostris – 

Fluttering shearwater Puffinus gavia At Risk 

Hutton's shearwater Puffinus huttoni At Risk 

Kermadec little shearwater Puffinus assimilis kermadecensis At Risk 

North Island little shearwater Puffinus assimilis haurakiensis At Risk 

Subantarctic little shearwater Puffinus elegans At Risk 

Northern diving petrel Pelecanoides urinatrix urinatrix At Risk 

Southern diving petrel Pelecanoides urinatrix chathamensis At Risk 

Subantarctic diving petrel Pelecanoides urinatrix exsul – 

South Georgian diving petrel Pelecanoides georgicus Threatened 

Grey petrel Procellaria cinerea At Risk 

Black (Parkinson's) petrel Procellaria parkinsoni Threatened 

Westland petrel Procellaria westlandica At Risk 

White-chinned petrel Procellaria aequinoctialis At Risk 

Kerguelen petrel Lugensa brevirostris – 

Southern Cape petrel Daption capense capense – 

Snares Cape petrel Daption capense australe At Risk 

Antarctic fulmar Fulmarus glacialoides – 

Southern giant petrel Macronectes giganteus – 

Northern giant petrel Macronectes halli At Risk 

Fairy prion Pachyptila turtur At Risk 

Chatham fulmar prion Pachyptila crassirostris crassirostris At Risk 

Lesser fulmar prion Pachyptila crassirostris flemingi At Risk 

Thin-billed prion Pachyptila belcheri – 

Antarctic prion Pachyptila desolata At Risk 

Salvin's prion Pachyptila salvini – 

Broad-billed prion Pachyptila vittata At Risk 

Blue petrel Halobaena caerulea – 

Pycroft's petrel Pterodroma pycrofti At Risk 

Cook's petrel Pterodroma cookii At Risk 

Black-winged petrel Pterodroma nigripennis – 

Chatham petrel Pterodroma axillaris Threatened 

Mottled petrel Pterodroma inexpectata At Risk 

White-naped petrel Pterodroma cervicalis At Risk 

Kermadec petrel Pterodroma neglecta At Risk 

Grey-faced petrel Pterodroma macroptera gouldi – 

Chatham Island taiko Pterodroma magentae Threatened 

66


White-headed petrel Pterodroma lessonii – 

Soft-plumaged petrel Pterodroma mollis – 

Wilson's storm petrel Oceanites oceanicus – 

Kermadec storm petrel Pelagodroma albiclunis Threatened 

New Zealand storm petrel Pealeornis maoriana Threatened 

Grey-backed storm petrel Garrodia nereis At Risk 

New Zealand white-faced storm petrel Pelagodroma marina maoriana At Risk 

Black-bellied storm petrel Fregetta tropica – 

White-bellied storm petrel Fregetta grallaria grallaria Threatened 

Yellow-eyed penguin Megadyptes antipodes Threatened 

Northern blue penguin** Eudyptula minor iredalei** At Risk 

Southern blue penguin** Eudyptula minor minor** At Risk 

Chatham Island blue penguin** Eudyptula minor chathamensis** At Risk 

White-flippered blue penguin** Eudyptula minor albosignata** Threatened 

Eastern rockhopper penguin Eudyptes filholi Threatened 

Fiordland crested penguin Eudyptes pachyrhynchus Threatened 

Snares crested penguin Eudyptes robustus At Risk 

Erect-crested penguin Eudyptes sclateri At Risk 

Red-tailed tropicbird Phaethon rubricauda Threatened 

Australasian gannet Morus serrator – 

Masked booby Sula dactylatra fullageri Threatened 

Black shag Phalacrocorax carbo novaehollandiae At Risk 

Pied shag Phalacrocorax varius varius Threatened 

Little black shag Phalacrocorax sulcirostris At Risk 

Little shag Phalacrocorax melanoleucos brevirostris – 

Stewart Island shag Leucocarbo chalconotus Threatened 

King shag Leucocarbo carunculatus Threatened 

Chatham Island shag Leucocarbo onslowi Threatened 

Bounty Island shag Leucocarbo ranfurlyi Threatened 

Auckland Island shag Leucocarbo colensoi Threatened 

Campbell Island shag Leucocarbo campbelli At Risk 

Spotted shag Stictocarbo punctatus punctatus – 

Blue shag Stictocarbo punctatus oliveri At Risk 

Pitt Island shag Stictocarbo featherstoni Threatened 

Subantarctic skua Catharacta antarctica lonnbergi At Risk 

South Polar skua Catharacta maccormicki – 

Pomarine skua Stercorarius pomarinus – 

Arctic skua Stercorarius parasiticus – 

Long-tailed skua Stercorarius longicaudus – 

Southern black-backed gull Larus dominicanus dominicanus – 

Red-billed gull Larus novaehollandiae scopulinus Threatened 

Black-billed gull Larus bulleri Threatened 

Caspian tern Hydroprogne caspia Threatened 

White-fronted tern*** Sterna striata striata*** At Risk 

Southern white-fronted tern*** Sterna striata aucklandorna*** Threatened 

Arctic tern Sterna paradisaea – 

New Zealand Antarctic tern Sterna vittata bethunei At Risk 

Eastern little tern Sternula albifrons sinensis – 

New Zealand fairy tern Sternula nereis davisae Threatened 

Sooty tern Onychoprion fuscata serratus At Risk 

Black-fronted tern Chlidonias albostriatus Threatened 

White-winged black tern Chlidonias leucopterus – 

Brown noddy Anous stolidus pileatus – 

Black noddy Anous tenuirostris minutus At Risk 

Grey noddy Procelsterna cerulea albivittata At Risk 

White tern Gygis alba candida Threatened 

Notes: 

* OSNZ (2010) classify New Zealand white-capped albatross as a subspecies Thalassarche cauta steadi. Full species status 

is used here following ACAP. 

** OSNZ (2010) classify a single species, little penguin Eudyptula minor. Multiple taxa are included here to reflect 

classification in the New Zealand Threat Classification Scheme. 

*** OSNZ (2010) classify a single species, white-fronted tern Sterna striata. Multiple taxa are included here to reflect 

classification in the New Zealand Threat Classification Scheme. 

67

5.2. Biology 


Taylor (2000) provided an excellent summary of the characteristics, ecology, and life history traits of 

seabirds (defined for the purpose of this document by the list in Table 5.1) which is further 

summarised here. 

All seabirds spend part of their life cycle feeding over the open sea. They have webbed feet, waterresistant 

feathering to enable them to fully immerse in salt water, and powerful wings or flippers. All 

have bills with sharp hooks, points, or filters which enable them to catch fish, cephalopods, 

crustaceans, and plankton. Seabirds can drink saltwater and have physiological adaptations to remove 

excess salt. 

Most seabird taxa are relatively long-lived; most live to 20 years and 30–40 years is typical for the 

oldest individuals. A few groups, notably albatrosses, can live for 50–60 years. Most taxa have 

relatively late sexual maturity. Red-billed gull and blue penguin have been recorded nesting as 

yearlings and diving petrels and yellow-eyed penguins can begin as 2-year-olds, but most seabirds 

start nesting only at age 3–6 years, and some albatross and petrel taxa delay nesting until 8–15 years 

old. In these late developers, individuals first return to colonies at 2–6 years old. Richard et al. (2011) 

list values for several demographic parameters that they used for a comprehensive seabird risk 

assessment. Most seabirds, and especially albatrosses and some petrels, usually return to the breeding 

colony where they were reared, or nest close-by. Seabirds also have a tendency to mate for long 

periods with the same partner, and albatross pairs almost always remain together unless one partner 

fails to return to the colony. 

The number of eggs laid varies among families. Albatrosses and petrels lay only one egg per year 

(sometimes nesting every other year) and do not replace it if it is damaged or lost. Other taxa such as 

gannets lay one egg but can replace it if the egg is lost. Most penguins lay two eggs but some raise 

only one chick and eject the second egg; replacement laying is uncommon. Blue penguins, gulls, and 

terns lay 1–3 eggs and can lay up to three clutches in a year if eggs are damaged or lost. Shags lay 2–5 

eggs, can replace clutches, and have several breeding seasons in a year. Incubation in albatrosses and 

petrels lasts 40–75 days and chick rearing 50–280 days. In gulls and terns, incubation is completed in 

20–25 days and chicks fledge in 20–40 days. In general, the lower the potential reproductive output of 

a taxon, the higher the adult survival rates and longevity. 

Some seabirds such as shags, blue penguins, and yellow-eyed penguins live their lives and forage 

relatively close to where they breed, but many, including most albatrosses and petrels, spend large 

parts of their lives in international waters or in the waters of other nations far away from their 

breeding locations. They can travel great distances across oceans during foraging flights and 

migratory journeys. 


Fishing related mortality of seabirds has been recognised as a serious, worldwide issue for only about 

20 years (Bartle 1991, Brothers 1991, Brothers et al. 1999, Croxall 2008) and the Food & Agriculture 

Organization of the United Nations (FAO) released its International Plan of Action for reducing 

incidental catch of seabirds in longline fisheries (IPOA-seabirds) in 1999 (FAO 1999). The IPOA- 

Seabirds called on countries with (longline) fisheries that interact with seabirds to assess their 

fisheries to determine if a problem exists and, if so, to develop national plans (NPOA–seabirds) to 

reduce the incidental seabird catch in their fisheries. Lewison et al. (2004) noted that, in spite of the 

recognition of the problem, few comprehensive assessments of the effects of fishing-related mortality 

had been conducted in the decade or so after the problem was recognised. They reasoned that: many 

vulnerable species live in pelagic habitats, making surveys logistically complex and expensive; 

capture data are sparse; and understanding of the potential for affected populations to sustain 

68


additional mortality is poor. Soykan et al. (2008) identified similar questions in a Theme Section 

published in Endangered Species Research, including: Where is bycatch most prevalent? Which 

species are taken as bycatch? Which fisheries and gear types result in the highest bycatch of marine 

megafauna? What are the population-level effects on bycatch species? How can bycatch be reduced? 

There has been substantial progress on these questions since 2004. Croxall et al (2012) reviewed the 

threats to 346 seabird taxa and concluded that: seabirds are more threatened than other comparable 

groups of birds; that their status has deteriorated faster over recent decades; and that fishing-related 

mortality is the most pervasive and immediate threat to many albatross and petrels. They listed the 

principal threats while at sea were posed by commercial fisheries (through competition and mortality 

on fishing gear) and pollution, and those on land were alien predators, habitat degradation and human 

disturbance. Direct exploitation, impacts of aquaculture, energy generation operations, and climate 

change were listed as threats for some taxa or areas where understanding was particularly poor. 

Croxall et al (2012) categorise responses to the issue of fishing-related mortality as 

• using long-term demographic studies of relevant seabird species, linked to observational and 

recovery data to identify the cause of population declines (e.g. Croxall et al. 1998, Tuck et al. 

2004, Poncet et al. 2006); 

• risk assessments, based on spatiotemporal overlap between seabird species susceptible to 

bycatch and effort data for fisheries likely to catch them (e.g. Waugh et al. 2008; Filippi et al. 

2010; Tuck et al. 2011); 

• working with multinational and international bodies (e.g. FAO and RFMOs) to develop and 

implement appropriate regulations for the use of best-practice techniques to reduce or 

eliminate seabird bycatch and; 

• working with fishers (and national fishery organisations) to assist cost-effective 

implementation of these mitigation techniques. 

Seabirds are ranked by the International Union for the Conservation of Nature (IUCN) as the world’s 

most threatened bird grouping (Croxall et al. 2012). Globally they face a number of threats to their 

long term viability, both at their breeding sites and while foraging at sea. Work at the global level on 

reducing threats at breeding sites is a major focus of the Agreement on the Conservation of 

Albatrosses and Petrels (ACAP) and, in New Zealand, is a DOC responsibility, but the key threat to 

seabirds at sea, especially albatrosses and petrels, is incidental capture and death through fishing 

operations. 

Some seabirds do not range far from their breeding or roosting sites and incidental captures of these 

taxa can be managed by a single jurisdiction. Conversely, conservation of highly migratory taxa such 

as albatrosses and petrels cannot be achieved by one country acting independently of other nations 

which share the same populations (e.g., ACAP). Because of this, in recent years countries which share 

populations of threatened seabirds have sought to take actions on an international level to complement 

policy and actions taken within their own jurisdictions. 

The ICES Working Group on Seabird Ecology agreed (WGSE 2011) that the three most important 

indirect effects of fisheries on seabird populations were: the harvesting of seabird food; discards as 

food subsidies; and modification of marine habitats by dredges and trawls. Many seabird prey species 

are fished commercially (e.g., Furness 2003) or can be impacted indirectly by fishing of larger 

predators. These relationships are complex and poorly understood but WGSE (2011) agreed that 

impacts on populations of seabirds were inevitable. Fishery discards and offal have the potential to 

benefit seabird species, especially those that ordinarily scavenge (Furness et al. 1992, Wagner and 

Boersma 2011). However, discarding can also modify the way in which birds forage for food (e.g., 

Bartumeus et al. 2010; Louzao et al. 2011), sometimes with farther-reaching behavioural 

consequences with negative as well as positive effects. Louzao et al. (2011) stated that discards can 

affect movement patterns (Arcos and Oro 1996), improve reproductive performance (Oro et al., 1997; 

69


1999) and increase survival (Oro and Furness, 2002; Oro et al. 2004). Benefits for scavengers and 

kleptoparasitic taxa (those that obtain food by stealing from other animals) feeding on discards can 

also have consequent negative impacts on other species, especially diving species, that share breeding 

sites or are subject to displacement (Wagner and Boersma 2011). Dredging and bottom trawling both 

affect benthic habitat and fauna (see Rice 2006 and the benthic effects chapter in this document) and 

WGSE (2011) agreed that this probably affects some seabird populations, although little work has 

been done in this area. 


Before the arrival of humans, the absence of mammalian predators in New Zealand made it a 

relatively safe breeding place for seabirds and large numbers of a wide variety of taxa bred here, 

including substantial numbers on the main North and South Islands. Today, New Zealand’s extensive 

coastline, numerous inshore and offshore islands (many of them predator free) and surrounding seas 

and oceans continue to make it an important foraging and breeding ground for about 145 seabird taxa, 

second only to the USA (GA Taylor, Department of Conservation, personal communication). Roughly 

95 of these taxa breed in New Zealand (Figures 5.1 and 5.2; Table 5.2), including the greatest number 

of albatrosses (14), petrels (32), shags (13) and penguins (9) of any area in the world (Miskelly et al. 

2008). More than a third are endemic (i.e. breed nowhere else in the world), giving New Zealand by 

far the largest number of endemic seabird taxa in the world. 

Figure 5.1 (after Croxall et al 2012). Number of endemic breeding seabird taxa by country. 

Some seabirds use New Zealand waters but do not breed here. Some visit here occasionally to feed 

(e.g. Indian Ocean yellow-nosed albatross and snowy wandering albatross), whereas others are 

frequent visitors (e.g. short-tailed shearwater and Wilson’s storm petrel), sometimes for extended 

durations (e.g. juvenile giant petrels). 

Taylor (2000) lists a wide range of threats to New Zealand seabird taxa including introduced 

mammals, avian predators (weka), disease, fire, weeds, loss of nesting habitat, competition for nest 

sites, coastal development, human disturbance, commercial and cultural harvesting, volcanic 

eruptions, pollution, plastics and marine debris, oil spills and exploration, heavy metals or chemical 

contaminants, global sea temperature changes, marine biotoxins, and fisheries interactions. Seabirds 

are caught in trawl, longline, set-net, and, occasionally, other fisheries (e.g, annual assessments by SJ 

Baird from 1994 to 2005, Baird & Smith 2008, Waugh et al. 2008, Abraham et al. 2010) and New 

Zealand released its National Plan of Action to reduce the incidental catch of seabirds (NPOAseabirds) 

in 2004. This stated there was, at that time, limited information about the level of incidental 

70


catch and population characteristics of different seabird taxa, and that this made quantifying the 

overall impact of fishing difficult. A key objective of New Zealand’s NPOA-seabirds was to improve 

this information and gain a better understanding of the impact of incidental catch on seabird taxa. 

Seabird taxa caught in New Zealand fisheries range in IUCN threat ranking from critically 

endangered (e.g. Chatham Island shag), to least concern (e.g. flesh-footed shearwater) (e.g., Vie et al. 

2009). 

Table 5.2 (after Taylor 2000): Number of species (spp.) and taxa of seabirds of different families in New 

Zealand and worldwide in 2000. Additional taxa may have been recorded since. 

NZ visitors, 

World breeding NZ breeding vagrants 

Family Common name N spp. N taxa N spp. N taxa N spp. N taxa 

Spheniscidae Penguins 17 26 6 10 8 10 

Gaviidae Divers, loons 4 6 – – – – 

Podicipedidae Grebes 10 20 2 2 – – 

Diomedeidae Albatrosses 24 24 13 13 7 7 

Procellariidae Petrels, shearwaters 70 109 28 31 20 23 

Hydrobatidae Storm-petrels 20 36 4 5 2 3 

Pelecanoididae Diving petrels 4 9 2 4 – – 

Phaethontidae Tropicbirds 3 12 1 1 1 1 

Pelecanidae Pelicans 7 12 – – 1 1 

Sulidae Gannets 9 19 2 2 1 1 

Phalacrocoracidae Shags 39 57 12 13 – – 

Fregatidae Frigatebirds 5 11 – – 2 2 

Anatidae Marine ducks 18 27 – – – – 

Scolopacidae Phalaropes 2 2 – – 2 2 

Chionididae Sheathbills 2 5 – – – – 

Stercorariidae Skuas 7 10 1 1 4 4 

Laridae Gulls 51 78 3 3 – – 

Sternidae Terns, noddies 43 121 10 11 8 8 

Rynchopidae Skimmers 2 4 – – – – 

Alcidae Auks, puffins 22 45 – – – – 

Total 359 633 84 96 56 62 

Figure 5.2 (from Croxall et al. 2012, supplementary material): The number of breeding and resident 

seabird species by country in each IUCN category (excluding Least Concern). FST, French Southern 

Territories; SGSSI, South Georgia & South Sandwich Islands; FI(M), Falkland Islands (Malvinas); 

H&M, Heard Island & McDonald Islands. 

71


Different taxa and populations face different threats from fishing operations depending on their 

biological characteristics and foraging behaviours. Biological traits such as diving ability, agility, size, 

sense of smell, eyesight and diet, foraging factors such as the season and areas they forage, their 

aggressiveness, the boldness (or shyness) they display in their attraction to fishing activity can all 

determine their susceptibility to capture, injury, or death from fishing operations. Some fishing 

methods pose particular threats to some guilds or types of seabirds. For example, penguins are 

particularly vulnerable to set net operations and large albatrosses appear to be vulnerable to all forms 

of longlining. The nature and extent of interactions differs spatially, temporally, seasonally and 

diurnally between sectors, fisheries and between fleets and vessels within fisheries. In 2010/11 the 

taxa most frequently observed caught in New Zealand commercial fisheries in descending order were 

white-chinned petrel, sooty shearwater, southern Buller’s albatross, white-capped albatross, Salvin’s 

albatross, and flesh footed shearwater, grey petrel, cape petrel, storm petrels, and black petrel. 

The management of fisheries to ensure the long-term viability of seabird populations requires an 

understanding of the risks posed by fishing and other anthropogenic drivers. Several studies have 

already estimated the number of seabirds caught annually within the New Zealand Exclusive 

Economic Zone (EEZ) in a range of fisheries (e.g., Baird & Smith 2008, Waugh et al. 2008, Abraham 

et al. 2010). In order to evaluate whether the viability of seabird populations is jeopardised by 

incidental mortality from commercial fishing, the number of annual fatalities needs to be compared 

with the capacity of the populations to replace those losses; this depends on the size and productivity 

of each population. Seabirds that breed in New Zealand die as a result of interactions with commercial 

or recreational fishing operations in waters under New Zealand jurisdiction, through interactions with 

New Zealand vessels or other nations’ vessels on the High Seas and through interactions with 

commercial, recreational or artisanal fishing operations in waters under the jurisdiction of other states. 

Unfortunately, sufficient data to build fully quantitative population models to assess risks and explore 

the likely results of different management approaches are available for only very few taxa (e.g., 

Fletcher et al. 2008, Francis and Bell 2010, Francis et al. 2008, Dillingham and Fletcher 2011). For 

this reason, broad seabird risk assessments need to rely on expert knowledge (level-1) or to be semiquantitative 

(level-2) (Hobday et al. 2007). Rowe 2010b described a level-1 seabird risk assessment 

and Baird and Gilbert (2010) described a semi-quantitative assessment for seabird taxa for which 

reasonable numbers of observed captures were available. These assessments were based on expert 

knowledge or not comprehensive and could not be used directly to assess risk for all seabird taxa and 

fisheries. 


Information with which to characterise seabird interactions with fisheries comes from a variety of 

sources. Some is opportunistically collected, whilst other information collection is targeted at 

specifically describing the nature and extent of seabird captures in fisheries. This section is focussed 

on the targeted information collection. 

Many New Zealand commercial fisheries have MPI observer coverage, much of which is funded by 

DOC’s CSP programme (e.g., Rowe 2009, 2010, Ramm 2011, 2012). Observers generate independent 

data on the number of captures of seabirds, the number of fishing events observed, and at-sea 

identification of the seabirds for these fisheries. Commercial fishers are required to provide effort data 

allowing estimation of the total number of fishing events in a fishery. In combination these data have 

been used for many years to assess the nature and extent of seabird captures in fisheries (e.g., 

Abraham et al. 2010, Abraham and Thompson 2009a, 2010, 2011 a&b, Ayers et al. 2004, Baird 1994, 

1995, 1996, 1997, 1999, 2000 a&b, 2001 a&b, 2003, 2004 a–c, 2005, Baird et al. 1998, 1999, Baird 

& Griggs 2004, Thompson and Abraham 2009). Fisher-reported captures (on NFPSR forms available 

since 1 October 2008) have not been used to estimate total captures because the reported capture rates 

72


are much lower than those reported by independent observers (Abraham and Thompson 2011) and the 

species identification is less certain. Specimens and photographs (especially for birds released alive) 

are also collected allowing verification of at-sea identifications (from carcasses or photographs) and 

description of biological characters (sex, age, condition, etc., available only from carcasses). 

In some fisheries observer data are temporally and spatially well stratified, whilst in others data are 

only available from a spatially select part of the fishery, or a limited part of the year. Where sufficient 

observer data are available, estimates of total seabird captures in the fishery are calculated. The 

methods currently used in estimating seabird captures in New Zealand fisheries are described in 

Abraham and Thompson (2011a). In this context, captures include all seabirds recovered on a fishing 

vessel except birds that simply land on the deck or collide with a vessel’s superstructure, 

decomposing animals, records of tissue fragments, and birds caught during trips carried out under 

special permit (e.g., for trials of mitigation methods). Observer coverage has been highly 

heterogeneous in that some fisheries and areas have had much higher coverage than others. This 

complicates estimation of the total number of seabirds captured, especially when estimates include 

more than one fishery, because the distribution of birds and captures is heterogeneous (Figure 5.3). 

Abraham and Thompson (2011, available at: http://fs.fish.govt.nz/Doc/22872/AEBR_79.pdf.ashx) made 

model-based estimates of captures in New Zealand trawl and longline fisheries for the following taxa 

or groups: sooty shearwater (Puffinus griseus); white-chinned petrel (Procellaria aequinoctialis); 

white-capped albatross (Thalassarche steadi); other albatrosses; and all other birds. The three 

individual species were chosen because they are the most frequently caught in trawl and longline 

fisheries. Captures of other albatrosses are mostly Salvin’s, southern Buller’s, Gibson’s or Antipodean 

wandering albatrosses, or Campbell albatrosses. The other birds category includes many taxa but 

grey, black, great-winged, and Cape petrels, flesh-footed shearwater, and spotted shag are relatively 

common observed captures (the latter based on few observations that included 31 captures in one 

event). Estimated captures up to and including the 2010/11 year are shown in Tables 5.3 and 5.4. 

Observed captures of seabirds in trawl fisheries were most common off both coasts of the South 

Island, along the Chatham Rise, on the fringes of the Stewart-Snares shelf, and around the Auckland 

Islands (Figure 5.4). This largely reflects the distribution of the major commercial fisheries for squid, 

hoki, and middle-depth species which have tended to have relatively high observer coverage. Whitecapped, 

Salvin's, and southern Buller's have been the most frequently observed captured albatrosses, 

and sooty shearwater and white chinned petrel have been the other species most frequently observed 

(Table 5.5). About 42% of observed captures were albatrosses. 

Observed captures of seabirds in surface longline fisheries were most common off the southwest coast 

of the South Island and the northeast coast of the North Island (Figure 5.5), again largely reflecting 

the distribution of the major commercial fisheries (for southern bluefin and other tunas). The charter 

fleet targeting tuna has historically had much higher observer coverage than the domestic fleet. 

Southern Buller's and white-capped have been the most frequently observed captured albatrosses, and 

grey, white-chinned, and black petrels have been the other species most frequently observed (Table 

5.6). About 77% of observed captures were albatrosses. 

Observed captures of seabirds in bottom longline fisheries were most common off the south coast of 

the South Island, along the Chatham Rise, scattered throughout the SubAntarctic, and off the northeast 

coast of the North Island, especially around the Hauraki Gulf (Figure 5.6). This distribution largely 

reflects the distribution of the ling and snapper longline fisheries that have received most observer 

coverage; other bottom longline fisheries have had much less coverage. Salvin’s and Chatham have 

been the most frequently observed captured albatrosses, and white chinned petrel, grey petrel, sooty 

shearwater, and black petrels have been the other species most frequently observed (Table 5.7). Only 

about 14% of observed captures were albatrosses. 

73


Figure 5.3 (reproduced from Abraham and Thompson 2011): All observed seabird captures in trawl, 

surface longline, and bottom longline fishing within the New Zealand region, between October 2008 and 

September 2009. The colour within each 0.2 degree cell indicates the number of fishing events (tows and 

sets, darker colours indicate more fishing) and the black dots indicate the number of observed events 

(larger dots indicate more observations). The coloured symbols indicate the location of observed seabird 

captures, randomly jittered by 0.2 degrees. The 500 m and 1000 m depth contours are shown. 

74


Table 5.3: Summary of observed and model-estimated total captures of all seabirds (top half) and whitecapped 

albatross (bottom half) by October fishing year in trawl (BT, effort in tows)), surface longline 

(SLL, effort in hooks) and bottom longline (BLL, effort in hooks) fisheries between 2002–30 and 2010–11. 

Observed and modelled rates are per 100 trawl tows or 1000 longline hooks. Caps, observed captures; 

% obs, percentage of effort observed; % incl, percentage of total effort included in the model. Data 

version v20121101. 

Models for all seabirds Fishing effort Seabirds Model estimates 

Year All effort Observed % obs Caps Rate Mean 95% c.i. % incl Rate 

BT 2002–03 130 344 6 834 5.2 269 3.94 3126 2451–4045 100.0 2.40 

BT 2003–04 121 498 6 546 5.4 262 4.00 2624 2034–3456 100.0 2.16 

BT 2004–05 120 585 7 709 6.4 483 6.27 4337 3358–5861 100.0 3.60 

BT 2005–06 110 234 6 553 5.9 356 5.43 3424 2696–4363 100.0 3.11 

BT 2006–07 103 529 7 928 7.7 211 2.66 2027 1559–2678 100.0 1.96 

BT 2007–08 89 537 9 046 10.1 234 2.59 1976 1515–2574 100.0 2.21 

BT 2008–09 87 589 9 804 11.2 469 4.78 2505 2059–3140 100.0 2.86 

BT 2009–10 92 886 9 006 9.7 256 2.85 2176 1672–2882 100.0 2.34 

BT 2010–11 86 074 7 445 8.6 370 4.97 2788 2172–3611 100.0 3.24 

SLL 2002–03 10764 588 2 195 152 20.4 115 0.05 2349 1735–3271 100.0 0.022 

SLL 2003–04 7 380 779 1 607 304 21.8 71 0.04 1582 1212–2064 100.0 0.021 

SLL 2004–05 3 676 365 783 812 21.3 41 0.05 660 499–885 100.0 0.018 

SLL 2005–06 3 687 339 705 945 19.1 37 0.05 785 589–1062 100.0 0.021 

SLL 2006–07 3 738 362 1 040 948 27.8 187 0.18 923 720–1239 100.0 0.025 

SLL 2007–08 2 244 339 426 310 19.0 41 0.10 509 397–650 100.0 0.023 

SLL 2008–09 3 115 633 937 233 30.1 57 0.06 642 502–814 100.0 0.021 

SLL 2009–10 2 992 285 665 883 22.3 135 0.20 903 702–1191 100.0 0.030 

SLL 2010–11 3 164 159 674 522 21.3 47 0.07 740 547–1019 100.0 0.023 

BLL 2002–03 37 671 038 10 772 020 28.6 296 0.03 1718 1250–2268 89.2 0.005 

BLL 2003–04 43 397 540 5 162 608 11.9 54 0.01 1151 761–1604 90.2 0.003 

BLL 2004–05 41 818 638 2 883 725 6.9 30 0.01 1191 802–1661 88.0 0.003 

BLL 2005–06 37 126 833 3 802 951 10.2 41 0.01 1037 701–1431 87.3 0.003 

BLL 2006–07 38 124 470 2 315 772 6.1 58 0.03 1236 833–1716 86.2 0.003 

BLL 2007–08 41 464 276 3 589 511 8.7 40 0.01 1193 824–1621 86.0 0.003 

BLL 2008–09 37 389 512 4 024 816 10.8 33 0.01 1037 699–1458 86.5 0.003 

BLL 2009–10 40 413 281 2 271 623 5.6 68 0.03 1062 716–1474 86.1 0.003 

BLL 2010–11 40 826 726 1 730 585 4.2 29 0.02 1403 955–1967 85.8 0.003 

White-capped albatross models 


BT 2002–03 130 344 6 834 5.2 85 1.24 861 648–1119 100.0 0.66 

BT 2003–04 121 498 6 546 5.4 148 2.26 905 701–1144 100.0 0.74 

BT 2004–05 120 585 7 709 6.4 243 3.15 1200 976–1502 100.0 1.00 

BT 2005–06 110 234 6 553 5.9 69 1.05 609 439–826 100.0 0.55 

BT 2006–07 103 529 7 928 7.7 57 0.72 437 315–591 100.0 0.42 

BT 2007–08 89 537 9 046 10.1 42 0.46 312 205–443 100.0 0.35 

BT 2008–09 87 589 9 804 11.2 97 0.99 471 352–625 100.0 0.54 

BT 2009–10 92 886 9 006 9.7 48 0.53 381 266–527 100.0 0.41 

BT 2010–11 86 074 7 445 8.6 39 0.52 356 236–496 100.0 0.41 

SLL 2002–03 10764 588 2 195 152 20.4 2 0.00 101 63–149 100.0 0.001 

SLL 2003–04 7 380 779 1 607 304 21.8 17 0.01 228 148–325 100.0 0.003 

SLL 2004–05 3 676 365 783 812 21.3 3 0.00 58 35–86 100.0 0.002 

SLL 2005–06 3 687 339 705 945 19.1 2 0.00 54 32–81 100.0 0.001 

SLL 2006–07 3 738 362 1 040 948 27.8 28 0.03 42 32–55 100.0 0.001 

SLL 2007–08 2 244 339 426 310 19.0 4 0.01 55 33–81 100.0 0.002 

SLL 2008–09 3 115 633 937 233 30.1 3 0.00 78 48–114 100.0 0.003 

SLL 2009–10 2 992 285 665 883 22.3 31 0.05 135 94–185 100.0 0.005 

SLL 2010–11 3 164 159 674 522 21.3 3 0.00 84 52–123 100.0 0.003 

BLL 2002–03 37 671 038 10 772 020 28.6 0 0.00 1 0–4 44.8 0.000 

BLL 2003–04 43 397 540 5 162 608 11.9 1 0.00 3 0–7 50.3 0.000 

BLL 2004–05 41 818 638 2 883 725 6.9 0 0.00 2 0–6 39.6 0.000 

BLL 2005–06 37 126 833 3 802 951 10.2 1 0.00 3 1–6 36.4 0.000 

BLL 2006–07 38 124 470 2 315 772 6.1 0 0.00 2 0–5 30.6 0.000 

BLL 2007–08 41 464 276 3 589 511 8.7 0 0.00 2 0–6 29.9 0.000 

BLL 2008–09 37 389 512 4 024 816 10.8 0 0.00 2 0–5 32.1 0.000 

BLL 2009–10 40 413 281 2 271 623 5.6 0 0.00 2 0–6 30.1 0.000 

BLL 2010–11 40 826 726 1 730 585 4.2 0 0.00 2 0–5 28.6 0.000 

75


Table 5.4: Summary of observed and model-estimated total captures of sooty shearwater (top half) and 

white-chinned petrel (bottom half) by October fishing year in trawl (BT, effort in tows), surface longline 

(SLL, effort in hooks) and bottom longline (BLL, effort in hooks) fisheries between 2002–30 and 2010–11. 

Observed and modelled rates are per 100 trawl tows or 1000 longline hooks. Caps, observed captures; 

% obs, percentage of effort observed; % incl, percentage of total effort included in the model. Data 


Sooty shearwater models Fishing effort Seabirds Model estimates 


BT 2002–03 130 344 6 834 5.2 120 1.76 999 642–1523 100.0 0.77 

BT 2003–04 121 498 6 546 5.4 54 0.82 370 224–590 100.0 0.30 

BT 2004–05 120 585 7 709 6.4 74 0.96 494 319–758 100.0 0.41 

BT 2005–06 110 234 6 553 5.9 169 2.58 976 657–1456 100.0 0.89 

BT 2006–07 103 529 7 928 7.7 84 1.06 497 328–748 100.0 0.48 

BT 2007–08 89 537 9 046 10.1 82 0.91 416 276–627 100.0 0.46 

BT 2008–09 87 589 9 804 11.2 152 1.55 521 371–744 100.0 0.59 

BT 2009–10 92 886 9 006 9.7 43 0.48 260 159–409 100.0 0.28 

BT 2010–11 86 074 7 445 8.6 110 1.48 488 331–722 100.0 0.57 

SLL 2002–03 10 771 388 2 195 152 20.4 8 0.00 14 8–31 100.0 0.000 

SLL 2003–04 7 386 864 1 607 304 21.8 3 0.00 7 3–19 100.0 0.000 

SLL 2004–05 3 679 865 783 812 21.3 0 0.00 2 0–9 100.0 0.000 

SLL 2005–06 3 689 879 705 945 19.1 0 0.00 2 0–9 100.0 0.000 

SLL 2006–07 3 739 962 1 040 948 27.8 2 0.00 4 2–10 100.0 0.000 

SLL 2007–08 2 245 939 426 310 19.0 0 0.00 2 0–6 100.0 0.000 

SLL 2008–09 3 115 633 937 233 30.1 0 0.00 2 0–8 100.0 0.000 

SLL 2009–10 2 992 285 665 883 22.3 0 0.00 2 0–7 100.0 0.000 

SLL 2010–11 3 166 559 674 522 21.3 0 0.00 2 0–9 100.0 0.000 

BLL 2002–03 37 789 058 10 772 020 28.6 32 0.00 97 45–216 100.0 0.000 

BLL 2003–04 43 493 500 5 162 608 11.9 17 0.00 82 30–202 100.0 0.000 

BLL 2004–05 41 868 788 2 883 725 6.9 3 0.00 81 20–213 100.0 0.000 

BLL 2005–06 37 138 783 3 802 951 10.2 3 0.00 46 6–151 100.0 0.000 

BLL 2006–07 38 150 820 2 315 772 6.1 1 0.00 53 7–169 100.0 0.000 

BLL 2007–08 41 502 096 3 589 511 8.7 6 0.00 61 17–157 100.0 0.000 

BLL 2008–09 37 424 356 4 023 916 10.8 0 0.00 54 6–169 100.0 0.000 

BLL 2009–10 40 445 221 2 279 233 5.6 7 0.00 53 10–165 100.0 0.000 

BLL 2010–11 40 878 991 1 728 765 4.2 0 0.00 69 6–235 100.0 0.000 

White-chinned petrel models 


BT 2002–03 130 344 6 834 5.2 13 0.19 148 67–280 100.0 0.11 

BT 2003–04 121 498 6 546 5.4 18 0.27 117 61–207 100.0 0.10 

BT 2004–05 120 585 7 709 6.4 55 0.71 266 169–403 100.0 0.22 

BT 2005–06 110 234 6 553 5.9 70 1.07 436 270–688 100.0 0.40 

BT 2006–07 103 529 7 928 7.7 29 0.37 135 82–216 100.0 0.13 

BT 2007–08 89 537 9 046 10.1 59 0.65 271 168–430 100.0 0.30 

BT 2008–09 87 589 9 804 11.2 104 1.06 316 222–453 100.0 0.36 

BT 2009–10 92 886 9 006 9.7 74 0.82 295 189–461 100.0 0.32 

BT 2010–11 86 074 7 445 8.6 130 1.75 540 359–817 100.0 0.63 

SLL 2002–03 10764 588 2 195 152 20.4 4 0.00 79 43–128 100.0 0.001 

SLL 2003–04 7 380 779 1 607 304 21.8 2 0.00 53 27–87 100.0 0.001 

SLL 2004–05 3 676 365 783 812 21.3 3 0.00 30 14–49 100.0 0.001 

SLL 2005–06 3 687 339 705 945 19.1 1 0.00 30 14–50 100.0 0.001 

SLL 2006–07 3 738 362 1 040 948 27.8 5 0.00 30 16–48 100.0 0.001 

SLL 2007–08 2 244 339 426 310 19.0 4 0.01 22 11–35 100.0 0.001 

SLL 2008–09 3 115 633 937 233 30.1 3 0.00 26 13–43 100.0 0.001 

SLL 2009–10 2 992 285 665 883 22.3 3 0.00 25 12–41 100.0 0.001 

SLL 2010–11 3 164 159 674 522 21.3 8 0.01 34 19–52 100.0 0.001 

BLL 2002–03 37 671 038 10 772 020 28.6 132 0.01 350 246–540 100.0 0.001 

BLL 2003–04 43 397 540 5 162 608 11.9 15 0.00 139 81–215 100.0 0.000 

BLL 2004–05 41 818 638 2 883 725 6.9 11 0.00 188 105–290 100.0 0.000 

BLL 2005–06 37 126 833 3 802 951 10.2 13 0.00 189 108–303 100.0 0.001 

BLL 2006–07 38 124 470 2 315 772 6.1 12 0.01 225 123–364 100.0 0.001 

BLL 2007–08 41 464 276 3 589 511 8.7 10 0.00 261 143–423 100.0 0.001 

BLL 2008–09 37 389 512 4 024 816 10.8 1 0.00 204 97–380 100.0 0.001 

BLL 2009–10 40 413 281 2 271 623 5.6 1 0.00 172 86–282 100.0 0.000 

BLL 2010–11 40 826 726 1 730 585 4.2 24 0.01 422 225–769 100.0 0.001 

76


Figure 5.4: Map of trawl fishing effort and all observed seabird captures in trawls, October 2003 to 

September 2011. Fishing effort is mapped into 0.2-degree cells, with the colour of each cell being related 

to the amount of effort (events). Observed fishing events are indicated by black dots, and observed 

captures are indicated by red dots. Fishing is shown only if the effort could be assigned a latitude and 

longitude, and if there were three or more vessels fishing within a cell (here, 96% of effort is displayed). 

77


Table 5.5: Summary of seabirds observed captured in trawl fisheries 2002–03 to 2010–11. Declared target 

species are: SQU, arrow squid; HOK+, hoki, hake, ling; Mid., other middle depth species silver, white, 

and common warehou, barracouta, alfonsinos, stargazer; SCI, scampi; ORH+, orange roughy and oreos; 

SBW, southern blue whiting; JMA, Jack mackerels; Ins., other inshore species for which one or more 

captures have been observed; tarakihi, red cod, spiny dogfish, John dory, snapper; FLA, flatfishes. Data 


Declared target species 

Species or group SQU HOK+ Mid. SCI ORH+ SBW JMA Ins. FLA Total 

White capped albatross 679 54 52 15 6 0 1 22 0 829 

Salvin's albatross 18 87 25 29 16 2 0 20 0 197 

Southern Buller's 49 41 19 4 3 0 1 1 0 118 

Campbell albatross 2 5 0 1 0 1 0 0 0 9 

Chatham Island albatross 0 0 0 1 8 0 0 0 0 9 

Southern royal albatross 5 0 0 0 0 1 0 0 0 6 

Southern black-browed 1 2 0 0 0 0 0 2 0 5 

Gibson's albatross 0 0 0 0 1 0 0 0 0 1 

Northern royal albatross 0 0 0 0 1 0 0 0 0 1 

Albatross indet. 10 10 1 5 0 4 1 1 0 32 

All albatrosses 764 199 97 55 35 8 3 46 0 1207 

Sooty shearwater 540 181 119 37 5 0 5 1 0 888 

White chinned petrel 387 43 42 48 1 0 9 0 0 530 

Cape petrels 1 34 1 3 19 1 2 0 0 61 

Flesh footed shearwater 0 1 0 35 0 0 0 2 0 38 

Spotted shag 0 0 0 0 0 0 0 0 32 32 

Grey petrel 1 2 0 0 3 22 0 0 0 28 

Common diving petrel 5 5 0 1 2 0 1 0 0 14 

Westland petrel 0 11 1 0 0 0 1 0 0 13 

Fairy prion 0 4 0 0 0 0 5 0 0 9 

Antarctic prion 7 0 0 0 0 0 0 0 0 7 

Northern giant petrel 0 3 1 1 1 0 0 0 0 6 

Giant petrel 3 1 0 0 0 0 0 0 0 4 

Grey-backed storm petrel 3 1 0 0 0 0 0 0 0 4 

Fulmar prion 0 0 0 0 0 0 3 0 0 3 

Black petrel 0 0 0 1 0 0 0 1 0 2 

Black-bellied storm petrel 1 1 0 0 0 0 0 0 0 2 

White-faced storm petrel 0 0 0 0 2 0 0 0 0 2 

Black backed gull 0 0 0 0 0 0 0 0 1 1 

Short tailed shearwater 0 0 1 0 0 0 0 0 0 1 

White headed petrel 1 0 0 0 0 0 0 0 0 1 

Other bird indet. 11 5 3 2 1 5 0 2 2 31 

All other birds 960 292 168 128 34 28 26 6 35 1677 

All observed birds 1724 491 265 183 69 36 29 52 35 2884 

Approx. proportion obs 0.23 0.14 0.06 0.09 0.26 0.35 0.25 0.01 0.01 0.08 

78


Figure 5.5: Map of surface longline fishing effort and all observed seabird captures by surface longlines, 

October 2003 to September 2011. Fishing effort is mapped into 0.2-degree cells, with the colour of each 

cell being related to the amount of effort (events). Observed fishing events are indicated by black dots, 

and observed captures are indicated by red dots. Fishing is shown only if the effort could be assigned a 

latitude and longitude, and if there were three or more vessels fishing within a cell (here, 75.3% of effort 

is displayed). 

79


Table 5.6: Summary of seabirds observed captured in surface longline fisheries 2002–03 to 2010–11. 

Declared target species are: SBT, southern bluefin tuna; BIG, bigeye tuna; SWO, broadbill swordfish; 

ALB, albacore tuna. Data version v20121101. 


Species or group SBT BIG SWO ALB Total 

Southern Buller's albatross 296 7 1 8 312 

White capped albatross 91 1 1 0 93 

Campbell albatross 18 3 2 17 40 

Antipodean albatross 4 8 15 3 30 

Gibson's albatross 8 6 9 7 30 

Wandering albatrosses 8 3 0 0 11 

Salvin's albatross 3 4 0 1 8 

Antipodean / Gibson's 0 2 5 0 7 

Black browed albatrosses 0 2 2 0 4 

Southern royal albatross 4 0 0 0 4 

Southern black-browed 2 0 0 0 2 

Light-mantled sooty 1 0 0 0 1 

Northern royal albatross 0 1 0 0 1 

Pacific albatross 1 0 0 0 1 

Albatrosses indet. 2 1 33 0 36 

Total albatrosses 438 38 68 36 580 

Grey petrel 38 0 3 5 46 

White chinned petrel 21 8 2 2 33 

Black petrel 0 23 2 1 26 

Great winged petrel 0 1 2 17 20 

Sooty shearwater 4 0 1 8 13 

Flesh footed shearwater 0 11 1 0 12 

Westland petrel 6 0 0 2 8 

Cape petrels 2 0 0 0 2 

Southern giant petrel 2 0 0 0 2 

White headed petrel 0 0 0 2 2 

Petrels indet. 0 1 0 0 1 

Total other birds 73 44 11 37 165 

All observed birds 511 82 79 73 745 

Approx. proportion obs 0.42 0.03 0.10 0.38 0.22 

80


Figure 5.6: Map of bottom longline fishing effort and all observed seabird captures by bottom longlines, 

October 2003 to September 2011. Fishing effort is mapped into 0.2-degree cells, with the colour of each 

cell being related to the amount of effort (events). Observed fishing events are indicated by black dots, 

and observed captures are indicated by red dots. Fishing is shown only if the effort could be assigned a 

latitude and longitude, and if there were three or more vessels fishing within a cell (here, 79.3% of effort 

is displayed). 

81


Table 5.7: Summary of seabirds observed captured in bottom longline fisheries 2002–03 to 2010–11. 

Declared target species are: LIN, ling; SNA, snapper; BNS, bluenose; HPB, hapuku or bass. Data version 

v20121101. 


Species or group LIN SNA BNS HPB Total 

Salvin's albatross 51 0 0 0 51 

Chatham Island albatross 18 0 0 0 18 

Southern Buller's albatross 4 0 3 0 7 

Campbell albatross 0 0 2 1 3 

Wandering albatrosses 2 0 1 0 3 

White capped albatross 2 0 0 0 2 

Black browed albatrosses 1 0 0 0 1 

Indian yellow-nosed albatross 1 0 0 0 1 

Southern royal albatross 1 0 0 0 1 

Albatross indet. 2 0 0 0 2 

All albatrosses 82 0 6 1 89 

White chinned petrel 217 0 2 0 219 

Grey petrel 79 0 0 0 79 

Sooty shearwater 68 0 0 1 69 

Black petrel 0 28 14 7 51 

Flesh footed shearwater 0 36 0 3 39 

Cape petrels 24 0 0 0 24 

Common diving petrel 23 0 0 0 23 

Great winged petrel 0 0 0 6 6 

Fluttering shearwater 0 4 0 0 4 

Northern giant petrel 4 0 0 0 4 

Prions 4 0 0 0 4 

Storm petrels 3 0 0 0 3 

Gannets 0 2 0 0 2 

Pied shag 0 2 0 0 2 

Black backed gull 0 1 0 0 1 

Buller's shearwater 0 1 0 0 1 

Crested penguins 1 0 0 0 1 

Giant petrel 1 0 0 0 1 

Red billed gull 0 1 0 0 1 

Other birds indet 1 10 0 0 11 

All other birds 425 85 16 17 545 

All birds observed 507 85 22 18 634 

Approx. proportion obs 0.20 0.01 0.01 0.01 0.10 

Model-based estimates of captures can be combined across trawl and longline fisheries (Figure 5.7). 

Summed across all bird taxa, trawl, surface longline, and bottom longline fisheries account for 55%, 

21%, and 24% of captures, respectively, but there are substantial differences in these proportions 

among seabird taxa. A high proportion (87% between 2003 and 2011) of white-capped albatross 

captures are taken in trawl fisheries with almost all of the remainder taken in surface longline 

fisheries. The trawl fishery also accounts for 89% of sooty shearwaters captured, with most of the 

remainder taken by bottom longliners. The proportion captured by trawl fisheries reduces to 53% for 

all other albatrosses combined, with 30% and 17% taken in surface and bottom longline fisheries, 

respectively. Bottom longline and trawl take similar proportions of the white-chinned petrels captured 

(43% and 50%, respectively). 

82


Over the 2003 to 2011 period, there appear to have been downward trends (across all fisheries) in the 

estimated captures of all birds combined, white-capped albatross, and non-albatross taxa other than 

sooty shearwaters and white-chinned petrel (Figure 5.7). Estimated captures of other albatrosses, 

sooty shearwaters, and white-chinned petrel appear to have fluctuated without much trend, although 

there is some evidence for an increasing trend for white-chinned petrel, especially in trawl fisheries. 

Because fishing effort often changes with time, estimates of total captures may not be the only index 

required for comprehensive monitoring. The number of captures (with certain caveats, see later) is 

clearly more biologically relevant for the birds, but capture rates by fishery may be more useful 

measures to assess fishery performance and the effectiveness of mitigation approaches. Dividing 

modelled catch estimates by the number of tows or hooks set in a particular fishery in each year 

provides catch rate indices by fishery. These are typically reported as the number of birds captured per 

100 trawl tows or per 1000 longline hooks (Figures 5.8 to 5.10). 


1400 

1200 

1000 

800 

600 

400 

200 

0 

1200 

1000 

800 

600 

400 

200 

0 

3000 

2500 

2000 

1500 

1000 

500 

0 

White-capped albatross 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

Sooty shearwater 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

Other birds 

BLL 

SLL 

Trawl 

BLL 

SLL 

Trawl 

BLL 

SLL 

Trawl 

83 

2500 

2000 

1500 

1000 

500 

0 

1200 

1000 

800 

600 

400 

200 

0 

8000 

7000 

6000 

5000 

4000 

3000 

2000 

1000 

0 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

Other albatrosses 

White-chinned petrel 

All birds combined 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

Figure 5.7: Model-based estimates of captures of the most numerous seabird taxa observed captured in 

trawl, surface longline, and bottom longline fisheries between 2002/03 and 2010/11. For confidence limits 

see Tables 3 and 4. Note this level of aggregation conceals any different trends within a fishing method 

(e.g., deepwater vs. inshore and flatfish trawl or large vs. small longliners). 

BLL 

SLL 

Trawl 

BLL 

SLL 

Trawl 

BLL 

SLL 

Trawl


For white-capped albatross, captures rates declined between 2002/03 and 2010/11, and especially up 

to 2006/07, in the major offshore trawl fisheries for squid and hoki (Figure 5.8) but showed no trend 

for inshore trawlers and increased for surface longliners targeting southern bluefin tuna. Together, 

these fisheries account for 82% of all estimated captures of white-capped albatross in these years. 

1000 

800 

600 

400 

200 

500 

400 

300 

200 

100 

0 

300 

250 

200 

150 

100 

50 

0 

200 

150 

100 

50 

0 

0 

White-capped albatross captures and capture rates 

Captures 

Squid trawl: 39% of captures 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

Inshore trawl: 26% of captures 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

SBT longline: 11% of captures 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

Hoki trawl: 6% of captures 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

Fishing year 

84 

10.0 

8.0 

6.0 

4.0 

2.0 

0.0 

1.2 

1.0 

0.8 

0.6 

0.4 

0.2 

0.0 

0.12 

0.10 

0.08 

0.06 

0.04 

0.02 

0.00 

0.7 

0.6 

0.5 

0.4 

0.3 

0.2 

0.1 

0.0 

Capture rate 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

Figure 5.8: Model-based estimates of captures (left panels) and capture rates (right panels, captures per 

100 trawl tows or 1000 longline hooks) of white capped albatross in the four fisheries estimated to have 

taken the most captures between 2002/03 and 2010/11 (cumulatively, 82% of all white-capped albatross 

captures). Data version v20121101.


For white-chinned petrel, captures rates increased between 2002/03 and 2010/11 in squid and scampi 

trawlers (Figure 5.9) but showed no trend for bottom longliners targeting ling and bluenose. Together, 

these fisheries account for 81% of all estimated captures of white-chinned petrel in these years. 

800 

600 

400 

200 

0 

600 

400 

200 

0 

200 

150 

100 

50 

0 

300 

250 

200 

150 

100 

50 

0 

White-chinned petrel captures and capture rates 

Captures Capture rate 

Ling longline: 32% of captures 

2003 2004 2005 2006 2007 2008 2009 2010 2011 


2003 2004 2005 2006 2007 2008 2009 2010 2011 

Bluenose longline: 11% of captures 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

Scampi trawl: 8% of captures 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

Fishing year 

85 

0.05 

0.04 

0.03 

0.02 

0.01 

0.00 

12.0 

10.0 

8.0 

6.0 

4.0 

2.0 

0.0 

0.03 

0.02 

0.01 

0.00 

6.0 

5.0 

4.0 

3.0 

2.0 

1.0 

0.0 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

2003 2004 2005 2006 2007 2008 2009 2010 2011 


100 trawl tows or 1000 longline hooks) of white chinned petrels in the four fisheries estimated to have 

taken the most captures between 2002/03 and 2010/11 (cumulatively, 81% of all white-chinned petrel 

captures). Data version v20121101.


For sooty shearwaters, captures rates decreased between 2002/03 and 2010/11 for bottom longliners 

targeting ling, but showed no trend in squid, middle-depth, and hoki trawlers (Figure 5.10). Together, 

these fisheries account for 80% of all estimated captures of sooty shearwaters in these years. 

1000 

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0 

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0 

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0 

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Sooty shearwater captures and capture rates 

Captures Capture rate 


2003 2004 2005 2006 2007 2008 2009 2010 2011 

mid-depth trawl: 18% of captures 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

Hoki trawl: 17% of captures 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

Ling longline: 3% of captures 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

Fishing year 

86 

10.0 

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2003 2004 2005 2006 2007 2008 2009 2010 2011 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

2003 2004 2005 2006 2007 2008 2009 2010 2011 

2003 2004 2005 2006 2007 2008 2009 2010 2011 


100 trawl tows or 1000 longline hooks) of sooty shearwaters in the four fisheries estimated to have taken 

the most captures between 2002/03 and 2010/11 (cumulatively, 80% of all sooty shearwater captures). 

Data version v20121101.


On-board captures recorded by observers represent the most reliable source of information for 

monitoring trends in total captures and capture rates, but these data have three main deficiencies with 

respect to estimating total fatalities, especially to species level. First, some captured seabirds are 

released alive (23% in trawl fisheries between 2002–03 and 2010–11, 29% in surface longline 

fisheries, and 25% in bottom longline fisheries), meaning that, all else being equal, estimates of 

captures may overestimate total fatalities, depending on the survival rate of those released. Second, 

identifications by observers are not completely reliable and sometimes use generic codes rather than 

species codes. A high proportion of dead captures are returned for necropsy and formal identification 

(87% in trawl fisheries between 2002–03 and 2010–11, 83% in surface longline fisheries, and 89% in 

bottom longline fisheries), but there remains uncertainty in the identity of 11–17% of dead captures 

and 100% of those released alive. Third, not all birds killed or mortally wounded by fishing gear are 

recovered on a fishing vessel. Some birds caught on longline hooks fall off before being recovered, 

and birds that collide with trawl warps may be dragged under the water and drowned or injured to the 

extent that they are unable to fly or feed. Excluding this “cryptic” mortality means that, all else being 

equal, estimates of captures will underestimate total fatalities. These deficiencies do not greatly affect 

the suitability of estimates of captures and capture rates for monitoring purposes, but they have 

necessitated the development of alternative measures for assessing risk and population consequences. 


New Zealand had taken steps to reduce incidental captures of seabirds before the advent of the IPOA 

in 1999 and the NPOA in 2004. For example, regulations were put in place under the Fisheries Act to 

prohibit drift net fishing in 1991 and prohibit the use of netsonde monitoring cables (“third wires”) in 

trawl fisheries in 1992. The use of tori lines (streamer lines designed to scare seabirds away from 

baited hooks) was made mandatory in all tuna longline fisheries in 1992. 

The fishing industry also undertook several initiatives to reduce captures include funding research into 

new or improved mitigation measures, and adopting voluntary codes of practice and best practice 

fishing methods. Codes of practice have been in place in the joint venture tuna longline fishery since 

1997–98, requiring, inter alia, longlines to be set at night and voluntary upper limits on the incidental 

catch of seabirds. That limit was steadily reduced from 160 “at risk” seabirds in 1997–98, to 75 in 

2003–04. Most vessels in the domestic longline tuna fishery had also voluntarily adopted night 

setting, by 2004. A code of practice was in place for the ling auto-line fishery by 2002–03. Other early 

initiatives included reduced deck lighting, the use of thawed rather than frozen baits, sound deterrents, 

discharging of offal away from setting and hauling, weighted branch lines, different gear hauling 

techniques and line shooters. Current regulated and voluntary initiatives are summarised by fishery in 

Table 5.8. 

In 2002, MFish, DOC, and stakeholders began working with other countries to reduce the incidental 

catch of seabirds. As a result, a group called Southern Seabird Solutions was formed and formally 

established as a Trust in 2003 (http://www.southernseabirds.org/) and received royal patronage in 2012. 

Southern Seabird Solutions exists to promote responsible fishing practices that avoid the incidental 

capture of seabirds in New Zealand and the southern ocean. Membership includes representatives 

from the commercial fishing industry, environmental and conservation groups, and government 

departments. The Trust’s vision is that: All fishers in the Southern Hemisphere avoid the capture of 

seabirds, and this is underpinned by the strategic goals on: Culture Change; Supporting Collaboration; 

Mitigation Development and Knowledge Transfer; Recognising Success; and Strengthening the Trust. 

Building on these initiatives, New Zealand’s 2004 NPOA established a more comprehensive 

framework to reducing incidental captures approach across all fisheries (because focussing on 

longline fisheries like the IPOA was considered neither equitable nor sufficient). 

87

It included two goals that set the overall direction: 


1. To ensure that the long-term viability of protected seabird species is not threatened by their 

incidental catch in New Zealand fisheries waters or by New Zealand flagged vessels in high 

seas fisheries; and 

2. To further reduce incidental catch of protected seabird species as far as possible, taking into 

account advances in technology, knowledge and financial implications. 

Together the two goals established the NPOA as a long-term strategy. The second goal was designed 

to build on the first goal by promoting and encouraging the reduction of incidental catch beyond the 

level that is necessary to ensure long term viability. The goals recognised that, although seabird deaths 

may be accidentally caused by fishing, most seabirds are absolutely protected under the Wildlife Act. 

The second goal balances the need to continue reducing incidental catch against the factors that 

influence how this can be achieved in practice (e.g., advances in technology and the costs of 

mitigation). The scope of the NPOA included: 

• all seabird species absolutely or partially protected under the Wildlife Act; 

• commercial and non-commercial fisheries; 

• all New Zealand fisheries waters; and 

• high seas fisheries in which New Zealand flagged vessels participate, or where foreign 

flagged vessels catch protected seabird species. 

Specific objectives were established in the NPOA as follows: 

1. Implement efficient and effective management measures to achieve the goals of the NPOA, 

using best practice measures where possible; 

2. Ensure that appropriate incentives and penalties are in place so that fishers comply with 

management measures; 

3. Establish mandatory bycatch limits for seabird species where they are assessed to be an 

efficient and effective management measure and there is sufficient information to enable an 

appropriate limit to be set; 

4. Ensure that there is sufficient, reliable information available for the effective implementation 

and monitoring of management measures; 

5. Establish a transparent process for monitoring progress against management measures; 

6. Ensure that management measures are regularly reviewed and updated to reflect new 

information and developments, and to ensure the achievement of the goals of the NPOA; 

7. Encourage and facilitate research into affected seabird species and their interactions with 

fisheries; 

8. Encourage and facilitate research into new and innovative ways to reduce incidental catch; 

9. Provide mechanisms to enable all interested parties to be involved in the reduction of 

incidental catch; 

10. Promote education and awareness programmes to ensure that all fishers are aware of the need 

to reduce incidental catch and the measures available to achieve a reduction. 

The NPOA-seabirds sets out the mix of voluntary and mandatory measures that would be used to help 

reduce incidental captures of seabirds, noted research into the extent of the problem and the 

techniques for mitigating it, and outlined mechanisms to oversee, monitor and review the 

effectiveness of these measures. It was not within the scope of the NPOA to address threats to 

seabirds other than fishing. Such threats are identified in DOC’s Action Plan for Seabird Conservation 

in New Zealand (Taylor 2000) and their management is undertaken by DOC. 

88


Since publication of the NPOA in 2004, more progress has been made in the commercial fishing 

sector, including: 

• in the deepwater fishing sector; 

o industry has implemented vessel specific risk management plans (VMPs) comprising 

non-mandatory seabird scaring devices offal management and other measures to 

reduce risks to seabirds, 

o Government has implemented mandatory measures to reduce risk to seabirds (e.g., 

use and deployment of seabird scaring devices), and 

o industry has taken a proactive stance in resourcing a 24/7 liaison officer to undertake 

incident response actions, mentoring, VMP and regime development and reviewing, 

and fleet wide training; 

• in the bottom and surface long-line sectors, Government has implemented mandatory 

measures including tori lines, night setting, line weighting and offal management; 

• a number of research projects have been or are currently being undertaken by government and 

industry into offal discharge, efficacy of seabird scaring devices, line weighting and longline 

setting devices; and 

• workshops organised by both industry bodies and Southern Seabird Solutions are being held 

for the inshore trawl and longline sectors. 

Areas still requiring progress identified in MPI’s 2012 consultation documents for a revision to the 

NPOA-seabirds included: 

• development and implementation of mitigation measures, and education, training and 

outreach in commercial set net fisheries and inshore trawl fisheries; 

• implementation of spatially and temporally representative at-sea data collection in inshore and 

some HMS fisheries; 

• development and implementation of mitigation measures for net captures in trawl fisheries; 

• development and implementation of mitigation measures, education, training and outreach in, 

and risk assessment of non-commercial fisheries (especially setnet and line fisheries). 

Mitigation has developed substantially since FAO’s IPOA was published and a number of recent 

reviews consider the effectiveness of different methods (Bull 2007, 2009) and summarise currently 

accepted best practice (ACAP 2011). In December 2010, FAO held a Technical Consultation where 

International Guidelines on bycatch management and reduction of discards were adopted (FAO2010). 

The text included an agreement that the guidelines should complement appropriate bycatch measures 

addressed in the IPOA-Seabirds and its Best Practice Technical Guidelines (FAO 2009). The 

Guidelines were subsequently adopted by FAO in January 2011. 

The most important factor influencing contacts between seabirds and trawl warp cables is the 

discharge of offal (Wienecke and Robertson 2002; Sullivan et al. 2006, ACAP 2011). Offal 

management methods used to reduce the attraction of seabirds to vessels include mealing, mincing, 

and batching. ACAP recommends (ACAP 2011) full retention of all waste material where practicable 

because this significantly reduced the number of seabirds feeding behind vessels compared with the 

discharge of unprocessed fish waste (Abraham 2009; Wienecke and Robertson 2002; Favero et al. 

2010) or minced waste (Melvin et al. 2010). Offal management has been found to be a key driver of 

seabird bycatch in New Zealand trawl fisheries (Abraham 2007; Abraham and Thompson 2009b; 

Abraham et al. 2009; Abraham 2010; Pierre et al 2010, 2012 a&b). Other best practice 

recommendations (ACAP 2011) are the use of bird-scaring lines to deter birds from foraging near the 

trawl warps, use of snatch blocks to reduce the aerial extent of trawl warps, cleaning fish and benthic 

material from nets before shooting, minimising the time the trawl net is on the surface during hauling, 

and binding of large meshes in pelagic trawl before shooting. 

89


Table 5.8 (after MPI 2012, consultation documents for a revised NPOA-seabirds): summary of current mitigation measures applied to New Zealand vessels fishing 

in New Zealand waters to avoid incidental seabird captures. R, regulated; SM, required via a self-managed regime (non-regulatory, but required by industry 

organisation and audited independently by Government); V, voluntary with at least some use known; N/A, measure not relevant to the fishery; years in parentheses 

indicate year of implementation; *, part of a vessel management plan (VMP). Note, this table may not capture all voluntary measures adopted by fishers. 

Mitigation Measure Surface longline Bottom longline Trawl >=28 m Trawl

AEBAR 2012: Non-protected bycatch 

In New Zealand, the three legally permitted devices used for mitigation by trawlers are tori lines (e.g., 

Sullivan et al. 2006), bird bafflers (Crysel 2002), and warp scarers (Carey 2005). Middleton and 

Abraham (2007) reported experimental trials of mitigation devices designed to reduce the frequency 

of collisions between seabirds and trawl warps on 18 observed vessels in squid trawl fishery in 2006. 

The frequencies of birds striking either warps or one of three mitigation devices (tori lines, 4-boom 

bird bafflers, and warp scarers) were assessed using standardised protocols during commercial 

fishing. Different warp strike mitigation treatments were used on different tows according to a 

randomised experimental design. Middleton and Abraham (2007) confirmed that the discharge of 

offal was the main factor influencing seabird strikes; almost no strikes were recorded when there was 

no discharge, and strike rates were low when only sump water was discharged (see also Abraham et 

al. 2009). In addition to this effect, tori lines were shown to be most effective mitigation approach and 

reduced warp strikes by 80–95% of their frequency without mitigation. Other mitigation approaches 

were only 10–65% effective. Seabirds struck tori lines about as frequently as they did the trawl warps 

in the absence of mitigation but the consequences are unknown. 

Recommended best practice for surface (pelagic) longline fisheries and bottom (demersal) longlines 

(ACAP 2011) includes weighting of lines to ensure rapid sinking of baits (including integrated 

weighted line for bottom longlines), setting lines at night when most vulnerable birds are less active, 

and the proper deployment of bird scaring lines (tori lines) over baits being set, and offal management 

(especially for bottom longlines). A range of other measures are offered for consideration. 

5.4.3. Modelling fisheries interactions and estimating risk 

5.4.3.1. Hierarchical structure of risk assessments 

Hobday et al (2007) described a hierarchical framework for ecological risk assessment in fisheries 

(see Figure 5.11). The hierarchy included three levels: Level 1 qualitative, expert-based assessments 

(often based on a Scale, Intensity, Consequence Analysis, SICA); Level 2 semi-quantitative analysis 

(often using some variant of Productivity Susceptibility Analysis, PSA); and Level 3 fully quantitative 

modelling including uncertainty analysis. The hierarchical structure is designed to “screen out” 

potential effects that pose little or low risk for the least investment in data collection and analysis, 

escalating to risk treatment or higher levels in the hierarchy only for those potential effects that pose 

non-negligible risk. This structure relies for its effectiveness on a low potential for false negatives at 

each stage, thereby identifying and screening out activities that are ‘low risk’ with high certainty. This 

focuses effort on remaining higher risk activities. In statistical terms, risk assessment tolerates Type I 

errors (false positives, i.e. not screening out activities that may actually present a low risk) in order to 

avoid Type II errors (false negatives, i.e. incorrectly screening out activities that actually constitute 

high risk), and it is important to distinguish this approach from normal estimation methods. Whereas 

normal estimation strives for a lack of bias and a balance of Type I and Type II errors, risk assessment 

is designed to answer the question “how bad could it be?” The divergence between the risk 

assessment approach and normal, unbiased estimation approaches should diminish at higher levels in 

the risk assessment hierarchy, where the assessment process should be informed by good data that 

support robust estimation. 

91


Figure 5.11 (from Hobday et al.): Diagrammatic representation of the hierarchical risk assessment 

process where activities that present low risk are progressively screened out by assessments of 

increasingly high data content, sophistication, and cost. 

5.4.3.2. Qualitative (Level 1) risk assessment 

Rowe (2010) summarised an expert-based, qualitative (Level 1) risk assessment, commissioned by 

DOC, for the incidental mortality of seabirds caused by New Zealand fisheries. The main focus was 

on fisheries operating within the NZ EEZ and on all seabirds absolutely or partially protected under 

the Wildlife Act 1953. New Zealand flagged vessels fishing outside the EEZ were included, but risk 

from non-NZ fisheries and other human causes were not included. 

The panel of experts who conducted the Level 1 risk assessment assessed the threat to each of 101 

taxa posed by 26 fishery groups, scoring exposure and consequence independently according to the 

schemas in Tables 5.9 and 5.10 (details in Rowe 2010b). The risk for a given taxon posed by a given 

fishery was calculated as the product of exposure and consequence scores. Potential risk was 

estimated as the risk posed by a fishery assuming no mitigation was in place, and residual risk (called 

“optimum risk” by Rowe 2010b) was estimated assuming that mitigation was in place throughout a 

given fishery and deployed correctly. The panel also agreed a confidence score for each taxon-fishery 

interaction using the schema in Table 5.11. 

Table 5.9: Exposure scores used by Rowe (2010) (modified from Fletcher 2005, Hobday et al 2007) 

Score Descriptor Description 

0 Remote The species will not interact directly with the fishery 

1 Rare Interactions may occur in exceptional circumstances 

2 Unlikely Evidence to suggest interactions possible 

3 Possible Evidence to suggest interactions occur, but are uncommon 

4 Occasional Interactions likely to occur on occasion 

5 Likely Interactions are expected to occur 

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Table 5.10: Consequence scores used by Rowe (2010) (modified from Fletcher 2005, Campbell & 

Gallagher 2007, Hobday et al. 2007) 

Score Descriptor Description 

1 Negligible Some or one individual/s impacted, no population impact. 

2 Minor Some individuals are impacted, but minimal impact on population structure or 

dynamics. In the absence of further impact, rapid recovery would occur 

3 Moderate The level of interaction / impact is at the maximum acceptable level that still meets 

an objective. In the absence of further impact, recovery is expected in years 

4 Major Wider and longer term impacts; loss of individuals; potential loss of genetic 

diversity. Level of impact is above the maximum acceptable level. In the absence 

of further impact, recovery is expected in multiple years 

5 Severe Very serious impacts occurring, loss of seabird populations causing local 

extinction; decline in species with single breeding population, measurable loss of 

genetic diversity. In the absence of further impact, recovery is expected in years to 

decades 

6 Intolerable Widespread and permanent / irreversible damage or loss occurring; local extinction 

of multiple seabird populations; serious decline of a species with a single breeding 

population, significant loss of genetic diversity. Even in the absence of further 

impact, long-term recovery period to acceptable levels will be greater than decades 

or may never occur 

Table 5.11: Confidence scores used by Rowe (2010) (after Hobday 2007) 

Score Descriptor Rationale for confidence score 

1a 

1b 

1c 

1d 

2a 

2b 

2c 

Low Data exists, but is considered poor or conflicting. 

No data exists. 

Agreement between experts, but with low confidence 

Disagreement between experts 

High Data exists and is considered sound. 

Consensus between experts 

High confidence exposure to impact can not occur (e.g. no spatial overlap of 

fishing activity and at-sea seabird distribution) 

Total potential and residual risk for a seabird taxon was estimated by summing the scores across all 

fisheries (Table 5.12 shows taxa with an aggregate score of 30 or higher), and total potential and 

residual risk posed by a fishery group was estimated by summing the scores across all seabird taxa 

(Table 5.13 shows the results for all 26 fishery groups). 

White-chinned petrel, Sooty shearwater, Black (Parkinson's) petrel, Salvin's albatross, White-capped 

albatross, and Flesh-footed shearwater were all estimated by this procedure to have an aggregate risk 

score of 90 or higher (range 92 to 123) even if mitigation was in place and deployed properly across 

all fisheries. Of the 101 seabird taxa considered, the aggregate risk score was less than 30 for 70 taxa 

with respect to potential risk and for 72 taxa with respect to residual risk. 

93


Table 5.12: Potential and residual risk scores for each seabird taxon with a potential risk score of >=30 in 

Rowe (2010). Residual risk (“optimal risk” in Rowe 2010b, not tabulated therein for grey-faced petrel or 

light-mantled albatross) is estimated assuming mitigation is deployed and correctly used throughout all 

interacting fisheries. 

Taxon Potential score Residual score Percent reduction 

White-chinned petrel 159 123 23 

Sooty shearwater 126 108 14 

Black (Parkinson's) petrel 139 106 24 

Salvin's albatross 161 106 34 

White-capped albatross 141 94 33 

Flesh-footed shearwater 117 92 21 

Southern Buller's albatross 123 85 31 

Grey petrel 123 84 32 

Black-browed albatross 114 80 30 

Northern Buller's albatross 107 72 33 

Chatham albatross 114 71 38 

Campbell albatross 97 66 32 

Westland petrel 89 59 34 

Antipodean albatross 89 55 38 

Gibson's albatross 89 55 38 

Wandering albatross 89 55 38 

Southern royal albatross 79 49 38 

King shag 48 48 0 

Pitt Island shag 46 46 0 

Chatham Island shag 45 45 0 

Hutton's shearwater 37 35 5 

Northern giant petrel 62 35 44 

Pied shag 35 35 0 

Indian yellow-nosed albatross 58 34 41 

Southern giant petrel 61 34 44 

Fluttering shearwater 34 32 6 

Spotted shag 31 31 0 

Stewart Island shag 31 31 0 

Yellow-eyed penguin 30 30 0 

Grey-faced petrel 31 – – 

Light-mantled albatross 30 – – 

Setnet and inshore trawl fisheries groups posed the greatest residual risk to seabirds (summed across 

all taxa); both had aggregate scores of over 200 and had no substantive mitigation. Surface and 

bottom longline fisheries and middle-depth trawl fisheries for finfish and squid also had aggregate 

risk scores of 100 or more. These risk scores were substantially reduced if mitigation was assumed to 

be deployed throughout these fisheries (reductions of 24 to 56%), but all remained above 100. 

Trawling for southern blue whiting and deep-water species, inshore drift net, various seine methods, 

ring net, diving, dredging, and hand gathering all had aggregate risk scores of 40 or less if mitigation 

was assumed to be deployed throughout these fisheries. Diving, dredging, and hand gathering were all 

judged by the panel to pose essentially no risk to seabirds. 

94


Table 5.13: Cumulative potential risk and residual risk scores across all seabird taxa for each fishery 

from Rowe (2010). Residual risk (“optimal risk” in Rowe 2010b) is estimated assuming mitigation is 

deployed and correctly used throughout a given fishery. 

Fishery group No. taxa Potential risk Residual risk Percent 

reduction 

Setnet 42 374 374 0 

Inshore trawl 44 225 225 0 

Surface longline: charter 25 313 191 39 

Surface longline: domestic 25 302 184 39 

Bottom longline: small 33 354 154 56 

Bottom longline: large 32 311 139 55 

Mid-depth trawl: finfish 22 160 122 24 

Mid-depth trawl: squid 21 156 118 24 

Mid-depth trawl: scampi 23 94 94 0 

Hand line 27 68 68 0 

Squid jig 44 62 62 0 

Dahn line 29 61 61 0 

Pots, traps 17 61 61 0 

Trot line 29 61 61 0 

Pelagic trawl 27 63 51 19 

Troll 23 50 50 0 

Mid-depth trawl: southern blue whiting 21 53 40 25 

Deep water trawl 21 46 35 24 

Inshore drift net 12 33 33 0 

Danish seine 15 32 32 0 

Beach seine 16 29 29 0 

Purse seine 11 22 22 0 

Ring net 12 13 13 0 

Diving 0 0 0 – 

Dredge 0 0 0 – 

Hand gather 0 0 0 – 

5.4.3.3. Semi-quantitative (Level 2) risk assessment 

The level 2 method developed by MPI arose initially from an expert workshop hosted by the Ministry 

of Fisheries in 2008 and attended by experts with specialist knowledge of New Zealand fisheries, 

seabird-fishery interactions, seabird biology, population modelling, and ecological risk assessment. 

The overall framework is described in Sharp et al. (2011) and has been variously applied and 

improved in multiple iterations (Waugh et al. 2008, developed further by Sharp 2009, Waugh and 

Filippi 2009, Filippi et al. 2010, Richard et al. 2011). The method applies the “exposure-effects” 

approach where exposure refers to the number of fatalities arising from an activity and effect refers to 

the consequence of that exposure for the population. The relative encounter rate of each seabird taxon 

with each fishery group is estimated as a function of the spatial overlap between seabird distributions 

(e.g., Figure 5.12) and fishing effort distributions (e.g., see Figures 5.4–5.6), and compares these 

estimates with observed captures from fisheries observer data to estimate vulnerability by taxon 

(capture rates per encounter) to each fishery group, yielding estimates of total observable captures and 

population-level potential fatalities from all New Zealand commercial fisheries. Impact estimates are 

subsequently compared with population estimates and biological characteristics to yield estimates of 

population-level risk. 

The current level 2 risk assessment (i.e., as described by Richard et al. 2011) estimated the risk posed 

to each of 64 seabird taxa by trawl and longline fisheries within New Zealand’s TS and EEZ. 

Insufficient information was available to include some other fisheries thought to pose substantial risk 

95


to seabirds, especially setnet. For each taxon, the risk was assessed by dividing the estimated number 

of potential fatalities by an estimate of Potential Biological Removals (PBR, after Wade 1998). This 

index represents the amount of human-induced mortality a population can sustain without 

compromising its ability to achieve and maintain a population size above its maximum net 

productivity (MNPL) or to achieve rapid recovery from a depleted state. In the risk assessment, PBR 

was estimated from the best available information on the demography of each taxon (Figure 5.13). 

Because estimates of seabirds’ demographic parameters and of fisheries related mortality are 

imprecise, the uncertainty around the demographic and mortality estimates was propagated through 

the analysis. This allowed uncertainty in the resulting risk to be calculated, and also allowed the 

identification of parameters where improved precision would reduce overly large uncertainties. 

However, not all sources of uncertainty could be included, and the results are best used as a guide in 

the setting of research and management priorities. In general, seabird demographics, the distribution 

of seabirds within New Zealand waters, and sources of cryptic mortality were poorly known. 

Amongst the 64 studied taxa, black (Parkinson’s) petrel (Procellaria parkinsoni) clearly stood out as 

at most risk from commercial fishing activities within the New Zealand Exclusive Economic Zone 

(estimated annual potential fishing-related fatalities almost 10 times higher than the PBR, Figures 

5.14 and 5.15). Seven other taxa had estimated annual potential fatalities with 95% confidence 

intervals of their risk ratios completely above one. These were grey-headed albatross, Chatham 

albatross, Westland petrel, light-mantled albatross, Salvin’s albatross, fleshfooted shearwater, and 

Stewart Island shag. For a further 12 taxa, the confidence interval of the risk ratio included one. 

Small inshore fisheries, especially trawl fisheries targeting flatfish, and small bottom and surface 

fisheries, were associated with the highest estimated risk to seabirds. This was due to a combination 

of low observer coverage, high effort, and overlap with the distributions of many seabirds. In fisheries 

where there were few observations, the number of potential fatalities was estimated in a precautionary 

way, with the estimates being biased toward the high end of the range of values that were consistent 

with the observer data. In these poorly observed fisheries, the risk estimates are often primarily 

associated with the lack of information. Of the taxa that had a risk ratio greater than one, the risk for 

four of them (grey-headed albatross, Westland petrel, Chatham albatross, and light-mantled albatross) 

was associated with low observer coverage in inshore fisheries that overlap with the distribution of 

these birds. Increasing the number of observations in inshore trawl and small vessel longline fisheries, 

especially in FMAs 1, 2, 3, and 7, would increase the precision of the estimated fatalities. The risk 

was estimated independently for each fishery, and it was assumed that the vulnerabilities of seabirds 

to capture in different fisheries were independent. This has the consequence that birds (such as lightmantled 

sooty albatross) may be caught infrequently in well observed fisheries, but still have high risk 

associated with poorly observed fisheries. 

96


Figure 5.12 (reproduced from Richard et al. 2011 supplementary material): Captures and relative density 

of White-capped albatross (top) and Chatham petrel (bottom) showing large differences in the extent of 

distributions and overlap with fishing effort (in grey), and in the number of observed captures. The 

97


distribution base maps were obtained from NABIS (white-capped albatross) and the BirdLife single-layer 

range maps (Chatham petrel). 

Figure 5.13 (reproduced from Richard et al. 2011): Diagram of the modelling approach to calculate the 

risk index for each taxon. NBP, number of annual breeding pairs; N, total number of birds over one year 

old; NBPmin, lower 25% of the distribution of NBP; Nmin, lower 25% of the distribution of the total number 

of birds over one year old; rmax, maximum population growth rate; f, recovery factor; PBR, Potential 

Biological Removal; P, proportion of adults breeding in a given year; A, age at first reproduction; S, 

annual adult survival rate. 

98


Figure 5.14 (reproduced from Richard et al. 2011): Mean annual potential seabird fatalities in the 

assessed fishery groups (colour bars) and the PBR (grey bars), for each of the 64 studied taxa. The bars 

indicate the 95% confidence intervals of the distributions. Taxa are sorted in decreasing order of the 

lower confidence level of the number of fatalities. 

99


Figure 5.15 (reproduced from Richard et al. 2011): Risk ratio (total annual potential fatalities / PBR) for 

each of the studied taxa except black-browed albatross. The risk ratio is displayed on a logarithmic scale. 

The threshold where the number of potential bird fatalities equals the PBR is presented by the vertical 

black line. The bars indicate the 95% confidence intervals of the distributions. Taxa are sorted in 

decreasing order of the lower confidence level of the risk ratio. 

Many limitations were identified in the risk assessment. These may result in biased estimates (either 

too high or too low) of the risk of fishing to some seabirds. Moreover, some fisheries were not 

included in our analysis, and other sources of human-induced mortality were ignored. The conclusions 

of our results should therefore be interpreted with caution, as some taxa might be at risk, even if their 

risk ratio was estimated to be lower than one. Conversely, the fisheries-related fatalities may be 

overestimated in poorly observed fisheries because the method is designed to answer the question 

“how bad could it be?” (e.g., Figure 5.16 which shows the results of different estimation approaches 

and questions). The method assumed a high number of captures in the absence of data to the contrary, 

so the estimated potential fatalities in poorly-observed fisheries may be higher than the actual 

fatalities. 

100


Figure 5.16 (reproduced from Richard et al. 2011): Comparison of the number of potential annual 

captures (without cryptic mortality) estimated using the risk assessment method used by Richard et al 

(2011), a simple ratio scalar, and statistical modelling, for white-chinned petrel, white-capped albatross, 

sooty shearwater, and all birds combined, in trawl, bottom longline, and surface longline fisheries. Each 

symbol represents the mean and the 95% confidence interval of an estimate. 

The method described by Richard et al. (2011) offers the following advantages that make it 

particularly suitable for assessing risk to multiple seabird populations from multiple fisheries: 

• risk is assessed separately for each seabird taxon; fisheries managers must assess risk to 

seabirds with reference to units that are biologically meaningful; 

• the method does not rely on the existence of universal or representative fisheries observer 

data to estimate seabird mortality (fisheries observer coverage is generally too low and/or too 

spatially unrepresentative to allow direct impact estimation at the species or subspecies level); 

the method can be applied to any fishery for which at least some observer data exists; 

• the method does not rely on detailed population models (the necessary data for which are 

unavailable for the great majority of taxa) because risk is estimated as a function of 

population-level potential fatalities and biological parameters that are generally available 

from published sources; 

• the method assigns risk to each taxon in an absolute sense, i.e. taxa are not merely ranked 

relative to one another; this allows the definition of biologically meaningful performance 

standards and ability to track changes in performance over time and in relation to risk 

management interventions; 

• risk scores are quantitative and objectively scalable between fisheries or areas, so that risk at a 

population level can be disaggregated and assigned to different fisheries or areas based on 

their proportional contribution to total impact to inform risk management prioritisation; 

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• the method allows explicit statistical treatment of uncertainty, and does not conflate 

uncertainty with risk; numerical inputs include error distributions and it is possible to track 

the propagation of uncertainty from inputs to estimates of risk; and 

• the method readily incorporates new information; assumptions in the assessment are 

transparent and testable and, as new data becomes available, the consequences for the 

subsequent impact and risk calculations arise logically without the need to revisit other 

assumptions or repeat the entire risk assessment process. 

The key disadvantages of the method are that: 

• fisheries for which no observer information on seabird interactions is available cannot be 

included in the analysis 

• the assumption that the vulnerabilities of particular seabirds to capture in different fisheries 

are independent does not allow “sharing” of scarce observer information between fisheries 

within the risk assessment 

• the spatial overlap method relies on appropriate spatial and temporal scales for the 

distributions of birds and fishing effort being used; use of inappropriate scales can lead to 

misleading results 

• strong assumptions have to be made about the distribution and productivity of some taxa, the 

relative vulnerability of different taxa to capture by particular fisheries, cryptic mortality 

associated with different fishing methods, and the applicability of the allometric method of 

estimating Potential Biological Removals. 

Most of these limitations are a result of the scarcity of relevant data on seabird populations and 

fisheries impacts and can be addressed only through the collection of more information or, in some 

cases, sensitivity testing. In particular, it was not possible to include some fishery groups identified by 

Rowe’s (2010b) level 1 analysis as posing substantial risk to seabirds. Notable among these fisheries 

was the commercial setnet fishery group. In the absence of quantitative information for these fishery 

groups, the Ministry of Fisheries combined the level 1 and level 2 results to generate a comprehensive 

assessment of seabird risk across all New Zealand seabirds and fisheries (Table 5.14). Apart from 

filling some important information gaps in the assessment, the level 1 results were also useful as a 

cross-check on the level 2 outputs. A number of likely misleading results were identified in this way, 

including those from poor input data (e.g. spatial distribution layers) or faulty structural assumptions 

for particular seabird taxa, and these were noted so that inappropriate conclusions were not made and 

to provide for better treatment in subsequent iterations of the level 2 analysis. 

At the time of going to press, a major update and revision of the level 2 risk assessment published by 

Richard et al. (2011) was undergoing final review. This revision includes several substantial 

improvements on the 2011 version including: 

• fisheries and observer data from 2006/07 onwards (i.e., post-mitigation only, allowing a better 

estimate of current risk) 

• inclusion of set net fisheries (obviating the need to combine level 1 and level 2 analyses) 

• revised bird distributions 

• inclusion of seasonal stratification of bird distribution and overlap with fisheries 

• an integrated approach to estimating species-specific vulnerability to particular fisheries 

• correction of a bias in the estimation of productivity from age at first reproduction and annual 

adult survival rate 

• inclusion of uncertainty in estimates of cryptic mortality 

This revised risk assessment is expected to be available early in 2013. 

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Table 5.14: Combined level 2 and level 1 risk assessments for seabird taxa with a risk ratio of 0.3 or 

greater (i.e., mean potential fatalities 30% of the estimated PBR or greater). INS, inshore trawl fisheries 

including for flatfish; SQU, squid trawl fisheries; SCI, scampi trawl fisheries; OFF, other offshore trawl 

fisheries; BLL, bottom longline fisheries; SLL, surface longline fisheries; SN, setnet (from level 1); Other, 

all other fisheries considered in the level 1 risk assessment. * indicates an unreliable assessment. 

Taxon INS SQU SCI OFF BLL SLL SN Other 

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Risk 

ratio 

Black (Parkinson's) petrel 4.37 0.12 0.17 0.37 5.56 0.41 0.00 0.45 11.45 

Black-browed albatross * 1.07 0.02 0.04 0.64 2.46 1.37 0.00 0.00 * 5.59 

New Zealand king shag 1.84 0.00 0.00 0.05 0.15 0.00 1.51 0.91 4.46 

Grey-headed albatross * 2.38 0.03 0.09 0.37 0.52 0.07 0.00 0.00 * 3.46 

Westland petrel 1.99 0.12 0.05 0.36 0.59 0.15 0.00 0.00 3.26 

Chatham albatross 1.81 0.04 0.08 0.19 0.55 0.03 0.00 0.00 2.70 

Stewart Island shag 1.59 0.00 0.00 0.00 0.01 0.00 1.01 0.00 2.62 

Northern giant-petrel 1.65 0.06 0.12 0.32 0.34 0.05 0.00 0.00 2.55 

Pitt Island shag 0.00 0.00 0.00 0.01 0.12 0.00 1.51 0.80 2.45 

Flesh-footed shearwater 0.72 0.01 0.31 0.08 1.12 0.19 0.00 0.00 2.42 

Chatham Island shag 0.00 0.00 0.00 0.02 0.17 0.00 1.51 0.60 2.31 

Salvin's albatross 1.43 0.05 0.22 0.22 0.34 0.03 0.00 0.00 2.29 

Light-mantled albatross * 1.46 0.02 0.05 0.22 0.34 0.04 0.00 0.00 * 2.14 

Northern royal albatross 0.96 0.05 0.03 0.21 0.31 0.54 0.00 0.00 2.09 

Campbell albatross 0.61 0.06 0.06 0.24 0.51 0.33 0.00 0.00 1.81 

New Zealand storm-petrel 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.51 1.51 

Yellow-eyed penguin 0.08 0.00 0.00 0.01 0.02 0.00 1.26 0.00 1.38 

Spotted shag 0.47 0.00 0.00 0.00 0.03 0.01 0.75 0.00 1.27 

Fiordland crested penguin 0.07 0.00 0.00 0.01 0.33 0.04 0.80 0.00 1.25 

Wandering albatross 0.00 0.00 0.00 0.00 0.00 1.21 0.00 0.00 1.21 

Southern Buller's albatross 0.36 0.17 0.03 0.38 0.05 0.20 0.00 0.00 1.19 

Gibson's albatross 0.23 0.02 0.01 0.07 0.15 0.67 0.00 0.00 1.16 

Antipodean albatross 0.22 0.02 0.01 0.06 0.14 0.64 0.00 0.00 1.10 

Hutton's shearwaters 0.05 0.00 0.00 0.01 0.04 0.00 1.01 0.00 1.10 

Pied shag 0.00 0.00 0.00 0.00 0.00 0.00 0.75 0.30 1.06 

South Georgia diving-petrel 0.00 0.00 0.00 0.00 0.00 0.00 0.60 0.30 0.91 

Indian yellow-nosed albatross 0.00 0.00 0.00 0.00 0.00 0.60 0.00 0.00 0.60 

White-capped albatross 0.32 0.34 0.02 0.09 0.02 0.01 0.00 0.00 0.79 

Sooty shearwater * 0.01 0.01 0.00 0.00 0.00 0.00 0.75 0.00 * 0.77 

White-chinned petrel 0.11 0.37 0.01 0.09 0.15 0.03 0.00 0.00 0.77 

Fluttering shearwater 0.00 0.00 0.00 0.00 0.00 0.00 0.75 0.00 0.75 

Little black shag 0.00 0.00 0.00 0.00 0.00 0.00 0.75 0.00 0.75 

Northern blue penguin 0.00 0.00 0.00 0.00 0.00 0.00 0.75 0.00 0.75 

White-flippered blue penguin 0.00 0.00 0.00 0.00 0.00 0.00 0.75 0.00 0.75 

Northern Buller's albatross 0.19 0.00 0.05 0.14 0.19 0.17 0.00 0.00 0.75 

Southern royal albatross 0.31 0.05 0.02 0.07 0.08 0.21 0.00 0.00 0.74 

Cape petrel * 0.27 0.00 0.03 0.14 0.21 0.03 0.00 0.00 * 0.69 

Southern giant petrel 0.00 0.00 0.00 0.00 0.15 0.00 0.00 0.00 0.15 

Chatham Island blue penguin 0.00 0.00 0.00 0.00 0.00 0.00 0.45 0.00 0.45 

Grey petrel 0.13 0.00 0.00 0.03 0.08 0.12 0.00 0.00 0.37 

Magenta petrel 0.00 0.00 0.00 0.00 0.02 0.00 0.00 0.30 0.33


5.4.3.4. Fully quantitative modelling 

Fully quantitative population modelling has been conducted only for southern Buller’s albatross, 

black (Parkinson’s) petrel, white capped albatross (mollymawk), and Gibson’s (wandering) albatross. 

Data of similar quality and quantity are available for Antipodean (wandering) albatross, and this work 

should be commissioned soon, but data for other species or populations appear unlikely to be 

adequate for comprehensive population modelling. The poor estimates of observable and cryptic 

fishing-related mortality have restricted such work to comprehensive population modelling rather than 

formal assessment of risk. 

5.4.3.4.1. Quantitative models for southern Buller’s 

albatross 

Francis et al. (2008, see also Francis and Sagar 2012) assessed the status of the Snares Islands 

population of southern Buller’s albatross (Thalassarche bulleri bulleri). They estimated (see also 

Sagar and Stahl 2005) that the adult population had increased about 5-fold since about 1950 (Figure 

5.17) at a rate of about 2% per year, and concluded from this that the risk to the viability of this 

population posed by fisheries had been small. This conclusion depends critically on the reliability of 

the first census of nesting birds conducted in 1969, but the authors give compelling reasons to trust 

that information. They noted, however, that population growth had slowed by about 2005 (and 

perhaps reversed) and adult survival rates were falling, but could discern neither the cause nor 

significance of these changes because they had included survival data only up to 2007. An additional 

5 years of survival and other demographic data have since been recorded (Sagar et al. 2010) and all 

monitored sites at the Snares Islands show substantial declines in the number of breeding pairs since 

2006. The modelling has not yet been repeated. 

Figure 5.17 (reproduced from Francis et al. 2008): Estimates from model SBA21 of numbers of breeders 

(solid line) and adults (broken line) in each year. Also shown are the census observations (after (Sagar 

and Stahl 2005) of numbers of breeders (crosses), with assumed 95% confidence intervals (vertical lines). 

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Fishery discards are an important component of the diet of chicks, but Francis et al. (2008) were not 

able to assess whether the associated positive effect on population growth (e.g., from increased 

breeding success) is greater or less than the negative effect of fishing-related mortality. 

5.4.3.4.2. Quantitative models for black petrel 

Francis and Bell (2010) analysed data from the main population of black (Parkinson’s) petrel 

(Procellaria parkinsoni), which breeds on Great Barrier Island. Abundance data from transect surveys 

were used to infer that the population was probably increasing at a rate between 1.2% and 3.1% per 

year. Mark-recapture data were useful in estimating demographic parameters, like survival and 

breeding success, but contained little information on population growth rates. Fishery bycatch data 

from observers were too sparse and imprecise to be useful in assessing the contribution of fishingrelated 

mortality. Francis and Bell (2010) suggested that, because the population was probably 

increasing, there was no evidence that fisheries posed a risk to the population at that time. They 

cautioned that this did not imply that there was clear evidence that fisheries do not pose a risk. 

Subsequent analysis (Bell et al. 2012) included an additional line transect survey in 2009/10 in which 

the breeding population was estimated to be ~22% lower than in 2004/05 (the latest available to 

Francis and Bell, 2010). Updating the model of Francis and Bell (2010) made little difference to 

estimates of demographic parameters such as adult survival, age at first breeding, and juvenile 

survival (which had 95% confidence limits of 0.67 and 0.91). The uncertainty in juvenile survival 

gave rise to uncertainty in the estimated population trend, with a mean rate of population growth over 

the modelling period ranging from ‐2.5% per year (if juvenile survival = 0.67) to +1.6% per year (if 

juvenile survival = 0.91, close to the average annual survival rate for older birds) (Figure 5.18). Bell et 

al. (2012) concluded that the mean rate of change of the population over the study period had not 

exceeded 2% per year, though the direction of change was uncertain. 

Figure 5.18 (reproduced from Bell et al. 2012): Likelihood profile for annual probability of juvenile 

survival showing: A, the loss of fit (the horizontal dotted line shows a 95% confidence interval for this 

parameter); and B, population trajectories corresponding to different values of juvenile survival, together 

with population estimates from transect counts (crosses with vertical lines indicating 95% confidence 

intervals. Note that the 1988 population estimate was not used in the model. 

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5.4.3.4.3. Quantitative models for white-capped albatross 

Francis (2012) described quantitative models for white-capped albatross (Thalassarche steadi), New 

Zealand’s most numerous breeding albatross, and the most frequently captured, focussing on the 

population breeding at the Auckland Islands. After a correction for a probable bias introduced by 

sampling at different times of day in one of the surveys, aerial photographic counts by Baker et al. 

(2007, 2008, 2009, and 2010, see also Table 5.15) suggest that the adult population declined at about 

9.8% per year between 2006 and 2009. However, this estimate is imprecise and is not easily 

reconciled with the high adult survival rate (0.96) estimated from mark-recapture data. Francis (2012) 

also compared the trend with his estimate of the global fishing-related fatalities of white-capped 

albatross (slightly over 17 000 birds per year, about 30% of which is taken in New Zealand fisheries) 

and found that fishing-related fatalities were insufficient to account for the number of deaths implied 

by a decline of 9.8% per year (roughly 22 000 birds per year over the study period). The scarcity of 

information on cryptic mortality makes these estimates and conclusions uncertain, however. 

Table 5.15 (data from Baker et al. 2007, 2008, 2009, 2010): Aerial-photographic counts of breeding pairs 

of white-capped albatrosses on three islands in the Auckland Islands group in December 2006–2009. 

Confidence limits for these counts published by Baker (op. cit.) were based on a Poisson model and were 

very narrow (although uncertainty introduced by the proportion of non-nesting birds at the colonies 

during photography was not included). 

Year Disappointment SW Cape Adams Total 

2006 110 649 6 548 – 117 197 

2007 86 080 4 786 79 90 945 

2008 91 694 5 264 131 97 089 

2009 70 569 4 161 132 74 862 

5.4.3.4.4. Quantitative models for Gibson’s albatross 

Francis et al. (in press) concluded there is cause for concern about status of the population of 

Gibson’s wandering albatross (Diomedea gibsoni) on the Auckland Islands. Since 2005, the adult 

population has been declining at 5.7%/yr (95% c.i. 4.5–6.9%) because of sudden and substantial 

reductions in adult survival, the proportion of adults breeding, and the proportion of breeding attempts 

that are successful (Figure 5.19). Forward projections showed that the most important of these to the 

future status of this population is adult survival (Figure 5.20). 

The population in 2011 was 64% (58–73%) of its estimated size in 1991. The breeding population 

dropped sharply in 2005, to 59% of its 1991 level, but has been increasing since 2005 at 4.2% per 

year (2.3–6.1%). The 2011 breeding population is estimated to be only 54% of the average of 5831 

pairs estimated by Walker & Elliott (1999) for 1991–97. 

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Figure 5.19: Estimated population trajectories for the whole Auckland Islands population of Gibson’s 

wandering albatross. These were calculated by scaling up Francis et al.’s (in press) GIB5 trajectories to 

match the Walker & Elliott (1999) estimate for the whole population. 

Figure 5.20: Estimated population trajectory for adults from Francis et al.’s (in press) model GIB5 with 

20-year projections under five alternative scenarios about three demographic parameters: adult survival 

(adsurv); breeding success (Psuccess); and proportion of adults breeding. These scenarios differ 

according to whether each parameter remains at its status quo (=2011) level or recovers immediately to 

its 1991 level. 

Francis et al. (in press) found it difficult to assess the effect of fisheries mortality on the viability of 

this population because, although some information exists about captures in New Zealand and 

Australian waters, the effect of fisheries in international waters is unknown. Three conclusions are 

possible from the available data: most fisheries mortality of Gibson’s is caused by surface longlines; 

mortality from fishing within the New Zealand EEZ is now probably lower than it was; and there is 

no indication that the sudden and substantial drops in adult survival, the proportion breeding, and 

breeding success were caused primarily by fishing. 

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5.4.3.4.5. Other quantitative models 

This section is not intended to cover all quantitative modelling of seabird populations, rather to focus 

on recent studies that sought to assess the impact of fishing-related mortality. 

Maunder et al. (2007) sought to assess the impact of commercial fisheries on the Otago Peninsula 

yellow-eyed penguins using mark-recapture data within a population dynamics model. They found the 

data available at that time inadequate to assess fisheries impacts, but evaluated the likely utility of 

additional information on annual survival or an estimate of bycatch for a single year. Including 

auxiliary information on average survival in the absence of fishing allowed estimation of the fishery 

impact, but with poor precision. Including an estimate of fishery-related mortality for a single year 

improved the precision in the estimated fishery impact. The authors concluded that there was 

insufficient information to determine the impact of fisheries on yellow-eyed penguins and that 

quantifying fishing-related mortality over several years was required to undertake such an assessment 

using population a modelling approach. 

Fletcher et al. (2008) sought to assess the potential impact of fisheries on Antipodean and Gibson’s 

wandering albatrosses (Diomedea antipodensis antipodensis and D. a. gibsoni); black petrel 

(Procellaria parkinsoni) and southern royal albatross (Diomedea epomophora). Because of problems 

with the available fisheries and biological data, they were unable to use their models to predict the 

impact of a change in fishing effort on the population growth rate of a given species. Instead, they 

used the models to estimate the impact that changes in demographic parameters like annual survival 

are likely to have on population growth rate. They found that: reducing breeder survival rate by k 

percentage points will lead to a reduction in the population growth rate of about 0.3k percentage 

points (0.4 for black petrel); and a reduction of k percentage points in the survival rate for each stage 

in the life cycle (juvenile, pre-breeder, non-breeder and breeder) will lead to a reduction in the 

population growth rate of approximately k percentage points. Fletcher et al. (2008) also made 

estimates of PBR for 23 New Zealand seabird taxa and summarise and tabulated non-fishing-related 

threats for 38 taxa. 

Newman et al. (2009) combined survey data with demographic population models to estimate the 

total population of sooty shearwaters within New Zealand. They estimated the total New Zealand 

population between 1994 and 2005 to have been 21.3 (95% c.i. 19.0–23.6) million birds. The harvest 

of “muttonbirds” was estimated to be 360 000 (320 000–400 000) birds per year, equivalent to 18% of 

the chicks produced in the harvested areas and 13% of chicks in the New Zealand region. This 

directed harvest is much larger than estimates of captures in key fisheries (Table 5.4) or potential 

fatalities in the level 2 risk assessment (Figure 5.16). Newman et al. (2009) did not assess the likely 

impact of fishing-related mortality but concluded that the much larger directed harvest was not an 

adequate explanation for the observed declines in the past three decades. 

5.4.3.4.6. General conclusions from quantitative modelling 

Fully quantitative modelling has now been conducted for four of the five seabird populations for 

which apparently suitable data are available. That modelling suggests very strongly that one 

population had been increasing steadily (southern Buller’s albatross, but note this trend may have 

reversed) and another is declining quite rapidly (Gibson’s albatross). White-capped albatross and 

black petrel both more likely to be declining than not but, even for these relatively data rich 

populations, the conclusions are uncertain. General conclusions from the modelling conducted to date, 

therefore, can be summarised as: 

• Very few seabird populations have sufficient data for modelling 

• Except for the two most complete data sets (southern Buller’s and Gibson’s albatross) it has 

been difficult to draw firm conclusions about trends in population size. 

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• Information from surveys or census counts is much more powerful for detecting trends in 

population size than data from the tagging programmes and plot monitoring implemented for 

New Zealand seabirds to date. 

• The available information on incidental captures in fisheries have not allowed rigorous tests 

of the role of fishing-related mortality in driving population trends 

• Although comprehensive modelling provides additional information to allow interpretation, 

we will have to rely on level 2 risk assessment approaches for much of our understanding of 

the relative risks faced by different seabird taxa and posed by different fisheries. 

5.4.3.5. Sources of uncertainty in risk assessments 

There are several outstanding sources of uncertainty in modelling the effects of fisheries interactions 

on sea birds, especially for the complete assessment of risk to individual seabird populations. 

5.4.3.5.1. Scarcity of information on captures and 

biological characteristics of affected 

populations 

These sources of uncertainty can be explored within the analytical framework of the level 2 risk 

assessment (Richard et al. 2011), noting that the results of that exploration are constrained by the 

structure of that analysis. Richard et al. (2011) provided plots of such an exploration for four example 

taxa (Figure 5.21). It can be concluded from this analysis that substantially more precise estimates of 

risk would be available for black petrel and Stewart Island shag if better estimates of potential 

captures were available. Conversely, substantially more precise estimates of risk would be available 

for Salvin’s albatross and flesh-footed shearwater if better estimates of average adult survival were 

available. This analysis is a powerful way of assessing the priorities for collection of new information, 

including research. 

Figure 5.21 (reproduced from Richard et al. 2011): Sensitivity of the risk ratio to the uncertainty in the 

mean number of annual potential fatalities (F, reflecting the uncertainty in vulnerability), the adult 

annual survival rate (S), the number of annual breeding pairs (N), the proportion of adults breeding in a 

given year (P), the age at first reproduction (A), and to the distribution map (D), for the taxa most at risk 

(lower bound of the 95% c.i. above 1). This sensitivity is expressed as the percentage reduction in the 95% 

confidence interval of the risk ratio when each parameter is fixed to its mean. 

5.4.3.5.2. Scarcity of information on cryptic mortality 

Cryptic mortality is particularly poorly understood but has substantial influence on the results of the 

risk assessment. Richard et al. (2011) provided a description of the method used to incorporate cryptic 

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mortality into their estimates of potential fatalities in the level-2 risk assessment (their Appendix B 

authored by B. Sharp, MPI). This method builds on the published information from Brothers et al. 

(2010) for longline fisheries and Watkins et al. (2008) and Abraham (2010) for trawl fisheries. 

Brothers et al. (2010) observed almost 6 000 seabirds attempting to take longline baits during line 

setting, of which 176 (3% of attempts) were seen to be caught. Of these, only 85 (48%) were retrieved 

during line hauling. They concluded that using only observed captures to estimate seabird fatalities 

grossly underestimates actual levels in pelagic longline fishing. Similarly, Watkins et al. (2008) 

observed 2454 interactions between seabirds and trawl warps in the South African hake fishery over 

189.8 hours of observation. About 11% of those interactions (263) involved birds, mostly albatrosses, 

being dragged under the water by the warps, and 30 of those submersions were observed to be fatal. 

Of the 30 birds observed killed on the warps, only two (both albatrosses) were hauled aboard and 

would have been counted as captures by an observer in New Zealand. Aerial collisions with the warps 

were about 8 times more common but appeared mostly to have little effect (although one whitechinned 

petrel suffered a broken wing which would almost certainly have fatal consequences). 

Given the relatively small sample sizes in both of these trials, there is substantial (estimatable) 

uncertainty in the estimates from the trials themselves and additional (non-estimatable) uncertainty 

related to the extent to which these trials are representative of all fishing of a given type, particularly 

as both trials were undertaken overseas. The binomial 95% confidence range (calculated using the 

Clopper-Pearson “exact” method) for the ratio of total fatalities to observed captures in Brothers et 

al.’s (2010) longline trial is 1.8–2.5 (mean 2.1), and that for Watkins et al.’s trawl warp trial is 5–122 

(mean 15.0 fatalities per observed capture). Abraham (2010) estimated that there were 244 (95% c.i. 

190–330) warp strikes by large birds for every one observed captured, and 6 440 (3400–20 000) warp 

strikes by small birds for every one observed captured (although small birds tend to be caught in the 

net rather than by warps). There is also uncertainty in the relative frequencies and consequences of 

different types of encounters with trawl warps in New Zealand fisheries (Abraham 2010, Richard et 

al. 2011 Appendix B). 

5.4.3.5.3. Mortalities in non-commercial fisheries. 

Little is known about the nature and extent of incidental captures of seabirds in non-commercial 

fisheries, either in New Zealand or globally (Abraham et al. 2010). In New Zealand, participation in 

recreational fishing is high and 2.5% of the adult population are likely to be fishing in a given week 

(mostly using rod and line). Because of this high participation rate, even a low rate of interactions 

between individual fishers and seabirds could have population-level impacts. A boat ramp survey of 

765 interviews at two locations during the summer of 2007–08 revealed that 47% of fishers recalled 

witnessing a bird being caught some time in the past. Twenty-one birds were reported caught on the 

day of the interview at a capture rate of 0.22 (95% c.i.: 0.13–0.34) birds per 100 hours of fishing. 

Observers on 57 charter trips recorded seabird captures at rate of 0.36 (0.09–0.66) birds per 100 fisher 

hours. The most frequently reported type of bird caught in rod and line fisheries were petrels and 

gulls. Captures of albatrosses, shags, gannets, penguins, and terns were also recalled. 

The ramp surveys reported by Abraham et al. (2010) were limited and covered only two widelyseparated 

parts of the New Zealand coastline. However, they also report two other pieces of 

information that suggest non-commercial captures are likely to be very widespread. First, the 

Ornithological Society of New Zealand’s beach patrol scheme records seabird hookings and 

entanglements as a common occurrence throughout New Zealand. Second, returns of banded birds 

caught in fisheries (separating commercial and non-commercial fisheries is very difficult) are very 

widely distributed around the coast (Figure 5.22). 

Noting that our understanding of seabird capture rates in amateur fisheries is very sketchy, it is 

possible to make first-order estimates of total captures using information on fishing effort. For 

example, in the north-eastern region where most of Abraham et al.’s (2010) interviews were 

conducted, there were an estimated 4.8 (4.4–5.2) million fisher hours rod and line fishing from trailer 

110


boats in 2004–05 (Hartill et al. 2007). Applying Abraham et al.’s (2010) capture rate leads to an 

estimate of 11 500 (6600–17 200) captures per year in this area. Based on estimates of nationwide 

recreational fishing effort, this could increase to as many as 40 000 bird captures annually. Most birds 

captured by amateur fishers were reported to have been released unharmed (77% of the incidents 

recalled) and only three people reported incidents where the bird died. Because of likely recall biases 

and the qualitative nature of the survey, the fate of birds that are captured by amateur fishers remains 

unclear. 

Non-commercial fishers are allowed to use setnets in New Zealand and two studies suggest that these 

have an appreciable bycatch of seabirds. A study of captures in non-commercial setnets in Portobello 

Bay, Otago Harbour, between 1977 and 1985 (Lalas 1991) suggested spotted shags were the most 

frequently caught taxa (82 recorded, compared with 14 Stewart Island shags and two little shags). 

Lalas (1991) suggested that up to 800 spotted shags (20% of the local population) may have been 

caught in the summer of 1981/82. A broader-scale study of yellow-eyed penguin mortality in setnets 

in southern New Zealand (Darby and Dawson 2000) suggested non-negligible captures of this species 

by non-commercial fishers, also reporting other seabirds like spotted shags and little blue penguin. 

Figure 5.22 (reproduced from Abraham et al. 2010): Distribution of the reported capture locations for 

banded seabirds reported as being captured in fishing gear, 1952–2007. Note, band recovery locations are 

reported with low spatial precision and some of the inland locations may be correct. 

5.4.3.5.4. Out of zone mortality. 

Robertson et al. (2003) mapped the distribution of the 25 breeding (mainly endemic) New Zealand 

seabird taxa they considered most at risk outside New Zealand waters. These ranged widely: 4 used 

the South Atlantic; 4 the Indian Ocean; 22 Australian waters and the Tasman Sea; 15 used the South 

Pacific Ocean as far afield as Chile and Peru; and 6 used the North Pacific Ocean as far north as the 

Bering Sea. These taxa therefore use the national waters of at least 18 countries. For example, the 

111


level-2 risk assessment described by Richard et al. (2011) includes only that part of the range of each 

taxon contained within New Zealand waters, but many including commonly-caught seabirds like 

white-capped albatross and white-chinned petrel range much further and are vulnerable to fisheries in 

other parts of the world. For instance, fatalities of white-capped albatross outside the New Zealand 

EEZ greatly exceed fatalities within the zone (Baker 2007, Francis 2012, Table 5.16), and more than 

10 000 white-chinned petrel are killed off South America each year (Phillips et al. 2006), noting that 

reliable records are not available for most of the fisheries involved. Based on similar analyses, Moore 

and Zydelis (2008) concluded that a population-based, multi-gear and multi-national framework is 

required to identify the most significant threats to wide-ranging seabird populations and to prioritize 

mitigation efforts in the most problematic areas. To that end, the Agreement for the Conservation of 

Albatrosses and Petrels (ACAP) adopted a global prioritisation framework at the Fourth Session of 

the Meeting of the Parties (MoP4) in April 2012 (ACAP 2012). 

Table 5.16 (after Francis 2012): Estimates of the number of white-capped albatrosses killed annually, by 

fishery. The first two columns are from Baker et al. (2007) (mid-point where a range was presented), 

including their assessment of reliability (L = low, M-H = medium-high, H = high). Updated estimates are 

from Watkins et al. (2008, *) and Petersen et al. (2009, **). Estimates not already corrected for cryptic 

mortality are either doubled to allow for this (***) or replaced by estimates of potential fatalities from 

Richard et al. (2011, ***), noting that potential fatalities may considerably overestimate actual fatalities. 

Fishery From Baker et al. 2007 Updated Incl. Cryptic 

mortality 

South African demersal trawl 4 750 (L) * 6650 6 650 

Asian distant-water longline 1 255 (L) – *** 2 510 

Namibian demersal trawl 910 (L) * 1270 1 270 

Namibian pelagic longline 180 (L) ** 195 *** 390 

NZ hoki and squid trawl 513 (MH) – **** 4 920 

NZ longline 60 (MH) – **** 199 

Australian (line fisheries) 15 (MH) – *** 30 

South African pelagic longline 570 (H) ** 570 *** 1 140 

Total 8 210 – – 17 110 

5.4.3.5.5. Other sources of anthropogenic mortality. 

Taylor (2000) listed a wide range of threats to New Zealand seabirds including introduced mammals, 

avian predators (weka), disease, fire, weeds, loss of nesting habitat, competition for nest sites, coastal 

development, human disturbance, commercial and cultural harvesting, volcanic eruptions, pollution, 

plastics and marine debris, oil spills and exploration, heavy metals or chemical contaminants, global 

sea temperature changes, marine biotoxins, and fisheries interactions. Relatively little is known about 

most of these factors, but the parties to ACAP have agreed a formal prioritisation process to address 

and prioritise major threats (ACAP 2012). Croxall et al. (2012) identified the main priorities as: 

protection of Important Bird Area (IBA) breeding, feeding, and aggregation sites; removal of 

invasive, especially predatory, alien species as part of habitat and species recovery initiatives. 

Lewison et al. (2012) identified similar research priorities (in addition to direct fishing-related 

mortality), including: understanding spatial ecology; tropho-dynamics; response to global change; and 

management of anthropogenic impacts such as invasive species, contaminants, and protected areas. 

Non fishing-related threats to seabirds in New Zealand are largely the mandate of the Department of 

Conservation and a detailed description is beyond the scope of this document (although causes of 

mortality other than fishing are clearly relevant to the interpretation of risk assessment restricted to the 

direct effects of fishing). These threats are identified in DOC’s Action Plan for Seabird Conservation 

in New Zealand (Taylor 2000). 

112



Population size Multiple species and populations: see Taylor (2000) 

Population trend Multiple species and populations: see Taylor (2000) 

Threat status Multiple species and populations: see Miskelly et al. (2008) and updates 

Number of 

interactions 

Trend in interactions 

In the 2010/11 October fishing year, there were an estimated 4931 seabird captures 

(excluding cryptic mortalities) across all trawl and longline fisheries (excluding about 

14% of bottom longline effort that could not be included in the models) (Data version 

v20121101). About 57% of the captures were in trawl fisheries, 15% in surface 

longline fisheries, and 28% in bottom longline fisheries: 

Bird group Trawl Surface 

longline 

113 

Bottom 

longline 

All these 

methods 

White-capped albatross 356 84 2 442 

Other albatrosses 808 287 257 1 352 

White-chinned petrel 540 34 422 996 

Sooty shearwater 488 2 69 559 

Other birds 596 333 652 1 581 

All birds combined 2 788 740 1 403 4 931 

Captures of all birds combined show a decreasing trend between 2002/03 and 2010/11 

(Data version v20121101) but there are substantial differences in trends between 

species and fisheries. Captures of white-capped albatross have decreased, especially in 

offshore trawl fisheries, whereas captures of white-chinned petrel have increased: 


1400 

1200 

1000 

White-capped albatross 

800 

BLL 

600 

SLL 

400 

200 

0 

Trawl 

2003 2005 2007 2009 2011 

1200 

1000 

800 

600 

400 

200 

0 

3000 

2500 

2000 

1500 

1000 

500 

0 

Sooty shearwater 

2003 2005 2007 2009 2011 

2003 2005 2007 2009 2011 

BLL 

SLL 

Other birds 

Trawl 

BLL 

SLL 

Trawl 

2500 

2000 

1500 

1000 

500 

0 

1200 

1000 

800 

600 

400 

200 

0 

Other albatrosses 

2003 2005 2007 2009 2011 

2003 2005 2007 2009 2011 

BLL 

SLL 

White-chinned petrel 

Trawl 

BLL 

SLL 

Trawl 

8000 

7000 

6000 

All birds combined 

5000 

4000 

BLL 

3000 

SLL 

2000 

1000 

0 

Trawl 

2003 2005 2007 2009 2011 

Capture rate trends (excluding cryptic mortalities) are described for the four fisheries 

estimated to account for most of captures of a species (accounting for 80% or more of 

the total). Capture rates of white-capped albatross have fallen in trawl fisheries for

Trend in interactions 

contd. 


hoki and squid but have remained steady in inshore trawl fisheries and increased in 

the southern bluefin tuna fishery. Capture rates for white-chinned petrel have 

increased in trawl fisheries for squid and scampi but have remained steady in longline 

fisheries. Capture rates of sooty shearwater have declined in the ling longline fishery 

but have fluctuated without trend in other key fisheries. 

114



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THEME 2: NON-PROTECTED BYCATCH 

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6. Non-protected species (fish and invertebrates) 

bycatch 

Scope of chapter This chapter outlines the main non-protected bycatch species (fish and 

invertebrates) and annual levels and trends in bycatch and discards in 

New Zealand’s major offshore fisheries. Research in this field is 

conducted fishery by fishery and this first summary of current 

knowledge reflects that strategy. It is expected that future summaries 

will be aligned to the general format used in other sections of this 

report, and be based on fishing method, habitat type, region, or a 

combination of these. 

The fisheries summarised are as follows: 

Trawl fisheries: Longline fisheries: Other fisheries 

Arrow squid Ling 

Albacore troll 

Hoki/hake/ling 

Jack mackerel 

Tuna 

Skipjack purse seine 

Area 

Southern blue whiting 

Orange roughy 

Oreo 

Scampi 

All areas and fisheries 

Focal localities Arrow squid: Auckland Islands and Stewart/Snares Shelf (80–300 m). 

Hoki/hake/ling: Chatham Rise, West Coast South Island, Campbell 

Plateau, Puysegur Bank, and Cook Strait (200–800 m). 

Jack mackerel: West Coast of the North and South Islands, Chatham 

Rise, and Stewart-Snares Shelf (0–300 m). 

Southern blue whiting: Campbell Plateau and Bounty Plateau (250–600 

m). 

Orange roughy: The entire New Zealand region (700–1200 m). 

Oreos: South Chatham Rise, Pukaki Rise, Bounty Plateau, and 

Southland (700–1200 m). 

Scampi: East coasts of the North and South Islands, Chatham Rise, and 

Auckland Islands (300–450 m). 

Ling longline: Chatham Rise, Bounty Plateau, and Campbell Plateau 

(150–600 m). 

Tuna longline: Surface waters off the east coast of the North Island and 

west coast of the South Island. 

Albacore troll fishery: Surface waters off the west coasts of the North 

and South Islands. 

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Skipjack purse seine fishery: Northern North Island 

Key issues Under-utilisation (including shark finning) of high volume, low value 

bycatch species, especially rattails, spiny dogfish, deepsea sharks, blue 

sharks, porbeagle sharks, and swimming crabs. 

Potential for considerable reduction of discards by discretionary fishing 

practices such as the use of mid-water nets, where practicable, and meal 

plants. 

Unseen mortality in longline fisheries due to predation by large fish and 

sharks, marine mammals, seabirds, and sea lice. 

Emerging issues Trends of increasing rates and levels of bycatch and discarding in 

several categories of catch, especially non-QMS fish species and 

invertebrates. 

The effect on bycatch rates in the ling longline fishery of a change to 

heavier fishing gear (including integrated weights) as used in the 

Antarctic toothfish fishery. 

Increasing trawl lengths in the squid, scampi, and orange roughy 

fisheries due to changes in fishing gear or reduction of target species 

catch rates—leading to greater bycatch levels in some categories. 

MPI Research (current) DAE201002 (bycatch and discards in deepwater fisheries) 

DEE201004 (ecological risk assessment in deepwater fisheries) 

DEE201005A (environmental indicators in deepwater fisheries) 

HMS200901 (bycatch in tuna longline fisheries) 

Other Govt Research (current) None 

Links to 2030 objectives Objective 6: Manage impacts of fishing and aquaculture. 

Related chapters/issues NPOA sharks 

6.1. Context 

Management of non-protected species bycatch aligns with Fisheries 2030 Objective 6: Manage 

impacts of fishing and aquaculture. 

The management of non-protected species bycatch in the deepwater and middle-depth fisheries is 

described in the National Fisheries Plan for Deepwater and Middle-depth Fisheries (the National 

Deepwater Plan). Under the National Deepwater Plan, the objective most relevant for management of 

non-protected species bycatch is Management Objective 2.4: Identify and avoid or minimise adverse 

effects of deepwater and middle-depth fisheries on incidental bycatch species. Specific objectives for 

the management of non-protected species bycatch will be outlined in the fishery-specific chapters of 

the National Deepwater Plan. Estimation of non-protected species bycatch is carried out for each of 

the Tier-1 deepwater fisheries on an annual rotational basis, with each of the following fisheries 

updated about every 4–5 years: 

• Arrow squid 

• ling bottom longline 

• hoki/hake/ling trawl 

• Jack mackerel trawl 

• southern blue whiting trawl 

• orange roughy/oreo trawl 

• scampi trawl 

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Non-protected fish species bycatch in the Highly Migratory Species (HMS) is addressed in the HMS 

fish plan. Tuna fisheries incidental bycatch has been regularly examined, with updates every 2–3 

years. Some data on bycatch in the Albacore troll fishery and the skipjack tuna purse seine fishery are 

also available. 

The three National Fisheries Plans for Inshore species (finfish, shellfish and freshwater fisheries) also 

include objectives which address non-protected species bycatch, but research on these objectives has 

yet to be conducted. However, summaries of the main bycatch species are occasionally included in 

reports from fisheries characterisation projects, for example school shark, red gurnard, and 

elephantfish (Starr In Prep; Starr et al. 2010a, b, c, Starr & Kendrick 2012). 

6.2. Global understanding 

Bycatch of unwanted, low value species and discarding of these and of target species that are 

damaged or too small to process are significant issues in many fisheries worldwide. Few, if any, 

fisheries are completely without bycatch and this issue has been the subject of innumerable studies 

and international meetings. Saila (1983) made the first comprehensive global assessment and 

estimated, albeit with very poor information, that at least 6.7 million tonnes was discarded each year. 

Alverson et al. (1994) extended that work and estimated the global bycatch at 27.0 (range 17.9–39.5) 

million tonnes each year. An update by Kelleher (2005) suggested global bycatch of about 8% of the 

global catch, or 7.3 million tonnes, in 1999–2001. 

Tropical shrimp trawl fisheries typically have the highest levels of unwanted bycatch, with an average 

discard rate of 62% (Kelleher 2005), accounting for about one-quarter to one-third of global bycatch. 

Discard rates in demersal trawl fisheries targeting finfish are typically much lower but, because they 

are so widespread, their contribution to global discards is considerable. Tuna longline fisheries have 

the next largest contribution and tend to have greater unwanted bycatch than other line fisheries 

(Kelleher 2005). 

The estimated global level of discards has reduced considerably since the first estimates were made, 

but differences in the methodology and definition of bycatch used (Kelleher 2005, Davies et al. 2009) 

make it difficult to quantify the decline. The main reasons for the decline in bycatch are thought to 

have been a combination of higher retention rates, better fisheries management, and improved fishing 

methods. 

Bycatch and discard estimation is frequently very coarse, and estimates of rates based on occasional 

surveys are often scaled up to represent entire fisheries and applied across years, or even to other 

fisheries (e.g., Bellido et al. 2011). Data from dedicated fisheries observers are also frequently used 

for individual fisheries, and these are considered to provide the most accurate results, providing that 

discarding is not illegal (leading to bias due to “observer effects”, Fernandes 2011). Ratio estimators 

similar to those applied in New Zealand fisheries are frequently used to raise observed bycatch and 

discard rates to the wider fishery, and the methods used in New Zealand fisheries are broadly similar 

to those used elsewhere (e.g., Fernandes 2011, Borges et al. 2005). 

Discard data are increasingly incorporated into fisheries stock assessments and management decisionmaking, 

especially with the move towards an Ecosystem Approach to Fisheries (EAF) (Bellido et al. 

2011), and as third party fishery certification schemes examine more closely the effects of fishing on 

the ecosystem. They can also be used to assess impacts on non-target species (e.g., Pope et al. 2000, 

Casini et al. 2003, Piet et al. 2009). 

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Estimation of annual bycatch and discard levels of non-protected species in selected New Zealand 

fisheries have been undertaken at regular intervals since 1998 (Table 6.1). 

Table 6.1: Summary of research into bycatch in New Zealand fisheries 

Fishery Report 

Arrow squid Anderson et al. (2000) 

Anderson (2004b) 

Ballara and Anderson (2009) 

Anderson (In Press) 

Ling bottom longline Anderson et al. (2000) 

Anderson (2008) 

Hoki trawl Clark et al. (2000) 

Anderson et al. (2001) 

Anderson and Smith (2005) 

Ballara et al. (2010) 

Hake trawl Ballara et al. (2010) 

Ling trawl Ballara et al. (2010) 

Jack mackerel trawl Anderson et al. (2000) 



Southern blue whiting trawl Clark et al. (2000) 

Anderson (2004a) 


Orange roughy Clark et al. (2000) 

Anderson et al. (2001) 



Oreo trawl Clark et al. (2000) 



Scampi trawl Anderson (2004b) 

Ballara and Anderson (2009) 

Tuna longline Francis et al. (1999a, 1999b) 

Ayers et al. (2004) 

Francis et al. (2004) 

Griggs et al. (2007) 

Griggs et al. (2008) 

Griggs & Baird (In Press) 

Albacore troll fishery Griggs et al. (In Press) 

Skipjack purse seine fishery Griggs (unpublished data) 

The estimation process uses rates of bycatch and discards in various categories (in most cases “all 

QMS species combined”, “all non-QMS species combined”, “all invertebrate species combined”) and 

fishery strata in the observed fraction of the fishery, and effort statistics from the wider fishery, to 

calculate annual bycatch and discard levels. This ratio-based approach calculates precision by 

incorporating a multi-step bootstrap algorithm which takes into account the effect of correlation 

between trawls in the same observed trip and stratum. Estimates of the annual bycatch of a wide range 

of individual species were also made in the most recent analysis of the arrow squid fishery (Anderson 

In Press). 

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The approach used in these analyses relies heavily on an appropriate level and spread of observer effort 

being achieved, and this is examined in detail in each report. Although details of bycatch and discards 

are also recorded directly by vessel skippers for the entire fishery, through catch effort forms, these data 

are often incomplete as the forms list only the top 5 catch species, discards are not well recorded, and 

they generally lack the accuracy and precision of observer data. Nevertheless, annual bycatch totals are 

also derived from these data, but only as secondary estimates. 

6.3.1. Arrow squid trawl fishery 

Since 1990–91 the level of observer coverage in this fishery has ranged from 6% to 53% of the total 

annual catch, and has been higher in more recent years due to the management measures imposed for the 

protection of New Zealand sealions (Phocarctos hookeri). This coverage has been spread across the fleet 

and annually 10–68% of all vessels targeting arrow squid have been observed, with this fraction 

increasing over time. Observers have covered the full size range of vessels operating in the fishery, 

although the smallest vessels have been slightly undersampled and the largest oversampled. 

The observer effort was mostly focussed on the main arrow squid fisheries around the Auckland 

Islands and Stewart-Snares Shelf, but the smaller fisheries on the Puysegur Bank and off Banks 

Peninsula were also covered, although less consistently. Observer coverage was more focussed on the 

central period of the arrow squid season, February to April, than the fleet was in general – with 

fishing in January and May slightly undersampled. 

Appropriate stratification for the analyses was determined using linear mixed-effect models (LMEs) 

to identify key factors influencing variability in the observed rates of bycatch and discarding. This 

approach addresses the significant vessel-to-vessel and trip-to-trip differences in bycatch and discard 

rates in this fishery by treating the trip variable as a random effect (whereby the trip associated with 

each record is assumed to be randomly selected from a population of trips) and treating other 

variables as fixed effects. This process consistently identified the separate fishery areas (Auckland 

Islands, Stewart-Snares Shelf, Puysegur Bank, Banks Peninsula) as having the greatest influence on 

bycatch and discard rates (with trawl duration of secondary importance) and so area was used in all 

cases to stratify the calculation of annual levels. 

Since 1990–91, over 470 bycatch species or species groups have been identified by observers in this 

fishery, most being non-commercial species (including invertebrate species) caught in low numbers. 

Arrow squid have accounted for about 80% of the total estimated catch recorded by observers. The 

main bycatch species or species groups were the QMS species barracouta (8.5%), silver warehou 

(2.5%), spiny dogfish (1.7%), and jack mackerel (1.1%); of these only spiny dogfish were mostly 

discarded (Figure 6.1). 

Of the other invertebrate groups crabs (0.8%), in particular smooth red swimming crabs (Nectocarcinus 

bennetti) (0.5%), were caught in the greatest amounts and these were mostly discarded. Smaller amounts 

of octopus and squid, sponges, cnidarians, and echinoderms were also often caught and discarded. 

When combined into broader taxonomic groups, bony fish (excluding rattails, tuna, flatfish, and eels) 

contributed the most bycatch (16.5% of the total catch), followed by sharks and dogfish (1.9%), 

crustaceans (0.8%), and rattails (0.2%). The combined bycatch of all other fish (tuna, rays & skates, 

chimaeras, flatfish, and eels) accounted for a further 0.5% of the total catch. 

More than 75% of the sharks & dogfish, rattails, and eels were discarded, whereas about half the flatfish 

were retained, as were most of the tuna, rays & skates, chimaeras, and other fish not in any of these 

groups. The fish species discarded in the greatest amounts were spiny dogfish, redbait, rattails, and 

silver dory. Of the invertebrates, virtually all the echinoderms, other squid, sponges, cnidarians, and 

polychaetes were discarded, but crustaceans, octopuses, and other molluscs were often retained. 

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Figure 6.1: Percentage of the total catch contributed by the main bycatch species (those representing 

0.05% or more of the total catch) in the observed portion of the arrow squid fishery, and the percentage 

discarded. The “Other” category is the sum of all bycatch species representing less than 0.05% of the 

total catch. 

Total annual bycatch in the arrow squid fishery ranged from about 4500 t to 25 000 t, with low levels 

in the early 1990s and after 2007–08, and a peak in the early 2000s (Figure 6.2). The large majority of 

the bycatch comprised QMS species, with less than 1000 t of non-QMS species and invertebrate 

species bycatch in most years. 

Estimated total annual discards ranged from just over 200 t in 1995–96 to about 5500 in 2001–02 and, 

like bycatch, peaked in the early 1990s and were at relatively low levels after 2006–07 (Figure 6.3). 

The majority of discards were QMS species (about 62% over all years), followed by non-QMS 

species (19%), invertebrate species (11%), and arrow squid (7%). 

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Figure 6.2: Annual estimates of bycatch in the arrow squid trawl fishery, for QMS species, non-QMS 

species, invertebrates (INV), and overall for 1990–91 to 2010–11. Also shown (in grey) are estimates of 

bycatch in each category (excluding INV) calculated for 1999–2000 to 2005–06 (Ballara & Anderson 

2009). Error bars indicate 95% confidence intervals. The red lines show the fit of a locally-weighted 

polynomial regression to annual bycatch. In the bottom panel the solid black line shows the total annual 

reported trawl-caught landings of arrow squid (Ministry of Fisheries 2011), with circles indicating years 

in which the fishery closed early after reaching the sea lion FRML; and the dashed line shows annual 

effort (scaled to have mean equal to that of total bycatch). 

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Figure 6.3: Annual estimates of discards in the arrow squid trawl fishery, for arrow squid (SQU), QMS 

species, non-QMS species, invertebrates (INV), and overall for 1990–91 to 2010–11. Also shown (in grey) 

are estimates of discards in each category (excluding INV) calculated for 1999–2000 to 2005–06 (Ballara 

& Anderson 2009). Error bars indicate 95% confidence intervals. The red lines show the fit of a locallyweighted 

polynomial regression to annual discards. 

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6.3.2. Ling longline fishery 

The first analysis of bycatch and discards in this fishery covered the period from 1990–91 to 1997–98, 

and the second (and latest) analysis covered the following years up to 2005–06. To enable a 

comparison of estimates between studies, which used slightly different methodologies, the 1994–95 

fishing year was re-assessed in the recent analysis. In addition to estimating the bycatch of all quota 

species combined, and all non-quota species combined, in the recent analysis annual bycatch was 

estimated separately for three commonly caught individual species, spiny dogfish, red cod, and 

ribaldo. Comparative estimates of only total annual bycatch are available from the first analysis for 

1990–91 to 1997–98. 

The ratio estimator used in these analyses to calculate bycatch and discard rates was based on the 

number of hooks set. The ratios were applied to hook number totals calculated from commercial 

catch-effort data to make annual estimates for the target fishery as a whole. 

Regression tree methods were used to minimise the number of levels of season and area variables 

used to stratify data for the calculation of annual discard bycatch totals in all categories with minimal 

loss of explanatory power. This reduced the number of areas in each category from eight down to 

between two and four, and split the year into three or four periods. The area variables created in this 

way tended to have more explanatory power. . 

Between 1998–99 and 2005–06 only 9% of the vessels operating in this fishery were observed 

(14 vessels in all) but these tended to be the main operators (including most of the larger autoliners) 

and accounted for between 7.7% and 52.5% of the annual target ling catch and 7.8% to 61% of the 

annual number of longlines set during these years. The annual number of observed sets ranged from 

324 to 1605 compared with the total target fishery effort of about 2500 to 4150 sets. Observer 

coverage before 1998–99 was very low, exceeding 5% of the annual target ling catch only in 1994–95 

and 1996–97. 

Ling accounted for 68% of the total estimated catch from all observed sets targeting ling between 

1998–99 and 2005–06, and spiny dogfish accounted for about a further 14%. About half of the 

remaining 18% of the catch comprised other commercial species; especially red cod (Pseudophycis 

bachus), (2.3%), ribaldo (Mora moro) (2.2%), rough skates (Zearaja nasuta, 1.9%), smooth skates 

(Dipturus innominatus) (1.8%), and sea perch (Helicolenus spp.) (1.2%). Altogether, 93% of the 

observed catch was comprised of QMS species, representing 40 of the 96 species in the QMS prior to 

1 October 2007. Over 130 species or species groups were identified by observers, the majority being 

non-commercial species caught in low numbers, especially black cod (Paranotothenia magellanicus) 

and Chondrichthyans, often unspecified but including shovelnose spiny dogfish (Deania calcea), 

Etmopterus species, and seal sharks (Dalatias licha). A surprising number of echinoderms, especially 

starfish (of which almost 200 000 were observed caught during the period), anemones, crustaceans, 

and other invertebrates were also recorded by observers. 

Total annual bycatch estimates for 1998–99 to 2005–06 ranged from about 2200 t to 3700 t, compared 

with approximate target species catches in the same period of between about 3500 and 8700 t. A large 

part of this bycatch (40–50%) comprised a single species, spiny dogfish, and 80% of the bycatch were 

quota species (Figures 6.4 & 6.5). Bycatch levels decreased during the period, in line with decreasing 

effort in the fishery. Total bycatch estimates for the years before 1998–99 ranged from about 880 t to 

3900 t. Differences in methodology between the two studies, coupled with generally low observer 

coverage, resulted in significantly different estimates of total bycatch for 1994–95. 

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Figure 6.4: Annual estimates of fish bycatch in the target ling longline fishery, calculated for commercial 

(QMS) species (COM), non-commercial (non-QMS) species (OTH), and overall (TOT) for the years 

1994–95 and 1998–99 to 2005–06 (in black). Also shown (in grey) are estimates of total bycatch calculated 

for the period 1990–91 to 1997–98 by Anderson et al. (2000). Error bars show the 95% confidence 

intervals. 

130


Figure 6.5: Annual estimates of the bycatch of spiny dogfish (SPD), red cod (RCO), and ribaldo (RIB) in 

the target ling longline fishery for the years 1994–95 and 1998–99 to 2005–06. Error bars show the 95% 

confidence intervals. 

Total annual discard estimates for 1998–99 to 2005–06 ranged from about 1400 t to 2400 t, and 

generally decreased during the period (Figure 6.6). About 70–75% of these discarded fish were quota 

species, and 60–70% spiny dogfish, the remainder being non-quota, generally non-commercial, 

species. Ling were discarded in small amounts (40–90 t per year), these discards generally being 

attributable to fish being lost on retrieval or predated by marine mammals and birds. Estimated annual 

discards were generally lower for the earlier period (1990–91 to 1997–98) and between about 350 t 

and 1600 t. Total discard estimates for 1994–95 were similar for the two studies. 

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Figure 6.6: Annual estimates of fish discards in the target ling longline fishery, calculated for ling (LIN), 

commercial (QMS) species (COM), non-commercial (non-QMS) species (OTH), and overall (TOT) for the 

years 1994–95 and 1998–99 to 2005–06 (in black). Also shown (in grey) are estimates of the ling and total 

discards calculated for 1990–91 to 1997–98 by Anderson et al. (2000). Error bars show the 95% 

confidence intervals. 

6.3.3. Hoki/hake/ling trawl fishery 

Earlier reports were limited to the hoki target fishery and only the most recent report considers 

bycatch and discards for the fishery as defined by the three target species combined—but hoki is 

dominant in this fishery, accounting for over 90% of the catch. 

Observer coverage in the hoki, hake, and ling trawl fishery between 2000–01 and 2006–07 ranged 

from 11% to 21% of the annual target fishery catch, and 78 separate vessels were observed, covering 

132


the full range of vessel sizes. The annual number of observed tows decreased from 3580 in 2000–01 

to 1999 in 2006–07. Coverage has been spread over the geographical range of this fishery, with high 

sampling throughout the west coast South Island (WCSI) and Chatham Rise fishing grounds and, less 

frequently, in the Sub-Antarctic. Lower levels of sampling have been achieved in the Cook Strait and 

Puysegur fisheries, and coverage was lower still around the North Island although this area accounts 

for very little of the overall catch. Good observer coverage was achieved during the hoki spawning 

season (July to early September), but coverage outside of this period was variable and underrepresentative 

in some months in some years, especially in the Sub-Antarctic, Chatham Rise and 

Puysegur fisheries. 

Hoki, hake, and ling accounted for 87% (77%, 6%, and 4% respectively) of the total observed catch 

from trawls targeting hoki, hake, and ling between 2000–01 and 2006–07. The remaining 13% 

comprised a large range of species, especially javelinfish (2.1%), silver warehou (1.7%), rattails 

(1.4%), and spiny dogfish (1.1%). In total, over 470 species or species groups have been identified by 

observers, the majority of which are non-commercial species caught in low numbers. 

Chondrichthyans in general, often unspecified but including spiny dogfish and basking shark, have 

accounted for much of the non-commercial catch. Echinoderms, squids, crustaceans, and other 

unidentified invertebrates were also well represented in the bycatch of this fishery. 

Total bycatch in the hoki, hake, and ling fishery between 2000–01 and 2006–07 ranged from about 36 

000 to 58 000 t per year (compared to the combined total landed catch of hoki, hake, and ling of 130 

000 to 238 000 t). Estimates of total bycatch for 1990–91 to 1998–99 from earlier projects (for the 

hoki target fishery alone), ranged from about 15 000 t to 60 000 t (Figure 6.7). Overall, total bycatch 

increased during the 1990s to a peak in the early 2000s, and has since declined slowly. Annual 

bycatch for the 1990–01 to 2006–07 period was also estimated for commercial species (QMS species 

and species which were generally retained (>75%) and comprised 0.1% or more of the total observed 

catch) and non-commercial species, rather than QMS and non-QMS species. Roughly similar amounts 

of these two categories were caught overall, and each showed a similar pattern over time to total 

bycatch. 

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Figure 6.7: Annual estimates of fish bycatch in the target hoki, hake and ling trawl fishery, calculated for 

commercial species, non-commercial species, and overall for 2000–01 to 2006–07 (black). Also shown (in 

light grey) are the equivalent bycatch estimates calculated for 1990–91 to 1998–99 by Anderson et al. 

(2001), and for the years 1990–91, 1994–95, 1998–99 and 1999–2000 to 2002–03 by Anderson and Smith 

(2004), (in dark grey). Error bars show the 95% confidence intervals. 

Total annual discard estimates for 2000–01 to 2006–07 ranged from about 5500 to 29 000 t per year 

with the main species being discarded including spiny dogfish, rattails, javelinfish, hoki, and 

shovelnose dogfish. Total annual discards for 1990–91 to 1998–99 were between 6600 t and 17 900 t, 

and overall there has been no obvious trend in total discards (Figure 6.8). The target species (hoki, 

hake, and ling) made up 9.7% of total observed discards. Discard rates were strongly influenced by 

the use of meal plants on fishing vessels; discards of non-commercial species on factory vessels 

without meal plants was up to twice the level of discards for vessels with meal plants. The use of meal 

plants, especially for species such as javelinfish and other rattails, has become more prevalent in 

recent years. 

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Figure 6.8: Annual estimates of fish discards in the target hoki, hake, and ling trawl fishery, calculated 

for commercial species, non-commercial species, hoki, and overall for the period 2000–01 to 2006–07 

(black). Also shown (in light grey) are the equivalent discard estimates calculated for the period 1990–91 

to 1998–99 by Anderson et al. (2001), and for 1990–91, 1994–95, 1998–99 and 1999–2000 to 2002–03 by 

Anderson and Smith (2004), (in dark grey). Error bars show the 95% confidence intervals. 

135


6.3.4. Jack mackerel trawl fishery 

Estimates of annual bycatch in this fishery are available for 1990–91 to 2004–05, with this fishery due 

to for reassessment in 2013. The annual level of observer coverage in this fishery has varied between 

8% and 27% of the target fishery catch but was usually between 15% and 20%. For the most recent 

period examined, 2001–02 to 2004–05, the majority of the observer effort has focussed on the main 

fishery, off the west coasts of the North and South Islands, with some additional coverage on the 

Stewart/Snares Shelf and Chatham Rise fisheries. However, in 2003–04 and 2004–05, there was a 

total of only 12 trawls observed outside of the western fishery. During this time the fishery was 

dominated by seven large trawlers and observers were able to complete a trip on each vessel in most 

years. The fishery runs year round, and although there were significant periods in each year when 

commercial fishing effort was not observed, coverage encompassed all seasons for the four years 

combined. 

Jack mackerel species accounted for 70% of the total estimated catch from all trawls targeting jack 

mackerel between 2001–02 and 2004–05. The remaining 30% mostly comprised other commercial 

species; especially barracouta (15.6%), blue mackerel (4.8%), frostfish (3.1%), and redbait (2.7%). 

Overall about 130 species or species groups were identified by observers, and about half of these were 

non-commercial, non-QMS species caught in low numbers. The species most discarded was the spiny 

dogfish, which comprised about 0.5% of the total catch. The bycatch of non-QMS invertebrate species 

has yet to be closely studied in this fishery, but species of squid, salps, jellyfish were the most 

commonly recorded by observers during this period. 

Total bycatch in the jack mackerel trawl fishery between 2001–02 and 2004–05 ranged from about 

7700 t to 11 900 t. Estimates of total bycatch for 1990–91 to 2003–04 from earlier projects ranged 

from about 5400 t to 15 500 t (Figure 6.9). After an abrupt increase in the late 1990s, annual bycatch 

steadily decreased to a level comparable to that of the 1990–91 to 1996–97 period. This bycatch 

almost entirely comprised commercial (mainly QMS) species. 

136


Figure 6.9: Annual estimates of fish bycatch in the target jack mackerel trawl fishery for the 2001-02 to 

2004-05 fishing years (in black), calculated for commercial species (COM), non-commercial species 

(OTH), and overall (TOT). Also shown (in grey) are estimates of overall bycatch calculated for 1990–91 to 

2000–01 by Anderson et al. (2000) and Anderson (2004a). Error bars show the 95% confidence 

intervals. 

Total annual discards decreased between 2001–02 and 2004–05, continuing a trend that began in 

1998–99, to a level of only 90–100 t per year. This is about 5% of the level of 1997–98 (1850 t), when 

annual discards were at their greatest, and is lower than in any year since 1990–91 (Figure 4.10). 

Discards of the target species were about 200–400 t per year prior to 1998–99 but thereafter decreased 

to only about 10 t per year, mainly due to the absence of recorded losses of large quantities of fish 

through rips in the net or intentional releases of fish during landing. Discards comprised a roughly 

equal amount of commercial and non-commercial species in the recent study, although commercial 

species discards were substantially greater in 2001–02. 

137


Figure 6.10: Annual estimates of fish discards in the target jack mackerel trawl fishery for the 2001-02 to 

2004–05 fishing years (in black), calculated for jack mackerel (JMA), commercial species (COM), noncommercial 

species (OTH), and overall (TOT). Also shown (in grey) are estimates of jack mackerel and 

overall discards calculated for 1990–91 to 2000–01 by Anderson et al. (2000) and Anderson (2004a). Error 

bars show the 95% confidence intervals. 

6.3.5. Southern blue whiting trawl fishery 

In the most recent study, covering the period 2002–03 to 2006–07, the ratio estimator used to 

calculate bycatch and discard rates in this fishery was based on trawl duration. Linear mixed-effect 

models (LMEs) identified fishing depth as the key variable influencing bycatch rates and discard rates 

in this fishery, and regression tree methods were used to optimise the number of levels of this variable 

in order to stratify the calculation of annual bycatch and discard totals in each catch category. 

The key categories of catch/discards examined were; southern blue whiting, other QMS species 

combined, commercial species combined (as defined above for hoki/hake/ling), non-commercial 

species combined, and three commonly caught individual species, hake, hoki, and ling. 

138


The level of observer coverage represented between about 22% and 53% of the target fishery catch 

between 2002–03 and 2006–07 and similar levels were reported from earlier reports, for 1990–91 to 

2001–02. The spread of observer data, across a range of variables, has shown no significant 

shortcomings, due to a combination of the highly restricted distribution of the southern blue whiting 

fishery over space and time of year, a stable and uniform fleet composition, and a high level of 

observer effort. 

Southern blue whiting accounted for more than 99% of the total estimated catch from all observed 

trawls targeting southern blue whiting between 2002–03 and 2006–07. About half the remaining total 

catch was made up of ling (0.2%), hake (0.1%), and hoki (0.1%). These three species, along with 

other QMS species, comprised over 80% of the total bycatch. In all, over 120 species or species 

groups were identified by observers, most being non-commercial species caught in low numbers. 

Porbeagle sharks (introduced into the QMS in 2004), javelinfish and other rattails, and silverside, 

accounted for much of remaining bycatch. Invertebrate species (mainly sponges, crabs, and 

echinoderms) were also recorded by observers, but no taxon accounted for more than 0.01% of the 

total observed catch. 

Total annual bycatch estimates for 2002–03 and 2006–07 ranged from about 40 t to 390 t, compared 

with approximate target species catches in the same period of about 22 000 to 42 000 t. This bycatch 

was fairly evenly split between commercial species (55%) and non-commercial species (45%), 

although QMS species accounted for about 80% of the total bycatch during this period. Total annual 

bycatch decreased during the period, to an all-time low of 40 t in 2006–07. Total annual bycatch 

estimates for 1990–91 to 2001–02, from earlier reports, were mostly between about 60 t and 500 t but 

reached nearly 1500 t in 1991–92 (Figure 6.11). This year immediately preceded the introduction of 

southern blue whiting into the QMS, and effort and catch were exceptionally high. 

139


Figure 6.11: Annual estimates of fish bycatch in the southern blue whiting trawl fishery, calculated for 

QMS species, non-commercial species (OTH), and overall (TOT) for 2002–03 to 2006–07 (in black). Also 

shown (in grey) are estimates of bycatch in each category (excluding QMS) for 1990–91 to 2001–02 

(Anderson 2004a). Error bars show the 95% confidence intervals. Note: the 98–00 fishing year 

encompasses the 18 months between September 1998 and March 2000, the transitional period between a 

change from an Oct–Sep to Apr–Mar fishing year. The dark line in the bottom panel shows the total 

annual estimated landings of SBW (Ministry of Fisheries 2009). 

Total annual discard estimates between 2002–03 and 2006–07 ranged from about 90 t to 250 t per 

year. Discard amounts sometimes exceeded bycatch due to the large contribution of the target species 

(50–230 t per year) to total discards – the result usually of fish losses during recovery of the trawl. 

Discarding of commercial species was virtually non-existent in most years and discards of noncommercial 

species amounted to only 10–50 t per year. The main species discarded were southern 

blue whiting, rattails and porbeagle sharks. Total annual discard estimates for 1990–91 to 2001–02, 

from earlier reports, were mostly between about 140 t and 750 t but were about 1200 t in 1991–92 

(Figure 6.12). Discards of southern blue whiting (and therefore total discards) decreased substantially 

at the end of the 1990s and have remained at low levels, below 250 t per year, at least up until 2006–0 

140


Figure 6.12: Annual estimates of fish discards in the southern blue whiting trawl fishery, calculated for 

the target species (SBW), QMS species, non-commercial species (OTH), and overall (TOT) for 2002–03 to 

2006–07 (in black). Also shown (in grey) are estimates of discards in each category (excluding QMS) 

calculated for 1990–91 to 2001–02 by Anderson (2004a). Error bars show the 95% confidence intervals. 

The dark line shows the total annual estimated landings of SBW (Ministry of Fisheries 2009). 

141


6.3.6. Orange roughy trawl fishery 


calculate bycatch and discard rates in the orange roughy fishery was based on the number of trawls. 

Linear mixed-effect models (LMEs) identified trawl duration as the key variable influencing bycatch 

rates and discard rates in this fishery, and regression tree methods were used to optimise the number 

of levels of this variable in order to stratify the calculation of annual bycatch and discard totals in each 

catch category. 

The key categories of catch/discards examined were; orange roughy, other QMS species (excluding 

oreos) combined, commercial species combined (as defined above for hoki/hake/ling), and noncommercial 

species combined. 

The level of observer coverage in this fishery has been relatively high over the entire period of the 

fishery—more than 10% (in terms of the total fishery catch) in all but one year, and over 50% in some 

years. Observer coverage was not evenly spread across all parameters of the orange roughy fishery, 

the most widespread of any New Zealand fishery, with notable undersampling of smaller vessels, the 

east coast fisheries in QMAs ORH 2A, ORH 2B, and ORH 3A, and some of the earlier years of the 

period. 

For the recent orange roughy fishery (since 2005–06), orange roughy accounted for about 84% of the 

total observed catch. Much of the remainder of the total catch (about 10%) comprised oreo species: 

mainly smooth oreo (8%), and black oreo (2.1%). Rattails (various species, 0.8%) and shovelnose 

spiny dogfish (Deania calcea, 0.6%) were the species most adversely affected by this fishery, with 

over 90% discarded. Other fish species frequently caught and usually discarded included deepwater 

dogfishes (family Squalidae), especially Etmopterus species, the most common of which is likely to 

have been Baxter’s dogfish (E. baxteri), slickheads, and morid cods, especially Johnson’s cod 

(Halargyreus johnsonii) and ribaldo. In total, over 250 bycatch species or species groups were 

observed, most being non-commercial species, including invertebrate species, caught in low numbers. 

Squid (mostly warty squid, Onykia spp.) were the largest component of invertebrate catch, followed 

by various groups of coral, echinoderms (mainly starfish), and crustaceans (mainly king crabs, family 

Lithodidae). 

Total annual bycatch in the orange roughy fishery since 1990–91 ranged from about 2300 t to 

27 000 t, and declined over time alongside the decline in catch and effort in this fishery to be less than 

4000 t in each of the last four years estimated (Figure 6.13). Bycatch mostly comprised commercial 

species, with non-commercial species accounting for only 5–10% of the total bycatch in the recent 

period. 

Estimated total annual discards also decreased over time, from about 3400 t in 1990–91 to about 300 t 

in 2007–08 (Figure 6.14), and since about 2000 were almost entirely non-commercial, non-QMS 

species. Large discards of orange roughy and other commercial species, more prevalent early in the 

fishery, were often due to fish lost from torn nets during hauling. 

142


Figure 6.13: Annual estimates of fish bycatch in the orange roughy trawl fishery, calculated for 

commercial species (COM), non-commercial species (OTH), QMS species, and overall for 1990–91 to 

2008–09 (black points). Also shown (grey points) are earlier estimates of bycatch in each category 

(excluding QMS) calculated for 1990–91 to 2004–05 (Anderson et al. 2001, Anderson 2009a). Error bars 

show the 95% confidence intervals. The black line in the bottom panel shows the total annual estimated 

landings of orange roughy (O. Anderson & M. Dunn (NIWA), unpublished data). 

143


Figure 6.14: Annual estimates of fish discards in the orange roughy trawl fishery, calculated for the target 

species (ORH), commercial species (COM), non-commercial species (OTH), QMS species, and overall for 

1990–91 to 2008–09 (black points). Also shown (grey points) are estimates of discards in each category 

(excluding QMS) calculated for 1990–91 to 2004–05 (Anderson et al. 2001, Anderson 2009a). Error bars 

show the 95% confidence intervals. The black line in the bottom panel shows the total annual estimated 

landings of orange roughy (O. Anderson & M. Dunn (NIWA), unpublished data). 

144


6.3.7. Oreo trawl fishery 


calculate bycatch and discard rates in the oreo fishery was based on the number of trawls. Linear 

mixed-effect models (LMEs) identified trawl duration as the key variable influencing bycatch rates 

and discard rates in this fishery, and regression tree methods were used to optimise the number of 

levels of this variable in order to stratify the calculation of annual bycatch and discard totals in each 

catch category. 

The key categories of catch/discards examined were; oreos, other QMS species (excluding orange 

roughy) combined, commercial species combined (as defined above for hoki/hake/ling), and noncommercial 

species combined. 

The oreo fishery is strongly linked to the orange roughy fishery, and only about 15% of the observed 

trips examined in the study predominantly targeted oreos, and nearly 30% of the observed trawls 

targeting oreos were from trips which predominantly targeted orange roughy. The coverage of the 

oreo fishery is therefore partly determined by the operations of the orange roughy fishery. 

The annual number of observed trawls in the oreo fishery ranged from 30 in 1991–92 to 1006 in 

2006–07 and the number of vessels observed ranged from 2 to 12. The level of coverage remained at a 

relatively consistent level after the mid-1990s, despite a decrease in the total catch and effort. 

Observer coverage was mostly restricted to the main fisheries on the South Chatham Rise and further 

south. Within this region, few locations were not covered by observers during the 19 years examined, 

but in the smaller fisheries, on the North Chatham Rise, Louisville Ridge, and the east coast from 

Kaikoura to East Cape, coverage was minimal. The match of observer coverage to commercial effort 

was relatively good, especially compared with the orange roughy fishery. Some oversampling on the 

south Chatham Rise occurred in some periods, e.g., 2001–2005 and 2008–09, and undersampling in 

the Pukaki/Bounty fisheries in 2005–06 and 2008–09, but elsewhere, and at other times, the spread of 

coverage was nearly ideal. The full range of vessel sizes (mainly between 300 t and 3000 t) was 

covered by observers, although small vessels were somewhat underrepresented and large vessels 

overrepresented. The fleet has shrunk in recent years and the remaining vessels are observed more 

regularly, with 30–60% of the fleet hosting observers annually since 2002–03. 

Oreo species accounted for about 92% of the total estimated catch from all observed trawls targeting 

oreos after 1 October 2002. Orange roughy (3.5%) was the main bycatch species, with no other 

species or group of species accounting for more than 0.6% of the total catch. Hoki were the next most 

common bycatch species, followed by rattails, deepwater dogfish (especially Baxter’s dogfish and 

seal shark (Dalatias licha)), slickheads, and basketwork eel (Diastobranchus capensis), all of which 

were usually discarded. Ling were also frequently caught, but only comprised about 0.25% of the total 

catch. In total, over 250 species or species groups were identified by observers in the target fishery, 

including numerous invertebrates. As in the orange roughy fishery, corals, squids and octopuses, king 

crabs, and echinoderms were the main groups caught. Coral, in particular, was a substantial part of the 

bycatch, accounting for almost 0.4% of the total catch. 

Total annual bycatch in the oreo fishery since 1990–91 has ranged from about 270 t to 2200 t and, 

apart from some higher levels in the late 1990s, not shown any obvious trends (Figure 6.15). Bycatch 

has been split almost evenly between commercial and non-commercial species overall, although after 

2002 about 60% of the bycatch comprised commercial species. 

Discards in the oreo fishery remained relatively stable over time, ranging from about 260 t to 750 t per 

year, with higher levels in the late 1990s than in the early 1990s or 2000s (Figure 6.16). Discards 

mainly comprised non-commercial, non-QMS species, but also included a significant component of 

the target species in most years. 

145


Figure 6.15: Annual estimates of fish bycatch in the oreo trawl fishery, calculated for commercial species 

(COM), non-commercial species (OTH), QMS species, and overall for 1990–91 to 2008–09 (black points). 

Also shown (grey points) are estimates of bycatch in each category (excluding QMS) calculated for 1990– 

91 to 2001–02 (Anderson 2004a). Error bars show the 95% confidence intervals. The black line in the 

bottom panel shows the total annual estimated landings of oreos (Ministry of Fisheries 2010). 

146


Figure 6.16: Annual estimates of fish discards in the oreo trawl fishery, calculated for the target species 

(OEO), commercial species (COM), non-commercial species (OTH), QMS species, and overall for 1990– 

91 to 2008–09 (black points). Also shown (grey points) are estimates of discards in each category 

(excluding QMS) calculated for 1990–91 to 2001–02 (Anderson 2004a). Error bars show the 95% 

confidence intervals. The black line in the bottom panel shows the total annual estimated landings of 

oreos (Ministry of Fisheries 2010). 

147


6.3.8. Scampi trawl fishery 


calculate bycatch and discard rates in the scampi fishery was based on the number of trawls. Linear 

mixed-effect models (LMEs) identified fishery area as the key variable influencing bycatch rates and 

discard rates. 

The key categories of catch/discards examined were; all QMS species combined, all non-QMS 

species combined, all invertebrate species combined, javelinfish, and all other rattail species 

combined. 

Observer coverage in the scampi fishery has been relatively low compared with most of the other 

fisheries assessed. The long-term level of observer coverage in the orange roughy, oreo, arrow squid, 

southern blue whiting, and ling longline fisheries is greater than 18% of the target fishery catch (and 

over 40% for southern blue whiting) whereas in the scampi fishery (and also in the jack mackerel 

fishery) long-term coverage has only been about 11–12%. However, annual coverage in the scampi 

fishery was greater than 10% in most years and fell below 5% only once (in 2000–01). 

The annual number of observed trawls in the fishery ranged from 142 to 797, but has been over 300 

trawls in most years. The number of vessels observed in each year ranged from 3 to 8 (equivalent to 

33–66% of the fleet) and was very constant—5 or 6 vessels in most years. Analysis of the spread of 

observer effort compared with that of the scampi fishery as a whole, across a range of variables, 

indicated that this coverage was reasonably well spread. Although some less important regions of the 

fishery received little or no coverage (e.g. the central Chatham Rise, where commercial scampi 

fishing has only recently developed, and west coast South Island), the main scampi fisheries were 

consistently sampled throughout the period examined. Vessels were mostly of a similar size, and the 

small amount of effort by larger vessels was adequately covered, as was the full depth range of the 

fishery and (despite highly intermittent sampling in several years) all periods of the year. 

Over 450 bycatch species or species groups were observed in the scampi target fishery catch, most 

being non-commercial species, including invertebrate species, caught in low numbers. Scampi 

accounted for only about 17% of the total estimated catch from all observed trawls targeting scampi 

since 1 October 1990. The main bycatch species or species groups were javelinfish (16%), other 

(unidentified) rattails (13%), sea perch (Helicolenus spp., 8.4%), ling (7.5%), and hoki (6.1%). The 

first three of these bycatch groups were mostly discarded (Figure 6.17). Of the other invertebrate 

groups, unidentified crabs (1.1%) and unidentified starfish (0.8%) were caught in the greatest 

amounts. When combined into broader taxonomic groups, bony fish (excluding rattails) contributed 

the most to total bycatch (40%), followed by rattails (29%), rays and skates (3.5%), sharks and 

dogfish (2.3%), crustaceans (2.2%), chimaeras (2.0%), echinoderms (1.6%), and cnidarians (0.6%). A 

large percentage of the bycatch in these groups was discarded, and was less than 85% only for bony 

fish (excluding rattails) (33%), rays and skates (67%), and chimaeras (28%). 

148


Figure 6.17: Percentage of the total catch contributed by the main bycatch species (those representing 1% 

or more of the total catch) in the observed portion of the scampi fishery, and the percentage discarded. 

The “Other” category is the sum of all other bycatch species (fish and invertebrates) representing less 

than 1% of the total catch. 

Total annual bycatch since 1990–91 ranged from about 2100 t to 9200 t and, although highly variable, 

showed a significant decline over the past 20 years – driven mainly by a decline in the bycatch of 

QMS species (Figure 6.18). Annual bycatch has generally been an even mixture of QMS and non- 

QMS species, with invertebrate species (although showing a significant increase over time) 

accounting for only about 7% of the total bycatch for the whole period. Rattails (split evenly between 

javelinfish and all other species combined) accounted for 30–80% of the annual non-QMS bycatch. 

Comparison of bycatch rates with relative biomass estimates from trawl surveys to test for similarity of 

trends over time was possible for the Chatham Rise and Auckland Islands fishery areas, but these were 

inconclusive. 

Total annual discards ranged from 6790 t in 1995–96 to 1430 t in 2005–06 and, although showing a 

general decrease since 2001–02, there was no significant trend in overall discard levels since 1990–91 

(Figure 6.19). Discards were dominated by non-QMS species (overall about 75%) followed by QMS 

species (16%) and invertebrates (9%). Rattail species accounted for nearly 60% of the non-QMS 

discards and about 45% of all discards. 

149


Figure 6.18: Annual estimates of bycatch in the scampi trawl fishery, for QMS species, non-QMS species, 

invertebrates (INV), and overall for 1990–91 to 2009–10. Also shown (in grey) are estimates of bycatch in 

each category (excluding INV) calculated for 1999–2000 to 2005–06 (Ballara & Anderson 2009). Error 

bars indicate 95% confidence intervals. The straight lines show the fit of a weighted regression to annual 

bycatch. In the bottom panel the solid black line shows the total annual reported landings of scampi 

(Ministry of Fisheries 2011) and the dashed line shows annual effort (scaled to have mean equal to that of 

total bycatch). 

150


Figure 6.19: Annual estimates of discards in the scampi trawl fishery, for QMS species, non-QMS species, 

invertebrates (INV), and overall for 1990–91 to 2009–10. Also shown (in grey) are estimates of discards 

in each category (excluding INV) calculated for 1999–2000 to 2005–06 (Ballara & Anderson 2009). Error 

bars indicate 95% confidence intervals. The straight lines show the fit of the weighted regression to 

annual discards. 

151


6.3.9. Tuna longline fishery 

The New Zealand tuna longline fishery was dominated by the foreign licensed vessels during the 

1980s, but is now comprised of chartered Japanese vessels and New Zealand domestic vessels. The 

domestic fishing fleet has been the dominant fleet in the fishery since 1993–94 (Figure 6.20). 

Number of hooks (millions) 

30.0 

25.0 

20.0 

15.0 

10.0 

5.0 

0.0 

1979-80 

1980-81 

1981-82 

1982-83 

1983-84 

1984-85 

1985-86 

1986-87 

1987-88 

1988-89 

1989-90 

1990-91 

1991-92 

1992-93 

1993-94 

1994-95 

1995-96 

1996-97 

Fishing year 

1997-98 

1998-99 

1999-00 

2000-01 

2001-02 

2002-03 

N.Z. Domestic 

Foreign + charter 

2003-04 

2004-05 

2005-06 

2006-07 

2007-08 

2008-09 

Figure 6.20: Effort (hooks set) in the tuna longline fishery. Black bars are Foreign and Charter vessels, 

white bars are NZ domestic vessels. 

The Japanese charter fleet mainly target southern bluefin tuna off the west coast South island (WCSI), 

and domestic vessels target mainly southern bluefin tuna and bigeye tuna and the fishery is 

concentrated on the east coast of the North Island (ECNI) with some fishing for southern Bluefin tuna 

on the WCSI. 

The most recent analysis of fish bycatch in tuna longline fisheries was the 2006−07 to 2009−10 

fishing years (Griggs & Baird 1012) 

Observer effort has mainly focused on the Japanese charter vessels (all vessels covered and usually 

about 80% of hooks observed), with lower coverage of the domestic fishery (approximately 7-8% 

during 2006−07 to 2009−10). Most of the fishing effort is carried out by the domestic fleet so this 

fleet is under-observed. 

During 2006−07 to 2009–10, 111 074 fish and invertebrates from at least 62 species or species groups 

were observed. Most species were rarely observed, with only 37 species (or species groups) exceeding 

100 observations between 1988–89 and 2009–10. The most commonly observed species over all years 

were blue shark, albacore tuna, and Ray’s bream, these three making up nearly 70% of the catch by 

numbers. Blue shark and Ray’s bream were the most abundant and second most abundant species in 

each of the four fishing years 2006–07 to 2009−10 (Table 6.2). Other important non-target species 

were albacore, lancetfish, bigscale pomfret, dealfish, porbeagle shark, swordfish, moonfish, mako 

shark, deepwater dogfish, sunfish, and oilfish. The catch composition varied with fleet and area 

fished. 

QMS bycatch species are blue sharks, mako sharks, porbeagle sharks, school shark, moonfish, Ray’s 

bream, and swordfish. Swordfish is also sometimes targeted. 

152 

2009-10


Table 6.2: Species composition of observed tuna longline catches. Number of fish observed are shown for 

2006-07 to 2009-10 and all fish observed since 1988-89. Top 30 species. 

1 

2 

3 

4 

5 

6 

7 

8 

9 

10 

11 

12 

13 

14 

15 

16 

17 

18 

19 

20 

21 

22 

23 

24 

25 

26 

27 

28 

29 

30 

2006–07 to Total 

Species Scientific Name 

2009–10 number 

Blue shark Prionace glauca 38162 182628 

Albacore tuna Thunnus alalunga 9854 101316 

Rays bream Brama brama 25277 98205 

Southern bluefin tuna Thunnus maccoyii 10373 43291 

Porbeagle shark Lamna nasus 2235 19011 

Dealfish Trachipterus trachypterus 2304 17185 

Lancetfish Alepisaurus ferox & A. brevirostris 5661 14383 

Moonfish Lampris guttatus 1683 9134 

Deepwater dogfish Squaliformes 1600 9112 

Swordfish Xiphias gladius 2213 8286 

Big scale pomfret Taractichthys longipinnis 2954 7818 

Oilfish Ruvettus pretiosus 711 7542 

Mako shark Isurus oxyrinchus 1676 6162 

Rudderfish Centrolophus niger 373 4907 

Butterfly tuna Gasterochisma melampus 617 4469 

Escolar Lepidocybium flavobrunneum 643 4422 

Bigeye tuna Thunnus obesus 1240 4390 

School shark Galeorhinus galeus 419 3620 

Yellowfin tuna Thunnus albacares 97 3342 

Sunfish Mola mola 1000 2755 

Pelagic stingray Pteroplatytrygon violacea 585 2398 

Hoki Macruronus novaezelandiae 265 2021 

Thresher shark Alopias vulpinus 169 1400 

Skipjack tuna Katsuwonus pelamis 38 1151 

Dolphinfish Coryphaena hippurus 134 608 

Flathead pomfret Taractes asper 158 516 

Striped marlin Tetrapturus audax 59 468 

Black barracouta Nesiarchus nasutus 51 386 

Barracouta Thyrsites atun 10 357 

Pacific bluefin tuna Thunnus orientalis 34 222 

Most blue, porbeagle, mako, and school sharks were processed in some way, either being finned or 

retained for their flesh, but there were significant fleet differences. Blue sharks were mainly just 

finned. Most albacore, swordfish, yellowfin tuna, moonfish and Ray’s bream were retained. Most 

bigscale pomfret, escolar, oilfish and rudderfish were discarded, with some year and fleet differences. 

Almost all deepwater dogfish, dealfish, and lancetfish were discarded. 

153


6.3.10. Albacore troll fishery 

This fishery is comprised entirely of small domestic vessels fishing over the summer months mainly 

on the west coast of the North and South Island, especially WCSI. 

Observers began to go to sea on troll vessels in 2007. The first 2 years were a trial period with one trip 

observed and targets were set in 2009. Coverage has ranged from 0.5-1.5% of days fished over the 

2009−10 to 2010−12 fishing years. 

Albacore has made up 93.5% of the observed catch over the past six years, followed by Ray’s bream 

(3.1%) and Skipjack tuna (2.1%) and small numbers (


6.3.11. Skipjack purse seine fishery 

Skipjack tuna makes up 98.9% of the catch observed on purse seine vessels in NZ waters. 

Catch composition from eight observed purse seine trips operating within New Zealand fisheries 

waters in 2010 and 2011 can be seen in Table 6.4. 

Table 6.4: Species composition of observed skipjack purse seine catches in 2010 and 2011. 

2010–2011 

Observed 

catch weight 

Common name Scientific name 

(kg) % Catch 

Skipjack tuna Katsuwonus pelamis 3 600 988 98.92 

Jack mackerel Trachurus spp. 22 090 0.61 

Jellyfish Scyphozoa 6 740 0.19 

Blue mackerel Scomber australasicus 4 040 0.11 

Manta ray Mobula japanica 2 122 0.06 

Sunfish Mola mola 1 456 0.04 

Striped marlin Tetrapturus audax 820 0.02 

Mako shark Isurus oxyrinchus 517 0.01 

Albacore tuna Thunnus alalunga 422 0.01 

Porcupine fish Tragulichthys jaculiferus 343 0.01 

Flying fish Exocoetidae 174



A standard measure that can be used to indicate the degree of wastefulness in a fishery is the level of 

annual discards as a fraction of the catch of the target species. The most recent estimates of this 

measure are provided in Table 6.5 for those fisheries where the necessary data were available. 

Table 6.5: Fishery efficiency. Kilograms of discards per kilogram of target species catch. The figures 

represent the most recent estimate, from published reports. 

Fishery Discards/target species catch (kg) 

Arrow squid trawl 0.02–0.07 

Ling longline 0.35 

Hoki/hake/ling trawl 0.03 

Jack mackerel trawl 0.011 

Southern blue whiting trawl 0.005 

Orange roughy trawl 0.03–0.06 

Oreo trawl 0.02–0.03 

Scampi trawl 3.5 

Some general trends have been identified in some fisheries, especially those examined within more 

recent MPI projects where the determination of trends in the rates and levels of bycatch over time has 

been an explicit objective (Table 6.6). 

Table 6.6: Trends in non-protected species bycatch from recent MPI projects where trend determination 

has been an objective. 

Fishery Trends 

Arrow squid trawl Linear regression modelling of observer catch data indicated increasing bycatch 

rates over time (positive slopes) in all species categories and areas except for 

QMS species in the Stewart-Snares Shelf and Banks Peninsula fisheries. These 

trends were statistically significant (p



Recent fleet-wide alterations to the nets providing escape gaps for larger 

unwanted fish species (e.g., skates) may be responsible for the above trends. 

These escape gaps allow for longer tows, as the nets fill up less rapidly, and may 

lead to greater catches of benthic invertebrates and smaller fish species. 

Alverson DL; Freeberg MH; Murawski SA; Pope JG (1994). A global assessment of fisheries bycatch and discards. FAO Technical Paper No. 

339. Rome. 233 p. 

Anderson, O.F. (2004a). Fish discards and non-target fish catch in the fisheries for southern blue whiting and oreos. New Zealand Fisheries 

Assessment Report 2004/9. 40 p. 

Anderson, O.F. (2004b). Fish discards and non-target fish catch in the trawl fisheries for arrow squid, jack mackerel, and scampi in New Zealand 

waters. New Zealand Fisheries Assessment Report 2004/10. 61 p. 

Anderson, O.F. (2007). Fish discards and non-target fish catch in the New Zealand jack mackerel trawl fishery, 2001–02 to 2004–05. New 

Zealand Aquatic Environment and Biodiversity Report 8. 36 p. 

Anderson, O.F. (2008). Fish and invertebrate bycatch and discards in ling longline fisheries, 1998–2006. New Zealand Aquatic Environment and 

Biodiversity Report 23. 43 p. 

Anderson, O.F. (2009a). Fish discards and non-target fish catch in the New Zealand orange roughy trawl fishery, 1999–2000 to 2004–05. New 

Zealand Aquatic Environment and Biodiversity Report 39. 40 p. 

Anderson, O.F. (2009b). Fish and invertebrate bycatch and discards in southern blue whiting fisheries, 2002–07. New Zealand Aquatic 

Environment and Biodiversity Report 43. 42 p. 

Anderson, O.F.; (2011). Fish and invertebrate bycatch and discards in orange roughy and oreo fisheries from 1990–91 until 2008–09. New 

Zealand Aquatic Environment and Biodiversity Report 67. 

Anderson, O.F. (In Press). Fish and invertebrate bycatch and discards in New Zealand arrow squid fisheries from 1990–91 until 2010–11. New 

Zealand Aquatic Environment and Biodiversity Report. 

Anderson, O.F., Clark, M.R., & Gilbert, D.J. (2000). Bycatch and discards in trawl fisheries for jack mackerel and arrow squid, and in the 

longline fishery for ling, in New Zealand waters. NIWA Technical Report 74. 44 p. 

Anderson, O.F., Gilbert, D.J., & Clark, M.R. (2001). Fish discards and non-target catch in the trawl fisheries for orange roughy and hoki in New 

Zealand waters for the fishing years 1990–91 to 1998–99. New Zealand Fisheries Assessment Report 2001/16. 57 p. 

Anderson, O.F.; Clark, M.R. (2003). Analysis of bycatch in the fishery for orange roughy, Hoplostethus atlanticus, on the South Tasman Rise. 


Anderson, O.F.; Smith, M.H. (2005). Fish discards and non-target fish catch in the New Zealand hoki trawl fishery, 1999–2000 to 2002–03. New 

Zealand Fisheries Assessment Report 2005/3. 37 p 

Ayers, D.; Francis, M.P.; Griggs, L.H.; Baird, S.J. (2004). Fish bycatch in New Zealand tuna longline fisheries, 2000–01 and 2001–02. New 


Ballara, S.L.; Anderson, O.F. (2009). Fish discards and non-target fish catch in the trawl fisheries for arrow squid and scampi in New Zealand 

waters. New Zealand Aquatic Environment and Biodiversity Report 38. 102 p. 

Ballara, S.L.; O’Driscoll, R.L.; Anderson, O.F. (2010). Fish discards and non-target fish catch in the trawl fishery for hoki, hake, and ling in New 

Zealand waters. New Zealand Aquatic Environment and Biodiversity Report 48. 

Bellido, J.M.; Santos, B. M.; Pennino, G. M.; Valeiras, X.; Pierce, G.J. (2011). Fishery discards and bycatch: solutions for an ecosystem 

approach to fisheries management? Hydrobiologia, 670. 317–333 

Borges, L.; Zuur, A. F.; Rogana, E.; Officer, R. 2005. Choosing the best sampling unit and auxiliary variable for discards estimations. Fisheries 

Research, 75: 29–39. 

Casini M; Vitale F; Cardinale M (2003). Trends in biomass and changes in spatial distribution of demersal fish species in Kattegatt and 

Skagerrak between 1981 and 2003. ICES CM 2003/Q:14 

Clark, M.R., Anderson, O.F., & Gilbert, D.J. (2000). Discards in trawl fisheries for southern blue whiting, orange roughy, hoki, and oreos in 

New Zealand waters. NIWA Technical Report 71. 73 p. 

Davies, R. W. D.; Cripps, S. J.; Nickson, A; Porter, G. (2009). Defining and estimating global marine fisheries bycatch. Marine Policy 33: 661– 

672. 

Fernandes, P. G.; Coull, K.; Davis, C.; Clark, P.; Catarino, R.; Bailey, N.; Fryer, R.; Pout, A. (2011). Observations of discards in the Scottish 

mixed demersal trawl fishery. ICES Journal of Marine Science, 68: 1734–1742. 

Francis, M. P.; Griggs, L. H.; Baird, S. J.; Murray, T. E.; Dean, H. A. (1999a). Fish bycatch in New Zealand tuna longline fisheries. NIWA 

Technical Report 55. 70 p. 

Francis, M. P.; Griggs, L. H.; Baird, S. J.; Murray, T. E.; Dean, H. A. (1999b). Fish bycatch in New Zealand tuna longline fisheries, 1988–89 to 

1997–98. NIWA Technical Report 76. 79 p. 

Francis, M.P.; Griggs, L.H.; Baird, S.J. (2004).Fish bycatch in New Zealand tuna longline fisheries, 1998–99 to 1999–2000. New Zealand 

Fisheries Assessment Report 2004/22. 62 p. 

Griggs, L.; Doonan, I. McKenzie, A.; Fu, D. (In Press). Monitoring the length structure of commercial landings of albacore (Thunnus alalunga) 

during the 2009–10 to 2011−12 fishing years. New Zealand Fisheries Assessment Report. 

Griggs, L.H.; Baird, S.J.; Francis, M.P. (2007). Fish bycatch in New Zealand tuna longline fisheries, 2002–03 to 2004–05. New Zealand 

Fisheries Assessment Report 2007/18. 58 p. 

Griggs, L.H.; Baird, S.J.; Francis, M.P. (2008). Fish bycatch in New Zealand tuna longline fisheries in 2005–06. New Zealand Fisheries 

Assessment Report 2008/27. 47 p. 

Griggs, L.H.; Baird, S.J.; (In Press). Fish bycatch in New Zealand tuna longline fisheries in 2006–07 to 2009−10. New Zealand fisheries 

Assessment Report. 

Kelleher, K.: (2005). Discards in the world’s marine fisheries. An update. FAO Fisheries Technical Paper No. 470. FAO, Rome: 131 pp. 

Ministry of Fisheries (2009). Report from the Fisheries Assessment Plenary, May 2010: stock assessments and yield estimates. Wellington, New 

Zealand Ministry of Fisheries. 1040p. 

157


Ministry of Fisheries (2010). Report from the Fisheries Assessment Plenary, May 2010: stock assessments and yield estimates. Wellington, New 

Zealand Ministry of Fisheries. 1158p. 

Ministry of Fisheries. (2011). Report from the Fisheries Assessment Plenary, May 2011: stock assessments and yield estimates. Ministry of 

Fisheries, Wellington, New Zealand. 1178p. 

Pope JG; MacDonald DS; Daan N; Reynolds JD; Jennings S (2000). Gauging the impact of fishing mortality on non-target species. ICES 

Journal of Marine Science 57: 689–696. 

Saila S (1983). Importance and assessment of discards in commercial fisheries. FAO Circular No. 765. Rome. 62 p. 

Starr P.J. (In prep). Stock assessment of east coast South Island elephantfish (ELE 3). New Zealand Fisheries Assessment Report xxxx/xx: 

32p. 

Starr P.J., Kendrick T.H. (2012). GUR 3 Fishery Characterisation and CPUE Report. SINS-WG-2012-14v2. 72 pp. 

Starr P.J., Kendrick T.H., Bentley, N. (2010a.) Report to the Adaptive Management Programme Fishery Assessment Working Group: 

Characterisation, CPUE analysis and logbook data for SCH 3. Document 2010/07-v2, 62 p. (Unpublished document held by the 

Ministry of Fisheries, Wellington, N.Z.) (http://cs.fish.govt.nz/forums/thread/3874.aspx) 

Starr P.J., Kendrick T.H., Bentley, N. (2010b). Report to the Adaptive Management Programme Fishery Assessment Working Group: 

Characterisation, CPUE analysis and logbook data for SCH 5. Document 2010/08-v2, 65 p. (Unpublished document held by the 

Ministry of Fisheries, Wellington, N.Z.) (http://cs.fish.govt.nz/forums/thread/3875.aspx) 

Starr P.J., Kendrick T.H., Bentley, N. (2010c). Report to the Adaptive Management Programme Fishery Assessment Working Group: 

Characterisation, CPUE analysis and logbook data for SCH 7 and SCH 8. Document 2010/09-v2, 149 p. (Unpublished document held 

by the Ministry of Fisheries, Wellington, N.Z.) (http://cs.fish.govt.nz/forums/thread/3876.aspx) 

158

AEBAR 2012: Benthic impacts 

THEME 3: BENTHIC IMPACTS 

159


7. Benthic (seabed) impacts 

Scope of chapter This chapter outlines the main effects of mobile bottom (or demersal) fishing 

gear on seabed habitats and communities All trawl gears contacting the 

seabed and shellfish dredges are included. Danish seines and more or less 

static methods like bottom longline and potting are excluded in this first 

version, as are fisheries outside the EEZ. 

Area All of the New Zealand Territorial Sea (TS) and Exclusive Economic Zone 

(EEZ). There will be some relevance for out-of-zone bottom trawl fisheries. 

Focal localities Areas that are fished more frequently and habitats that are more sensitive to 

disturbance are likely to be most affected; areas that are closed to bottom 

impacting methods will not be directly affected. Bottom trawling in the EEZ 

is most intense on the western flanks and to the southwest of the Chatham 

Rise, the edge of the Stewart-Snares Shelf, south of the Auckland Islands, 

and off the northwest coast of the South Island. Because of the low spatial 

resolution of reporting up to 2006/07, the spatial distribution of trawling 

within the TS is less well understood. Shellfish dredges probably have the 

greatest effect but their footprint is much smaller than that of bottom trawl 

fisheries and in generally shallow waters. 

Key issues Habitat modification, potential loss of biodiversity, potential loss of benthic 

productivity, potential modification of important breeding or juvenile fish 

habitat leading to reduced fish recruitment. 

Emerging issues Potential for effects on habitats of particular significance to fisheries 

management (HPSFM). The need for (and opportunities presented by) better 

spatial information on inshore fisheries from finer scale reporting of fishing 

locations (including logbooks). Cumulative effects and interactions with 

other stressors (including existing effects, especially in the coastal zone, and 

MFish Research 

(current) 

NZ Government 


Links to 2030 

objectives 

Related chapter/ 

issues 

climate change. 

BEN2007/01, Assessing the effects of fishing on soft sediment habitat, fauna, 

and processes; DAE2010/04, Monitoring the trawl footprint for deepwater 

fisheries; DAE2010/01, Taxonomic identification of benthic samples; 

DEE2010/05, Development of a suite of environmental indicators for 

deepwater fisheries; DEE2010/06, Design a programme to monitor trends in 

deepwater benthic communities; BEN2012-01, Spatial overlap of mobile 

bottom fishing methods and coastal benthic habitats. 

MSI (ex-FRST) programmes: C01X0907, Coastal Conservation 

Management; C01X0906, Impacts of resource use on vulnerable deep-sea 

communities; C01X0808, Deepsea mining of the Kermadec Ridge. Previous 

OBI programmes Coasts & Oceans C01X0501 and Marine Biodiversity & 

Biosecurity C01X0502 are now part of NIWA core funding. 

Objective 6: Manage impacts of fishing and aquaculture 

Habitats of particular significance for fisheries management (HPSFM), 

marine environmental monitoring, marine mining/sand extraction, land-based 

effects. 

160

7.1. Context 


For the purpose of this document, mobile bottom fishing methods include all types of trawl gear that 

are used in contact with the seabed, Danish seines, and various designs of shellfish dredges. The 

information available on the distribution and effects of Danish seining is poor relative to that on 

trawls and dredges, so that method is not considered here in detail. The benthic effects of other 

methods of catching fish on or near the seabed that do not involve deliberately towing or dragging 

fishing gear across the seabed are thought to be considerably less than those of the mobile methods 

(although not always negligible) and these methods are not considered in this version. 

Trawls and dredges are used to catch a relatively high proportion of commercial landings in New 

Zealand and such methods can represent the only effective and economic way of catching some 

species. However, the resulting disturbance to seabed habitats and communities may have 

consequences for biodiversity and ecosystem services, including fisheries and other secondary 

production. The guiding sections of the Fisheries Act 1996 for managing the effects fishing, including 

benthic effects, are s.8(2)(b) which specifies that “ensuring sustainability” (s.8(1)) includes “avoiding, 

remedying, or mitigating any adverse effects of fishing on the aquatic environment” and s.9 which 

specifies a principle that “biological diversity of the aquatic environment should be maintained”. Also 

potentially relevant is the principle in s.9 that “habitat of particular significance for fisheries 

management should be protected” (see the chapter on Habitats of Particular Significance for Fisheries 

Management for more details). 

One approach to managing the effects of mobile bottom fishing methods is through the use of spatial 

controls. A wide variety of such controls apply in New Zealand waters (Figure 7.1). Some of these 

controls were introduced specifically to manage the effects of trawling, shellfish dredging, and Danish 

seining in areas or habitats considered sensitive to such disturbance (e.g., the bryozoans beds off 

Separation Point, between Golden and Tasman Bays, and the sponge-dominated fauna to the north of 

Spirits and Tom Bowling Bays in the far north). Other closures exist for other reasons but have the 

effect of protecting certain areas of seabed from disturbance by mobile bottom fishing methods. These 

include no-take marine reserves, pipeline and power cable exclusion zones, and areas set aside to 

protect marine mammals (e.g., see Figure 7.2 for trawl closures introduced in 2008 to protect Hector’s 

and Maui’s dolphins). Marine reserves provide marine protection in a range of habitats within the 

Territorial Sea. Although marine reserves provide a higher level of protection by prohibiting all 

extractive activities, most tend to be small. New Zealand’s 34 marine reserves protect about 7.6% of 

New Zealand’s Territorial Sea; however, 99% of this is in two marine reserves in the territorial seas 

around offshore island groups in the far north and far south of New Zealand’s EEZ (Helson et al. 

2009). Until 2000, most closures that had the effect of protecting areas of seabed from disturbance by 

trawling and dredging were in the Territorial Sea. 

In the Exclusive Economic Zone, 18 seamount closures were established in 2000 to protect 

representative underwater topographic features from bottom trawling and dredging (Brodie and Clark 

2003, see Figure 7.1). These areas include 25 features, including 12 large seamounts >1000 m high, 

covering 2% (81, 000 km 2 ) of the EEZ. The seamount areas are closed to all types of trawling and 

dredging. In 2006, members of the fishing industry proposed the closure of about 31% of the EEZ to 

bottom trawling and dredging in Benthic Protection Areas (BPAs), including the existing seamount 

closures. The design criteria for the BPAs were they should be large, relatively unfished, have simple 

boundaries, and be broadly representative of the marine environment. After a consultation process, a 

substantially revised package of BPAs (including three additional areas totalling 13,887 km 2 , 10 

additional active hydrothermal vents, and 35 topographic features) that complemented the existing 

seamount closures was implemented by regulation in 2007 (Helson et al. 2009, Figure 7.3). BPAs 

cover about 1.1 million km 2 (30%) of New Zealand’s EEZ and are closed to trawling on or close to 

the bottom. Midwater trawling well off the bottom is permitted in the BPAs if two observers are on 

161


board and an approved net monitoring system is used. Much of the seabed within BPAs is below 

trawlable depth (maximum trawlable depth is about 1600 m) and all are outside the Territorial Sea. In 

combination, the seamount closures and the BPAs include: 28% of topographic features (a term that 

includes underwater hills, knolls, and seamounts); 52% of seamounts over 1000 m high; and 88% of 

known active hydrothermal vents. 

Figure 7.1: Map, from Baird and Wood 2010, of the major spatial restrictions to trawling present at some stage 

during 1989–90 to 2004–05 and the Ministry for Primary Industries Fishery Management Areas (FMAs) within the 

outer boundary of the New Zealand EEZ. Vessels longer than 28 m may not trawl within the TS and additional 

restrictions are specified in the Fisheries (Auckland Kermadecs Commercial Fishing) Regulations 1986, the Fisheries 

(Central Area Commercial Fishing) Regulations 1986, the Fisheries (Challenger Area Commercial Fishing) 

Regulations 1986 the Fisheries (South East Area Commercial Fishing) Regulations 1986, and the Fisheries (Southland 

and Sub-Antarctic Areas Commercial Fishing) Regulations 1991. 

162


Figure 7.2: Maps from Ministry of Fisheries website showing the general locations of areas closed to trawling to 

protect Hector’s and Maui’s dolphins. Note scales differ. (http://www.fish.govt.nz/ennz/Consultations/Archive/2008/Hectors+dolphins/Decisions.htm?wbc_purpose=Basic&WBCMODE=PresentationUnpublis 

hed%2525252525252cPresentationUnpublished) 

163


Figure 7.3: Map from Ministry of Fisheries website showing the general locations of Benthic Protection Areas (BPAs) 

(http://www.fish.govt.nz/ennz/Environmental/Seabed+Protection+and+Research/Benthic+Protection+Areas.htm?wbc_purpose=basic&WBCMODE=pr 

esentationunpublished&MSHiC=65001&L=10&W=BPA%20&Pre=%3Cspan%20class%3d'SearchHighlight'%3E&Post=% 

3C/span%3E). See also Helson et al. 2009. 


Concerns about the use of towed fishing gear on benthic habitats were first raised by fishermen in the 

fourteenth century in the UK (Lokkeborg 2005). They were worried about the capture of juvenile fish 

and the detrimental effects on food sources for harvestable fish. Despite this long history of concern, 

it is really only in the last 20 years that research efforts have focused strongly on the effects of mobile 

bottom fishing methods on benthic (seabed) communities, biodiversity, and production. This activity, 

combined with controversy around fishing effects, has spawned numerous reviews in the past 10 years 

that seek to summarise or synthesise the information (Jones 1992, Dayton et al. 1995; Jennings and 

Kaiser 1998; Watling and Norse 1998; Lindeboom and deGroot 1998, Auster and Langton 1999; Hall 

1999; ICES 2000a and b, Kaiser and de Groot 2000; NMFS 2002, NRC 2002, Dayton et al. 2002; 

Thrush and Dayton 2002; Lokkeborg 2005, Barnes and Thomas 2005, Clark and Koslow 2007). 

Benthic habitats provide shelter and refuge for juvenile fish and the associated fauna can be the prey 

of demersal fish species. Towed fishing gears (particularly trawl doors), affect benthic habitats and 

organisms and the level of effect will depend on the type of trawl doors and ground gear used, and the 

physical and biological characteristics of seabed habitats in the fishing grounds. The effects are 

164


difficult to assess because of the complexity of benthic communities and their temporal and spatial 

variations, and interpretation can be complicated by environmental gradients or change. For reasons 

of accessibility, cost, and tractability, most research on seabed disturbance caused by human activities 

worldwide has been carried out in coastal systems, and our understanding of the effects of physical 

disturbance in the sparse but highly diverse communities of the deep sea has developed only recently. 

The reviews above broadly indicate that numerical abundance of many invertebrates declines 

(sometimes substantially) after mining, trawling, or other major disturbance. Trawling and dredging 

can re-suspend sediment and can, depending on sediment and local currents, alter sediment 

characteristics. Physical effects include furrows and berms from trawl doors, furrows from the 

bobbins and rock hoppers, and sediment resorting, but the magnitude of these depends on sediment 

type, currents, and wave action (if any). Bottom trawling can also alter natural sediment fluxes and 

reduce the depth of the oxic layer in sediments (Churchill 1989, Warnken et al. 2003, Bradshaw et al. 

2012), and trawling can modify the shape of the upper continental slope (Puig et al 2012), reducing 

morphological complexity and benthic habitat heterogeneity. The mixing of sediments and overlying 

water can alter the chemical makeup of the sediment and have considerable effects in deep, stable 

waters (Rumohr, 1998). Chemical release from the sediment can also be changed, as shown for 

phosphate in the North Sea (ICES 1992, noting lower fluxes were observed after trawling events). 

Trawling can alter benthic communities, reduce total biomass of benthic species, and increase 

predation by scavengers. Sites subject to greater natural disturbance are generally thought less 

susceptible to change from bottom contact fishing (but see Schratzberger et al. 2009 who concluded 

that common anthropogenic disturbances differ fundamentally from natural disturbance). 

There has been less work on the effects of other methods of catching demersal fish or crustaceans that 

do not involve deliberately towing or dragging fishing gear across the seabed, but some such methods 

can have non-negligible effects (e.g., Sharp et al. 2009, Williams et al. 2011). Studies of recovery 

dynamics are rarer still, but a return to pre-disturbance levels after such changes can take up to several 

years, even in some sites subject to considerable natural disturbance (see Kaiser et al. 2006 for a 

summary). In shallow regions with mobile sediments, the effects are generally difficult to detect and 

recovery can be rapid (e.g., Jennings et al. 2005). Hard-bottom fauna is predicted to recover most 

slowly and Williams et al. (2010) concluded that hard-bottom fauna on seamounts did not show signs 

of recovery within 5–10 years on Australasian seamounts. Recovery rate is typically correlated with 

the spatial extent of a disturbance event (e.g., Hall 1994, Kaiser et al. 2003, see also Figure 7.4) and 

the effects of some “catastrophic” natural disturbance events, such as large-scale marine mudslides, 

can be detected for hundreds of years, even for taxa thought to be robust to physical disturbance such 

as nematodes (Hinz et al. 2008). 

Recovery time 

10 y 

5y 

1y 

1 mo 

eider 

rays 

1 day macrofauna 

fishing 

hurricanes 

bait digging fishing anoxia 

Ice scour hurricanes 

Hydraulic dredging 

walrus grey whales 

10 mm² 1 m² 100 m² 108 10 mm² 1 m² 100 m² 10 m² 8 m² 

Patch size 

165 

tidal currents 

Figure 7.4: General relation between the spatial extent of disturbance events and the time taken to recover from such 

events in marine systems (after Kaiser et al. 2003). Blue dots signal human impacts, including fishing in habitats of 

different abilities to recover, and black dots signal natural disturbance.


Rice (2006) summarised the findings of five major reviews of the effects of mobile bottom-contacting 

fishing gears on benthic species, communities, and habitats (available at: http://www.dfompo.gc.ca/CSAS/Csas/DocREC/2006/RES2006_057_e.pdf). 

In this “review of reviews” Rice (2006) 

summarised the findings of the multiple working groups that contributed to the reviews as follows: 

Rice’s (2006) conclusions about the effects on habitats of mobile bottom fishing gears were that 

they: 

• can damage or reduce structural biota (All reviews, strong evidence or support). 

• can damage or reduce habitat complexity (All reviews, variable evidence or support). 

• can reduce or remove major habitat features such as boulders (Some reviews, strong evidence 

or support). 

• can alter seafloor structure (Some reviews, conflicting evidence for benefits or harm). 

Other emergent conclusions on habitat effects included: 

• There is a gradient of effects, with greatest effects on hard, complex bottoms and least effect 

on sandy bottoms (All reviews, strong support, with qualifications). 

• There is a gradient of effects, with greatest effects on low energy environments and least 

(often negligible) effect on high-energy environments (All reviews, strong support). 

• Trawls and mobile dredges are the most damaging of the gears considered (Three of the 

reviews considered other gears; all drew this conclusion, often with qualifications). 

Mobile bottom gears affect benthic species and communities in that they: 

• can change the relative abundance of species (All reviews, strong evidence or support). 

• can decrease the abundance of long-lived species with low turnover rates (All reviews, 

moderate to strong evidence or support). 

• can increase the abundance of short-lived species with high turnover rates (All reviews, 

moderate to occasionally strong evidence or support). 

• affect populations of surface-living species more often and to greater extents than populations 

of burrowing species (All reviews, weak to occasionally strong evidence or support). 

• have lesser effects in high-energy or frequent natural disturbance environments than in low 

energy environments where natural disturbances are uncommon (Four reviews (the other did 

not address the factor), strong evidence or support). 

• affect populations of structurally fragile species more often and to greater extents than 

populations of “robust” species (All reviews, variable evidence and support). 

• Abundance of scavengers increases temporarily in areas where bottom trawls have been used 

(Three reviews, variable support or evidence, all argue for the effects being transient). 

• Rates of nutrient cycling or sedimentation are increased in areas where bottom trawls have 

been used (Two reviews, mixed views on magnitude of effects and conditions under which 

they occur). 

Considerations in the application or adoption of mitigation measures: 

• The effect of mobile fishing gears on benthic habitats and communities is not uniform. It 

depends on: 

o the features of the seafloor habitats, including the natural disturbance regime (All 

reviews, strong evidence or support); 

o the species present (All reviews, strong evidence or support, though not mentioned by 

NMFS panel); 

o the type of gear used and methods of deployment (All reviews, moderate to strong 

evidence support); 

o the history of human activities, particularly past fishing, in the area of concern (All 

reviews, strong evidence or support). 

166


• Recovery time from trawl-induced disturbance can take from days to centuries, and depends 

on the same factors as listed above. (All reviews, strong evidence or support). 

• Given the above considerations, the effect of mobile bottom gears has a monotonic 

relationship with fishing effort, and the greatest effects are caused by the first few fishing 

events (All reviews, moderate to strong evidence or support). 

• Application of mitigation measures requires case specific analyses and planning; there are no 

universally appropriate fixes (Three reviews, moderate to strong evidence or support. The 

issue of implementing mitigation was not addressed in the FAO review. It was also stressed in 

the US National Academy of Sciences review and discussed in the ICES review that extensive 

local data are not necessary for such case-specific planning. The effects of mobile bottom 

gears on seafloor habitats and communities are consistent enough with well-established 

ecological theory, and across studies, that cautious extrapolation of information across sites 

is legitimate). 

Rice (2006) concluded “These overall conclusions on impacts and mitigation measures, and 

recommendations for management action form a coherent and consistent whole. They are relevant to 

the general circumstances likely to be encountered in temperate, sub-boreal, and boreal seas on 

coastal shelves and slopes, and probably areas … beyond the continental shelves. They allow use of 

all relevant information that can be made available on a case by case basis, but also guide 

approaches to management in areas where there is little site-specific information.” 

Since Rice’s (2006) paper, Kaiser et al. (2006) published a meta-analysis of 101 separate 

manipulative experiments that confirms many of Rice’s findings. Shellfish dredges have the greatest 

effect of the various mobile bottom fishing gears, biogenic habitats are the most sensitive to such 

disturbance (especially for attached fauna on hard substrates) and unconsolidated, coarse sediments 

(e.g., sands) are the least sensitive. Kaiser et al. (2006) concluded that recovery from disturbance 

events can take months to years, depending on the combination of fishing method and benthic habitat 

type. This meta-analysis of manipulative experiments was an important development, reinforcing the 

inferences drawn from multiple mensurative observations at much larger scale (“fisheries scale”) in 

New Zealand (e.g., Thrush et al. 1998, Cryer et al. 2002) and overseas (e.g., Craeymeersch et al. 

2000, McConnaughey et al. 2000, Bradshaw et al. 2002, Blyth et al. 2004, Tillin et al. 2006, Hiddink 

et al. 2006). This is a powerful combination that implies substantial generality of the findings. 

The international literature is, therefore, clear that bottom (demersal) trawling and shellfish dredging 

are likely to have largely predictable and sometimes substantial effects on benthic community 

structure and function. However, the positive or negative consequences for ecosystem processes such 

as production had not been addressed until more recently (e.g., Jennings et al. 2001, Reiss et al. 2009, 

Hiddink et al. 2011). It has been mooted that frequent disturbance should lead to the dominance of 

smaller species with faster life histories and that, because smaller species are more productive than 

larger ones, system productivity and production should increase under trawling disturbance. However, 

when this proposition has been tested, it has not been supported by data in real fishing situations (e.g., 

Jennings 2002, Hermsen et al. 2003, Reiss et al.2009) and where overall productivity has been 

assessed, it decreases with increasing trawling disturbance. 

For example, Veale et al. (2000) examined spatial patterns in the scallop fishing grounds in the Irish 

Sea and found that total abundance, biomass, and secondary production (including that of most 

individual taxa examined) decreased significantly with increasing fishing effort. Echinoids, 

cnidarians, prosobranch molluscs, and crustaceans contributed most to the differences. Jennings et al. 

(2001) showed that, in the North Sea, trawling led to significant decreases in infaunal biomass and 

production in some areas even though production per unit biomass rose with increased trawling 

disturbance. The expected increase in relative production did not compensate for the loss of total 

production that resulted from the depletion of large-bodied species and individuals. Hermsen et al. 

(2003) found that mobile fishing gear disturbance had a conspicuous effect on benthic megafaunal 

production on Georges Bank, and cessation of such fishing led to a marked increase in benthic 

167


megafaunal production, dominated by scallops and urchins. Hiddink et al. (2006) estimated that more 

than half of the southern North Sea was trawled sufficiently frequently to depress benthic biomass by 

10% or more, and that 27% was in a state where benthic production was depressed by 10% or more. 

They estimated that recovery from this situation would take 2.5–6 years or more once fishing effort 

had been eliminated. They further estimated that fishing reduced benthic biomass and production by 

56% and 21%, respectively, compared with an unfished situation. Reiss et al. (2009) found that, 

although sediment composition was the most important driver of benthic community structure in their 

North Sea study area, the intensity of fishing effort was also important and reductions in the 

secondary production of the infaunal community could be detected even within this heavily fished 

region. 

The types of models developed by Hiddink et al. (2006, 2011, but see also Ellis and Pantus 2001 and 

Dichmont et al.(2008) can be used to assess the likely performance of different management 

approaches or levels of fishing intensity. Such management-strategy-evaluation (MSE) methods 

involve specifying management objectives, performance measures, a suite of alternative management 

strategies, and evaluating these alternatives using simulation (Sainsbury et al. 2000). For instance, the 

early study by Ellis and Pantus (2001) assessed the effect of trawling on marine benthic communities 

by combining an implementation of the spatial and temporal behaviour of the local fishing fleet with 

realistic ranges for the removal and recovery of benthic organisms. The model was used to compare 

the outcomes of two radically different management approaches, spatial closures and reductions in 

fishing effort. Lundquist et al. (2007, 2010) used a more sophisticated spatially explicit landscape 

mosaic model with variable connectivity between patches to assess the implications of different 

spatial and temporal patterns of disturbance in the model landscape. They found that the scale of the 

disturbance regime (which could be trawling or any other physical disturbance) and the dispersal 

processes interact, and that the scales of these processes greatly influenced changes in the structure 

and diversity of the model community, and that recovery across the mosaic depended strongly on 

dispersal. System stability also decreased as dispersal distance decreased. 


To understand the effects of mobile bottom fishing methods on benthic habitats, it is necessary to 

have knowledge on 

• the distribution of such habitats, 

• the extent to which mobile bottom fishing methods are used in each habitat (the overlap), 

• the consequences of any such disturbance (potentially in conjunction with other disturbances 

or stressors), and 

• the nature and speed of recovery from the disturbance. 

These components will be dealt with in turn. 

7.3.1. Distribution of Habitats 

Mapping of benthic habitats at the large scales inherent in fisheries management is expensive and 

time-consuming so the New Zealand government commissioned an environmental classification to 

provide a spatial framework that subdivided the TS and EEZ into areas having similar environmental 

and biological character. This Marine Environment Classification (MEC) was launched in 2005 

(Snelder et al. 2004, 2005, 2006) using available physical and chemical predictors, and because 

environmental pattern was thought a reasonable surrogate for biological pattern. The authors 

suggested that the MEC provided managers with a useful spatial framework for broad scale 

management, but cautioned that the full utility and limitations would become clear only as the MEC 

was applied to real issues. They described the MEC as a tool to organise data, analyses and ideas, and 

as only one component of the information that would be employed in any analysis. The 20-class 

version (Figure 7.5, Table 7.1) has been the most widely cited, although additional classification 

168


levels provide more detail that is significantly correlated with biological layers. The 2005 MEC was 

not optimised for any specific ecosystem component but was “tuned” against data for demersal fish, 

phytoplankton, and benthic invertebrates. It performed least well as a classification of benthic 

invertebrates and, at the 20-class level, grouped most of the Chatham Rise and Challenger Plateau into 

a single class. Although separation of these two areas was evident as the MEC was driven to larger 

numbers of classes, their inclusion in a single class in the 20-class classification was considered 

counter-intuitive because their productivity and fisheries are known to be very different. 

This disquiet with the predictions of the original MEC for benthic habitat classes led to the 

development of alternatives that might perform better for benthic systems. First of these was a 

classification optimised for demersal fish (Leathwick et al. 2006). Several variants of this 

classification all out-performed the original MEC for demersal fish, particularly at lower levels of 

classification detail and was adopted by the Ministry for the Environment for their indicators related 

to bottom trawling and their 2010 Environmental Snapshot where the trawl footprint is compared with 

putative habitats (Ministry for the Environment 2010, see also: 

http://www.mfe.govt.nz/environmental-reporting/report-cards/seabed-trawling/2010/index.html). 

Figure 7.5: The 20-class version of the 2005 general purpose Marine Environment Classification (MEC, from Snelder 

et al. 2005). The class numbers are nominal; for attributes of each class at this level, see Table 7.1. 

169


Based partly on this experience, the Ministry of Fisheries commissioned a Benthic-Optimised Marine 

Environment Classification, BOMEC. Many more physical, chemical, and biological data layers were 

available for the development and tuning of this classification than for the 2005 MEC. Especially 

relevant for benthic invertebrates was the inclusion of a layer for sediment grain size (notably absent 

from the MEC). Generalised Dissimilarity Modelling (GDM, Ferrier et al. 2002, 2006, Leathwick et 

al. 2011) was used to define the classification because this approach is well suited to the sparse and 

unevenly distributed biological data available. The BOMEC classes (Figure 7.6) were strongly driven 

by depth, temperature, and salinity into five major groups: inshore and shelf; upper slope; northern 

mid-depths; southern mid-depths; and deeper waters (generally beyond the fishing footprint, down to 

3000 m, the limit of the analysis). Waters deeper than 3000 m could be considered an additional class. 

Recent testing (Bowden et al. 2011) has indicated that the BOMEC out-performs the original MEC at 

predicting benthic habitat classes on and around the Chatham Rise, but that none of the available 

classifications is very good at predicting the abundance and composition of benthic invertebrates at 

the fine scale of the sampling undertaken (10s of metres to kilometres). This, in conjunction with the 

findings of Leathwick et al. (2006), reinforces the role of environmental classifications as broad-scale 

predictors of general patterns at broad scale (tens to hundres of kilometres) when more specific 

biological information is not available. 

Where broad scale classification methods are not applicable, other approaches have been taken. The 

trawl fisheries for orange roughy, oreos, and cardinalfish take place to a large extent on seamounts or 

other features (Clark and O’Driscoll 2003, O’Driscoll and Clark 2005). These features are often 

geographically small and, in common with other, localised habitats like vents, seeps, and sponge beds, 

do not appear on broad-scale habitat maps (e.g., at EEZ scale) and cannot realistically be predicted by 

broad-scale environmental classifications. Many features have been extensively mapped in recent 

years (e.g., Rowden et al. 2008), and seamount classifications based on biologically-referenced 

physical and environmental “proxies” have also been developed, in New Zealand waters by Rowden 

et al. (2005), and globally by Clark et al. (2010a&b), and Davies and Guinotte (2011) developed a 

method of predicting the framework-forming (i.e, physically structuring) coldwater corals that are a 

focus for benthic biodiversity in deepwater systems. Work continues worldwide, including in New 

Zealand, on the development of sampling, analytical, and modelling techniques to provide costeffective 

assessments of the distribution of marine habitats at a range of scales. MPI project 

DEE2010/06 has been commissioned to design a monitoring programme to assess trends in deepwater 

benthic communities using information from trawl surveys, observers, and directed sampling. MPI 

project DEE2010/05 has been commissioned to develop a suite of environmental indicators for 

deepwater fisheries using, to the extent possible, existing data collection processes. This is an area of 

rapid change in the science and better techniques and data sets for predicting and mapping marine 

benthic habitats are likely to become available in the short to medium term. MPI project 

BEN2012/01will use existing information and classifications to describe the distribution of benthic 

habitats in the coastal zone. NIWA has a MBIE-funded project “Predicting the occurrence of 

vulnerable marine ecosystems for planning spatial management in the South Pacific region” in 

collaboration with Victoria University of Wellington and the Marine Conservation Institute (USA). 

The research will develop a model to predict the locations of VMEs to inform New Zealand and South 

Pacific Regional Fisheries Management Organisation (SPRFMO) initiatives on spatial management in 

the South Pacific region. There may be applications within the New Zealand EEZ. 

170


Table 7.1: Average values for each of the eight defining environmental variables in each class of the 20-class level of 

the MEC classification. After Snelder et al. 2005. 

Figure 7.6: Map of the distribution of Benthic Optimised Marine Environment Classification (BOMEC) classes 

defined by multivariate classification of environmental data transformed using results from GDM analyses of 

relationships between environment and species turnover averaged across eight taxonomic groups of benthic species. 

From Leathwick et al. 2010. 

171

7.3.2. Distribution of Fishing 


Since 1989/90, mobile bottom fishing has been reported on one of three standardised reporting forms 

(Table 7.2). Trawl Catch Effort and Processing Returns (TCEPRs) contain detailed spatial and other 

information for each trawl tow, whereas Catch Effort and Landing Returns (CELRs) include only 

summarised information for each day’s fishing, with very limited spatial resolution. Since 2007/08, 

Trawl Catch and Effort Returns (TCERs) have been available for smaller, predominantly inshore 

trawlers. These include spatial and other information for each trawl tow but in less detail than on 

TCEPRs. Between 1989/90 and 2004/05, only about 25% of all mobile bottom fishing events were 

reported on TCEPRs. Another 25% were bottom trawls reported on CELRs, and the remaining 50% 

were dredge tows for shellfish reported on CELRs. The distribution of trawling reported on CELRs is 

not the same as that reported on TCEPRs (Figure 7.8); the smaller trawlers using CELRs are much 

more likely than the larger boats to fish close to the coast and target inshore species such as flatfish, 

red cod, tarakihi, and red gurnard (collectively 73% of all trawl tows reported on CELRs). MPI 

project BEN2012/01will update the work in BEN2006/01 producing maps of swept area and footprint 

for more recent years. 

Table 7.2: Attributes, usage, and resolution of spatial reporting required on Trawl Catch Effort and Processing 

Returns (TCEPRs) Trawl Catch and Effort Returns (TCERs) and Catch Effort and Landing Returns (CELRs). 

Year of introduction 

Trawl catch and effort reporting forms 

TCEPR TCER CELR 

1988/89 2007/08 1988/89 

Vessels using All trawlers >28 m 

Other vessels as directed 

Other vessels optional 

Trawl tow reporting Tow by tow, start and finish 

locations, speed, depth, gear 

All trawlers 6–28 m unless 

exempted 

Tow by tow, start location, 

speed, depth, gear 

172 

Trawlers not using TCER or 

TCEPR 

Shellfish dredgers 

Daily summary, number of 

tows, effort, gear 

Spatial resolution 1 minute (lat/long) 1 minute (lat/long) Statistical reporting area 

(optionally lat/long) 

Baird et al. (2002) and Baird et al. (2001) described the distribution and frequency of reported fishing 

by mobile bottom fishing gear (dredge, Danish seine, bottom trawl, bottom pair trawl, and mid-water 

trawl in contact with the bottom) in New Zealand’s TS and EEZ during the 1990s and up to 2004/05, 

respectively. They showed that fishing was highly heterogeneous (spatially), but had considerable 

consistency among years; sites that were fished heavily in one year were likely to be fished heavily in 

other years and vice versa. A similar but more detailed analysis was conducted for the Chatham Rise 

and SubAntarctic areas by Baird et al. (2006). Tows reported on TCEPRs were included in the main 

spatial analysis but some additional analysis was possible using tows reported on CELRs. Until 

2006/07, many inshore vessels used CELRs and these comprised a substantial proportion of reported 

trawling, even for some “deepwater” species. For instance, Cryer and Hartill (2002) estimated that, in 

the Bay of Plenty, 78%, 75%, and 39% of trawl tows for tarakihi, gemfish, and hoki, respectively, 

were reported on CELR forms in the 1990s. Since 2007/08, almost all trawling effort has been 

reported on TCEPR or TCER forms. 

Baird et al. (2011) calculated three annual measures of fishing effort: the number of tows, the 

aggregate swept area (using assumed door spreads, see Figure 7.7), and the coverage (“footprint”) of 

the total trawl contact. Trawls were represented spatially as tracklines between the reported start and


finish positions buffered by the assumed door spread to generate trawl polygons. The aggregate swept 

area for a year is the sum of the areas of the polygons and the “footprint” is the estimated area of the 

seabed that is covered by the polygons overlaid. The estimated swept areas and footprint do not 

account for any modification that might occur alongside the trawl path as represented by the swept 

area polygon (e.g., by suspended sediments transported by currents away from the trawl track). Baird 

et al. (2011) produced maps of the aggregate swept area by year for each of the 22 main target species 

or species groups, and various tables and figures describing trends. The annual number of trawls 

peaked in 1997–98 at 78 610 tows (swept area ~ 180 450 km 2 ). In 2007/08, fewer than 55 000 tows 

were reported on TCEPRs (~ 130 800 km 2 ) 

Figure 7.7: Map from Baird et al. 2011 showing the intensity of bottom-contacting trawling effort reported on 

TCEPR forms 1989–90 to 2004–05. The colour scale indicates the aggregate swept area estimated by Baird et al. for 

each 5 x 5 km cell, all target species combined (e.g., the 36 most intensively fished 25 km 2 cells all had an aggregate 

swept area of over 2290 km 2 over 16 years, which translates to the seabed in those cells being swept by some part of a 

trawl 92 times in 16 years, or an average of 5.8 or more times each year). Updates for deepwater trawl fisheries are 

expected in 2013. 

173


Baird et al. (2011) used reported tows on small topographic features that are a focus for orange 

roughy and cardinalfish fisheries by defining polygons for these tows as radii around the reported start 

position with the area swept estimated from the reported duration and speed of the tow. These short 

tows do not appear to contribute substantially to broad-scale plots like Figure 7.7, yet can represent 

intense fishing effort on particular, small seamount features (e.g. Rowden et al. 2005, O’Driscoll and 

Clark 2005). 

Figure 7.8: Broad-scale distribution from Baird et al. 2011 of bottom trawl effort reported on CELRs (left) and on 

CELRs and TCEPRs combined (right), for all fishing years 1989–90 to 2004–05. Updates for deepwater trawl 

fisheries (but not inshore fisheries reporting on TCER) are expected in 2013. 

After the peak of over 140 000 reported trawl tows in 1996/97 and 1997/98 (Figure 7.9) when slightly 

over half of all tows were reported on TCEPRs, overall trawling effort declined to less than 100 000 

tows per year by 2006/07. The reported number of trawl tows has remained relatively stable at about 

174


85–90 000 tows per year, only about 44% of which is reported on TCEPRs (virtually all other tows 

are reported on TCERs) 

Dredging for shellfish (oysters and scallops) is conducted in a number of specific areas that have 

separate, smaller statistical reporting areas (Figure 7.10). Over the 16-year dataset, there were almost 

1.5 million scallop dredge tows in the four main scallop fisheries and over 0.6 million oyster dredge 

tows in the two dredge oyster fisheries . These data are collected on CELRs, usually at the spatial 

scale of a scallop or oyster fishery area and the data have been summarised as the number of dredge 

tows. No estimates of the area swept by these dredges have been made, but the number of reported 

tows has declined markedly since the early 1990s (Figure 7.11). 

Total reported trawls 

160,000 

140,000 

120,000 

100,000 

80,000 

60,000 

40,000 

20,000 

- 

1990 

1991 

1992 

1993 

1994 

1995 

1996 

1997 

1998 

1999 

2000 

2001 

2002 

2003 

2004 

2005 

2006 

2007 

2008 

2009 

2010 

2011 

2012 

175 

Fishing year 

TCER 

CELR 

TCEPR 

Figure 7.9: The number of trawl tows reported on Trawl Catch Effort and Processing Returns (TCEPR), Catch 

Effort and Landing Returns (CELR) and Trawl Catch and Effort Return (TCER) between the 1989/90 and 2007/08 

fishing years. Data for the 2011/12 year may be incomplete. 

Our knowledge of the distribution of mobile bottom fishing effort within our TS and EEZ is, by 

international standards, very good; since 2007/08 we have had tow-by-tow reporting of almost all 

trawling with a spatial precision of about 1 nautical mile. The distribution of dredge tows for shellfish 

is not reported with such high precision, but records kept by fishers in industry logbooks are often 

much more detailed than the Ministry for Primary Industries standard returns, and have sometimes 

been used to support spatial analyses that would not have been possible using the standard returns 

(e.g., Tuck et al. 2006 for project ZBD2005/15 on the Coromandel scallop fishery and Michael et al. 

2006 for project ZBD2005/04 on the Foveaux Strait oyster fishery). These studies indicate the value 

of records with higher spatial precision.


Figure 7.10: Maps taken from Baird et al. 2011 of statistical reporting areas for the main oyster and scallop dredge 

fisheries (scales differ). Note that these reporting areas are generally much smaller than the standard statistical 

reporting areas used for most finfish reporting. 

176

Total reported dredge tows 

200,000 

180,000 

160,000 

140,000 

120,000 

100,000 

80,000 

60,000 

40,000 

20,000 

0 


1990 

1991 

1992 

1993 

1994 

1995 

1996 

1997 

1998 

1999 

2000 

2001 

2002 

2003 

2004 

2005 

2006 

2007 

2008 

2009 

2010 

2011 


177 

Fishing Year 

oysters 

scallops 

Figure 7.11: The number of dredge tows for scallop or oysters reported on Catch Effort and Landing Returns 

(CELR) between the 1989/90 and 2007/08 fishing years (data from Baird et al. 2011 and MPI databases). Data for the 

2011/12 year may be incomplete. 

7.3.3. Overlap of Fishing and Predicted Habitat Classes 

Baird and Wood (2010, project BEN200601) overlaid the 16-year trawl footprint up to 2004-05 on the 

15-class BOMEC to estimate the proportion of each class that had been trawled (and reported on 

TCEPRs). They found that the size of the footprint and the proportion of each class trawled varied 

substantially between habitat classes (Figure 7.12, Table 7.3). Class O is the largest BOMEC class but 

has almost no reported fishing effort. Conversely, class I is one of the smaller classes but has a larger 

trawl footprint that overlaps about 70% of the total class area. Two contrasting classes, together with 

their trawl footprints, are shown in Figure 7.13. The cumulative trawl footprint from Baird and 

Wood’s analysis overlaps about 8% of the 4.1 million km 2 of seafloor within the New Zealand EEZ 

boundary (i.e., including the Territorial Sea). However, this overlap and that for some individual 

BOMEC classes (particularly coastal classes A–E) will be underestimated because of the omission of 

CELR data from these analyses. This analysis is being updated for offshore (middle depth and 

deepwater) trawl fisheries under project DAE2010/04, Monitoring the trawl footprint for deepwater 

fisheries, and the results are expected to be available in early 2013. MPI project BEN2012/01, Spatial 

overlap of mobile bottom fishing methods and coastal benthic habitats, will update the work in 

BEN2006/01, particularly focussing on the overlap between fishing and habitats in the coastal zone.

Area (1000 sq.km) 

Area (1000 sq.km) 

Percentage 


1000 

800 

600 

400 

200 

0 

100 

80 

60 

40 

20 

0 

100 

90 

80 

70 

60 

50 

40 

30 

20 

10 

0 

Area of BOMEC Classes 

A B C D E F G H I J K L M N O 

BOMEC Cl a s s 

Fishing footprint area 



Footprint percentage 



Figure 7.12: Plots from Baird and Wood (2010) of the areas of each BOMEC Class (top), the fishing footprint up to 

2004/05 shown in Figure 7.8 (centre), and percentage of each BOMEC Class area covered by the fishing footprint 

(bottom). 

Table 7.3: Estimated area of each BOMEC class (within the outer boundary of the EEZ), the minimum and 

maximum values for the trawl footprint in each, and cumulative footprint over the 16 years studied by Baird and 

Wood (2010). 

BOMEC class Area (km 2 ) Min. annual footprint 

area (km 2 ) 

178 

Max. annual 

footprint area (km 2 ) 

Cumulative (16 yr) 

proportion overlapped 

A* 27 557 121 4 026 0.42 

B* 12 420 40 484 0.19 

C* 89 710 4 271 11 374 0.58 

D* 27 268 377 1 602 0.30 

E* 60 990 4 046 7 108 0.40 

F 38 608 517 1 391 0.13 

G 6 342 132 833 0.34 

H 138 550 9 583 20 344 0.45 

I 52 224 5 511 18 016 0.70 

J 311 361 10 469 15 975 0.18 

K 1 290 - 2 0.01 

L 198 577 4 238 13 599 0.24 

M 233 825 895 4 390 0.06 

N 493 034 601 1 054 0.02 

O 935 315 2 28 0.00 

TS & EEZ 4 115 806 46 300 90 940 0.08


Figure 7.13: Maps from Baird and Wood (2010) showing BOMEC classes I (left) and M (right) overlaid with the 

footprint of trawls on or near the seafloor reported on TCEPR forms to 2004–05 for each 25-km 2 cell. 

7.3.4. Studies of the Effects of Mobile Bottom Fishing Methods in 


The widespread nature of bottom trawling suggests that fishing is the main anthropogenic disturbance 

agent to the seabed throughout most of New Zealand’s EEZ. Wind waves are certainly very 

widespread, but both field studies and modelling (Green et al. 1995) suggest that erosion of the 

seabed deeper than 50 m by waves occurs only very rarely in the New Zealand EEZ. Despite their 

widespread distribution at the surface, therefore, wind-waves are not a dominant feature of the longterm 

disturbance regime throughout most of the EEZ. In some places, especially in the coastal zone 

and in areas close to headlands, straits, or islands, currents and tides may dominate the natural 

disturbance regime and a community adapted to this type of disturbance will have developed. 

However, over most of the EEZ between about 100 and 1000 m depth, especially in areas where there 

are few strong currents, fishing is probably the major broad-scale disturbance agent. 

Several studies have been conducted since 1995 in New Zealand, focussing on the effects of various 

dredge and trawl fishing methods on a variety of different habitats in several geographical locations 

(Table 7.4). Despite the diversity of these studies, and their different depths, locations, and habitat 

types, the results are consistent with the global literature on the effects of mobile bottom fishing gear 

on benthic communities. Generally, there are decreases in the density and diversity of benthic 

communities and, especially, the density of large, structure-forming epifauna, and long-lived 

organisms along gradients of increasing fishing intensity. Large, emergent epifauna like sponges and 

framework-forming corals that provide structured habitat for other fauna are particularly noted as 

being susceptible to disturbance by mobile bottom fishing methods (Cranfield et al. 1999, 2001, 2003, 

Cryer et al. 2000), especially on hard (non sedimentary) seabeds (Clark & Rowden 2009, Clark et al. 

2010a&b, Williams et al. 2011). Even though large emergent fauna seem most susceptible, however, 

effects have also been shown in the sandy or silty sedimentary systems usually considered to be most 

resistant to disturbance (Thrush et al. 1995, 1998, Cryer et al. 2002). Also typical of the international 

literature is a substantial variation in the extent to which individual New Zealand studies have shown 

clear effects. For instance, in Foveaux Strait, Cranfield et al. (1999, 2001, 2003) inferred substantial 

179


changes in the benthic system caused by over 130 years of oyster dredging, but Michael et al. (2006) 

did not support such conclusions in the same system. Subsequent review of these studies found much 

common ground but no overall consensus on the long-term effects of dredging on the benthic 

community of the strait. 

These studies have focussed predominantly on changes in patterns in biodiversity associated with 

trawling and/or dredging and less work has been done to assess changes in ecological process or to 

estimate the rate of recovery from fishing. Projects that have started on recovery rates are focussed on 

relatively few habitats and primarily those that are known to be sensitive to physical disturbance, 

including by trawling or dredging (e.g., seamounts, project ENV2005/16, and areas of high current 

and natural biogenic structure, projects ENV9805, ENV2005/23 and BEN2009/02). Thus, the 

understanding of the consequences of fishing (or ceasing fishing) for sustainability, biodiversity, 

ecological integrity and resilience, and fish stock productivity in the wide variety of New Zealand’s 

benthic habitats remains incomplete. Reducing this uncertainty would allow the testing of the utility 

and likely long-term productivity of a variety of management strategies, and enable a move towards a 

regime that maximises value to the nation consistent with Fisheries 2030. 

Table 7.4: Summary of studies of the effects of bottom trawling and dredging in New Zealand waters. 

Location Approach Key findings References 

Mercury 

Islands sandy 

sediments. 

Scallop dredge 

Hauraki Gulf 

various soft 

sediments. 

Bottom trawl & 

scallop dredge. 

Bay of Plenty 

continental 

slope. Scampi 

and other 

bottom trawls. 

Foveaux Strait, 

sedimentary & 

biogenic reef. 

Oyster dredge. 

Spirits Bay, 

sedimentary & 

Experimental Density of common macrofauna at both sites decreased as a result 

of dredging at two contrasting sites; some populations were still 

significantly different from reference plots after 3 months. 

Observational, 

gradient 

analysis 


multiple 

gradient 

analyses 


various 


gradient 

Decreases in the density of echinoderms, longlived taxa, epifauna, 

especially large species, the total number of species and 

individuals, and the Shannon-Weiner diversity index with 

increasing fishing pressure (including trawl and scallop dredge). 

Increases in the density of deposit feeders, small opportunists, and 

the ratio of small to large heart urchins. 

Depth and historical fishing activity (especially for scampi) at a site 

were the key drivers of community structure for large epifauna. 

The Shannon-Weiner diversity index generally decreased with 

increasing fishing activity and increased with depth. Many species 

were negatively correlated with fishing activity; fewer were 

positively correlated (including the target species, scampi). 

Interpretations of the authors differ. Cranfield et al’s papers 

concluded that dredging biogenic reefs for their oysters damages 

their structure, removes epifauna, and exposes associated sediments 

to resuspension such that, by 1998, none of the original bryozoan 

reefs remained. 

Michael et al. concluded that there are no experimental estimates of 

the effect of dredging in the strait or on the cumulative effects of 

fishing or regeneration, that environmental drivers should be 

included in any assessment, and that the previous conclusions 

cannot be supported. 

The authors agree that biogenic bycatch in the fishery has declined 

over time in regularly-fished areas, that there may have been a 

reduction in biogenic reefs in the strait since the 1970s, and that 

simple biogenic reefs appear able to regenerate in areas that are no 

longer fished (dominated by byssally attached mussels or reefbuilding 

bryozoans). There is no consensus that reefs in Foveaux 

Strait were (or were not) extensive or dominated by the bryozoan 

Cinctopora. 

In 1999, depth was found to be the most important explanatory 

variable for benthic community composition but a coarse index of 

180 

Thrush et al. 

1995 

Thrush et al. 

1998 

Cryer et al. 

1999 

Cryer et al. 

2002 

Cranfield et al. 

1999, 2001, 

2003 

Michael et al. 

2006 

Cryer et al. 

2000

iogenic areas. 

Scallop dredge. 

Tasman & 

Golden Bays. 

Bottom trawl, 

scallop & 

oyster dredge 

Graveyard 

complex 

“seamounts”, 

northern 

Chatham Rise. 

Orange roughy 

bottom trawl. 


analysis dredge fishing intensity was more important than substrate type for 

many taxonomic groups. Sponges seemed most affected by scallop 

dredging, and samples taken in an area once rich in sponges had 

few species in 1999. This area had probably been intensively 

dredged for scallops. Analysis of historical samples of scallop 

survey bycatch showed a marked decline in sponge species 

richness between 1996 and 1998. 

In 2006, significant differences were identified among areas within 

which fishing was or was not allowed. Species contributing to these 

differences included those identified as being most vulnerable to 

the effects of fishing. These differences could not be attributed 

specifically to fishing because of interactions with environmental 

gradients and uncertainty over the history of fishing. No significant 

change between 1999 and 2006 was identified. 

In 2010, analysis of both epifaunal and infaunal community data 

identified change since 2006, and significant depth, habitat and 

fishing effects. The combined fishing effects accounted for 15 – 

30% of the total variance (about half of the explained variance). 

Individual species responses to fishing were examined, and those 

identified as most sensitive to fishing in this analysis had 

previously been categorised as sensitive on the basis of life history 

characteristics within the 2006 study. 


gradient 

analysis 


multiple 

analyses 

A gradient analysis was adopted to investigate the importance of 

the different factors affecting epifaunal and infaunal communities 

in Tasman and Golden Bays. Fishing was consistently identified as 

an important factor in explaining variance in community structure, 

with recent trawl and scallop effort being more important than 

other fishing terms. Important environmental variables included 

maximum current speed, maximum wave height, depth, % mud, 

and salinity. Fishing accounted for 31–50% of the explained 

variance in epifaunal and infaunal community composition, species 

richness, and Shannon-Weiner diversity. Overall, models explained 

30–54% of variance, and additional spatial patterns identified in the 

analysis explained a further 5–16% of variance. 

From surveys in 2001 and 2006, substrate diversity and the amount 

of intact coral matrix were lower on fished seamounts. Conversely, 

the proportions of bedrock and coral rubble were higher. No 

change in the megafaunal assemblage consistent with recovery 

over 5–10 years on seamounts where trawling had ceased. Some 

taxa had significantly higher abundance in later surveys. This may 

be because of their resistance to the direct effects of trawling, their 

protection in natural refuges, or because these taxa represent the 

earliest stages of seamount recolonisation. 

181 

Tuck et al. 

2009 

Tuck & Hewitt 


Tuck et al. 

2011 

Clark et al. 

2010a&b 

Williams et al. 

2011 

An expert based assessment of 65 threats to 62 marine habitats from saltmarsh to the abyss 

(MacDiarmid et al. 2012) concluded that only 7 of the 20 most important threats to New Zealand 

marine habitats were directly related to human activities within the marine environment. The most 

important of these was bottom trawling (ranked third equal most important), but invasive species, 

coastal engineering, and aquaculture were also ranked highly. However, the two top threats, five of 

the top six threats, and over half of the 26 top threats stemmed largely or completely from human 

activities external to the marine environment (the most important being ocean acidification, rising sea 

temperatures, and sedimentation resulting from changes in land-use). The assessment suggested that 

the number and severity of threats to marine habitats declines with depth, particularly deeper than 

about 50 m. Shallow coastal habitats face up to 52 non-trivial threats whereas most deep water 

habitats are threatened by fewer than five. Coastal and estuarine reef, sand, and mud habitats were 

considered to be the most threatened habitats whereas slope and deep water habitats were among the 

least threatened.

7.3.5. Current research 


Project BEN2007/01 is a 5-year project to assess the effects of fishing on soft sediment habitat, fauna, 

and processes across the range of habitat types in the TS and EEZ. Sampling and analytical strategies 

for such broad-scale assessments have been developed and the project has moved into a phase of data 

collection, collation, and analysis. Two field-based “case studies” in different habitat types will be 

assessed, and a variety of existing information will be drawn together and analysed to provide a TS & 

EEZ-wide perspective. The focus of this study is on the relative sensitivities of different habitats in 

the TS and EEZ to disturbance by mobile bottom fishing methods. 

Project DAE2010/04 provides for an annual assessment of the “footprint” of middle depth and 

deepwater trawl fisheries, including the overlap of the footprint with various depth ranges and habitat 

classes. Inshore fisheries, including shellfish dredge fisheries, are not covered under this project, so 

the focus is on offshore fisheries and habitats. 

Project DEE2010/05 provides for the development of a suite of ecosystem and environmental 

indicators for deepwater trawl fisheries. The focus of this study is on developing a cost-effective 

approach to monitoring ecosystem status (e.g., providing a mechanism to detect ocean climatic 

changes or regime shifts that could affect fisheries production) or the potential effects of deepwater 

trawl fisheries (such as changes to benthic invertebrate diversity). The suite could include information 

that may stem from project DEE2010/06 which provides for a desk-top assessment of the extent to 

which information can be collected cost-effectively on trends in benthic systems inside and outside of 

the trawled areas. 

Project BEN2012/01will use existing data and classifications to describe the distribution of benthic 

habitats, estimate the sensitivity to fishing disturbance of the species within these habitats, and then 

describe the spatial pattern of fishing using bottom trawls, Danish seine and dredges, to assess the 

overlap with each habitat class. 

Several MBIE-funded projects also have strong linkages with MPI research on benthic impacts. These 

include “Vulnerable Deep-Sea Communities” (CO1X0906) which is analysing the time series of data 

from the “Graveyard seamounts” (surveys in 2001, 2006, 2009, all carried out with support from 

MFish or the cross-departmental Oceans Survey 20/20 programme), as well as evaluating the relative 

vulnerability of benthic communities in several deep-sea habitats (e.g., seamounts, canyons, 

continental slope, hydrothermal vents, seeps) and their risk from bottom trawling. 

182


Annual number 

of tows 

Trend in 

number of tows 

Annual and 

cumulative (16 

year) overlap of 

BOMEC habitat 

classes up to 

2004/05 

This analysis 

will be updated 

for deepwater 

trawl fisheries 

in 2013 


2010/11 fishing year: 

86 024 trawl tows 

35 150 shellfish dredge tows 

Trawl effort stable, dredge effort decreasing: 

BOMEC 

class 

Total reported dredge tows 

Total reported trawls 

160,000 

140,000 

120,000 

100,000 

80,000 

60,000 

40,000 

20,000 

- 

200,000 

180,000 

160,000 

140,000 

120,000 

100,000 

80,000 

60,000 

40,000 

20,000 

Area 

(km 2 ) 

0 

1990 

1991 

1992 

1993 

1994 

1995 

1996 

1997 

1998 

1999 

2000 

2001 

2002 

2003 

2004 

2005 

2006 

2007 

2008 

2009 

2010 

2011 


183 

Fishing year 

TCER 

CELR 

TCEPR 

1990 

1991 

1992 

1993 

1994 

1995 

1996 

1997 

1998 

1999 

2000 

2001 

2002 

2003 

2004 

2005 

2006 

2007 

2008 

2009 

2010 

2011 


Min. annual 

footprint area 

(km 2 ) 

Fishing Year 

Max. annual 

footprint area 

(km 2 ) 

oysters 

scallops 

Cumulative (16 yr) 

proportion 

overlapped 

A* 27 557 121 4 026 0.42 

B* 12 420 40 484 0.19 

C* 89 710 4 271 11 374 0.58 

D* 27 268 377 1 602 0.30 

E* 60 990 4 046 7 108 0.40 

F 38 608 517 1 391 0.13 

G 6 342 132 833 0.34 

H 138 550 9 583 20 344 0.45 

I 52 224 5 511 18 016 0.70 

J 311 361 10 469 15 975 0.18 

K 1 290 - 2 0.01 

L 198 577 4 238 13 599 0.24 

M 233 825 895 4 390 0.06 

N 493 034 601 1 054 0.02 

O 935 315 2 28 0.00 

TS & EEZ 4 115 806 46 300 90 940 0.08 

* the trawl footprint and proportion overlapped in coastal classes A–E will be grossly underestimated because CELR data 

are excluded.



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186

AE&B Annual review: Ecosystem effects 

THEME 4: ECOSYSTEM EFFECTS 

187

AEBAR 2012: Ecosystem effects: NZ regional climate and oceanic setting 

8. New Zealand Climate and Oceanic Setting 

Scope of chapter Overview of primary productivity, oceanography, bentho-pelagic coupling 

and oceanic climate trends in the SW Pacific region. 

Area covered New Zealand regional setting 

Focal localities Pan New Zealand waters 

Key issues • Climate and oceanographic variability and change are of relevance to 

fisheries and the broader marine environment 

• Allows for improved understanding of the links between observed 

patterns and drivers of biological processes. 

Emerging issues • New Zealand’s oceanic climate is changing 

MPI Research 

(current) 

NZ Research 

(current) 

Links to Fisheries 

2030 and MPI’s 

Our Strategy 

Related issues 

and/or Chapters 

• Causal mechanisms that link the dynamics of a variable marine 

environment to variation in biological productivity, particularly of 

fisheries, are not well understood in New Zealand. 

• Need for improved understanding of the linkages between the pelagic and 

benthic environment (i.e., bentho-pelagic coupling). 

• The cumulative effects of ocean climate change and other anthropogenic 

stressors on aquatic ecosystems (productivity, structure and function) are 

likely to be high. 

• Some long-term trends in the marine environment are available at a 

national scale but are not reported. 

Growing recognition that stressors will act individually & interactively, 

confounding prediction of net effects of climate change 

Projects include ZBD2005-05: Long-term effects of climate variation and 

human impacts on the structure and functioning of New Zealand shelf 

ecosystems; ZBD2008-11 Predicting plankton biodiversity & productivity 

with ocean acidification; ZBD2009-13. Ocean acidification impact on key 

NZ molluscs; ZBD2010-40. Marine Environmental Monitoring Programme; 

ZBD2010-41 Deepsea fisheries habitat and ocean acidification. 

NIWA Coast & Oceans Centre, Climate Centre; University of Otago-NIWA 

shelf carbonate geochemistry & bryozoans; Munida time-series transect; 

Geomarine Services-foraminiferal record of human impact; Regional Council 

monitoring programmes; Statistics New Zealand Environmental Domain 

review. 

Environmental Outcome Objective 1; environmental principles of Fisheries 

2030; MPI’s “Our Strategy 2030”: two key stated focuses are to maximise 

export opportunities and improve sector productivity; increase sustainable 

resource use, and protect from biological risk. 

• Ocean related climate variability and change are predicted to have major 

implications for fishstock distributions and abundance, reproductive 

success, ecosystem goods and services, deepsea coral habitat and Habitats 

of Particular Significance to Fisheries Management, 

• A significant warming event occurred in the late 1990s 

• A regime shift to the negative phase of the IPO occurred in about 2000, 

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8.1. Context 

which is likely to result in fewer El Niño events for a 20–30 year period, 

i.e., less zonal westerly winds (already apparent compared to the 1980– 

2000 period) and increased temperatures; this is the first regime shift to 

occur since most of our fisheries monitoring time series have started (the 

previous shift was in the late 1970s), and will likely impact on fish 

productivity 

• New Zealand trends of increasing air and sea temperatures and ocean 

acidification are consistent with global trends. 

Climate and oceanographic conditions play an important role in driving the productivity of our oceans 

and the abundance and distribution of our fishstocks, and hence fisheries. A full analysis of trends in 

climate and oceanographic variables in New Zealand is given in Hurst et al. (2012) and is now being 

developed as an Ocean Climate Change Atlas for New Zealand waters (Boyd and Law.2011). 

New Zealand is essentially part of a large submerged continent (Figure 8.1). 

Figure 8.1: New Zealand land mass area 250,000 km 2 ; EEZ & territorial sea area (pink) 4,200,000 km 2 ; extended 

continental shelf extension area (light green) 1,700,000 km 2 ; Total area of marine jurisdiction 5,900,000 km 2 . The 

black line shows the boundary of the New Zealand EEZ, the yellow line indicates the extension to New Zealand’s 

legal continental shelf, and the red line the agreed Australia/New Zealand boundary under UNCLOS Article 76. 

Image courtesy of GNS. 

The territorial sea (TS extending from mean low water shore line to 12 nautical miles) and Exclusive 

Economic Zone (the EEZ, extending from 12 nautical miles to 200 miles offshore) and the extended 

continental shelf (ECS) combine to produce one of the largest areas of marine jurisdiction in the 

world, an area of almost 6 million square kilometres, (Figure 8.1). New Zealand waters straddle more 

than 25 degrees of latitude from 30º S in warm subtropical waters to 56º S in cooler, subantarctic 

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waters, and 28 degrees of longitude from 161º E in the Tasman Sea to 171º W in the west Pacific 

Ocean. New Zealand’s coastline, with its numerous embayments, is also long, with estimates ranging 

from 15,000 to 18,000 km, depending on the method used for measurement (Gordon et al. 2010). 

New Zealand lies across an active subduction zone in the western Pacific plate, tectonic activity and 

volcanism have resulted in a diverse and varied seascape within the EEZ. The undersea topography 

comprises a relatively narrow band of continental shelf down to 200 m water depth, extensive 

continental slope areas from 200 to 1000 m, extensive abyssal plains, submarine canyons and deep sea 

trenches, ridge systems and numerous seamounts and other underwater topographic features such as 

hills and knolls. There are three significant submarine plateaus, the Challenger Plateau, the Campbell 

Plateau in the subantarctic, and the Chatham Rise (Figure 8.2). 

Disturbance of current flow across the plateaus and around the New Zealand landmass gives rise to 

higher ocean productivity than might be expected, given New Zealand’s isolated location in the 

generally oligotrophic western Pacific Ocean (Figure 8.3). Higher ocean colour, reflecting higher 

levels of productivity, is typically found around the coast and to the east across the Chatham Rise 

(Figure 8.3; Pinkerton et al. 2005). The coastal waters and plateaus support a range of commercial 

shellfish and finfish fisheries from the shoreline to depths of about 1500 m. Seamounts, seamount 

chains and ridge structures in suitable depths provide additional localized areas of upwelling and 

increased productivity sometimes associated with commercial fisheries. 

Figure 8.2 Undersea topography of New Zealand (red shallow to blue deep). White dash line shows the EEZ 

boundary. Image courtesy of NIWA. 

. 

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Figure 8.3: SeaWIFS image showing elevated chlorophyll a (green) near New Zealand. Image courtesy of NOAA 

Both Figures 8.3 and 8.4 (left panel) show that the strongest chlorophyll a and ocean colour are 

associated with the coastal shelf around New Zealand and the Chatham Rise. Although remote 

sensing cannot readily distinguish between primary productivity (from phytoplankton) and sediments 

in freshwater runoff, so interpretation of the relative productivity levels inshore has to be made in 

conjunction with knowledge of river flow, it is clear that the Chatham Rise has the highest 

productivity levels in the region. Globally, New Zealand net primary productivity levels in the sea are 

higher compared with most of Australasia, but lower than most coastal upwelling systems around the 

world (Willis et al., 2007). 

Figure 8.4: Left panel: Ocean colour in the New Zealand region from satellite imagery. Red shows the highest 

intensity of ocean colour typically associated with higher primary productivity. Right panel: The relative 

concentrations of particulate organic carbon (POC) that reach the seafloor. Red shows the highest levels, which are 

likely to be associated with areas of enhanced benthic productivity (based on the model of Lutz et al. (2007)). Images 

courtesy of NIWA. 

Patterns in surface waters of primary productivity are mirrored to an extent in the amount of “energy” 

that sinks to the seafloor (Figure 8.4). This POC flux is based on a model which accounts for sinking 

rates of dead organisms and predation in the water column (Lutz et al. 2007). This is a potential 

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surrogate of benthic production, and indicates where bentho-pelagic coupling may be strong. Highest 

levels of POC flux match with surface productivity to a large extent, with coastal waters (including 

around the offshore islands) and the Chatham Rise having high estimated production. 

The Tasman Sea (west of New Zealand) is separated from the South Pacific Gyre by the New Zealand 

landmass (Figure 8.5). The South Pacific Western Boundary Current, the East Australian Current 

(EAC) flows down the east coast of Australia, before separating from the Australian landmass in a 

variable eddy field at about 31 or 32°S (Ridgway & Dunn 2003). The bulk of the separated flow 

crosses the Tasman Sea as the Tasman Front (Stanton 1981; Ridgway & Dunn 2003), before a portion 

of the flow attaches to New Zealand, flowing down the northeast coast as the East Auckland Current 

(Stanton et al. 1997). In the southern limit of the Tasman Sea is the Subtropical Front, which passes 

south of Tasmania and approaches New Zealand at the latitude of Fiordland (Stanton 1988), before 

diverting southward around New Zealand, and then northward up the southeast coast of New Zealand 

where it is locally called the Southland Front (Heath 1985; Chiswell 1996; Sutton 2003). 

Figure 8.5: Circulation around New Zealand. TF Tasman Front (large red arrows), WAUC West Auckland Current, 

EAUC East Auckland Current, NCE North Cape Eddy, ECE East Cape Eddy, ECC East Cape Current, WE 

Wairarapa Eddy, DC D’Urville Current, WC Westland Current, SC Southland Current, SF Southland Front, STW 

Subtropical Water, STF Subtropical Front (left diagonal hashed area), SAW Subantarctic Water, SAF Subantarctic 

Front (right diagonal hashed area), ACC Antarctic Circum-Polar Current, CSW Circum-Polar Surface Water, 

DWBC Deep Western Boundary Current (large purple arrows) (after Carter et al. 1998). 

The water in the eastern central Tasman Sea south of the Tasman Front, east of the influence of the 

EAC and north of the Subtropical Front is thought to be relatively quiescent. Ridgway & Dunne 

(2003) show eastward surface flow across the interior of the Tasman Sea sourced from the 

southernmost limit of the EAC, with the flow bifurcating around Challenger Plateau and, ultimately, 

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New Zealand. Reid’s (1986) analysis indicates that a small anticyclonic gyre exists in the western 

Tasman Sea at 1000–2500 m depth. This gyre is centred at about 35°S, 155°E on the offshore side of 

the EAC and west of Challenger Plateau. All indications are that the eastern Tasman region overlying 

Challenger Plateau is not very energetic. 

This is in contrast with the east coast of both the North and South Islands, and Cook Strait, which are 

highly energetic. Campbell Plateau waters are well mixed though nutrient limited (iron), leading to 

tight coupling between trophic levels (Bradford-Grieve et al. 2003). The Subtropical Front lies along 

the Chatham Rise and turbulence and upwelling results in relatively high primary productivity in the 

area. 


8.2.1. Sea temperature 

Sea surface temperature (SST), sea surface height (SSH), air temperature and ocean temperature to 

800m depth, all exhibit some correlation with each other over seasonal and inter-annual time scales 

(Hurst et al. 2012). Air temperatures have increased by about 1°C since 1900 (Figure 8.6). 

Figure 8.6: Annual time series in New Zealand. NOAA annual mean sea surface temperatures (blue line) 25 and 

NIWA’s seven-station annual mean air temperature composite series (red line), expressed as anomalies relative to the 

1971-2000 climatological average. Linear trends over the period 1909-2009, in °C/century, are noted under the graph. 

(Image Source Mullan et al. 2010) 

Although a linear trend has been fitted to the seven-station temperatures in Figure 8.6, the variations 

in temperature over time are not completely uniform. For example, a markedly large warming 

occurred through the periods 1940-1960 and 1990-2010. These higher frequency variations can be 

related to fluctuations in the prevailing north-south airflow across New Zealand (Mullan et al. 2010). 

Temperatures are higher in years with stronger northerly flow, and are lower in years with stronger 

southerly flow. One would expect this, since southerly flow transports cool air from the Southern 

Oceans up over New Zealand 

25 http://www.ncdc.noaa.gov/oa/climate/research/sst/ersstv3.php 

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The unusually steep warming in the 1940-1960 period is paralleled by an unusually large increase in 

northerly flow during this same period Mullan et al. (2010). On a longer timeframe, there has been a 

trend towards less northerly flow (more southerly) since about 1960 Mullan et al. (2010). However, 

New Zealand temperatures have continued to increase over this time, albeit at a reduced rate 

compared with earlier in the 20 th century. This is consistent with a warming of the whole region of the 

southwest Pacific within which New Zealand is situated (Mullan et al. 2010). 

Mullan et al. 2010 describe the pattern of warming in New Zealand as consistent with changes in sea 

surface temperature and prevailing winds. Their review shows enhanced rates of warming (in units of 

°C/decade) down the Australian coast and to the east of the North Island, and much lower rates of 

warming south and east of the South Island (Figure 8.7). 

Figure 8.7: Trends in sea surface temperature, in °C/decade over the period 1909-2009, calculated from the 

NOAA_ERSST_v3 data-set (provided by NOAA’s ESRL Physical Sciences Division, Boulder, Colorado, USA, from 

their web site at http://www.esrl.noaa.gov/psd/). The data values are on a 2° latitude-longitude grid. The box around 

New Zealand denotes the region used to produce the area-averaged sea temperatures plotted in Figure 2. (Image 

Source Mullan et al. 2010.) 

Figure 8.8 gives a broader spatial picture at much higher resolution (but a shorter period, since 1982). 

It is apparent that sea temperatures are increasing north of about 45°S; they are increasing more 

slowly, and actually decreasing in recent decades, off the Otago coast and south of New Zealand. This 

regional pattern of cooling (or only slow warming) to the south, and strong warming in the Tasman 

and western Pacific can be related to increasing westerly winds and their effect on ocean circulation 

Mullan et al. (2010). Thompson and Solomon (2002) discuss the increase in Southern Hemisphere 

westerlies and the relationship to global warming; Roemmich et al. (2007) describe recent ocean 

circulation changes; Thompson et al. (2009) discuss the consequent effect on sea surface temperatures 

in the Tasman Sea. 

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Figure 8.8: Trends in sea surface temperature, in °C/decade over the period 1982-2009. The data are again taken 

from NOAA, but are based on daily interpolated satellite measurements over a much finer 0.25° grid. See 

http://www.ncdc.noaa.gov/oa/climate/research/sst/oi-daily.php. This product is the result of an objective analysis, an 

optimum interpolation rather than a pure satellite retrieval, so as to correct for issues like the effect of the Mt 

Pinatubo eruption aerosols on satellite detected radiances. It is described in Reynolds et al. (2007) 

Sea surface temperatures (SST) derived from satellite data have been compared to empirical CTD 

measurements made from relevant sub-areas of the Chatham Rise and Sub-Antarctic during trawl 

surveys. This showed good correlations, reassuring us that satellite-derived SST provided a realistic 

measure of sea surface temperature for these regions in years before CTD data were available 

O’Driscoll et al. 2011). 

Coastal SST data, particularly the longer time series from Leigh and Portobello, have been used in 

studies attempting to link processes in the marine environment with temperature. The negative 

relationship between SST and SOI is broadly consistent across the 40 years of data although the 

pattern is less clear post 1997 (Figure 8.9). The clearest fisheries example of a link between coastal 

SST and fish recruitment and growth is for northern stocks of snapper (Pagras auratus), where 

relatively high recruitment and faster growth rates have been correlated with warmer conditions from 

the Leigh SST series (Francis 1993, 1994a). 

Figure 8.9: Sea surface temperature (SST) anomolies from SST measurements at Leigh (Auckland University Marine 

Laboratory) and Southern Oscillation Index (SOI) anomalies. (Image from Hurst et al 2012.) 

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Temperature fluctuations also occur at depth in the ocean as demonstrated by changes in temperature 

down to 800 m in the eastern Tasman Sea between 1992 and 2008 (Figure 8.10). 

The ocean temperature between Sydney and Wellington has been sampled about four times per year 

since 1991. The measurements are made in collaboration with the Scripps Institution of 

Oceanography. Analyses of the subsurface temperature field using these data include Sutton & 

Roemmich (2001) and Sutton et al. (2005). The index presented for this transect (Figure 8.10) is for 

the most eastern section closest to New Zealand (161.5°E and 172°E). The eastern Tasman is chosen 

because it is closer to New Zealand, and because it has less oceanographic variability which can mask 

subtle interannual changes. The section of the transect shown is along fairly constant latitude is 

therefore unaffected by latitudinal temperature and seasonal cycle variation. The upper panel shows 

the temperature averaged along the transect between the surface and 800m and from 1991 to the most 

recent sampling. 

Figure 8.10: Eastern Tasman ocean temperature: Wellington to Sydney 1991–2008. Coloured scale to the right is 

temperature °C. (Image from Hurst et al. 2012, after Sutton et al. 2005) 

The seasonal cycle is clearly visible in the upper 100–150m. There is a more subtle warming signal 

that occurred through the late 1990s, which is apparent by the isotherms increasing in depth through 

that time period. This warming was significant in that it extended to the full 800m of the 

measurements (effectively the full depth of the eastern Tasman Sea). It also began during an El Niño, 

period when conditions would be expected to be cool. Finally, it was thought to be linked to a largescale 

warming event centred on 40°S that had hemispheric and perhaps global implications. This 

warming has been discussed by Sutton et al. (2005) who examined the local signals, Bowen et al. 

(2006) who studied the propagation of the signal into the New Zealand area, and Roemmich et al. 

(2007), who examined the broad-scale signal over the entire South Pacific Ocean. Roemmich et al. 

(2007) hypothesized that the ultimate forcing was due to an increase in high latitude westerly winds 

effectively speeding up the entire South Pacific gyre. 

Other phenomena have led to periods of warming that are not as yet fully understood. In particular a 

period of widespread warming in the Tasman Sea to depths of at least 800 m, 1996–2002 (Sutton et 

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al. 2005). Both stochastic environmental variability and predictable cycles of change influence the 

productivity and distribution of marine biota in our region. 

8.2.2. Climate variables 

The Interdecadal Pacific Oscillation (IPO) is a Pacific-wide reorganisation of the heat content of the 

upper ocean and represents large-scale, decadal temperature variability, with changes in phase (or 

“regime shifts”) over 10–30 year time scales. In the past 100 years, regime shifts occurred in 1925, 

1947, 1977 and 2000 (Figure 8.11). The latest shift should result in New Zealand experiencing 

periods of reduced westerlies, with associated warmer air and sea temperatures and reduced upwelling 

on western coasts (Hurst et al. 2012). 

Figure 8.11: Smoothed index of the Interdecadal Pacific Oscillation (IPO) since 1900. (Image source NIWA based on 

data from the United Kingdom Meteorological Office, UKMO). 

The El Niño-Southern Oscillation (ENSO) cycle in the tropical Pacific has a strong influence on New 

Zealand. ENSO is described here by the Southern Oscillation Index (SOI), a measure of the difference 

in mean sea-level pressure between Tahiti (east Pacific) and Darwin (west Pacific). When the SOI is 

strongly positive, a La Niña event is taking place and New Zealand tends to experience more north 

easterlies, reduced westerly winds, and milder, more settled, warmer anticyclonic weather and warmer 

sea temperatures (Hurst et al. 2012). When the SOI is strongly negative, an El Niño event is taking 

place and New Zealand tends to experience increased westerly and south-westerly winds and cooler, 

less settled weather and enhanced along shelf upwelling off the west coast South Island and north east 

North Island (Shirtcliffe 1990, Zeldis et al. 2004, Chang & Mullan 2003). The SOI is available 

monthly from 1876 (Mullan 1995) (Figure 8.12). 

Figure 8.12: Southern Oscillation Index (SOI) 13-month running mean 1876-2010. Red indicates warmer 

temperatures, blue indicates cooler conditions for New Zealand. (Image courtesy of NIWA.) 

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8.2.3. Ocean acidification 

An increase in atmospheric CO2 since the industrial revolution has been paralleled by an increase in 

CO2 concentrations in the upper ocean (Sabine et al. 2004), with global ocean uptake on the order of 

~2 gigatonnes (Gt) per annum (~30% of global anthropogenic emissions, IPCC, 2001a). The 

anthropogenic CO2 signal is apparent to an average depth of ~1000m. 

The increasing rate of CO2 input from the atmosphere has surpassed the ocean’s natural buffering 

capacity and so the surface of the ocean ocean is becoming more acidic. This is because carbon 

dioxide absorbed by seawater reacts with H2O to form carbonic acid, the dissociation of which 

releases hydrogen ions, so raising the acidity and lowering pH of seawater. Since1850, average 

surface ocean pH has decreased by 0.1 units, with a further decrease of 0.4 units to 7.9 predicted by 

2100 (Houghton et al, 2001). The pH scale is logarithmic, so a 0.4 pH decrease corresponds to a 

150% increase in hydrogen ion concentration. Both the predicted pH in 2100 and the rate of change in 

pH are outside the range experienced by the oceans for at least half a million years. In the absence of 

any decrease in CO2 emissions this trend is proposed by Caldeira & Wickett, (2003) to continue. 

In New Zealand, the projected change in surface water pH between 1990 and 2070 is a decrease of 

0.15-0.18 pH units (Hobday et al. 2006). The only time series of dissolved pCO2 and pH in NZ 

waters is the bimonthly sampling of a transect across neritic, subtropical and subantarctic waters off 

the Otago shelf since 1998 (University of Otago/NIWA Munida Otago Shelf Time Series). Dissolved 

pCO2shows some indication of an increase although this is not linear and does not correlate with rise 

in atmospheric CO2 (see Fig 8.13). 

Figure 8.13: pCO 2 (partial pressure of CO 2) in subantarctic surface seawater from the R.V. Munida transect, 1998– 

2012. (Image courtesy of K. Currie, NIWA) 

The Munida time-series pH data shows a decline in subantarctic surface waters since 1998 (Fig 8.14). 

Addition of a sine-wave function to the pH data suggests a) a linear decline in surface water pH and b) 

that winter time pH values are consistent with that expected from equilibrium with atmospheric CO2 

as recorded at the NIWA Baring Head atmospheric station (K. Hunter (U. Otago) & K. Currie 

(NIWA), pers comm.). The oscillations are primarily due to seasonal changes in water temperature 

and biological removal of dissolved carbon in the seawater. The time series sampling period is 

currently too short to distinguish long-term changes from seasonal and interannual variability, and it is 

not yet possible to attribute observed changes to uptake of anthropogenic carbon dioxide. 

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Figure 8.14: pH in Sub- Antarctic surface seawater on the R.V. Munida transect, 1998–2006. The blue points and 

joining lines are the actual measurements, and the red line a best fit to the points using a sine wave function (to 

represent seasonal change). The black line represents what pH assuming equilibrium with the atmosphere 

concentration in the Year 1750. The yellow line is the pH assuming equilibrium with actual CO2 concentrations 

measured at the NIWA Baring Head Atmospheric Station. pH 25 is the pH measured at 25 o C (Image Source: A 

Southern Hemisphere Time Series for CO2 Chemistry and pH K. Hunter, K.C. Currie, M.R. Reid, H. Doyle. A 

presentation made at the International Union of Geodesy and Geophysics (IUGG) General Assembly Meeting, 

Melbourne June 2011.) 

Globally, open ocean seawater pH shows relatively low spatial and temporal variability, compared to 

coastal waters where pH may vary by up to 1 unit in response to precipitation, biological activity in 

the seawater and sediment and other coastal processes. Surface pH in the open ocean has been 

determined on a monthly basis at the BATS (Bermuda Time Series Station) in the North Atlantic 

since 1983 (Bates 2001, 2007), and at HOT (Hawaiit Time Series Station) in the North Pacific since 

1988 (Brix et al. 2004, Dore et al. 2009). Both time series records show long term trends of increasing 

pCO2 (partial pressure of CO2) and decreasing pH, with the pCO2 increasing at a rate of 1.25 μatm per 

year, and pH decreasing by 0.0012 pH units per annum since 1983 at Bermuda (Figure 8.15). Placed 

in the context of these longer time series of atmospheric CO2 measurements, the short record of the 

Munida SubAntarctic Water time series shows pCO2 and pH in surface seawater tracking the 

atmospheric CO2 (Figure 8.14). In addition, the regional means of seawater pH differ significantly 

with temperature, with the South Pacific at the lower end (Feely et al 2009). 

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Figure 8.15: Time series of atmospheric carbon dioxide at Moana Loa, seawater carbon dioxide and surface ocean pH 

at Ocean station ALOHA in the subtropical North Pacific Ocean near Hawaii. pH is shown as in situ pH, based on 

direct measurements and calculated from dissolved inorganic carbon and alkalinity in the surface layer (after Dore et 

al. 2009). (Image directly sourced from Feely et al. 2009 with permission.) 

Biological implications of ocean acidification result from increasing dissolved pCO2, increasing 

hydrogen ions (decreasing pH) and decreasing carbonate availability. The concern about ocean 

acidification is that the resulting reduction in carbonate availability may potentially impact organisms 

that produce shells or body structures of calcium carbonate, resulting in a redistribution of an 

organism’s metabolic activity and increased physiological stress. Organisms most likely to be affected 

are those at the base of the food chain (bacteria, protozoa, plankton), coralline algae, rhodoliths, 

shallow and deepwater corals, echinoderms, molluscs, and possibly cephalopods (e.g., squids) and 

high-activity pelagic fish (e.g., tunas) (see Feely et al. 2004 and references therein; Orr et al. 2005, 

Langer et al. 2007). This is particularly of concern for deep-sea habitats such as seamounts, which can 

support structural reef-like habitat composed of stony corals (Tracey et al. 2011) as well as 

commercial fisheries for species such as orange roughy (Clark 1999). A shoaling carbonate saturation 

horizon could push such biogenic structures to the tops of seamounts, or cause widespread die-back 

(e.g., Thresher et al. 2012). This has important implications for the structure and function of benthic 

communities, and perhaps also for the deep-sea ecosystems that support New Zealand’s key 

deepwater fisheries. Conversely some groups, including phytoplankton and sea-grass, may benefit 

from the increase in dissolved pCO2 due to increased photosynthesis. 

Direct effects of acidification on the physiology and development of fish have also been investigated. 

This has particularly focussed on the freshwater stages of salmonids (due to the widespread 

occurrence of pollution-derived acid rain) but increasingly in marine fish, where adverse effects on 

physiology development have been documented (e.g. Franke, and Clemmesen, 2011). Such studies 

highlight the potential for increasing acidification to impact larval growth and development, with 

implications for survival and recruitment of both forage fish and fish harvested commercially. 

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8.3. Ocean climate trends and New Zealand fisheries 

This section has been quoted almost directly from the summary in Hurst et al. (2012). Some general 

observations on recent trends in some of the key ocean climate indices that have been found to be 

correlated with a variety of biological processes among fish (including recruitment fluctuations, 

growth, distribution, productivity and catch rates) are: 

The Interdecadal Pacific Oscillation (IPO): available from 1900; time scale 10–30 years. The IPO 

has been found to have been correlated with decadal changes (‘regime shifts’) in northeast Pacific 

ecosystems (e.g., Alaska salmon catches). In the New Zealand region, there is evidence of a 

regime shift into the negative phase of the IPO in about 2000. During the positive phase, from the 

late 1970’s to 2000, New Zealand experienced periods of enhanced westerlies, with associated 

cooler air and sea temperatures and enhanced upwelling on western coasts. Opposite patterns are 

expected under a negative phase. For most New Zealand fisheries, monitoring of changes in 

populations began since the late 1970’s, so there is little information on how New Zealand 

fishstocks might respond to these longer-term climatic fluctuations. Some of the recent changes in 

fish populations since the mid 1990s, for example, low western stock hoki recruitment indices 

(Francis 2009) and increases in some elasmobranch abundance indices (Dunn et al. 2009) may be 

shorter-term fluctuations that might be related in some way to regional warming during the period 

and only longer-term monitoring will establish whether they might be related to longer-term 

ecosystem changes. 

The Southern Oscillation Index: available from 1876; best represented as annual means. Causal 

relationships of correlations of SOI with fisheries processes are poorly understood but probably 

related in some way to one or more of the underlying ocean climate processes such as winds or 

temperatures. When the index is strongly negative, an El Niño event is taking place and New 

Zealand tends to experience increased westerly and south-westerly winds, cooler sea surface 

temperatures and enhanced upwelling in some areas (see, for example, the correlation of monthly 

SST at Leigh and SOI indices, Figure 8.13). Upwelling has been found to be related to increased 

nutrient flux and phytoplankton growth in areas such as the west coast South Island, Pelorus 

Sound and north-east coast of the North Island (Willis et al. 2007, Zeldis et al. 2008). El Niño 

events are likely to occur on 3–7 year time scales and are likely to be less frequent during the 

negative phase of the IPO which began in about 2000. This is likely to impact positively on 

species that show stronger recruitment under increased temperature regimes (e.g., snapper, 

Francis 1993, 1994a, b). 

Surface wind and pressure patterns: available from 1940s; variation in patterns can be high over 

monthly and annual time scales and many of the indices are correlated with each other, and with 

SOI and IPO indices (e.g., more zonal westerly winds, more frequent or regular cycles in 

southerlies in the positive IPO, 1977–2000). Correlations with biological process in fish stocks 

may occur over short time scales (e.g., impact on fish catchability) as well as seasonal and annual 

scales (e.g., impact on recruitment success). Wind and pressure patterns have been found to be 

correlated with fish abundance indices for southern gemfish (Renwick et al. 1998), hake, red cod 

and red gurnard (Dunn et al. 2008), rock lobster (Booth et al. 2000), and southern blue whiting 

(Willis et al. 2007, Hanchet & Renwick, 1999). Causal relationships of these correlations are 

poorly understood but can be factored into hypothesis testing as wind and pressure patterns affect 

surface ocean conditions through heat flux, upwelling and nutrient availability on exposed coasts. 

Temperature and sea surface height: available at least monthly over long time scales (air 

temperatures from 1906) or relatively short time scales (ocean temperatures to 800m, SST and 

SSH variously from 1987). Ocean temperatures, SST and SSH are all correlated with each other 

and smoothed air temperatures correlate well with SST in terms of interannual and seasonal 

variability; there are also some correlations of SST and SSH with surface wind and pressure 

patterns (see Dunn et al. 2009). SST has been found to be correlated with relative fish abundance 

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indices (derived from fisheries and/or trawl surveys) for elephantfish, southern gemfish, hoki, red 

cod, red gurnard, school shark, snapper, stargazer and tarakihi (Francis 1994a,b, Renwick et al 

1998, Beentjes & Renwick 2001, Gilbert & Taylor 2001, Dunn et al 2009). Air temperatures in 

New Zealand have increased since 1900; most of the increase occurred since the mid 1940s. 

Increases from the late 1970s to 2000 may have been moderated by the positive phase of the IPO. 

Coastal SST records from 1954 (at Portobello) also show a slight increase through the series and, 

in general, show strong correlations with SOI (i.e., cooler temperatures in El Niño years). Other 

time series (SSH, ocean temperature to 800m) are comparatively short but show cycles of warmer 

and cooler periods on 1–6 year time scales. All air and ocean temperature series show the 

significant warming event during the late 1990s which has been followed by some cooling, but 

not to the levels of the early 1990s. 

Ocean colour and upwelling: these will be important time series because they potentially have a 

more direct link to biological processes in the ocean and are more easily incorporated into 

hypothesis testing. The ocean colour series starts in late 1997, so is not able to track changes that 

may have occurred since before the late 1990s warming cycle. These indices also need to be 

analysed with respect to SST, SSH and wind patterns, at similar locations or on similar spatial 

scales. The preliminary series developed exhibit some important spatial differences and trends 

that may warrant further investigation in relation to fish abundance indices. Of note are the 

increased chlorophyll indices off the west and south-west coast of the South Island in 

spring/summer during the last 5–6 years and the relatively low upwelling indices off the west 

coast South Island during winter in the late-1990s (Hurst et al. 2012). 

Currents: there are no general indices of trends or variability at present. Improvements in 

monitoring technology (e.g., satellite observations of SSH; CTD; ADCP; ARGO floats) have 

resulted in more information becoming available to enable numerical models of ocean currents to 

be developed. On the open ocean scale, there is considerable complexity in the New Zealand zone 

(e.g., frontal systems, eddy systems of the east coast). In the coastal zone, this is further 

complicated in coastal areas by the effects of tides, winds and freshwater (river) forcing, and a 

more limited monitoring capability. Nevertheless, the importance of current systems is starting to 

become more recognised and incorporated into analysis and modelling of fisheries processes and 

trends. Recent examples include the retention of rock lobster phyllosoma (mid-stage larvae) in 

eddy systems (Chiswell & Booth 2005, 2007), the apparent bounding of orange roughy nursery 

grounds by the presence of a cold-water front (Dunn et al. 2009) and the drift of toothfish eggs 

and larvae (Hanchet et al. 2008). 

Acidification: The increase in atmospheric CO2 has been paralleled by an increase in CO2 

concentrations in the upper ocean, resulting in a decrease in pH. Maintenance of the one existing 

New Zealand monitoring programme for pH and pCO2, and development of new programmes to 

monitor the impacts of pH on key groups of organisms are critical. Potentially vulnerable groups 

include organisms that produce shells or body structures of calcium carbonate (corals, molluscs, 

plankton, coralline algae), and also non-calcifying groups including plankton, squid and highactivity 

pelagic fishes. Potentially positive impacts of acidification include increased 

phytoplankton carbon fixation and vertical export and increased productivity of sub-tropical 

waters due to enhanced nitrogen fixation by cyanobacteria. Secondary effects at the ecosystem 

level, such as productivity, biomass, community composition and biogeochemical feedbacks, also 

need to be considered. 

Climate change was not specifically addressed as part of the report by Hurst et al. (2012), although 

indices described are an integral part of monitoring the speed and impacts of climate change. As noted 

under the air temperature section, the slightly increasing trend in temperatures since the mid 1940s is 

likely to have been moderated by the positive phase of the IPO, from the late 1970s to the late 1990s. 

With the shift to a negative phase of the IPO in 2000, it is likely that temperatures will increase more 

steeply. Continued monitoring of the ocean environment and response is critical. This includes not 

only the impacts on productivity, at all levels, but also on increasing ocean acidification. 

202


For the New Zealand region, key ocean climate drivers in the last decade have been: 

• the significant warming event in the late 1990s 

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fewer El Niño events for a 20–30 year period, i.e., less zonal westerly winds (already apparent 

compared to the 1980–2000 period) and increased temperatures; this is the first regime shift 

to occur since most of our fisheries monitoring time series have started (the previous shift was 

in the late 1970s), and 

• global trends of increasing air and sea temperatures and ocean acidification. 


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AEBAR 2012: Ecosystem effects: Habitats of particular significance to fisheries management 

9. Habitats of particular significance for fisheries 

management 

Scope of chapter This chapter highlights subject areas that might contribute to the management 

of HPSFM and hence provides a guide for future research in the absence of 

an approved policy definition of HPSFM 

Area All of the New Zealand EEZ and territorial sea (inclusive of the freshwater 

and estuarine areas). 

Locality hotspots None formally defined, but already identified likely candidates include areas 

of biogenic habitat, e.g. Separation Point and Wairoa Hard, and areas 

identified with large catches and/or vulnerable populations of juveniles, e.g. 

Hoki Management Areas, packhorse crayfish legislated closures and toheroa 

beaches. 

Key issues Defining and identifying likely HPSFM and potential threats to them. 

Emerging issues Connectivity and intra-population behaviour variability, multiple use 

MPI Research 

(current) 

NZ Government 


Links to 2030 

objectives 

Related 


9.1. Context 

Biogenic habitats as areas of particular significance for fisheries management 

(HAB2007/01), Toheroa abundance (TOH2007/03), Research on Biogenic 

Habitat-Forming Biota and their functional role in maintaining Biodiversity 

in the Inshore Region (5-150M Depths) (ZBD2008/01 – this is also partfunded 

by Oceans Survey 2020, NIWA and MBIE) , Habitats of particular 

significance for fisheries management: Kaipara Harbour (ENV2009/07), 

Habitats of particular significance for inshorefinfish fisheries management 

(ENV2010/03) Spatial Mixing of GMU1 using Otolith Microchemistry 

(GMU2009/01). 

Ministry of Business, Innovation and Employment (MBIE) funded 

programmes (Coastal Conservation Management: protecting the functions of 

marine coastal habitats that support fish assemblages at local, regional and 

national scales (C01X0907) Predicting the occurrence of vulnerable marine 

ecosystems for planning spatial management in the South Pacific region 

(C01X1229) and Impacts of resource use on vulnerable deep-sea 

communities (C01X0906). 

NIWA Core funding in the ’Managing marine stressors’ area under the 

’Coasts and Oceans’ centre, specifically the programme ’Managing marine 

resources’ and the project ’Measuring mapping and conserving (C01X0505)’ 

Under the Environment Outcome habitats of special significance to fisheries 

need to be protected. 

Land-based impacts on fisheries and supporting biodiversity, bycatch 

composition, marine environmental monitoring. 

The Fisheries Act 1996, in Section 9 (Environmental principles) states that: 

“All persons exercising or performing functions, duties, or powers under this Act, in 

relation to the utilisation of fisheries resources or ensuring sustainability, shall take 

into account the following environmental principles: 

(a) Associated or dependent species should be maintained above a level that ensures 

their long-term viability: 

(b) Biological diversity of the aquatic environment should be maintained: 

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(c) Habitat of particular significance for fisheries management should be 

protected.” 

No policy definition of habitat of particular significance for fisheries management (HPSFM) exists, 

although work is currently underway to generate one. Some guidance in terms of defining HPSFM is 

provided by Fisheries 2030 which specifies as an objective under the Environment Outcome that 

“habitats of special significance to fisheries are protected”. This wording suggests that a specific 

focus on habitats that are important for fisheries production should be taken rather than a more 

general focus that might also include other habitats that may be affected by fishing. 

Fisheries 2030 re-emphasises that HPSFM should be protected. No specific strategic actions are 

proposed to implement this protection in Fisheries 2030; although action 6.1 “To implement a revised 

MPA policy and legal framework” could potentially be relevant to protecting HPSFM. The 

management of activities other than fishing, such as land-use and vehicle traffic, are outside the 

control of the Ministry for Primary Industries but Fisheries 2030 specifies actions to “Improve 

fisheries sector input to processes that manage RMA-controlled effects on the marine and freshwater 

environment” (Action 8.1) and to “Promote the development and use of RMA national policy 

statements, environmental standards, and regional coastal and freshwater plans” (Action 8.2). This 

suggests that the cooperation of other parties outside of the fisheries sector may be necessary in some 

cases to protect HPSFM. 

In the absence of a policy definition of HPSFM this chapter will focus on examples of habitats shown 

to be important for fisheries and concepts likely to be important to HPSFM. Examples of potential 

HPSFM include: sources of larvae; larval settlement sites; habitat for juveniles; habitat that supports 

important prey species; migration corridors; and spawning, pupping or egg-laying grounds. Some of 

these habitats may be important for only part of the life cycle of an organism, or for part of a year. 

The location or relative importance of habitats, compared with other limiting factors, is largely 

unknown for most stocks. For example, some stocks may be primarily habitat limited, whereas others 

may be limited by oceanographic variability, food supply, predation rates (especially during juvenile 

phases), or a mixture of these and other factors. In the case of stocks that are habitat limited, a 

management goal might be to preserve or improve some aspect of the habitat for the stock. 

Hundreds of legislated spatial fisheries restrictions already apply within New Zealand’s territorial sea 

and exclusive economic zone (www.nabis.govt.nz), but until further policy work and research is 

conducted we cannot be sure the contribution they make to protecting HPSFM. Examples of these are 

listed below: 

• Separation Point in Tasman Bay, and the Wairoa Hard in Hawke Bay, were created to protect 

biogenic habitat which was believed to be important as juvenile habitat for a variety of fish 

species (Grange et al. 2003). 

• An area near North Cape is currently closed to packhorse lobster fishing to mitigate sub-legal 

handling disturbance in this area. This closure was established because of the small size of 

lobsters caught there and a tagging study that showed movement away from this area into 

nearby fished areas (Booth 1979). 

• The largest legislated closure are the Benthic Protection Areas (BPAs) which protect ~ 1.2 

million square km (about 31% of the EEZ) outside the territorial sea from contact of trawl 

and dredge gear with the bottom (Helson et al. 2010). 

• Commercial fishers must not use New Zealand fishing vessels or foreign-owned New Zealand 

fishing vessels over 46 m in overall length for trawling in the territorial sea. 

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In addition to legislated closures, a number of non-regulatory management measures exist. For 

example: 

• Spatial closures 

o Trawlers greater than 28 m in length are excluded from targeting hoki in four Hoki 

Management Areas – Cook Strait, Canterbury Banks, Mernoo Bank, and Puysegur 

Bank (DeepWater Group 2008). These areas were chosen because of the larger 

number of juveniles caught, relative to adults in these areas. 

o Trawling and pair trawling are both closed around Kapiti Island 

• Seasonal closures 

o A closure to trawling exists from November the first until the 30 th of April each year 

in Tasman Bay. 

o A closure to commercial potting exists for all of CRA3 for the whole of the month of 

December each year. 

The high-level objectives and actions in Fisheries 2030 have been interpreted in the highly migratory, 

deepwater and middle-depths (deepwater) inshore national fish plans. The highly migratory fish plan 

addresses HPSFM in environment outcome 8.1 “Identify and where appropriate protect habitats of 

particular significance to highly migratory species, especially within New Zealand waters”. In the 

deepwater fish plan the Ministry proposes in management objective 2.3 “to develop policy guidelines 

to determine what constitutes HPSFM then apply these policy guidelines to fisheries where 

necessary”. Inshore fisheries management plans (freshwater, shellfish and finfish) all contain 

references to identifying and managing HPSFM. These plans recognise that not all impacts stem from 

fisheries activities, therefore managing them may include trying to influence others to better manage 

their impacts on HPSFM. Work is underway on a policy definition of HPSFM that will assist 

implementing these outcomes and objectives. 


This section focuses upon those habitats protected overseas for their value to fisheries and discusses 

important concepts that may help gauge the importance of any particular habitat to fisheries 

management. This information may guide future research into HPSFM in New Zealand and any 

subsequent management action. 

9.2.1. Habitats protected elsewhere for fisheries management 

Certain habitats have been identified as important for marine species: shallow sea grass meadows, 

wetlands, seaweed beds, rivers, estuaries, rhodolith beds, rocky reefs, crevices, boulders, bryozoans, 

submarine canyons, seamounts, coral reefs, shell beds and shallow bays or inlets (Kamenos et al. 

2004; Caddy 2008, Clark 1999, Morato et al. 2010). Discrete habitats (or parts of these) may have 

extremely important ecological functions, and/or be especially vulnerable to degradation. For 

example, seabeds with high roughness are important for many fisheries and can be easily damaged by 

interaction with fishing gear (Caddy 2008). Examples of these include: 

1. The Oculina coral banks off Florida were protected in 1994 as an experimental reserve in 

response to their perceived importance for reef fish populations (Rosenberg et al. 2000). Later 

studies confirmed that this area is the only spawning aggregation site for gag (Mycteroperca 

microlepis) and scamp (M. phenax) (both groper species), and other economically important 

reef fish in that region (Koenig et al. 2000). The size of the area within which bottom-tending 

gears were restricted was subsequently increased based on these findings (Rosenberg et al. 

2000). 

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2. Lophelia cold-water coral reefs are now protected in at least Norway (Fosså et al. 2002), 

Sweden (Lundälv, & Jonsson 2003) and the United Kingdom (European Commission 2003) 

due to their importance as habitat for many species of fish (Costello et al. 2005). 

3. The Western Pacific Regional Fishery Management Council identified all escarpments between 

40 m and 280 m as Habitat Areas of Particular Concern (HAPC) for species in the bottom-fish 

assemblage. The water column to a depth of 1000 m above all shallow seamounts and banks 

was categorised as HAPC for pelagic species. Certain northwest Hawaiian Island banks 

shallower than 30 m were categorised as HAPC for crustaceans, and certain Hawaiian Island 

banks shallower than 30 m were classified as Essential Fish Habitat (EFH) for precious corals. 

Fishing is closely regulated in the precious-coral EFH, and harvest is only allowed with highly 

selective gear types which limit impacts, such as manned and unmanned submersibles (West 

Pacific Fisheries Management Council 1998) 

Examples of habitats protected for their freshwater fishery values also exist. For example, the U.S. 

Atlantic States Interstate fishery management plan (Atlantic States Marine Fisheries Commission 

2000) notes the Sargasso Sea is important for spawning, and that seaweed harvesting provides a threat 

of unknown magnitude to eel spawning. Habitat alteration and destruction are also listed as probably 

impacting on continental shelves and estuaries/rivers, respectively, but the extent to which these are 

important is unknown. 

It is also possible that HPSFM may be defined by the functional importance of an area to the fishery. 

For example, large spawning aggregations can happen in mid-water for set periods of time 

(Schumacher and Kendall 1991, Livingston 1990) these could also potentially qualify as HPSFM. 

9.2.2. Concepts potentially important for HPSFM 

Many nations are now moving towards formalised habitat classifications for their coastal and ocean 

waters, which may include fish dynamics as part of their structure, and could potentially help to 

define HPSFM. Such systems help provide formal definitions for management purposes, and to ‘rank’ 

habitats in terms of their relative values and vulnerability to threats. Examples include the Essential 

Fish Habitat (EFH) framework being advanced in North America (Benaka 1999, Diaz et al. 2004, 

Valavanis et al. 2008), and in terms of habitat, the developing NOAA Coastal and Marine Ecological 

Classification Standard for North America (CMECS) (Madden et al. 2005, Keefer et al. 2008), and 

the European Marine Life Information Network (MarLIN) framework which has developed habitat 

classification and sensitivity definitions and rankings (Hiscock and Tyler-Walters 2006). 

Habitat connectivity (the movement of species between habitats) operates across a range of spatial 

scales, and is a rapidly developing area in the understanding of fisheries stocks. These movements 

link together different habitats into ‘habitat chains’, which may also include ‘habitat bottlenecks’, 

where one or more spatially restricted habitats may act to constrain overall fish production (Werner et 

al. 1984). Human driven degradation or loss of such bottleneck habitats may strongly reduce the 

overall productivity of populations, and hence ultimately reduce long-term sustainable fisheries 

yields. The most widely studied of these links is between juvenile nursery habitats and often spatially 

distant adult population areas. Most studies published have been focussed on species that uses 

estuaries as juveniles; e.g. blue grouper Achoerodus viridis (a large wrasse) (Gillanders and Kingsford 

1996) and snapper Pagrus auratus (Hamer et al. 2005) in Australia; and gag (Mycteroperca- 

Microlepis) in the United States (Ross and Moser 1995) which make unidirectional ontogenetic 

habitat shifts from estuaries and bays out to the open coast as they grow from juveniles to adults. The 

extent of wetland habitats in the Gulf of Mexico has also been linked to the yield of fishery species 

dependent on coastal bays and estuaries. Reduced fishery stock production (shrimp and menhaden (a 

fish)) followed wetland losses and, conversely, stock gains followed increases in the area of wetlands 

(Turner and Boesch 1987). Juvenile production was limited by the amount of available habitat but, 

equally, reproduction, larval settlement, juvenile or adult survivorship, or other demographic factors 

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could also be limited by habitat loss or degradation, and these could have knock-on effects to stock 

characteristics such as productivity and its variability. Other examples include movements which may 

be bidirectional and regular in nature e.g., seasonal migrations of adult fish to and from spawning 

and/or feeding grounds, e.g. grey mullet Mugil cephalus off Taiwan (Chang et al. 2004). 

How habitats are spatially configured to each other is also important to fish usage and associated 

fisheries production. For example, Nagelkerken et al. (2001) showed that the presence of mangroves 

in tropical systems significantly increases species richness and abundance of fish assemblages in 

adjacent seagrass beds. Jelbart et al. (2007) sampled Australian temperate seagrass beds close to 

(< 200 m) and distant from (> 500 m) mangroves. They found seagrass beds closer to mangroves had 

greater fish densities and diversities than more distant beds, especially for juveniles. Conversely, the 

densities of fish species in seagrass at low tide that were also found in mangroves at high tide were 

negatively correlated with the distance of the seagrass bed from the mangroves. This shows the 

important daily habitat connectivity that exists through tidal movements between mangrove and 

seagrass habitats. Similar dynamics may occur in more sub-tidal coastal systems at larger spatial and 

temporal scales. For example, Dorenbosch et al. (2005) showed that adult densities of coral reef fish, 

whose juvenile phases were found in mangrove and seagrass nursery habitats, were much reduced or 

absent on coral reefs located far distant from such nursery habitats, relative to those in closer 

proximity. 

A less studied, but increasingly recognised theme is the existence of intra-population 

variability in movement and other behavioural traits. Different behavioural phenotypes within 

a given population have been shown to be very common in land birds, insects, mammals, and 

other groups. An example of this is a phenomenon known as ‘partial migration’, where part 

of the overall population migrates each year, often over very large distances, while another 

component does not move and remains resident. By definition, this partial migration also 

results in differential use of habitats, often over large spatial scales. Recent work on white 

perch (Morone americana) in the United States shows this population is made up of two 

behavioural components: a resident natal freshwater contingent; and a dispersive brackishwater 

contingent (Kerr et al. 2010). The divergence appears to be a response to early life 

history experiences which influence individuals’ growth (Kerr 2008). The proportion of the 

overall population that becomes dispersive for a given year class ranges from 0% in drought 

years to 96% in high-flow years. Modelling of how differences in growth rates and 

recruitment strengths of each component contributed to the overall population found that the 

resident component contributed to long-term population persistence (stability), whereas the 

dispersive component contributed to population productivity and resilience (defined as 

rebuilding capacity) (Kerr et al. 2010). Another species winter flounder Pseudopleuronectes 

americanus has also shown intra-population variability in spawning migrations; one group 

stays coastally resident while a second smaller group migrate into estuaries to spawn 

(DeCelles & Cadrin 2010). The authors went on to suggest that coastal waters in the Gulf of 

Maine should merit consideration in the assignment of Essential Fish Habitat for this species. 

Kerr and Secor (2009) and Kerr et al. (2010) argue that such phenotypic dynamics are probably very 

common in marine fish populations but have not yet been effectively researched and quantified. The 

existence of such dynamics would have important implications for fisheries management, including 

the possibility of spatial depletions of more resident forms and variability in the use of potential 

HPSFM between years. For instance, recent work on snapper in the Hauraki Gulf has shown that fish 

on reef habitats are more resident (ie have less propensity to migrate) than those of soft sediment 

habitats, and can experience higher fishing removals (Parsons et al. 2011). 

The most effective means of protecting a HPSFM in terms of the benefit to the fishery may differ 

depending on the life-history characteristics of the fish. A variety of modelling, theoretical, and 

observational approaches have lead to the conclusion that spatial protection performs best at 

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enhancing species whose adults are relatively sedentary but whose larvae are broadcast widely 

(Chiappone and Sealey 2000, Murawski et al. 2000, Roberts 2000, Warner et al. 2000). The sedentary 

habit of adults allows the stock to accrue the maximum benefit from the protection, whereas the 

broadcasting of larvae helps ‘seed’ segments of the population outside the protection. However, the 

role of spatial protection in directly protecting juveniles after they have settled to seafloor habitats (via 

habitat protection/recovery, and/or reduced juvenile bycatch), or their interaction with non-fisheries 

impacts has not yet been explicitly considered. 


9.3.1. Potential HPSFM in New Zealand 

Important areas for spawning, pupping, and egg-laying are potential HPSFM. These areas (insofar as 

these are known) have been identified and described using science literature and fisheries databases 

and summarised within two atlases, one coastal (< 200 m) and one deepwater (> 200 m). Coastally, 

these HPSFM areas were identified for 35 important fish species by Hurst et al. (2000). This report 

concluded that virtually all coastal areas were important for these functions for one species or other. 

The report also noted that some coastal species use deeper areas for these functions, either as 

juveniles, or to spawn (e.g., red cod, giant stargazer) and some coastal areas are important for 

juveniles of deeper spawning species (e.g., hake and ling). Some species groupings were apparent 

from this analysis. Elephant fish, rig, and school shark all preferred to pup or lay eggs in shallow 

water, and very young juveniles of these species were found in shallow coastal areas. Juvenile 

barracouta, jack mackerel (Trachurus novaezelandiae), kahawai, rig, and snapper were all relatively 

abundant (at least occasionally) in the inner Hauraki Gulf. Important areas for spawning, pupping, and 

egg-laying were identified for 32 important deepwater fish species (200 to 1500 m depth), 4 pelagic 

fish species, 45 invertebrate groups, and 5 seaweeds (O'Driscoll et al. 2003). This study concluded 

that all areas to 1500 m deep were important for either spawning or juveniles of one or more species 

studied. The relative significance of areas was hard to gauge because of the variability in the data, 

however the Chatham Rise was identified as a “hotspot”. 

Areas of high juvenile abundances of certain species may be useful indicators of HPSFM for some 

species. A third atlas (Hurst et al. 2000b) details species distributions (mainly commercial) of adult 

and immature stages from trawl, midwater trawl and tuna longline where adequate size information 

was collected. No conclusions are made in this document, and generalisations across species are 

inherently difficult, therefore like the previous two atlases, this document is probably best examined 

for potential HPSFM in a species specific way. 

Certain locations within New Zealand already seem likely to qualify as HPSFM under any likely 

definition. The Kaipara Harbour has been identified as particularly important for the SNA 8 stock. 

Analysis of otolith chemistry showed that, for the 2003 year-class, a very high proportion of new 

snapper recruits to the SNA 8 stock were sourced as juveniles from the Kaipara Harbour (Morrison et 

al. 2008). This result is likely to be broadly applicable into the future as the Kaipara provides most of 

the biogenic habitat available for juvenile snapper on this coast. The Kaipara and Raglan harbours 

also showed large catches of juvenile rig and the Waitemata, Tamaki and Porirua harbours moderate 

catches (Francis et al. 2012). Recent extensive fish-habitat sampling within the harbour in 2010 as 

part of the MBIE Coastal Conservation Management programme showed juvenile snapper to be 

strongly associated with sub-tidal seagrass, horse mussels, sponges, and an introduced bryozoan. 

Negative impacts on such habitats have the potential to have far-field effects in terms of subsequent 

fisheries yields from coastal locations well distant from the Kaipara Harbour. Beaches that still retain 

substantive toheroa populations, e.g. Dargaville and Oreti beaches, may also potentially qualify as 

HPSFM (Beentjes 2010). 

210


Consistent with the international literature, biogenic (living, habitat forming) habitats have been found 

to be particularly important juvenile habitat for some coastal fish species in New Zealand. For 

example: bryozoan mounds in Tasman Bay are known nursery grounds for snapper, tarakihi and john 

dory (Vooren 1975); northern subtidal seagrass meadows fulfil the same role for a range of fish 

including snapper, trevally, parore, garfish and spotties (Francis et al. 2005, Morrison et al. 2008, 

Schwarz et al. 2006, Vooren 1975); northern horse mussel beds for snapper and trevally (Morrison et 

al. 2009); and mangrove forests for grey mullet, short-finned eels, and parore (Morrisey et al. 2010). 

Many other types of biogenic habitats exist, and some of their locations are known (e.g. see Davidson 

et al. 2010 for biogenic habitats in the Marlborough Sounds), but their precise role as HPSFM 

remains to be quantified. Examples include open coast bryozoan fields, rhodoliths, polychaete (worm) 

species ranging in collective form from low swathes to large high mounds, sea pens and sea whips, 

sponges, hydroids, gorgonians, and many forms of algae, ranging from low benthic forms such as 

Caulerpa spp. (sea rimu) through to giant kelp (Macrocystis pyrifera) forests in cooler southern 

waters. Similarly, seamounts are well-known to host reef-like formations of deep-sea stony corals 

(e.g., Tracey et al. 2011), as well as being major spawning or feeding areas for commercial deepwater 

species such as orange roughy and oreos (e.g., Clark 1999, O’Driscoll & Clark 2005). However, the 

role of these benthic communities on seamounts in supporting fish stocks is uncertain, as spawning 

aggregations continue to form even if the coral habitat is removed by trawling (Clark & Dunn 2012). 

Hence the oceanography or physical characteristics of the seamount and water column may be the key 

drivers of spawning or early life-history stage development, rather than the biogenic habitat. 

Freshwater eels are reliant upon rivers as well as coastal and oceanic environments. GIS modelling 

estimates that for longfin eels, about 30% of longfin habitat in the North Island and 34% in the South 

Island is either in a reserve or in rarely/non-fished areas, with ~ 49% of the national longfin stock 

estimate of about 12 000 tonnes being contained in these waterways (Graynoth et al. 2008). More 

regional examination of the situation for eels also exists, e.g., for the Waikato Catchment (Allen 

2010). Shortfin eels prefer slower-flowing coastal habitats such as lagoons, estuaries, and lower 

reaches of rims (Beentjes et al. 2005). In-stream cover (such as logs and debris) has been identified as 

important habitat, particularly in terms of influencing the survival of large juvenile eels (Graynoth et 

al. 2008). Short-fin eel juveniles and adults have also been found to be relatively common in estuarine 

mangrove forests, and their abundance positively correlated with structural complexity (seedlings, 

saplings, and tree densities) (Morrisey et al. 2010). In addition oceanic spawning locations are clearly 

important for eels, the location of these are unknown, although it has been suggested that these may 

be northeast of Samoa and east of Tonga for shortfins and longfins respectively (Jellyman 1994). 

Many of the potential HPSFM are threatened by either fisheries or land-based effects, the reader 

should look to the land-based effects chapter in this document and the eel section of the Stock 

assessment plenary report for further details. 

9.3.2. Habitat classification and prediction of biological 

characteristics 

Habitat classification schemes focused upon biodiversity protection have been developed in New 

Zealand at both national and regional scales, these may help identify larger habitats which HPSFM 

may be selected from, but are unlikely to be useful in isolation for determining HPSFM. The Marine 

Environment Classification (MEC), the demersal fish MEC and the benthic optimised MEC 

(BOMEC) are national scale classification schemes have been developed with the goal of aiding 

biodiversity protection (Leathwick et al. 2004, 2006, 2012). A classification scheme also exists for 

New Zealand’s rivers and streams based on their biodiversity values to support the Department of 

Conservations Waters of National Importance (WONI) project (Leathwick and Julian 2008). Regional 

211


classification schemes also exist such as ones mapping the Marine habitats of Northland, or 

Canterbury in order to assist in Marine Protected Area planning (Benn 2009; Kerr 2010). 

Another tool which may help in terms of identifying HPSFM is the predictions of richness, 

occurrence and abundance of small fish in New Zealand estuaries (Francis et al. 2011). This paper 

contains richness predictions for 380 estuaries and occurrence predictions for 16 species. This could 

help minimise the need to undertake expensive field surveys to inform resource management, 

although environmental sampling may still be needed to drive some models. 


Prior to 2007 research within New Zealand has not been explicitly focused on identifying HPSFM. 

However, in line with international trends, this situation has changed in recent times, with recognition 

of some of the wider aspects of fisheries management and the move towards an ecosystem approach 

foreshadowed in Fisheries 2030. 

A number of Ministry and other research projects are underway, or planned, concerning HPSFM in 

the 2010/11 year. Project ENV200907, “Habitat of particular significance to fisheries management: 

Kaipara Harbour”, is underway and has the overall objective of identifying and mapping areas and 

habitats of particular significance in the Kaipara Harbour which support coastal fisheries; and 

identifying and assessing threats to these habitats. Included in this work is the reconstruction of 

environmental histories through interviews of long time local residents who have experience of the 

harbour, and associated collation and integration of historical data sources (e.g., catch records, 

photographs, diaries, maps, and fishing logs). Another output of this work will be recommendations 

on the best habitats and methods of monitoring to detect change to HPSFM within Kaipara harbour. 

Biogenic habitats on the continental shelf from ~5 to 150 m depths are currently being characterised 

and mapped through the biodiversity project ZBD2008/01, this will also provide new information on 

fisheries species utilisation of these habitats. Interviews with 50 retired fishers have provided valuable 

information on biogenic habitat around New Zealand. A national survey to examine the present 

occurrences and extents of these biogenic habitats was completed in 2011 in collaboration with 

Oceans Survey 2020, NIWA and Ministry of Business, Innovation and Employment (MBIE) funding. 

A number of other national scale projects are also underway. A desktop review is collating 

information on the importance of biogenic habitats to fisheries across the entire Territorial Sea and 

Exclusive Economic Zone (project HAB2007/01). A project has been approved to review the 

literature and recommend the relative urgency of research on habitats of particular significance for 

inshore finfish species (project ENV2010/03). 

The Ministry of Business, Innovation and Employment (MBIE) funded project Coastal Conservation 

Management started in 2009 and runs for six years. This programme aims to integrate and add to 

existing fish-habitat association work to develop a national scale marine fish-habitat classification and 

predictive model framework. This project will also attempt to develop threat assessments at local, 

regional and national scales. MPI is maximising the synergies between its planned research and this 

project. As part of that synergy, work on the connectivity and stock structure of grey mullet (Mugil 

cephalus) is underway in collaboration with MFish project GMU2009/01. Otolith chemistry is being 

assessed for its utility in partitioning the GMU 1 stock into more biologically meaningful 

management units, and in quantifying the suspected existence of source and sink dynamics between 

the various estuaries that hold juvenile grey mullet nursery habitats. 

MBIE also funded in 2012 the three year project delivered by NIWA entitled Predicting the 

occurrence of vulnerable marine ecosystems for planning spatial management in the South Pacific 

region. The development of predictive models of species occurrence under this project may also aid in 

212


identifying HPSFM. Identification of biogenic habitat has been part of the MBIE project “Vulnerable 

deep-sea communities”since 2009 (and its predecessor seamount programme) which includes survys 

of a range of habiatts that may be important for various life-history stages of commercial fish species: 

seamounts, canyons, continental slope, hydrothermal vents, seeps. 


As no HPSFM are defined this section cannot be completed. 


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Warner R.R., Swearer S.E., Caselle J.E. 2000. Larval accumulation and retention: Implications for the design of marine reserves and 

essential fish habitat. Bulletin of Marine Science (66): 821-830. 

Western Pacific Regional Fishery Management Council 1998. Magnuson-Stevens Act definitions and required provisions. Western Pacific 

Regional Fishery Management Council, Hawaii. 

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AEBAR 2012: Ecosystem effects: Land-based effects 

10. Land-based effects on fisheries, aquaculture and 

supporting biodiversity 

Scope of chapter This chapter outlines the main known threats from land-based activities to 

fisheries, aquaculture and supporting biodiversity. It also describes the 

present status and trends in land-based impacts. 

Area All of the New Zealand freshwater, EEZ and territorial sea. 

Focal localities Freshwater habitats and areas closest to the coast are likely to be most 

impacted; this will be exacerbated in areas with low water movement. 

Anthropogenically increased sediment run-off is particularly high from the 

Waiapu and Waipaoa river catchments on the east coast of the North Island. 

Areas of intense urbanisation or agricultural use of catchments are also likely 

to be impacted by bacteria, viruses, heavy metals and nutrients. 

Key issues Habitat modification, sedimentation, aquaculture, shellfish, terrestrial landuse 

change (particularly for urbanisation, forestry or agriculture) water 

quality and quantity, contamination, consequences to seafood production of 

increased pollutants, freshwater management and demand. 

Emerging issues Impacts on habitats of particular significance to fisheries management 

(HPSFM), linkages through rainfall patterns to climate change, shellfish bed 

closures, habitat remediation, domestic animal diseases in protected marine 

MPI Research 

(current) 

NZ Government 


Links to 2030 

objectives 

Related 


10.1. Context 

species, proposed aquaculture expansion, water abstraction impacts. 

Habitats of particular significance for fisheries management: Kaipara 

Harbour (ENV2009/07), Toheroa abundance (TOH2007/03), Biogenic 

habitats as areas of particular significance for fisheries management 

(HAB2007/01), Research on Biogenic Habitat-Forming Biota and their 

functional role in maintaining Biodiversity in the Inshore Region, 5-150m 

depths (ZBD2008/01 – this is also part-funded by Oceans Survey 2020, 

NIWA and MBIE). 

Ministry of Business, Innovation and Employment (MBIE) funded programs: 

(After the outfall: recovery from eutrophication in degraded New Zealand 

estuaries (UOCX0902). 

NIWA Core funding in two areas. Firstly, The ’Managing marine stressors’ 

area under the ’Coasts and Oceans’ centre, specifically the programme 

’Managing marine resources’ and the project ’Measuring mapping and 

conserving (C01X0505)’. Secondly, in the ’Fisheries’ Centre programme 3 

which deals with ecosytem-based management approaches in conjunction 

with the ’Coasts and Oceans’ centre. 

Objective 8: Improve RMA fisheries interface. Objective 4: Support 

aquaculture development 

Habitats of particular significance for fisheries management (HPSFM), 

marine environmental monitoring. 

It has been acknowledged for some time now that land-based activities can have important effects on 

seafood production. The main threats to the quality and use of the world’s oceans are (GESAMP 

2001): 

• alteration and destruction of habitats and ecosystems; 

• effects of sewage on human health; 

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• widespread and increased eutrophication; 

• decline of fish stocks and other renewable resources; and 

• changes in sediment flows due to hydrological changes 

. Coastal development is projected to impact 91% of all inhabited coasts by 2050 and will contribute 

to more than 80% of all marine pollution (Nellemann et al. 2008). 

Aquaculture and land-based activities that may have impacts on seafood production are primarily 

regulated under the Resource Management Act 1991 (and subsequent amendments). Fisheries are 

controlled under the Fisheries Act 1996. Fisheries 2030 is a long-term policy strategy and direction 

paper of the Ministry for Primary Industries. It was released in 2009 and states that improving the 

Fisheries/Resource Management Act interface is a priority (objective 8). Strategic actions to achieve 

this priority are listed as: 

8.1 Improve fisheries sector input to processes that manage RMA-controlled effects on the 

marine and freshwater environment. 

8.2 Promote the development and use of RMA national policy statements, environmental 

standards, and regional coastal and freshwater plans 

The Government’s ‘Fresh Start for Freshwater Programme 26 ’ (lead by MfE and MPI) is addressing a 

range of issues through a water reform strategy that includes governance, setting objectives and limits, 

managing within limits (quality and quantity) and that better reflects Maori/Iwi rights and interests in 

water management. The Coastal Policy Statement (2010) also has relevance to matters of fisheries 

interest, e.g. Policy 20(1) (paraphrased) controls the use of vehicles on beaches where (b) harm to 

shellfish beds may result. MPI also works with other agencies, principally DOC, MfE and regional 

councils and through the Natural Resource Cluster to influence these processes to ensure 

consideration of land-based impacts upon seafood production. 

Land-based effects on seafood production and supporting biodiversity in this context are defined as 

resulting either from the inputs of contaminants from terrestrial sources or through engineering 

structures (e.g., breakwaters, causeways, bridges) that change the nature and characteristics of coastal 

habitats and modify hydrodynamics. The major route for entry of land-based contaminants into the 

marine environment is associated with freshwater flows (rivers, streams, direct runoff and ground 

water), although contaminants may enter the marine environment via direct inputs (e.g., landslides) or 

atmospheric transport processes. 

The most important land-based effect in New Zealand is arguably increased sediment deposition 

around our coasts (Morrison et al. 2009). This deposition has been accelerated due to increased 

erosion from land-use, which causes gully and channel erosion and landslides (Glade 2003). Inputs of 

sediments to our coastal zone, although naturally high in places due to our high rainfall and rates of 

tectonic uplift (Carter 1975), have been accelerated by human activities (Goff 1997). Sediment inputs 

are now high by world standards and make up ~1% of the estimated global detrital input to the oceans 

(Carter et al. 1996). By contrast New Zealand represents only ~ 0.3% of the land area that drains into 

the oceans (Griffiths and Glasby 1985, Milliman and Syvitski 1992). 

Different land use effects act over different scales; for example localised effects act on small streams 

and adjacent estuarine habitats, large scale effects extend to coastal embayments and shelf 

ecosystems. Associated risks will vary according to location and depend on the relevant ecosystem 

services (e.g. high value commercial fishery stocks) and their perceived sensitivities. The risk from 

stormwater pollutants will be more important near urban areas and the effects of nutrient enrichment 

will be more important near intensively farmed rural areas. 

26 http://www.mfe.govt.nz/issues/water/freshwater/fresh-start-for-fresh-water/ 

217


The risk from land-based impacts for seafood production is that they will limit the productivity of a 

stock or stocks. For example, the bryozoan beds around Separation Point in Golden Bay, were 

protected from fishing, amongst other reasons, due to their perceived role as nursery grounds for a 

variety of coastal fish species in 1980 (Grange et al. 2003). Recent work has suggested the main threat 

to these bryozoans is now sedimentation from the Motueka River, which may inhibit recovery of any 

damaged bryozoans (Grange et al. 2003, Morrison et al. 2009). Any declines in this bryozoan bed and 

associated ecological communities could also affect the productivity of adjacent fishery stocks. 

The New Zealand aquaculture industry has an objective of developing into a billion dollar industry by 

2025 (Aquaculture New Zealand 2012). Government supports well-planned and sustainable 

aquaculture through its Aquaculture Strategy and Five-year Plan. One of the desired outcomes of 

actions by the New Zealand Government is to enable more space to be made available for 

aquaculture. This outcome is likely to heighten the potential for conflict between aquaculture 

proponents and those creating negative land-based effects. 

MPI mainly manage in the marine environment, therefore this topic area will be dealt with first. MPI 

also manages the freshwater eel fishery; this will be dealt with latterly within relevant sections. 


10.2.1. Land-based influences 

The importance of different land-based influences differ regionally but the South Pacific Regional 

Environmental Programme (SPREP, which includes New Zealand) defines waste management and 

pollution control as one of its four strategic priorities for 2011-2015 (SPREP 2010). “ 

Influences, including land-based influences, seldom work in isolation; for example the development 

of farming and fishing over the last hundred years has meant that increased sediment and nutrient 

runoff has to some degree occurred simultaneously with increased fishing pressure. However, the 

impact of these influences has often been studied in isolation. In a review on coastal eutrophication, 

Cloern (2001) stated that “Our view of the problem [eutrophication] is narrow because it continues to 

focus on one signal of change in the coastal zone, as though nutrient enrichment operates as an 

independent stressor; it does not reflect a broad ecosystem-scale view that considers nutrient 

enrichment in the context of all the other stressors that cause change in coastal ecosystems”. These 

influences (in isolation or combination) can also cause indirect effects, such as decreasing species 

diversity which then lessens resistance to invasion by non-indigenous species or species with different 

life-history strategies (Balata et al. 2007, Kneitel and Perrault 2006, Piola and Johnston 2008). Studies 

that research a realistic mix of influences are rare. 

Sediment deposition can be an important influence, particularly in areas of high rainfall, tectonic uplift, 

and forest clearances, or areas where these activities coincide. Sediments are known to erode from the 

land at an increased rate in response to human use, for example, estimates from a largely deforested 

tropical highland suggest erosion rates 10-100 times faster than pre-clearance rates (Hewawasam et al. 

2003). Increased sediment either deposited on the seafloor or suspended in the water column can 

negatively impact upon invertebrates in a number of ways including: burial, scour, inhibiting 

settlement, decreasing filter-feeding efficiency and decreasing light penetration, generally leading to 

less diverse communities, with a decrease in suspension feeders (Thrush et al. 2004). These impacts 

can affect the structure, composition and dynamics of benthic communities (Airoldi 2003, Thrush et al. 

2004). Effects of this increased sediment movement and deposition on finfish are mostly known from 

freshwater fish and can range from behavioural (such as decreased feeding rates) to sublethal (e.g., gill 

tissue disruption) and lethal as well as having effects on habitat important to fishes (Morrison et al. 

2009). These effects differ by species and life-stages and are dependant upon factors that include the 

218


duration, frequency and magnitude of exposure, temperature, and other environmental variables 

(Servizi and Martens 1992). 

Increased nutrient addition to the aquatic environment can initially increase production, but with 

increasing nutrients there is an increasing likelihood of harmful algal blooms and cascades of effects 

damaging to most communities above the level of the plankton (Kennish 2002; Heisler et al. 2008). 

This excess of nutrients is termed eutrophication. Eutrophication can stimulate phytoplankton growth 

which can decrease the light availability and subsequently lead to losses in benthic production from 

seagrass, microalgae or macroalgae and their associated animal communities. Algal blooms then die 

and their decay depletes oxygen and blankets the seafloor. The lack of oxygen in the bed and water 

column can lead to losses of finfish and benthic communities. These effects are likely to be location 

specific and are influenced by a number of factors including: water transparency, distribution of 

vascular plants and biomass of macroalgae, sediment biogeochemistry and nutrient cycling, nutrient 

ratios and their regulation of phytoplankton community composition, frequency of toxic/harmful algal 

blooms, habitat quality for metazoans, reproduction/growth/survival of pelagic and benthic 

invertebrates, and subtle changes such as shifts in the seasonality of ecosystems (Cloern 2001). These 

effects of eutrophication abound in the literature, for example, the formation of dead (or anoxic) zones 

is exacerbated by eutrophication, although oceanographic conditions also play a key role (Diaz and 

Rosenberg 2008). Dead zones have now been reported from more than 400 systems, affecting a total 

area of more than 245,000 square kilometres (Diaz and Rosenberg 2008). This includes anoxic events 

from New Zealand in coastal north-eastern New Zealand and Stewart Island (Taylor et al. 1985, 

Morrissey 2000). 

Other pollutants such as heavy metals and organic chemicals can have severe effects, but are more 

localised in extent than sediment or nutrient pollution (Castro and Huber 2003, Kennish 2002). 

Fortunately the concentration of these pollutants in most New Zealand aquatic environments is 

relatively low, with a few known exceptions. Examples of this include naturally elevated levels of 

arsenic in Northland 27 , Cadmium levels in Foveaux Strait oysters (Frew et al. 1996) and levels of 

Nickel and chromium within the Motueka river plume in Tasman Bay (Forrest et al. 2007). The 

Cadmium levels have caused market access issues for Foveaux Strait Oysters. Some 

anthropogenically generated pollutants such as copper, lead, zinc and PCBs are high in localised 

hotspots within urban watersheds. In the Auckland region these hotspots tend to be in muddy 

estuarine sites and tidal creeks that receive runoff from older urban catchments 28 . There is a lack of 

knowledge on the impacts of these pollutants upon fisheries. 

Climate change is likely to interact with the effect of land-based impacts as the main delivery of landbased 

influences is through rainfall and subsequent freshwater flows. Global climate change 

projections include changes in the amount and regional distribution of rainfall over New Zealand 

(IPCC 2007). More regional predictions include increasing frequency of heavy rainfall events over 

New Zealand (Whetton et al. 1996). This is likely to exacerbate the impact of some land-based 

influences as delivery peaks at times of high rainfall, e.g. sediment delivery (Morrison et al. 2009). 

Physical alterations of the coast are generally, but not exclusively (i.e. wetland reclamation for 

agriculture), concentrated around urban areas and can have a number of consequences on the marine 

environment (Bulleri and Chapman 2010). Changes in diversity, habitat fragmentation or loss and 

increased invasion susceptibility have all been identified as consequences of physical alteration. The 

effects of physical alterations upon fisheries remain largely unquantified; however the habitat loss or 

alteration portion of physical alterations will be dealt with under the habitats of particular significance 

for fisheries management (HPSFM) section. 

27 Accessible on the www.os2020.org.nz website. 

28 Available from the State of the Auckland Region report 2010, Chapter 4.4 Marine, at 

http://www.arc.govt.nz/albany/index.cfm?FD6A3403-145E-173C-986A-A0E3C199B8C5 

219


An area of emerging interest internationally is infectious diseases from land-based animals affecting 

marine populations. Perhaps the most well-known example of this is the canine distemper outbreak in 

Caspian seals that cause a mass mortality in the Caspian sea in 2000 (Kennedy et al. 2000) 

10.2.2. Habitat restoration 

Habitat restoration or rehabilitation has been the subject of much recent research. Habitat restoration 

or rehabilitation rarely, if ever, replaces what was lost and is most applicable in estuarine or enclosed 

coastal areas as opposed to exposed coastal or open ocean habitats (Elliott et al. 2007). Connectivity 

of populations is a key consideration when evaluating the effectiveness of any marine restoration or 

rehabilitation (Lipcius et al. 2008). In the marine area, seagrass replanting methodologies are being 

developed to ensure the best survival success (Bell et al. 2008) and artificial reefs can improve 

fisheries catches, although whether artificial reefs boost population numbers or merely attract fish is 

unclear (Seaman 2007). In addition, The incorporation of habitat elements in engineering structures, 

e.g., artificial rockpools in seawalls, shows promise in terms of ameliorating impacts of physical 

alterations (Bulleri 2006). Spatial approaches to managing land-use impacts, such as marine reserves, 

will be covered under the section about HPSFM. 

Freshwater rehabilitation has been reviewed by Roni et al. (2008). Habitat reconnection, floodplain 

rehabilitation and instream habitat improvement are all suggested to result in improved habitat and 

local fish abundances. Riparian rehabilitation, sediment reduction, dam removal, and restoration of 

natural flood regimes have shown promise for restoring natural processes that create and maintain 

habitats, but there is a lack of long-term studies to gauge their success. Wild eel fisheries in America 

and Europe have declined over time (Allen et al. 2006, Atlantic States Marine Fisheries Commission 

2000, Haro et al. 2000). Declines in wild eel fisheries have been linked to a number of factors 

including: barriers to migration; hydro turbine mortality; and habitat loss or alteration. Information to 

quantitatively assess these linkages is however often lacking (Haro et al. 2000). 


Land-based effects will be most pronounced closest to the land, therefore it is freshwater, estuarine, 

coastal, middle depths and deepwater fisheries, in decreasing order, that will be most affected. The 

scale of land-use effects will, however, differ depending upon the particular influence. The most 

localised of these are likely to be direct physical impacts; for example, the replacement of natural 

shorelines with seawalls; although even direct physical impacts can have larger scale impacts, such as 

affecting sediment transport and subsequently beach erosion, or contributing to cumulative effects 

upon ecosystem responses. Point-source discharges are likely to have a variable scale of influence, 

and this influence is likely to increase where a number of point-sources discharge, particularly when 

this occurs into an embayed, low-current environment. An example of this is the multiple stormwater 

discharges into the Waitemata harbour in Auckland (Hayward et al. 2006). The largest influence can 

be from diffuse-source discharges such as nutrients or sediment (Kennish 2002). For example, the 

influence of diffuse-source materials from the Motueka river catchment in Golden Bay on subtidal 

sediments and assemblages and shellfish quality can extend up to tens of kilometres offshore (Tuckey 

et al. 2006; Forrest et al. 2007), with even a moderate storm event extending a plume greater than 

6km offshore (Cornelisen et al. 2011). Terrestrial influences on New Zealand’s marine environment 

can, at times be detected by satellites from differences in ocean colour and turbidity extending many 

kilometres offshore from river mouths (Gibbs et al. 2006). 

All coastal areas are unlikely to suffer from land-based impacts in the same way. The quantities of 

pollutants or structures differ spatially. Stormwater pollutants, seawalls and jetties are more likely to 

be concentrated around urban areas. Nutrient inputs are likely to be concentrated either around sewage 

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outlets or associated with areas of intensive agriculture or horticulture. Sediment production has been 

mapped around the country and is greatest around the west coast of the South Island and the East 

coast of the North Island (Griffiths and Glasby 1985, Hicks and Shankar 2003, Hicks et al. 2011). 

Notably the catchments where improved land management may result in the biggest changes to 

sediment delivery to coastal environments are likely to be the Waiapu and Waipaoa river catchments 

on the East coast of the North Island. In addition to this, the sensitivity of receiving environments is 

also likely to differ; this will be covered in subsequent sections. 

A MPI funded survey of scientific experts (MacDiarmid et al. 2012) addressed the vulnerability to a 

number of threats of marine habitat types within the New Zealand’s Territorial Sea and Exclusive 

Economic Zone (EEZ). Each vulnerability score was based on an assessment of five factors including 

the spatial scale, frequency and functional impact of the threat in the given habitat as well as the 

susceptibility of the habitat to the threat and the recovery time of the habitat following disturbance 

from that threat. The study found that the number of threats and their severity were generally 

considered to decrease with depth, particularly below 50m. Reef, sand, and mud habitats in harbours 

and estuaries and along sheltered and exposed coasts were considered to be the most highly threatened 

habitats. The study also reported that over half of the twenty-six top threats fully, or in part, stemmed 

from human activities external to the marine environment itself. The top six threats in order were: 

1. ocean acidification, 

2. rising sea temperatures resulting from global climate change, 

3 rd equal bottom trawling fishing, 

3 rd equal increased sediment loadings from river inputs 

5 th equal change in currents from climate change 

5 th equal increased storminess from climate change 

The reader is guided to MacDiarmid et al. (2012) for more detail including tables of threats-by-habitat 

and habitats-by-threat. Climate change and ocean acidification, although they can be considered landbased 

effects, are covered under the Chapters in this document called “New Zealand Regional climate 

and oceanic setting” and “Biodiversity”. 

The protozoan Toxoplasma gondii has been identified as the cause of death for 7 of 28 Hector’s and 

Maui’s dolphins examined since 2007 (W. Roe, Massey University, unpubl. data, 31 July 2012). 

Land-based runoff containing cat faeces is believed to be the means by which Toxoplasma gondii 

enters the marine environment (Hill & Dubey 2002). A Hectors dolphin has also tested positive for 

Brucella abortus (or a similar organism) a pathogen of terrestrial mammals that can cause late 

pregnancy abortion, and has been seen in a range of cetacean species elsewhere 29 . 

10.3.1. Completed research 

A MPI funded project (IPA2007/07) reviewed the impacts of land based influences on coastal 

biodiversity and fisheries (Morrison et al. 2009). This review used a number of lines of evidence to 

conclude that in this context, sedimentation is probably New Zealand’s most important pollutant. The 

negative impacts of sediment include decreasing efficiency of filter-feeding shellfish (such as cockles, 

pipi, and scallops), reduced settlement success and survival of larval and juvenile phases (e.g., paua, 

kina), and reductions in the foraging abilities of finfish (e.g., juvenile snapper). Indirect effects 

include the modification or loss of important nursery habitats, particularly biogenic habitats (greenlipped 

and horse mussel beds, seagrass meadows, bryozoan and tubeworm mounds, sponge gardens, 

29 http://www.doc.govt.nz/Documents/conservation/native-animals/marine-mammals/maui-tmp/mauis-tmp- 

discussion-document-full.pdf 

221


kelps/seaweeds, and a range of other structurally complex species). Inshore filter-feeding bivalves and 

biogenic habitats were identified as the most likely to be adversely affected by sedimentation. 

Eutrophication was also identified as a potential threat from experience overseas. 

Marine restoration studies published in New Zealand have focused on the New Zealand cockle 

Austrovenus stutchburyi. The first of these studies identified a tagging methodology to aid relocation 

of transplanted individuals (Stewart and Creese 1998). Subsequent studies stressed the use of adults in 

restoration and the importance of site selection, either from theoretical or modelling viewpoints 

(Lundquist et al. 2009, Marsden and Adkins 2009). Detailed restoration methodology has been 

investigated in Whangarei Harbour and recommends replanting adults at densities between 222 and 

832 m -2 (Cummings et al. 2007). 

Multiple influences in areas relevant to seafood production in New Zealand have been addressed by 

three studies. A field experiment near Auckland showed greater effects of three heavy metals 

(Copper, lead and Zinc) in combination compared to isolation on infaunal colonisation of intertidal 

estuarine sediments (Fukunaga et al. 2010). A survey approach looking at the interaction of sediment 

grain size, organic content and heavy metal contamination upon densities of 46 macrofaunal taxa 

across the Auckland region also showed a predominance of multiplicative effects (Thrush et al. 2008). 

Although influences can work in unexpected directions; as in a study on large suspension feeding 

bivalves off estuary mouths where the anticipated negative impacts from sediment were not observed 

and these species benefited from food resources generated from those estuaries (Thrush et al. In 

Press). 

Toheroa populations are currently closed to all but customary harvesting but have failed to recover to 

former population levels even though periodic (and sometimes substantial) pulses in young recruits 

have been detected in both Northland and Southland (Beentjes 2010, Morrison and Parkinson 2008). 

Current thinking suggests a mix of influences are probably responsible for these declines including 

over-harvesting, land-use changes leading to changes in freshwater seeps on the beaches and vehicle 

traffic (Morrison et al. 2009). A number of discrete pieces of research have been completed in this 

area. A review of the wider impact of vehicles on beaches and sandy dunes has been completed, and 

suggested more research was needed on the impacts of vehicle traffic on the intertidal (Stephenson 

1999). A four day study over a fishing contest on 90 mile beach showed the potential of traffic to 

produce immediate mortalities of juvenile toheroa, but the temporal importance of this could not be 

gauged (Hooker and Redfearn 1998). Mortalities of toheroa from the Burt Munro Classic motorcycle 

race on Oreti beach have been quantified and recommendations made for how to minimise these, but 

again the importance of vehicle traffic for toheroa survival over longer time periods was unclear 

(Moller et al. 2009). 

The effects of large-scale habitat loss and modification on eels in New Zealand are clearly significant, 

but difficult to quantify (Beentjes et al. 2005). Significant non-fisheries mortality of New Zealand 

freshwater longfin and shortfin eels are caused by mechanical clearance of drainage channels, and 

damage by hydro-electric turbines and flood control pumping. Eels prefer habitat that offers cover and 

in modified drains aquatic weed provides both daytime cover and nighttime foraging areas. Loss of 

weed and natural debris can thus result in significant displacement of eels to other areas. In addition, 

wetlands drainage has resulted in greatly reduced available habitat for eels, particularly shortfins 

which prefer slower-flowing coastal habitats such as lagoons, estuaries, and lower reaches of rims. 

Water abstraction is one of a number of information requirements identified in this paper to better 

define the effects on eel populations. 

Rhodolith beds have been surveyed in the Bay of Islands and high diversity reported even in areas of 

abundant fine sediments (Nelson et al. 2012). It is unclear if the increasing sedimentation occurring in 

the Te Rawhiti Reach is negatively impacting rhodoliths and whether this atypical rhodolith bed (i.e., 

with abundant fine sediments) is at risk if current sedimentation and mobilisation rates continue. 

222


A number of Integrated Catchment Management (ICM) projects are underway in New Zealand. These 

take a holistic view to land management incorporating aquatic effects; this approach could help 

restore water quality of both fresh and coastal waters. An overview of these projects is given in a 

Ministry for the Environment Report on integrated catchment management (Environmental 

Communications Limited 2010). Many of these projects employ restoration techniques such as 

riparian planting, but few assessments of the effectiveness of riparian planting exist. One assessment 

of the effect of nine riparian zone planting schemes in the North Island on water quality, physical and 

ecological indicators concluded that riparian planting could improve stream quality; in particular rapid 

improvements were seen in terms of visual clarity and channel stability (Parkyn et al. 2003). Nutrient 

and faecal contamination results were more variable. Improvement in macroinvertebrate communities 

did not occur in most streams and the three factors needed for these were canopy closure (which 

decreased stream temperature), long lengths of riparian planting and protection of headwater 

tributaries. A modelling study also demonstrated the long time lag needed to grow large trees which 

then provide wood debris to structure channels which achieves the best stream rehabilitation results 

(Davies-Colley et al. 2009). Although some of these studies extend into the marine realm (at least in 

terms of monitoring) it is difficult to gauge the impact of these activities upon fisheries or aquaculture, 

particularly on wider scales because ICM studies have been localised at small scales. 

The review of land based effects (Morrison et al. 2009) identified knowledge gaps and made 

suggestions for more relevant research on these influences: 

• identification of fisheries species/habitat associations for different life stages, including 

consideration of how changing habitat landscapes may change fisheries production; 

• better knowledge of connectivity between habitats and ecosystems at large spatial scales; 

• the role of river plumes; 

• the effects of land-based influences both directly on fished species, and indirectly through 

impacts on nursery habitats; 

• a better spatially-based understanding, mapping and synthesis of the integrated impacts of 

land-based and marine-based influences on coastal marine ecosystems. 

The locations where addressing land-based impacts is likely to result in a lowering in risk to seafood 

production or increased seafood production, excluding those already mentioned, are undefined. 


A number of ongoing research projects exist that will improve the knowledge of land-based impacts 

upon seafood production. Project ENV2009/07 investigates habitats of particular significance for 

fisheries management within the Kaipara Harbour and one objective is to assess fishing and landbased 

threats to these habitats. Current research is investigating the impact of a range of influences 

upon toheroa at Ninety-Mile Beach (project TOH2007/03). Environmental factors, including landbased 

impacts (particularly vehicle use and changing land-use patterns) are implicated in poor 

recovery of this population since the closure of this commercial and recreational fishery in the 1960s. 

A MPI biodiversity project also has components that address land-based effects; the threats to 

biogenic habitats are addressed in project ZBD2008/01. 

Research is also ongoing on land-use effects at a national scale. A national scale threat analysis is also 

being carried out for biogenic habitats, given their likely importance for fisheries management 

(project HAB2007/01). A Ministry of Business, Innovation and Employment (MBIE) funded project 

30 of particular relevance is (project number and lead agencies in brackets): Nitrogen reduction and 

benthic recovery (UOCX0902, University of Canterbury). This research aims to determine the 

trajectories and thresholds of coastal ecosystem recovery following removal of excessive nutrient 

30 http://www.msi.govt.nz/update-me/who-got-funded/ 

223


loading (called "eutrophication") and earthquake impacts. This will be achieved by monitoring the 

effects of diverting all of Christchurch’s treated wastewater discharge from the eutrophied Avon- 

Heathcote (Ihutai) Estuary and the subsequent earthquake induced disturbances to this diversion. 

Although not current research, the Department of Conservations suggested research priorities in 

the “Review of the Maui’s dolphin Threat management plan: Consultation paper” include 

objectives to determine the presence, pathways and possible mitigation of the threat from 

Toxoplasmosis gondii 31 . 


A national view of the impacts of land-based influences upon seafood production does not exist; this 

could be facilitated by better coordination and planning of the many disparate marine monitoring 

programmes running around the country. Monitoring of marine water quality and associated 

communities is carried out through a variety of organisations, including, universities, regional 

councils and aquaculture or shellfisheries operations. Regional council monitoring of water quality 

and associated biological communities is often reported through web sites such as the Auckland 

Regional Council environmental monitoring data which is available on the internet 32 

224 

or summary 

reports such as the Hauraki Gulf state of the Environment 2011 report 33 Water quality and 

associated communities may also be monitored for a regional council as part of a consent application 

or as a stipulation for a particular marine development. The data from aquaculture and shellfisheries 

water quality monitoring is not generally available. Improved coordination and planning of marine 

monitoring has been achieved in some places, e.g., the United Kingdom 34 The Marine Environmental 

Monitoring Programme (ZBD2010-42), is a step towards this goal, more information is available on 

this project in the Biodiversity chapter of this document. Possible national scale proxies for coastal 

faecal contamination may exist after collating information from sanitation area monitoring for 

shellfish harvesting or shellfish harvesting closure information. 

Marine water quality indicators are available nationally from 407 coastal bathing beaches which have 

been monitored for human health issues, rather than environmental purposes, over the last six years 35 . 

No temporal trends were detectable in this relatively short time period, however changes in sites 

monitored over this time may have confounded this analysis. Over the 2007-8 and 2008-9 summers, 

79% of the swimming sites met the guidelines for contact recreation almost all the time. At least 95% 

of the samples at these sites had safe Enterococci levels (which is an indicator of human and animal 

sewage). Two percent of the sites (located within the Manukau harbour and on the West coast of 

Auckland), breached the guidelines more than 25% of the time. In general, the most polluted sites 

were embayed locations with poor natural flushing. 

The Ministry for the Environment (MfE) also reports on freshwater quality. River water quality 

indicators that have been assessed have direct relevance to the eel, and other freshwater fisheries, and 

this water will flow through estuaries and enter the marine environment. The National River Water 

Quality Network (NRWQN) has national coverage, and has been running for over 20 years and has 

recently reported upon the following 8 variables: temperature, dissolved oxygen, visual clarity, 

dissolved reactive and total phosphorous, and ammoniacal, oxidised and total nitrogen (Ballantine and 

31 http://www.doc.govt.nz/Documents/conservation/native-animals/marine-mammals/maui-tmp/mauis-tmp- 

discussion-document-full.pdf 

32 

http://maps.auckland.govt.nz/aucklandregionviewer/?widgets=HYDROTEL 

33 

http://www.arc.govt.nz/albany/fms/main/Documents/Environment/Coastal%20and%20marine/hgfstateoftheen 

vreport2011.pdf 

34 

http://www.cefas.co.uk/data/marine-monitoring/national-marine-monitoring-programme-(nmmp).aspx 

35 

http://www.mfe.govt.nz/environmental-reporting/freshwater/recreational/snapshot/coastal.html#results


Davies-Colley 2009). Dissolved oxygen showed few meaningful trends and the ammoniacal nitrogen 

data suffered from a processing artefact. An upward, although not significant trend in temperature and 

an improvement of water clarity were seen at the national scale. However, a negative correlation was 

seen between water clarity and percent of catchment in pasture, which suggests any expansion of 

pasture lands may have impacts on clarity. Strong increasing trends over time were seen in oxidised 

nitrogen, total nitrogen, total phosphorous and dissolved reactive phosphorous. These latter trends all 

signify deteriorating water quality and are mainly attributable to increased diffuse-source pollution 

from the expansion and intensification of pastoral agriculture. 

Total Nitrogen and Phosphorous loads to the coast in New Zealand have been modelled and were 

estimated at 167,300 and 63,100 t yr -1 , respectively (Elliot et al. 2005) 36 . The main sources of 

Nitrogen and Phosphorous were from pastoralism (70%) and erosion (53%), respectively. The dairy 

herd in New Zealand has approximately doubled (increased 211%) since 1981 (whilst other grazer 

numbers have been relatively stable or declining) 9 . The amount of Urea and Superphosphate (New 

Zealand’s most common nitrogen and phosphorous fertiliser) have increased 27.7 and 1.6 fold, 

respectively over the same period 37 . The use of Urea is currently around 100 kg.ha -1 for dairying and 

~10 kg.ha -1 for sheep and beef farms (MPI 2012). The area in dairy farming is ~ 2 million hectares 

compared to 3.6 million hectares for sheep and 2 million hectares in beef farming (MPI 2012). 

Therefore Urea use in New Zealand is dominated by the dairy industry. These statistics provide strong 

circumstantial evidence that the expansion in dairying is primarily responsible for these declines in 

water quality from agricultural sources. 

High faecal coliform counts (primarily from mammal or bird faeces) can impact upon the value 

gained from shellfish fisheries and aquaculture. Area closures to commercial harvesting usually 

depend on an areas rainfall/runoff relationship and areas closer to significant farming areas or urban 

concentrations are likely to be closed more frequently, due to high faecal coliform counts, than areas 

where the catchment is unfarmed or not heavily populated, e.g. Inner Pelorus sound is likely to be 

closed more frequently than outer Pelorus Sound (Marlborough Sounds) 38 . For coastal areas of the 

Marlborough Sounds, the Coromandel Peninsula and Northland closures can range from a few days to 

over 50 percent of the time in a given year 39 . Certain fisheries may in practice be limited by the 

amount of time where water quality is sufficient to allow harvesting, e.g. the cockle fishery in COC1A 

(Snake bank in Whangarei harbour) was closed for 101, 96, 167, 96 and 117 days for the 2006-7, 

2007-8, 2008-9, 2009-10 and 2010-11 fishing years, respectively due to high faecal coliform counts 

from sewage spills or runoff 40 . Models also now exist that allow real-time prediction of E. coli pulses 

associated with storm events, e.g. Wilkinson et al. 2011, which may help harvesters to better cope 

with water quality issues. 


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227

AEBAR 2012: Marine Biodiversity 

THEME 5: MARINE BIODIVERSITY 

228

11. Biodiversity 

AEBAR 2012: Marine biodiversity 

Scope of chapter Provide an overview of the MPI Biodiversity Programme and address: 

National and global context of NZ marine biodiversity research; Research 

findings and progress of the MPI Biodiversity Research Programme from 

2000–2012; including one-off whole-of-government research initiatives 

administered under this programme (e.g. Ocean Survey 20/20 Biodiversity 

and Fisheries projects; International Polar Year Census of Antarctic Marine 

life project 2007) 

Geographic area New Zealand Territorial Seas, EEZ and Continental shelf extension 

(BioInfo); South-west Pacific Region associated with South Pacific Regional 

Fisheries Management Organisation (SPRFMO);Antarctic Ross Sea region 

(BioRoss) 

Focal issues New Zealand waters have globally significant levels of marine biodiversity, 

and productivity particularly coastal habitats, offshore island habitats and 

underwater topographical features such as seamounts, and canyons. With the 

exception of shallow sea ice impacted coastal habitats, these features apply 

also to the Ross Sea region. Adjacent international waters in the SPRFMO 

area contain areas likely to constitute Vulnerable Marine Ecosystems 

Key progress 

2011-12 

(VMEs), 

• Predictive habitat modelling has identified potential areas of VMEs in 

SPRFMO areas 

• Significant progress has been made on mapping deepsea fisheries 

habitat at risk from ocean acidification; research on shellfish has 

identified thermal stress and ocean acidification as two areas of concern 

for New Zealand in an increasing CO2 world. 

• Progress has been made towards developing a national Marine 

Environmental Monitoring Programme 

• A major project on changes in marine shelf systems over the past 1000 

years has almost reached completion. 

• IPY and Chatham Challenger completed with many outputs and 

leveraging opportunities 

Emerging issues • The combined effects of multiple stressors arising from climate change 

and a range of otheranthropogenic activities on biodiversity and marine 

ecosystems (structure and function) are likely to be large and complex. 

• Keen interest in the development of ecosystem approaches to marine 

resource management is developing. 

• The nature and functional role of marine microbial biodiversity in large 

scale biogeochemical and ecosystem processes are important but not 

well understood. 

• Genetic and life-history stage connectivity between and within large 

scale habitats may be important to the size and placement of protection 

zones. 

• Apart from fisheries data, long-term (eg decadal to millenia) 

observations of variability and change in the marine environment 

(including biodiversity) are not yet generally available at geographic 

scales appropriate for national reporting . 

• Metrics for assessing the effectiveness of current protection measures in 

safeguarding marine biodiversity and aquatic ecosystem health in NZ 

and Ross Sea region are inadequate. 

• Economic value of ecosystem goods and services provided by marine 

biodiversity to current and future generations are not addressed in 

extractive business models. 

• Marine biodiversity and its monitoring, loss reduction and enhancement 

229

MPI Research 

(current) 

NZ Research and 

associated 

initiatives (current) 

Links to Fisheries 

2030 and MPI’s 

Our Strategy 2030 

Related 



are emerging requirements for signatories (including New Zealand) to 

the CBD Aichi-Nagoya Agreement 2010 

• Geo-engineering methods including ocean fertilisation continues to be 

advocated in some areas of international climate change mitigation 

• Meeting New Zealand responsibilities participate in international data 

collection programmes, e.g., IMOS, SOCPR ARGO, BIO-ARGO, 

55 biodiversity projects commissioned over the period 2000-12; Currently in 

4th year of a 5 year programme to address seven science objectives in the 

Biodiversity Programme: 1 characterisation and description; 2 ecosystem 

scale biodiversity; 3 functional role of biodiversity; 4 genetics; 5 ocean 

climate effects; 6 indicators; 7 threats to biodiversity. MPI biodiversity 

research has strong synergies with marine research funded by MPI Aquatic 

and Environment Working Group (AEWG), Ministry of Business Innovation 

and Employment (MBIE), Department of Conservation (DOC), Land 

Information New Zealand (LINZ), other sections within the Ministry for 

Primary Industries (MPI), Ministry for the Environment (MfE),Statistics New 

Zealand (Stats NZ), Te Papa and Crown Research Institutes 

Research programmes and database initiatives on Marine Biodiversity are run 

at University of Auckland (World Register of Marine Species (WoRMS), 

marine reserves, rocky reef ecology, Ross Sea meroplankton, genetics); 

Auckland University of Technology, University of Waikato (soft sediment 

functional ecology and biodiversity), Victoria University of Wellington 

(monitoring marine reserves, population genetics), University of Canterbury 

(intertidal and subtidal ecology, kelp forests and biodiversity), University of 

Otago (land-use effects, bryozoans, inshore ecology, ocean acidification), 

National Institute of water and Atmospheric Research (NIWA) and Cawthron 

Institute. Former MBIE programmes i.e., Coasts & Oceans OBI C01X0501, 

Marine Biodiversity & Biosecurity OBI C01X0502, are now part of Core 

Funding managed by NIWA through the Coast and Oceans Centre; Protecting 

Ross Sea Ecosystems C01X1001, Climate Change Effects in the Ross Sea 

C01X1226, Coastal Conservation Management C01X0907, Impacts of 

resource use on vulnerable deep-sea communities C01X0906; DOC, MPI, 

NIWA and Landcare Research - NZ Organisms Register. 

Fisheries 2030 Environmental Outcome Objective 1; environmental 

principles of Fisheries 2030 include: Ecosystem-based approach, Conserve 

biodiversity: Environmental bottom lines, Precautionary approach, 

Responsible international citizen, Inter-generational equity, Best available 

information, Respect rights and interests (MPI 2009). MPI’s Strategy “Our 

Strategy 2030”: two key stated focuses are to maximise export opportunities 

and improve sector productivity; increase sustainable resource use, and 

protect from biological risk 

Multiple use, land-based effects, variability and change, marine monitoring, 

cumulative effects of use and extraction in the marine environment, protected 

areas; benthic impacts, ecosystem approaches to fisheries and marine 

resource management. 

230

11.1. Introduction 


This chapter summarises the development and progress of the MPI Marine Biodiversity Research 

Programme 2000-2012 and reviews the work commissioned in the context of national and global 

concerns about biodiversity and the maintenance of the marine ecosystem in a healthy functioning 

state, as identified by the New Zealand Biodiversity Strategy (NZBS, Anon 2000). 

11.1.1. Halting the decline in biodiversity 

In June 2000, the ‘New Zealand Biodiversity Strategy– Our Chance to Turn the Tide’ (NZBS) with the 

over-arching objectives “to halt the decline of biodiversity in New Zealand and protect and enhance 

the environment” was launched as part of New Zealand’s commitment to the international Convention 

on Biological Diversity 1993 (Anon 2000). To meet long-term goals of the NZBS, a comprehensive 

plan, with stated objectives and actions 

1 , was developed to address biodiversity issues in terrestrial, freshwater and marine systems. The 

Desired Outcomes by 2020 for the marine environment (Coasts and Oceans, Theme 3) in the NZBS 

were stated as: 

• “New Zealand's natural marine habitats and ecosystems are maintained in a healthy 

functioning state and degraded marine habitats are recovering. 

• A full range of marine habitats and ecosystems representative of New Zealand's indigenous 

marine biodiversity is protected. 

• No human-induced extinctions of marine species within New Zealand's marine environment 

have occurred. 

• Rare or threatened marine species are adequately protected from harvesting and other human 

threats, enabling them to recover. 

• Marine biodiversity is appreciated, and any harvesting or marine development is done in an 

informed, controlled and ecologically sustainable manner.” 

In the marine environment, biodiversity decline is characterised not only by extinctions or reduction 

in species richness and abundance, but also by environmental degradation such as species invasion 

and hybridisations, habitats that have been diminished or removed, and the disruption of ecosystem 

structure and function, as well as ecological processes (e.g. biological cycling of water, nutrients and 

energy). Measuring the decline of marine biodiversity is complicated by the ‘shifting baseline 

syndrome’, a common obstacle to useful biodiversity assessment and monitoring 2 . Furthermore the 

size range of organisms sampled is often limited to macroscopic. Changes (declines) in biodiversity 

metrics at a macroscopic level may not detect potentially large changes in biodiversity in smaller 

sized organisms below our sampling threshold that may also be critical to marine ecosystem health 

and well-being. 

Responsibility for addressing Theme 3 of the Biodiversity Strategy was allocated across government 

departments with active roles in the management of the marine environment, including the 

Department of Conservation (DOC), the Ministry for Environment (MfE), and the Ministry of 

Fisheries (now MPI) 3 . 

1 

The New Zealand Biodiversity Strategy with its stated goals, objectives and actions can be viewed at 

http://www.biodiversity.govt.nz 

2 

A National Approach to Addressing Marine Biodiversity Decline (Australian Government-available on line at 

www.environment.gov.au/coasts/publications/marine-diversity-decline/index.html 

3 

https://www.biodiversity.govt.nz/picture/doing/programmes/index.html 

231

11.1.2. Defining biodiversity 


New Zealand’s Biodiversity Strategy defines biodiversity as: 

“The variability among living organisms from all sources including inter alia, terrestrial, marine and 

other aquatic ecosystems and the ecological complexes of which they are a part [as defined by the 

CBD]; this includes diversity within species, between species and of ecosystems [as further 

disaggregated for New Zealand purposes]. Components include: 

• Genetic diversity: the variability in the genetic make-up among individuals within a 

single species. In more technical terms, it is the genetic differences among populations of 

a single species and those among individuals within a population. 

• Species diversity – the variety of species—whether wild or domesticated— within a 

particular geographic area. 

• Ecological diversity – the variety of ecosystem types (such as forests, deserts, grasslands, 

streams, lakes wetlands and oceans) and their biological communities that interact with 

one another and their non-living environments.” 

MPI’s Biodiversity programme is concerned primarily with research to underpin NZBS Theme 3: 

Biodiversity in Coastal and Marine Ecosystems: 

“Coastal and marine ecosystems include estuaries, inshore coastal areas and offshore areas, and 

all the resident and migratory marine species that live in them. 

New Zealand’s ocean territory (including territorial sea and the recent continental shelf extension 4 ) is 

very large relative to the area of land 5 and includes some 15-18,000 kilometres of coastline extending 

from the sub-tropical north to the cool Subantarctic waters to the south. New Zealand also has a rich 

marine biodiversity that has been recognised as being globally significant with up to 44% estimated as 

endemic and comprising up to 10% of global marine biodiversity Gordon et al. 2010. 

An estimated 34,400 marine species and associated ecosystems around New Zealand deliver a wide 

range of environmental goods and services that sustain considerable fishing, aquaculture and tourism 

industries as well as drive major biogeochemical and ecological processes. Several factors would 

suggest that this estimate of marine species number is conservative. Such factors include the region’s 

size, the depth range, geomorphological and hydrological complexity as well as limited water column 

sampling and limited benthic sampling, especially below 1500 metres. If recent indications of massive 

oceanic microbial diversity are taken into account (e.g. Sogin et al. 2006) then the number above is 

certainly conservative. 

New Zealand’s marine biodiversity is affected by many uses of the marine environment, particularly 

fishing, aquaculture, shipping, petroleum and mineral extraction, renewable energy, tourism and 

recreation 6 . Impacts from changing land use, including agricultural, urban run-off and coastal 

development can also affect marine biodiversity (Morrison et al. 2009). The potential loss of marine 

biodiversity and possible functionality caused by climate change and ocean acidification are of 

increasing concern worldwide (e.g., Guinotte et al., 2006; Ramirez-Llodra et al. 2011; as well as in 

New Zealand–see NZ Royal Society Workshop papers 7 ). The growing arrival of non-indigenous 

4 http://www.mfat.govt.nz/Treaties-and-International-Law/04-Law-of-the-Sea-and-Fisheries/NZ-Continental- 

Shelf-and-Maritime-Boundaries.php 

5 2 th 

NZ sea area is ~5.8 million km including TS, EEZ and continental shelf extension; 4 largest in the world; 

www.linz.govt.nz 

6 

http://www.royalsociety.org.nz/media/Future-Marine-Resource-Use-web.pdf 

http://www.stats.govt.nz/browse_for_stats/environment/natural_resources/fish.aspx 

7 

: http://www.royalsociety.org.nz/publications/policy/yr2009/ocean-acidification-workshop/ 

232


(sometimes invasive) marine species is also a threat to local biodiversity (e.g., Coutts and Dodgshun 

2003, Cranfield et al. 2003, Gould et al. 2008 Russel et al. 2008, Williams et al. 2008). 

Understanding about New Zealand’s coastal marine environment and its land-sea interactions has 

progressed although knowledge about the state of the marine environment and marine biodiversity on 

a national scale remains limited. Current knowledge about New Zealand’s and the Ross Sea’s marine 

biodiversity suggests that it may generally be in better shape than that of many other countries 

(Costello et al. 2010, Gordon et al. 2010). However, New Zealand is less well placed when it comes 

to understanding the threats to marine biodiversity (Costello et al. 2010, MacDiarmid et al. 2012) and 

the nature of their impacts. There are significant concerns with the decline of some key species (MfE 

2007), localised impacts on habitats and conditions (Thrush and Dayton 2002, Cryer et al. 2002, Clark 

et al. 2010a., Gordon et al. 2010, Clark & Dunn 2012) and emerging threats to the marine 

environment (MacDiarmid et al. 2012) despite the combined efforts of New Zealand’s government 

and stakeholders. Global scale threats associated with the potential effects of ocean acidification on 

microbial diversity and their roles in biogeochemical processes have yet to be quantified but could 

have EEZ wide implications (Bostock et al. 2012). 

New Zealanders increasingly value environmental, economic and social aspects of marine 

biodiversity and the ecosystem services that a healthy marine environment provides. They also value 

the need to sustainably manage the use of coastal and marine environments and maintain biological 

diversity as reflected by recent policy statements by the New Zealand Government. 8 9 A broad range 

of legislation, regulations and policies are in place to manage and regulate uses of the marine 

environment, to protect marine biodiversity, to improve management of the coastal and marine 

environment and to meet world-wide consumer demands for improved sustainability. The most recent 

introduction is the Exclusive Economic Zone and Continental Shelf (Environmental Effects) Act 2012 

which will come into effect once the first set of regulations is promulgated. However, progress on an 

integrated oceans policy and strategic direction for implementation of New Zealand’s Biodiversity 

Strategy has been slow compared with other countries such as Canada, the UK, the USA and 

Australia (Peart et al. 2011). 

11.1.3. Implementation of New Zealand’s Biodiversity Strategy 

A number of initiatives have been supported by MPI to meet the goals of the NZBS. Commitments 

include the creation of NABIS (the National Aquatic Biodiversity Information System) 10 , the 

administration of the MPI Biodiversity Research Programme, convening and chairing the Biodiversity 

Research Advisory Group 11 , and developing a Marine Protected Area policy with DOC. DOC also 

surveys and monitors aspects of marine biodiversity, particularly in marine reserves 12 . MfE has 

encouraged Regional Councils to develop coastal monitoring programmes and with MPI and DOC, 

initiated an approach to Marine Environmental Classification 13 . Biodiversity related research has also 

been carried out through MPI’s Biosecurity Science Strategy. One result includes mapping and 

valuation of marine biodiversity around New Zealand’s coastline 14 . 

8 

MfE Proposed National Policy Statement on Indigenous Biological Diversity (biodiversity) under the 

Resource Management Act 1991 www.mfe.govt.nz/publications/biodiversity/indigenous-biodiversity/proposednational-policy-statement/statement.pdf 

9 

New Zealand Coastal Policy Statement 2010 www.doc.govt.nz/conservation/marine-and-coastal/coastalmanagement/nz-coastal-policy-statement/ 

10 

NABIS is an interactive database accessible at www.nabis.govt.nz 

11 

www.fish.govt.nz/en-nz/Research+Services/Background+Information/Biodiversity+background.htm 

12 

www.doc.govt.nz 

13 

www.mfe.govt.nz/issues/biodiversity/initiatives/marine.html#regional 

14 

www.biosecurity.govt.nz/biosec/research 

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Marine biodiversity research is also supported through public good funding and is conducted mainly 

by Universities and CRIs. Both have contributed to New Zealand’s high profile on the international 

scientific network for marine biodiversity through participation in global initiatives such as the 

Census of Marine Life as well as to local programmes that have improved understanding of the role of 

biodiversity in the marine ecosystem. The Museums of Auckland, Canterbury, Otago and Wellington 

(Te Papa) also conduct biodiversity sampling expeditions and national collections of specimens have 

been set up within Museums and also at NIWA. Regional Councils give effect to NZBS; Coastal 

Biodiversity Policy Statement 2011, protected areas and spatial planning. 

11.1.4. New challenges and agendas 

Since the launch of the Biodiversity Stratey, there have been substantial changes in Government goals 

for New Zealand. In July 2009, the Minister of Science set an overarching goal for research science 

and technology 15 : 

“to improve New Zealand’s economic performance while continuing to strengthen our society 

and protect our environment”. 

This goal is reflected in first progress report on “Building Natural Resources” as part of the Business 

Growth Agenda 16 released December 2012. The Business Growth Agenda sets an ambitious goal of 

increasing the ratio of exports to GDP to 40% by 2025. Meeting the target will require the value of 

our exports to double in real terms by 2025. The report states that one of the goals is to “Make the 

most of the considerable opportunities for New Zealand to gain much greater value from its extensive 

marine and aquaculture resources”. 

The biological economy of the sea (currently largely fisheries and aquaculture, oil and gas, minerals) 

is a significant part of the overall economy and may have potential for growth (e.g. unlocking the 

potential of the fisheries sector–Fisheries 2030 (MPI 2009 17 ). It is essential that the aquatic 

environment and biodiversity on which industry depends are not adversely affected by these or other 

impacting activities. 

Bodies such as the Marine Stewardship Council (MSC 18 ) require fisheries to satisfy stringent 

environmental requirements to achieve certification. Many fisheries management systems throughout 

the globe have begun to develop policies that are ecosystem based. Implementation has met with 

varied success, and measurement of success is a challenge. 

The large scale threats to the marine environment posed by increasing global impacts of 

anthropogenic stressors such as climate change and ocean acidification, increasing exploitation of 

resources (living or non-living) and the cumulative effect of multiple uses of the marine environment 

(e.g., renewable energy, commercial fisheries, recreational fisheries, aquaculture, hydrocarbon and 

mineral extraction) remain. 

Scientific research has provided information about the predicted distribution and abundance of marine 

biodiversity in some areas of New Zealand’s coasts and oceans, but progress on validation in areas 

that remain unsampled has been slow. The structure and function of biodiversity of macrofauna within 

some New Zealand and Ross Sea marine ecosystems is well understood and available information has 

15 

MoRST feedback document on New Zealand’s research science and technology: 

www.morst.govt.nz/Documents/publications/policy 

16 

https://www.mbie.govt.nz/what-we-do/business-growth-agenda/pdf-folder/BGA-Natural-Resources-report- 

December-2012.pdf 

17 

MFish (2009). Fisheries 2030 report. New Zealanders maximising benefits from the use of fisheries within 

environmental limits available from http://www.fish.govt.nz/en-nz/Fisheries+2030/default.htm 

18 

Marine Stewardship Council www.msc.org 

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been used to assess the habitat types at greatest risk from disturbance, particularly fishing. However, 

the proportions of marine habitat types should be or can be protected to maintain a healthy aquatic 

environment is unknown. 

There is growing awareness of the likely importance of the huge diversity, biomass and species mix of 

micro-organisms, nano- and pico-plankton, and is a fast developing field of research. The rate of 

change and the resilience of biodiversity to the cumulative effect of multiple stressors across large 

spatial scales (e.g. ocean acidification, temperature increase and oxygen depletion), particularly as 

utilisation of marine resources increases, remain semi-quantified (Ramerez-Llodra et al. 2011). 

Understanding the dynamics of climate change and predicting the impacts on food webs and fisheries 

are only just being investigated (e.g., Fulton 2004, Brown et al. 2010, Garcia and Rosenberg 2010). 

11.2. Global understanding and developments 

In April 2002, the Parties to the Convention on Biological Diversity (CBD) committed to achieve by 

2010 a significant reduction of the current rate of biodiversity loss at the global, regional and national 

level as a contribution to poverty alleviation and to the benefit of all life on Earth. This target was 

subsequently endorsed by the World Summit on Sustainable Development and the United Nations 

General Assembly and was incorporated as a target under the Millennium Development Goals 19 . 

The third edition of the Global Biodiversity Outlook confirmed that the 2010 biodiversity target had 

not been met, and the CBD 2010 Strategic Plan notes that “actions [to achieve the 2010 target] have 

not been on a scale sufficient to address the pressures on biodiversity 20 . Moreover there has been 

insufficient integration of biodiversity issues into broader policies, strategies, programmes and 

actions, and therefore the underlying drivers of biodiversity loss have not been significantly reduced”. 

The Strategic Plan includes a new series of targets for 2020 under the heading “Taking action now to 

decrease the direct pressures on biodiversity”. The Strategic Plan for 2011–2020 was updated, 

revised and adopted by over 200 countries, including New Zealand 21 . 

The eleventh meeting of the Conference of the Parties to the Convention on Biological Diversity (held 

8-19 Oct 2012) 22 generated some agreed outcomes of relevance for New Zealand, in particular: 

• There was confirmation that the application of the scientific criteria for EBSAs and the 

selection of conservation and management measures is a matter for states and relevant intergovernmental 

bodies but that it is an open and evolving process that should continue to allow 

ongoing improvement and updating as new information comes to hand 

• It was recognised that there was a need to promote additional research and monitoring in 

accordance with national and international laws, to improve the ecological or biological 

information in each region with a view to facilitating the further description of the areas 

described 

• There is a tentative schedule of further regional workshops to facilitate the description of 

areas meeting the criteria for EBSAs. 

19 UNEP's work to promote environmental sustainability, the object of Millenium Development Goal 7, 

underpins global efforts to achieve all of the Goals agreed by world leaders at the Millennium Summit 

http://www.unep.org/MDGs/ 

20 www.cbd.int/2010-target 

21 draft updated and revised Strategic Plan for the Convention on Biological Diversity for the post-2010 period 

(UNEP/CBD/WG-RI/3/3) http://www.cbd.int/nagoya/outcomes/ 

22 http://www.cbd.int/doc/?meeting=cop-11 UNEP/CBD/COP/11/23 Marine and Coastal Biodiversity: 

Revised Voluntary Guidelines for the Consideration of Biodiversity in Environmental Impact Assessments and 

Strategic Environmental Assessments in Marine and Coastal Areas 

235


New Zealand government agencies will need to consider how to update the NZBS to better align with 

the Aichi Biodiversity targets. 

11.2.1. The decade of biodiversity 2011-2020 

The United Nations General Assembly at its 65th session declared the period 2011-2020 to be “the 

United Nations Decade on Biodiversity, with a view to contributing to the implementation of the 

Strategic Plan for Biodiversity for the period 2011-2020” (Resolution 65/161). It will serve to support 

and promote implementation of the objectives of the Strategic Plan for Biodiversity and the Aichi- 

Nagoya Biodiversity Targets. The principal instruments for implementation are to be National 

Biodiversity Strategies and Action Plans or equivalent instruments (NBSAPs). CBD signatory nations 

are expected to revise their NBSAPs and to “ensure that this strategy is mainstreamed into the 

planning and activities of all those sectors whose activities can have an impact (positive and negative) 

on biodiversity” (http://www.cbd.int/nbsap/). Throughout the United Nations Decade on Biodiversity, 

governments are encouraged to develop, implement and communicate the results of progress on their 

NBSAPs as they implement the CBD Strategic Plan for Biodiversity. 

There are five strategic goals and 20 ambitious yet achievable targets. Collectively known as the 

Aichi Targets, they are part the Strategic Plan for Biodiversity. The five Strategic Goals are: 

• Goal A - Address the underlying causes of biodiversity loss by mainstreaming biodiversity 

(NBSAPs) across government and society 

• Goal B - Reduce the direct pressures on biodiversity and promote sustainable use 

• Goal C - Improve the status of biodiversity by safeguarding ecosystems, species and genetic 

diversity 

• Goal D - Enhance the benefits to all from biodiversity and ecosystem services 

• Goal E - Enhance implementation through participatory planning, knowledge management and 

capacity building 

Targets 6-11 specifically refer to fisheries and marine ecosystems and are provided in Appendix 1 to 

this Chapter. 

The CBD also calls for renewed efforts specifically on coastal and marine biodiversity: “The road 

ahead for coastal areas lies in better and more effective implementation of integrated marine and 

coastal area management in the context of the Convention’s ecosystem approach. This includes 

putting in place marine and coastal protected areas to promote the recovery of biodiversity and 

fisheries resources and controlling land-based sources of pollution. For open ocean and deep sea 

areas, sustainability can only be achieved through increased international cooperation to protect 

vulnerable habitats and species.” 23 The CBD held regional workshops during 2011 to identify 

information sources that might inform the location of Ecologically or Biolologically Sensitive Areas 

(EBSAs). New Zealand participated in the SW Pacific workshop, and EBSAs were identified 24 The 

criteria for identifying EBSAs and Vulnerable Marine Ecosystems as recommended through UNGA 

and managed by Regional Fisheries Management Organisations 25 . The 2012 SPRFMO Science 

Working Group noted that the differing approaches to identifying VMEs and EBSAs could lead to 

conflicts in how areas possible in need of protection are defined. 

23 www.cbd.int/marine/done.shtml 

24 www.cbd.int/doc/meetings/cop/cop-11/official/cop-11-03-en.doc 

25 http://www.un.org/Depts/los/consultative_process/documents/no4_spc2.pdf 

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11.2.2. Global marine assessment 

The biological diversity of the 72% of the planet covered by seawater is a crucial component of global 

resource security, ecosystem function and to climate dynamics. The Marine Biodiversity Outlook 

Reports and Summaries prepared by UNEP’s Regional Seas Programme for the 10th Conference of 

Parties of the Convention on Biological Diversity (CBD) held in 2010 provide the first systematic 

overview at a sub-global scale of the state of knowledge of marine biodiversity, the pressures it faces 

currently and the management frameworks in place for addressing those pressures 26 . 

The regional reports reflect a poor outlook for the continuing well being of marine biodiversity, which 

faces increasing pressures in all regions from land sourced pollution, ship sourced pollution and 

impacts of fishing. These pressures are serious and generally increasing despite measures in place to 

address them. They are amplified by predicted impacts of ocean warming, acidification and habitat 

change arising from climate and atmospheric change. Without significant management intervention 

marine biological diversity is likely to deteriorate substantially in the next 20 years with growing 

consequences for resource and physical security of coastal nations. 

With respect to fisheries, the main findings of the reports are that in most regions fisheries peaked at 

some point between the mid-1980s and mid-2000s that catch expansion is not possible in many cases 

and that increased exploitation levels would lead to lower catch levels. 

All regions report increases in shipping at levels which generally reflect annual economic growth. All 

regions report progress in the establishment of Marine Protected Areas but current levels of 1.2% of 

global ocean surface or 4.3% of continental shelf areas fall far short of the 10% target set by CBD 

COP7 in 2004. It is likely to be many years before this target is reached. The figures do not include 

some managed fishery areas that have objectives consistent with multiple sustainable use and overall 

objectives for conservation but even if these are taken into account the proportion managed with 

objectives that explicitly address sustainability of biodiversity or ecosystem processes is inadequate. 

The need to plan and implement ecosystem scale and ecosystem-based management of the seas is 

urgent. 

After many years of international negotiations on the need to strengthen the science‐policy interface 

on biodiversity and ecosystem services at all levels, more than 90 governments (including New 

Zealand) agreed in April 2012 to officially establish the Intergovernmental Science-Policy Platform 

on Biodiversity and Ecosystem Services (IPBES) 27 . It will be a leading global body providing 

scientifically sound and relevant information to support more informed decisions on how biodiversity 

and ecosystem services are conserved and used around the world. 

The United Nations Conference on Sustainable Development (UNCSD), also known as the Rio+20 

Conference (June 2011) 28 had a strong sustainability focus and generated an outcome document 

entitled "the future we want" which had a section on oceans (para 158 - 177) including: 

• Support for the Regular Process of Global Reporting and Assessment of the State of the 

Marine Environment established under the General Assembly and looked forward to the 

completion of the first global integrated assessment of the state of the marine environment by 

2014 29 . 

26 UNEP (2003) Global Marine Assessments: a survey of global and regional marine environmental assessments 

and related scientific activities. UNEP-WCMC/UNEP/UNESCO-IOC. 132p available online at www.unepwcmc.org/resources/publications/ss1/GMA_Review.pdf 

27 http://www.iucn.org/what/ 

28 http://sustainabledevelopment.un.org/futurewewant.html Rio +20 outcome document 

29 Integrated assessment of the state of the marine environment by 2014. 

http://www.un.org/depts/los/global_reporting/Santiago_Regular_Proceess_Workshop_Presentations/GRAME_ 

Outline_of_the_First_Integrated_Assessment_Report.pdf 

237


• The ongoing work of the Ad Hoc Open-ended Informal Working Group on Study Issues 

Relating to the Conservation and Sustainable Use of Marine Biodiversity Beyond Areas of 

National Jurisdiction and the wish to, by the end of the 69th session (2014) make a decision 

about the development of an international instrument under UNCLOS. 

• A concern about the health of oceans and marine biodiversity and the work of the IMO and 

relevant conventions including initiatives like the London Protocol on ocean fertilisation and 

teh global programme of action for the protection of the marine environment from land based 

activities. 

• The Rio+20 outcome also endorsed a process to develop sustainable development goals (to 

apply to all countries) which will include oceans issues. (This is still in its nascent stage and a 

clear work programme will be finalised by Sept 2013). 

11.2.3. Ocean climate change and ocean acidification 

Ocean climate change at the global scale overshadows the existing challenges of managing local 

impacts causing declines in marine biodiversity in the face of current levels of human use and impact. 

The projected increases in temperature, acidity, severe storm incidence and sea level present major 

challenges for biodiversity management. This is reflected in changes at the Great Barrier Reef in 

Australia, which is a globally iconic marine ecosystem that has been subject to adaptive scientificallybased 

ecosystem-based management for more than 30 years. An Outlook Report by the Great Barrier 

Reef Marine Park Authority (2009) concluded that “without significant additional management 

intervention, some components of the ecosystem will deteriorate in the next 20 years and only a few 

areas are likely to be healthy and resilient in 50 years.” Without strong ecosystem based management 

the global threats to marine biodiversity may be similar and their implications for food and physical 

security could be substantial. 

The Outlook Report provides a reasonable understanding of the nature and extent of the problems 

facing marine biodiversity and marine resources. There are examples of effective actions to address 

some of these problems but management performance is generally insufficient and inadequately 

coordinated to address the growing problems of marine biodiversity decline and ecosystem change. 

Climate change can adversely impact on the spatial patterns of marine biodiversity and ecosystem 

function through changes in species distributions, species mix and habitat availability, particularly at 

critical stages of species life histories. A study of the global patterns of climate change impacts on 

ocean biodiversity projected the distributional ranges of a sample of 1066 exploited marine fish and 

invertebrates for 2050 using a newly developed dynamic bioclimate envelope model which showed 

that climate change may lead to numerous local extinctions in the sub-polar regions, the tropics and 

semi-enclosed seas (Cheung et al. 2009). Simultaneously, species invasion is projected to be most 

intense in the Arctic and the Southern Ocean. With these elements taken together, the model predicted 

dramatic species turnovers of over 60% of the present biodiversity, implying ecological disturbances 

that potentially disrupt ecosystem services (Cheung et al. 2009). 

The World Bank, together with IUCN and Environmental Services Association released a brief for 

decision-makers entitled, "Capturing and Conserving Natural Coastal Carbon – Building Mitigation, 

Advancing Adaptation 30 ". This brief highlights the crucial importance of carbon sequestered in 

coastal wetlands and in submerged vegetated habitats such as seagrass beds, for climate change 

mitigation. 

30 UNFCCC COP-16 event. Cancun Messe, Jaguar. ‘Blue Carbon: Valuing CO2 Mitigation by Coastal Marine 

Systems. Sequestration of Carbon Along Our Coasts: Are We Missing Major Sinks and Sources?’ 

238


The Intergovernmental Panel on Climate Change (IPCC) is preparing material for the 5 th IPCC Report 

in 2014 and for the first time includes chapters to explicitly address ocean climate change issues 31 . 

The Working Group I and Working Group II Contributions to the Fifth Assessment Report include 

chapters on the ocean (WG I) and Climate Change 2014: Impacts, Adaptation, and Vulnerability 

including Chapters on Coastal and Oceans ecosystems, and sections on biodiversity(WGII). Working 

Group I will consider "Ocean biogeochemical changes, including ocean acidification" in their Chapter 

3 (Observations - Ocean), and "Processes and understanding of changes, including ocean 

acidification" in their Chapter 6 on "Carbon and other biogeochemical cycles". Working Group II will 

consider "Water property changes, including temperature and ocean acidification" in their Chapter 6 

on "Ocean Systems". In addition, "Carbon Cycle including Ocean Acidification" has been identified 

as a "Cross-Cutting Theme" across (predominantly) WG1 and WG2. 

Hobday et al. (2006) reported on the relative risks and likely impacts of ocean climate change and 

ocean acidification to marine life in Australian waters (Figure 11.1). This approach was extremely 

useful for summarising risks and threats of climate change on marine systems to policy makers and 

the subsequent development of the Commonwealth Environment Research Facilities (CERF) Marine 

Biodiversity Hub in Australia 32. 

The Hub analysed patterns and dynamics of marine biodiversity through four research programmes to 

determine the appropriate units and models for effectively predicting Australia’s marine biodiversity. 

These programmes were designed to develop and deliver tools needed to manage Australia’s marine 

biodiversity in a changing ocean climate. The final report from three years intense research is 

available at the website 33. Australia also has The Marine Adaptation Network that comprises a 

framework of five connecting marine themes (integration; biodiversity and resources; communities; 

markets and policy) that cut across climate change risk, marine biodiversity and resources, socioeconomics, 

policy and governance, and includes ecosystems and species from the tropics to 

Australian Antarctic waters 34 . 

In late June 2011, two science-based reports heightened concerns about the critical state of the 

world’s oceans in response to ocean climate change. One focuses on the potential impacts of ocean 

acidification on fisheries and higher trophic level ecology and takes a modelling approach to scaling 

from physiology to ecology (Le Quesne and Pinnegar 2011) and the other assesses the critical state of 

the world’s oceans in relation to climate change and other stressors (Rogers and Laffoley (2011). 

11.2.1. Census of Marine Life 2000–2010 

In 2010, the international initiative to conduct a Census of Marine Life 35 was concluded after ten 

years of accessing and databasing existing records, sampling and exploration around the globe. The 

Census is an unprecedented collaboration among researchers from more than 80 nations to assess and 

explain the diversity, distribution, and abundance of life in the oceans. During the last decade, the 

2,700 scientists involved in the Census have mounted 540 expeditions, identified more than 6,000 

potentially new species, catalogued upward of 31 million distribution records, and generated 2,600 

scientific publications. NIWA scientists were part of the team that led CenSeam 36 , the seamount 

component of the Census of Marine Life, and scientists from NIWA and the University of Auckland 

played significant roles in a number of other programmes.The New Zealand IPY-CAML voyage to 

the Ross Sea in 2008 was a major contribution to CAML. 

31 http://www.global-greenhouse-warming.com/IPCC-5th-Report.html 

32 www.marinehub.org/ 


34 arnmbr.org/content/index.php/site/aboutus/ 

35 www.coml.org/results-publications 

36 www.coml.org/global-census-marine-life-seamounts-censeam 

239


Figure 11.1: Potential biological impacts of climate change on Australian marine life. The ratings in this table are 

based on the expected responses to predicted changes in Sea Surface Temperature (SST), salinity, wind, pH, mixed 

layer depth and sea level, and from literature reviews for each species group. The implicit assumption underlying this 

table is that Australian marine species will respond in similar ways to their counterparts throughout the world 

(Hobday et al. 2006.) Note: phenology means life cycle. 

The Census increased the total number of known marine species by about 20,000, from 230,000 in 

2000 to about 250,000 in 2010. Among the millions of specimens collected in both familiar and 

seldom-explored waters, the Census found more than 6,000 potentially new species and completed 

formal descriptions of more than 1,200 of them. It also found that some species considered to be rare 

are more common than previously thought (Ausubel et al. 2010). The digital archive (the Ocean 

Biogeographic Information System OBIS (http://www.iobis.org/) has now grown to 31 million 

observations, and the Census compiled the first regional and global comparisons of marine species 

diversity. It helped to create the first comprehensive list of the known marine species, and also helped 

to compose web pages for more than 80,000 species in the Encyclopaedia of Life 37 . 

Applying genetic analysis on an unprecedented scale to a dataset of 35,000 species from widely 

differing major groupings of marine life, the Census graphed the proximity and distance of relations 

37 www.eol.org/ 

240


among distinct species, providing new insight into the genetic structure of marine diversity. With the 

genetic analysis often called barcoding, the Census sometimes decreased diversity but generally its 

analyses expanded the number of species, especially the number of different microbes, including 

bacteria and archaea. 

The Census has overwhelmingly demonstrated that the total number of species in the ocean remain 

largely unknown. The Census also demonstrated that evidence of human impacts on the oceans 

extends to all depths and habitats and that we still have much to learn to integrate use of resources 

with stewardship of a healthy marine ecosystem. The Census results could logically extrapolate to at 

least a million kinds of eukaryotic marine life that earn the rank of species and to tens or even 

hundreds of millions of kinds of microbes. 

A summary of the overall state of knowledge about marine biodiversity after the Census by Costello 

et al. (2010) places New Zealand 6 th out of 18 national regions based on the collective knowledge 

assembled by the Census National and Regional Implementation Committees (NRIC) and comparing 

the Spearman rank correlation coefficients between known diversity (total species richness, alien 

species, and endemics) and available resources, such as numbers of taxonomic guides and experts. 

(Figure 11.2). 

Figure 11.2: The regions are ranked by their state-of-knowledge index (mean ± standard error) across taxa. Dashed 

line represents the overall mean. (Image Source Costello et al. 2010). 

All NRICs reported what they considered the main threats to marine biodiversity in their region, 

citing published data and expert opinions. Although the reports were not standardised, the threats 

identified were grouped into several overarching issues. We integrated these data on biodiversity 

threats so as to rank each threat from 1 (very low) to 5 (very high threat) in each region. New Zealand 

was placed 12 th out of 1 8 regions in terms of overall threat levels to biodiversity, overfishing and 

alien species invasion. Habitat loss and ocean acidification were identified as the biggest threats to 

marine biodiversity in New Zealand (Costello et al. 2010). 

241


11.2.2. Global monitoring and indicators for marine biodiversity 

There are numerous schemes within and between nations to monitor the marine environment, 

including physical, chemical and biological components. Marine biodiversity indicators have been 

developed for the UK and the EU 38 . Marine environmental monitoring networks have been developed 

in the USA, Canada, Australia and South Africa. Global networks include the Global Ocean 

Observing System (GOOS) which is a permanent global system for observations, modelling and 

analysis of marine and ocean variables; Global Climate Observing System (GCOS 39 ) which 

stimulates, encourages, coordinates and otherwise facilitates observations by national or international 

organizations. A Southern Ocean Observing System (SOOS) is under development. 40 

Others include: 

• ARGO an international deepwater monitoring system of free floating buoys that are part of 

the integrated global observation strategy 41 . 

• The Ocean Observation Systems (OOS) in Canada have demonstrated many positive benefits. 

• The Continuous Plankton Recorder (CPR) Surveys have been collecting data from the North 

Atlantic and the North Sea on the ecology and biogeography of plankton since 1931 42 . Sister 

CPR surveys around the globe include the SCAR SO-CPR Survey established in 1991 by the 

Australian Antarctic Division to map the spatial-temporal patterns of zooplankton and then to 

use the sensitivity of plankton to environmental change as early warning indicators of the 

health of the Southern Ocean. It also serves as reference for other monitoring programs such 

as CCAMLR's Ecosystem Monitoring Program C- EMP and the developing Southern Ocean 

Observing System 43 . 

• The Marine Environmental Change Network (MECN) is a collaboration between 

organisations in England, Scotland, Wales, Isle of Man and Northern Ireland collecting longterm 

time series information for marine waters 44 . 

• The MECN has developed links with other networks coordinating long-term data collection 

and time series. These networks include the Marine Biodiversity and Ecosystem Functioning 

European Union Network of Excellence (MarBEF 45 ) which coordinates long-term marine 

biodiversity monitoring at a European level. 

• New Zealand has now formed a partnership with Australia’s Integrated Marine Observing 

System (IMOS 46 ) was established in 2007. IMOS is designed to be a fully integrated national 

array of observing equipment to monitor the open oceans and coastal marine environment 

around Australasia, covering physical, chemical and biological variables. All IMOS data is 

freely and openly available through the IMOS Ocean Portal for the benefit of Australian and 

New Zealand marine and climate science as a whole. Oceans 2025 47 is an initiative of the 

Natural Environment Research Council (NERC) funded Marine Research Centres. This 

addresses environmental issues that require sustained long-term observations. 

A challenge for MPI and New Zealand researchers is how to assimilate any or all of the above 

monitoring approaches as a means of measuring biodiversity baseline levels and the nature and extent 

38 http://jncc.defra.gov.uk/page-4233 

39 www.ioc-goos.org/index.php?option=com_content&view=article&id=12&Itemid=26&lang=en 

40 http://www.scar.org/soos/ 

41 http://www.qc.dfo-mpo.gc.ca/publications/science/evaluation-assessment-eng.asp. 

42 www.sahfos.ac.uk/ 

43 www.sahfos.ac.uk/sister-survey/sister-surveys/-southern-ocean-continuous-plankton-recorder-survey- 

(scar).aspx 

44 http://www.mba.ac.uk/MECN/ 

45 http://www.marbef.org/ 

46 http://imos.org.au/ 

47 http://www.oceans2025.org/ 

242


of biodiversity changes, especially as a means of assessing the effectiveness of management measures 

to protect or enhance biodiversity or halt its decline. 

11.2.3. Economic valuation of biodiversity 

The national and global responsibility for New Zealand to maintain a strong environmental record in 

fisheries and other marine-based industries is increasing. There is growing awareness of international 

treaties and agreements that New Zealand is party to. Global markets are becoming increasingly 

sensitive to our national environmental record. Fishing companies who meet rigorous standards 

receive Marine Stewardship Council Certification for certain fisheries (currently, hoki trawl, southern 

blue whiting pelagic trawl and albacore tuna troll fisheries). Proposals to exploit other living marine 

resources or extract non-living marine resources are increasingly under scrutiny to ensure that such 

activities do not adversely degrade the marine environment or impact on marine living resource 

industries. 

The invisibility of biodiversity values has often encouraged inefficient use or even destruction of the 

natural capital that is the foundation of our economies. A recent international initiative “The 

Economics of Ecosystems and Biodiversity” (TEEB) 48 demonstrates the application of economic 

thinking to the use of biodiversity and ecosystem services. This can help clarify why prosperity and 

poverty reduction depend on maintaining the flow of benefits from ecosystems; and why successful 

environmental protection needs to be grounded in sound economics, including explicit recognition, 

efficient allocation, and fair distribution of the costs and benefits of conservation and sustainable use 

of natural resources. Valuation is seen as a tool to help recalibrate the faulty economic compass that 

has led to decisions about the environment (and biodiversity) that are prejudicial to both current wellbeing 

and that of future generations. 


The past 750 years of human activity have impacted on marine environments. For example, depletion 

of fur seals and sea lions occurred from the earliest days of human settlement, not just with European 

arrival (Smith 2005, 2011). There was also a pulse of sedimentation coinciding with the initial 

clearance of 40% of NZ forests within 200 years of Polynesian settlement (McWethy et al. 2010). 

Impacts have occurred near population centres, as well as more remote areas and to depths in excess 

of 1000 metres (MacDiarmid et al. 2012, Ministry for Primary Industries 2012). In some cases by 

looking back over historical records it becomes apparent how much biodiversity loss has occurred. 

Over long time spans incremental impacts can lead to major shifts in biodiversity composition. An 

analysis of marine biodiversity decline over a couple of decades could miss the major changes that 

can occur incrementally over long periods. 

While New Zealand has reasonable archaeological, historical and contemporary data on the decline in 

abundance of individual marine species, in some cases over a period of 750 years (e.g., MacDiarmid 

et al. in press), current trends in the status of New Zealand’s marine biodiversity are difficult to 

determine for several reasons. These include a lack of both pre-disturbance baseline and recent 

information, and a lack of a nationally coordinated approach to assessing and monitoring marine 

biodiversity 

A re-evaluation of the threat status of New Zealand's marine invertebrates was undertaken by the 

Department of Conservation in 2009, and identified no taxa that had improved in threat status as a 

result of past or ongoing conservation management action, nor any taxa that had worsened in threat 

48 TEEB (2010) The Economics of Ecosystems and Biodiversity: Mainstreaming the Economics of Nature: A 

synthesis of the approach, conclusions and recommendations of TEEB. www.teebweb.org/ 

243


status because of known changes in their distribution, abundance or rate of population decline 

(Freeman et al. 2010). The authors cautioned however that only a small fraction of New Zealand's 

marine invertebrate fauna had been evaluated for their threat status and that many taxa remain ‘data 

deficient’ or unlisted. 

A re-evaluation of marine mammal threat status found that relative to the previous listing, the threat 

status of two species worsened: the NZ sea lion (Phocarctos hookeri) was uplisted to Nationally 

Critical and the bottlenose dolphin (Tursiops truncatus) was uplisted to Nationally Endangered. No 

species was considered to have an improved status (See Chapter on marine mammales and also Baker 

et al. 2010). 

The most recent State of the Environment Report in New Zealand (MfE 2007) covers terrestrial and 

freshwater organisms in its Biodiversity section 49 . Comment on marine biodiversity is provided in the 

Oceans section which states: 

“Of the almost 16,000 known marine species in New Zealand, 444 are listed as threatened. 

Well-known species of particular concern include both subspecies of Hector’s dolphin, New 

Zealand sea lion, southern right whale, Fiordland crested penguin, and New Zealand fairy 

tern. Land-based pressures on the inshore marine environment, as well as pressures on 

fisheries stocks, can be expected to persist and, therefore, continue to pose a challenge to the 

health of the marine environment. The increasing number of introduced species brought to 

New Zealand through marine-based trade and travel, and climate change may exacerbate 

existing pressures. Further information about our marine environment is needed if we are to 

help set priorities for future use and protection of our oceans”. 

Two major knowledge gaps identified by MfE 2007 that hinder resource management are sparse 

biodiversity baseline information; and the lack of a systematic national-scale approach to monitoring 

biodiversity trends (i.e. by comparing subsequent studies to the baseline information) in New Zealand. 

The most recent summary of knowledge about marine biodiversity in New Zealand is provided by 

Gordon (2009, 2010, 2012) and Gordon et al. (2010). Figure 11.3 gives a tally of 17,058 living 

species in the EEZ, including 4,320 known undescribed species in collections. 

The Hub analysed patterns and dynamics of marine biodiversity through four research programmes to 

determine the appropriate units and models for effectively predicting Australia’s marine biodiversity. 

These programmes were designed to develop and deliver tools needed to manage Australia’s marine 

biodiversity in a changing ocean climate. The final report from three years intense research is 

available at the website 50. Australia also has The Marine Adaptation Network that comprises a 

framework of five connecting marine themes (integration; biodiversity and resources; communities; 

markets and policy) that cut across climate change risk, marine biodiversity and resources, socioeconomics, 

policy and governance, and includes ecosystems and species from the tropics to 

Australian Antarctic waters 51 . 

Species diversity for the most intensively studied animal phyla (Cnidaria, Mollusca, Brachiopoda, 

Bryozoa, Kinorhyncha, Echinodermata, Chordata) is more or less equivalent to that in the ERMS 

(European Register of Marine Species) region, an area 5.5 times larger than the New Zealand EEZ 

(Gordon et al. 2010), suggesting that the NZ region biodiversity is proportionately richer than the 

ERMS region (Figure 11.3). 

49 State of the Environment MfE 2007. 


51 arnmbr.org/content/index.php/site/aboutus/ 

244


Taxonomic group No. Species 1 State of No. Introduced No. Experts No. ID 

knowledge 

species 

guides 2 

Domain Prokaryota 3 

79 

3 

>1 

3 

1 

Cyanobacteria 

40 

2 

1 

1 

1 

Domain Eukaryota 3 16,979 3-4 159 58 75 

Kingdom Chromista 3 2,643 3-4 11 7 2 

Ochrophyta 858 4-5 11 1 1 

Myzozoa incl. Dinoflagellata 249 3-4 0 2 0 

Foraminifera 1141 4-5 3 2 2 

Kingdom Plantae 3 702 4-5 12 12 3 

Chlorophyta 156 3-4 0 12 1 

Rhodophyta 541 3-4 12 0 1 

Tracheophyta 5 5 0 3 2 

Kingdom Protozoa 3 43 2-3 4 5 4 

Kingdom Fungi 89 3 0 1 0 

Kingdom Animalia 3 13,502 3-4 150 40 66 

Porifera 742 3 7 1 4 

Cnidaria 1,116 4 23 0 6 

Platyhelminthes 323 2 2 1 1 

Mollusca 3,813 4 14 1 3 

Annelida 792 4 32 1 2 

Arthropoda (esp. Crustacea) 2,926 3-4 27 13 17 

Bryozoa 953 4 24 1 4 

Echinodermata 623 5 0 3 6 

Tunicata 192 5 0 3 6 

Other invertebrates 456 2-5 3 7 12 

Vertebrata (Pisces) 1,387 4-5 6 6 7 

Other vertebrates 179 5 0 4 4 

TOTAL REGIONAL 

17,058 3-4 177 62 76 

DIVERSITY 3 

1 

Sources of the tallies: scientific literature, books, field guides, technical reports, museum collections. 

2 

Identification guides cited in Gordon et al. 2010. 

3 

Totals from Gordon 2010, 2012 and Gordon et al. 2010 and unpublished NIWA data. 

Figure 11.3: Diversity of marine species found in the New Zealand region (after Gordon 2010, 2012; Gordon et al. 

2010 and current unpublished NIWA data). 

In late June 2011, two science-based reports heightened concerns about the critical state of the 

world’s oceans in response to ocean climate change. One focuses on the potential impacts of ocean 

acidification on fisheries and higher trophic level ecology and takes a modelling approach to scaling 

from physiology to ecology (Le Quesne and Pinnegar 2011) and the other assesses the critical state of 

the world’s oceans in relation to climate change and other stressors (Rogers and Laffoley (2011). 

In New Zealand, new marine research projects initiated in 2012 include ‘Marine Futures’ that aims to 

develop an agreed decision-making framework, enabling participation of all stakeholders (public, iwi, 

industry, government), that facilitates economic growth, improves marine stewardship and ensures 

that cumulative stresses placed on the environment do not degrade the ecosystem beyond its 

ecological adaptive capacity.( C01X1227). The ‘Ross Sea Climate & Ecosystem’will model likely 

future changes in the physical environment of the region and potential consequences of these changes 

on the ecosystem in terms of functional links between the environment and the marine food web. 

(C01X1226). ‘Management of offshore mining’will develop a clear framework that will guide 

appropriate and robust environmental impact assessments and the development of integrated 

environmental management plans for the marine-mining sector, other resource users and resource 

management agencies. (C01X1228) 

Core purpose funding within the Coasts and Oceans Centre at NIWA include “Managing Marine 

Stressors: Quantifying and predicting the effects of natural variability, climate change and 

anthropogenic stressors to enable ecosystem-based approaches to the management of New Zealand’s 

marine resources” and within the Fisheries Centre, “Ecosystem Approaches to Fisheries Management: 

Determine the impact of fisheries on the aquatic environment to inform an ecosystem-based approach 

245


to fisheries management and contribute to broader ecosystem-based management approaches in 

conjunction with the Coasts & Oceans Centre. 

11.3.1. The MPI Biodiversity Research Programme 

The recognition of increasing societal expectation to use fisheries management measures that will 

achieve biodiversity conservation has signalled by MPI through Fisheries 2030 52 in its long-term 

commitment to– “ecosystem based fisheries management” and to ensuring that “biodiversity and the 

function of ecological systems, including trophic linkages, are conserved”. While New Zealand’s 

environmental record with regard to fishing is perceived to be relatively high on an international 

scale, the Ministry is not complacent about the ongoing requirement to monitor and provide evidence 

that measures to achieve biodiversity conservation needs are being met. This is particularly true of the 

need to better understand and mitigate the effects of fishing on the areas impacted by fishing.The 

effects of fishing on the aquatic environment and risks to biodiversity and marine ecosystems are 

recognised in Fisheries Plans. Research continues to be supported through the Deepwater Research 

Plan, as well as the Aquatic Environment and Biodiversity Research Programmes. 

There are also a range of societal values beyond commercial, customary and recreational take from 

the sea that are recognised as part of “strengthening our society” (see footnote 12). These include 

aesthetic and cultural values as well as other economic values such as tourism and marine recreation 

other than fishing 53 . To link socio-economic values of biodiversity to science supporting fisheries 

management will require a multi-disciplinary approach only just beginning in New Zealand. 

MPI responded to the NZBS in 2000 with the establishment of the MPI Biodiversity Programme 

which has run successfully for more than 10 years with 55 research projects and a large number of 

published outputs, presentations and contributions to NZ and CCAMLR management measures. 

The Ministry is one of several New Zealand government agencies with a strong interest and a 

statutory management mandate in the Ross Sea region of Antarctica through the Antarctic Marine 

Living Resources Act 1981. MPI Antarctic science contributes strongly to New Zealand’s whole-ofgovernment 

involvement in contributions to the Commission for the Convention on Antarctic Marine 

Living Resources (CCAMLR) and the Antarctic Treaty. Research conducted under the MPI Antarctic 

Biodiversity Programme seeks to help New Zealand deliver on its international obligations to support 

an ecosystem-based approach to management in Antarctic waters. There are strong links with the MPI 

Antarctic Working Group research and with other Ross Sea ecosystems research carried out under 

NIWA core purpose Fisheries, and Coast and Oceans Centres (e.g., Sharp et al. 2010). 

The biodiversity research programme set up under the NZBS was established with a multi-stakeholder 

biodiversity research advisory group (BRAG), chaired by the former Ministry of Fisheries (now MPI). 

The research commissioned for the period 2001–2005 reflected goals set by the NZBS and the 

BRAG, while remaining compatible with the Ministry of Fisheries Statements of Intent (SOIs). 

During the first three years of this period, MPI also commissioned marine biosecurity research under 

NZBS, but this was transferred to Biosecurity New Zealand (MAFBNZ) in 2004. From 2006 to 2010, 

the programme evolved further with the development of a new 5-year work programme to address 

shortcomings identified in the review of the NZBS by Clark and Green (2006). An overview of the 

Biodiversity Programme at a glance is given in Figure 11.4. 

52 Fisheries 2030 The full document can be downloaded from www.fish.govt.nz/en-nz/Fisheries+2030 

53 MARBEF: The Valencia Declaration 2008 www.marbef.org/worldconference 

246


BIODIVERSITY THEMES KEY QUESTIONS 

BIODIVERSITY PATTERNS & 

DISTRIBUTION 

• Fauna and flora (taxonomy, 

biosystematics) 

• Distribution & abundance of major 

groups 

• Reviews of existing knowledge 

• Biogeography 

• Drivers of observed patterns 

HABITAT DIVERSITY 

• Biogenic reefs 

• Rocky reefs 

• Rhodolith beds 

• Seamounts 

• Soft sediments 

• Habitat mapping EEZ 

• Deepsea habitats 

• Physical and biological characterisation 

FUNCTIONAL DIVERSITY 

• The role of different animal/plant groups 

in the ecosystem 

• Trophic processes 

• Bentho-pelagic processes 

GENETIC DIVERSITY 

• Barcode of Life 

• Connectivity (populations, areas) 

THREATS TO BIODIVERSITY 

• Climate change and variability 

• Invasive organisms; fishing 

• Land-use effects 

• Cumulative effects 

METHODS 

• Measuring biodiversity 

• Classification 

• Predictive modelling 

• Biodiversity indicators 

• Monitoring biodiversity 

• Ecosystem approaches 

BIOROSS/ & IPY RESEARCH 

• Bioross coastal biodiversity 

• Subtidal ice-sea interface 

• Census of Antarctic marine Life survey 

for IPY, Ross Sea 

• Trophic modelling Ross Sea 

• Balleny Islands survey for MPA 

• Functional habitats 

Figure 11.4: Summary of MPI Biodiversity Research Programme 2000–2012. 

247 

• What is the abundance and distribution of marine 

biodiversity in NZ? 

• What are the key drivers of observed patterns in 

biodiversity? 

• How much marine endemism is there in NZ 

waters? 

• What is the organism size distribution? 

• How do patterns in biodiversity change over time? 

• What are the relative goods and services offered 

by each habitat to aquatic environment health? 

• Can the assemblages and biodiversity of marine 

habitats in the EEZ be predicted by modelling? 

• Which habitats are at greatest risk from extraction 

practices? 

• What proportion of a given habitat needs to remain 

intact for healthy ecosystem functioning? 

• How does biodiversity contribute to the resilience 

of ecosystems to perturbation? 

• Can we use ecosystem function to classify 

biodiversity? 

• Which key processes need to be retained? 

• What barriers drive connectivity within species? 

• What is the role of endemism in characterising the 

evolutionary history and taxonomy? 

• What are the key threats? 

• Does biodiversity increase resilience to climate 

change? 

• Which components of the ecosystem will be most 

at risk from climate change? 

• How can we best measure and portray 

biodiversity? 

• How scalable are results from a local scale to an 

ecosystem scale? 

• What do we need to monitor to measure risks and 

change to ecosystem health? 

• How can we measure the economic value of 

biodiversity and ecosystem services? 

• What is the connectivity between biodiversity in 

the Ross Sea and NZ? 

• How are biota adapted to polar conditions and 

what is their sensitivity to perturbation? 

• Are MPAs a useful protection tool for the Ross 

Sea? 

• Are climate change effects on the ocean already 

impacting on the Ross Sea biota?


ACHIEVEMENTS & KNOWLEDGE TO DATE CURRENT WORK 

• Taxonomy of coralline algae and bryozoans ( 2 ID Guides) 

• New species from surveys added to benthic ID Guides 

• Review of macroalgae distribution on soft sediments 

• Contribution to several books on marine biodiversity in NZ 

• EEZ surveys on Fjordland, Spirit’s Bay, Kermadec seamounts, 

Farewell Spit, Norfolk Ridge, Chatham Rise and Challenger Plateau. 

• Links to MAFBNZ biodiversity mapping; MEC, MFish BOMEC 

• Extensive new data sets and specimen collections obtained 

• Ecological input to improve MEC (fish, benthic invertebrates) 

• Deep-sea habitats , biogenic habitat and soft-sediment reviewed 

• Ocean Survey 20/20 habitats mapped Chatham-Challenger 

• Biodiversity of Kermadec and Chatham Rise seamounts mapped 

• Foveaux Strait habitats mapped 

• Classification of seamounts and VMEs developed 

• Testing of MEC with Chatham Challenger data 

• Rhodolith beds as havens of biodiversity in NZ 

• Rocky reef ecosystem function studied 

• Chatham Rise fish feeding study completed 

• Productivity in horse mussel and echinoderm benthic communities 

determined 

• Bioindicators in estuarine systems in Otago determined 

• Chatham-Challenger functional component analysis completed 

• Shellhash habitat function in the coastal zone 

• Molecular ID of certain fish and plankton determined 

• EEZ and Ross Seaspecies added to Barcode of Life Database, 

• Genetic assessment of ocean microbe diversity 

• Seamount connectivity reviewed 

• Threats and impacts to biodiversity and ecosystem functioning 

beyond natural environmental variation identified 

• Monitoring of plankton on transect NZ to Ross Sea annually 

• Changes in coccolithophore diversity and abundance in NZ waters 

and predicted change as temp and acidification increase asessed 

• Long-term effects of climate change on shelf ecosystems determined 

• Diversity metrics and other indicators to monitor change developed 

• Large-scale sampling protocols for habitat mapping determined 

• Acoustic habitat mapping tools developed 

• Workshop held on qualitative modelling and marine environment 

monitoring 

• Development of “OFOP” and DTIS-visual analytical methods 

• Predictive modelling techniques progressed for biodiversity on 

different scales 

• Development of data to end-user portal interfaced with NABIS 

• Latitudinal gradient project and ICECUBE completed in Ross sea 

• Fish taxonomy and ID guide developed for the Ross Sea 

• Foodweb and role of silverfish vs krill studied 

• IPY-CAML 2008; Ross Sea 2006, BioRoss 2004 surveys done 

• Subtidal and offshore biodiversity sampled, Balleny Islands 2006 

• Seaweed diversity determined at Balleny Islands 

• Bioregionalisation of the Ross Sea region completed 

248 

• Ongoing taxonomic work in 

relation to deep sea corals 

(VMEs) 

• Ongoing taxonomic work on 

specimens collected from the 

Chatham-Challenger project 

and from the IPY –CAML 

project. 

• Mapping biogenic structures 

• Mapping deepsea fisheries 

habitats in relation to ocean 

acidification threats from 

changing saturation horizons 

• Modelling benthic impacts 

• Ocean acidification on 

shellfish 

• Response and recovery of 

seabed to disturbancemodelling 

project 

• Connectivity among coastal 

fish populations 

• Experimental response of 

shellfish pH and temp. 

• CPR monitoring 

• Initial appraisal for MEMP 

• Acidification in deepwater 

fish habitat 

• Development of functional 

biota model for habitat 

classification 

• Qualitative and quantitative 

modelling of rocky reef 

ecosystem 

• Predictive modelling VMEs 

• Measuring risk and resilience 

(Chat-Chall objective) 

• finalisation IPY analyses 

• Uptake of biodiversity 

results to CCAMLR trophic 

modelling and biomass 

estimation, VMEs 

• New spp logged for CAML 

• Review of squids, octopus 

Figure 11.4: Continued Summary of MPI Biodiversity Research Programme 2000–2012.


11.3.2. Overall progress in MPI marine biodiversity research 

The MPI Biodiversity Research programme has three overarching science goals: 

• To describe and characterise the distribution and abundance of fauna and flora, as expressed 

through measures of biodiversity, and improving understanding about the drivers of the 

spatial and temporal patterns observed. 

• To determine the functional role of different organisms or groups of organisms in marine 

ecosystems, and assess the role of marine biodiversity in mitigating the impacts of 

anthropogenic disturbance on healthy ecosystem functioning. 

• To identify which components of biodiversity are required to ensure the sustainability of 

healthy marine ecosystems as well as to meet societal values on biodiversity. 

More specific Science Objectives developed below have been modified by BRAG over time and are 

used to focus the research commissioned: 

1. To classify and characterise the biodiversity, including the description and documentation of 

biota, associated with nearshore and offshore marine habitats in New Zealand. 

2. To develop ecosystem-scale understanding of biodiversity in the New Zealand marine 

environment. 

3. To investigate the role of biodiversity in the functional ecology of nearshore and offshore 

marine communities. 

4. To assess developments in all aspects of diversity, including genetic marine biodiversity and 

identify key topics for research. 

5. To determine the effects of climate change and increased ocean acidification on marine 

biodiversity, as well as effects of incursions of non-indigenous species, and other threats 

and impacts. 

6. To develop appropriate diversity metrics and other indicators of biodiversity that can be used 

to monitor change. 

7. To identify threats and impacts to biodiversity and ecosystem functioning beyond natural 

environmental variation. 

To date, 55 research projects have been commissioned. Early studies focused primarily on Objectives 

1 and 2 and resulted in reviews, Identification Guides, habitat and community characterisations, and 

revised taxonomy for certain groups of organisms. These objectives have also resulted in large 

collaborative ship-based surveys that have contributed to improved seabed classification in New 

Zealand waters and the exploration of new habitats in the region and in Antarctic waters. Over time, 

the complexity and scale of studies has increased with projects on the functional ecology of marine 

ecosystems from localised experimental manipulation to broad-scale observations across 100s km 2 

under Objective 3. Such studies have also pursued the development of improved measures of 

biodiversity and indicators under Objectives 6 and 7. A study on changes in shelf ecosystems over the 

past 1000 years is yielding insights into the effects of long-term climate change, land-use effects and 

fishing on marine ecosystems while more recently, some studies have begun to address the effects of 

ocean acidification on marine biodiversity under Objective 5. A study underway has reviewed genetic 

variation in the New Zealand marine environment and is conducting field observations on several 

species to examine genetic variation across latitudinal gradients. Aspects of the seven Objectives have 

also been addressed through a range of biodiversity projects in the Ross Sea region including the 

International Polar Year Census of Antarctic Marine Life project (IPY-CAML). A key to study 

findings is consideration of biodiversity within the context of the carrying capacity of the system and 

the natural assemblages of biota supported by that system in the absence of human disturbance. 

Progress in the MPI Biodiversity Programme is summarised in Figure 11.5. 

249

Progression of research 

understanding 

1. Review extent of 

knowledge of 

biodiversity (desktop) 

2. Identify & characterise 

species and habitat 

diversity (field work, 

qualitative analysis, 

taxonomy & systematics) 

3. Quantify biodiversity 

distribution, abundance 

(replication, purpose 

designed surveys) 

4. Model and predict 

biodiversity distribution 

and abundance 

5. Assess or measure 

functional processes in 

healthy marine 

ecosystems 

(experiments, process 

studies) 

6. Assess the role of 

genetic diversity 

7. Assess interactions and 

connectivity on 

ecosystem scale, 

(genetics, modelling) 

8. Develop indicators and 

measures to monitor 

bio-diversity, 

ecosystem health 

9. Define key risks and 

threats to biodiversity 

10. Define standards for 

maintaining 

biodiversity and healthy 

ecosystem functioning 

11. Examine strategies to 

mitigate remedy or 

avoid threats to 

biodiversity 

12. Monitor risks and 

compliance with 

standards 

Science 

objective † 

1-7 

1 

1 

1 

2, 3 

4 

2, 5 

6 

5, 7 

6 

6 

6 


Estuarine/ 

Coastal 0-30 m 

250 

Shelf 

30-200 m 

Slope 

200-1500 m 

Deep/Abyss 

>1500 m 

Antarctica 

All depths 

Figure 11.5. Progress on biodiversity research commissioned by MPI 2000–2010. Dark grey: Significant progress 

(several projects completed and results emerging from research underway). Light grey: Limited progress (some 

results emerging, more research needed). White: no substantive research. Diagonal-hatch: progress linked to large 

whole-of-government projects (e.g. Ocean Survey 2020) and/or other funding outside MPI (e.g. MBIE (MSI) funded 

Outcome Based Investment projects, DOC Marine Coastal Services, MAFBNZ marine biosecurity research). 

† 

Science objectives are- 1 characterisation and description; 2 ecosystem scale biodiversity; 3 functional role of 

biodiversity; 4 genetics; 5 ocean climate effects; 6 indicators; 7 threats to biodiversity. The objectives are 

detailed in MPI Biodiversity Programme: Part 2. Medium Term Research Plan 2011-2014. 

The chart depicts a logical flow down the page of increasing conceptual complexity from cataloguing 

of biodiversity to increasingly complex understanding of environmental drivers and functionality of 

biodiversity; and ultimately methods to develop standards and protection of biodiversity. Across the


chart, the marine environment is graded from the coastline to offshore regions, and Antarctica. A full 

list of projects can be obtained from the MPI Biodiversity Medium Term research programme 2010- 

2014. 

Greatest progress has been made in the shallower inshore parts of the marine environment, not least 

because of cost and ease of access. However, by leveraging from existing offshore projects, 

significant progress has also been made to depths of 1500 m. 

MPI Biodiversity research based in Antarctica lags behind EEZ-based research, simply because of the 

difficulty in securing additional funding to access and work in such a remote and hostile marine 

environment. While the top left side of the figure shows the area of greatest progress, it would be a 

mistake to conclude that biodiversity work is completed here. 

11.3.1. Progress on Science Objective 1. Characterisation and 

Classification of Biodiversity 

The characterisation and classification of biodiversity requires an assessment of the abundance and 

distribution of marine life. Building on earlier research to map fish and squid species (Anderson et al. 

1998, Bagley et al. 2000) and the biodiversity of the New Zealand ecoregion (Arnold 2004), literature 

reviews, taxonomic studies and habitat mapping surveys have been undertaken. 

Reviews and books 

The following lists scientific reviews and books on biodiversity that were commissioned by the 

programme: 

ZBD2000-01 A review of current knowledge describing the biodiversity of the Ross Sea 

region (Bradford-Grieve and Fenwick 2001, 2002; Fenwick and Bradford-Grieve 2002a, 

2002b, Varian 2005) 

ZBD2000-06 “The Living Reef: The Ecology of New Zealand's Rocky Reefs” (eds. Andrew 

and Francis 2003) 

ZBD2000-08 A review of current knowledge describing New Zealand’s Deepwater Benthic 

Biodiversity (Key 2002), 

ZBD2000-09 Antarctic fish taxonomy (Roberts and Stewart 2001) 

ZBD2001-02 Documentation of New Zealand Seaweed (Nelson et al. 2002) 

ZBD2001-04 “Deep Sea New Zealand” (Batson 2003) 

ZBD2001-05 Crustose coralline algae of New Zealand (Harvey et al. 2005, Farr et al. 2009, 

Broom et al. 2008) 

ZBD2001-06 Biodiversity of New Zealand’s soft-sediment communities (Rowden et al. 

2011) 

ZBD2003-09 Macquarie Ridge Complex Research Review (Grayling 2004) 

ZBD2008-27 Scoping investigation into New Zealand abyss and trench biodiversity (Lörz et 

al. 2012). 

In addition a major work which includes marine species – “The New Zealand Inventory of 

Biodiversity” (Gordon 2009, Gordon 2010, Gordon 2012), has been completed. Field identification 

guides have also been published by MPI on deepsea invertebrates (–projects ENV2005-20 and 

ZBD2010-39, Tracey et al. 2005, 2007, 2011), bryozoans (project IPA2009/14 Smith and Gordon 

2011) and on fish species (IDG2006-01 MacMillan et al. (2011 a, b, c) which further contribute to the 

accurate monitoring and identification of biodiversity in New Zealand waters. 

Projects 

Several hundred new species of marine organisms have been discovered, and the known range of 

species extended, through exploratory surveys such as the NORFANZ project ZBD2002-16 (Clark 

251


and Roberts 2008); MSI’s Seamount Programme, mainly commissioned through public-good science, 

supplemented by MPI projects ZBD2000-04, e.g., Rowden et al. 2002 and 2003, ZBD2001-10 

(Rowden et. al 2004), ZBD2004-01 (Rowden et al. 2010) and MPI projects ENV2005-15, ENV2005- 

16 (Clark et al. 2010, Rowden et al. 2008) and the Ocean Survey 20/20 programme (Clark et al. 

2009); inshore surveys of bryozoans at Tasman Bay ZBD2000-03 (Grange et al. 2003); Farewell Spit, 

ZBD2002-18 (Battley et al. 2005), Fiordland, ZBD2003-04 (Wing 2005); coralline algae ZBD2001- 

05, ZBD2004-07 (Harvey et al. 2005, Farr et al. 2009); soft sediment environments ZBD2003-08 

(Neill et al. 2011); rhodolith community study ZBD2009- 03 (Nelson et al. 2012); offshore surveys of 

the Chatham Rise and Challenger Plateau funded through Ocean Survey 20/20 programme, 

ZBD2006-04 (Nodder 2008) and ZBD2007-01 (Nodder et al. 2011; Hewitt et al. 2011; Bowden 2011, 

Bowden and Hewitt 2012; Bowden et al. 2011b; Bowden et al. in press). 

Research in the Ross Sea Region (BioRoss projects) have also generated records of new species 

including MPI projects ZBD2000-02 (Page et al. 2001), ZBD2001-03 (Norkko et al. 2002), 

ZBD2002-02 (Sewell et al. 2006, Sewell 2005, 2006), ZBD2003-02 (Cummings et al. 2003, 2006), 

ZBD2003-03 (Rowden et al. 2012a, Rowden et al. in press), ZBD2005-03 (MacDiarmid and Stewart 

2012), ZBD2006-03 (Cummings et al. 2003, 2006; Norkko et al. 2002), ZBD2008-23 (Nelson et al. 

2010)and IPY2007-01 (Bowden et al. 2011a, Clark et al. 2010, Eakin et al. 2009, Hanchet, et al. 

2008a Hanchet 2008b, Hanchet 2008c, Hanchet et al. 2008d. Hanchet 2009, Hanchet 2010, Koubbi et 

al. in press, Lörz and Coleman 2009, Lörz in press, Lörz et al. in press, Mitchell 2008, O’Driscoll et 

al. 2009. O'Driscoll 2009, O’Driscoll, et al. 2010, O’Loughlin et al. 2010) 

Habitat diversity, classification and characterisation 

The development of the Marine Environment Classification or “MEC” (Snelder et al. 2006) was an 

important step in the delineation of areas with similar environmental attributes in the offshore 

environment. However, significant environmental drivers of variability in marine biodiversity, such as 

substrate type for seafloor organisms, were absent from the classification. In 2005, DOC and MPI 

jointly commissioned a project to optimise the MEC using fish distribution data. This project 

(ZBD2005-02) demonstrated a substantial improvement in the MEC classification for offshore 

habitats (Leathwick et al. 2006a, b, c). In 2006, three projects to map coastal biodiversity were 

completed in the Coromandel scallop, Foveaux Strait oyster and southern blue whiting fisheries as 

part of fishery plan development for these fisheries (ZBD2005-04, ZBD2005-15, ZBD2005-16). 

These projects found that the biological distribution of organisms and their habitats were not well 

predicted by the MEC. MPI project (BEN2006-01) aimed to further optimise the MEC by producing a 

methodology for a Benthic Optimised MEC (Leathwick et al. 2009).MPI Ecological studies to 

improve habitat classification and vulnerability indices have also been completed through MPI 

AEWG projects on seamounts (ENV2005-15, ENV2005-16) (e.g., Clark et al. 2010), and to 

supplement other studies funded by MPI, and MSI (e.g. ZBD2004-01, ZBD2001-10, ZBD2000-04, 

and CO1X0508). 

Distribution maps providing indicative abundance and characterisation of biodiversity are now 

emerging and have been produced through projects using predictive modelling tools e.g., Compton et 

al. 2012; the fish optimised MEC in project ZBD2005-02 (Leathwick et al. 2006a, 2006b, 2006c), the 

benthic optimised MEC (Leathwick et al. 2009) and Chatham-Challenger project ZBD2007-01 

(Hewitt et al. 2011, Bowden et al. 2012, Compton et al. in press). 

Progress has advanced considerably in recent years with the introduction of the whole-of-government 

Ocean Survey 20/20 Programme and Biosecurity New Zealand mapping projects (Beaumont et al. 

2008, 2010) In addition, MPI implemented spatial management tools (Benthic Protection Areas 54 ) 

implemented on the basis of the Marine Environment Classification 55 56 to address broader statutory 

responsibilities on the environmental effects of fishing on biodiversity. 

54 www.fish.govt.nz/en-nz/Environmental/Seabed+Protection+and+Research/Benthic+Protection+Areas.htm 

55 Marine Environmental Classification. (2005). Can be viewed online at 

http://www.mfe.govt.nz/publications/ser/marine-environment-classification-jun05/index.html 

252


ZBD2007-01 Chatham-Challenger seabed habitats-post voyage analyses. 

This large project has been completed. Progress for each objective is as follows: 

1. To count, measure, and identify to species level (where possible, otherwise to genus) all 

macro invertebrates (>2 mm) and fish collected during Oceans Survey 20/20 voyages. 

Completed (Figure 6, Bowden 2011). 

2. To count, measure and identify to species-level (where possible, otherwise to genus or family) 

all meiofauna (>45μm to


Survey 20/20 samples. Completed. (Bowden et al.in press, Bowden et al 2011b, Compton et 

al 2012). 

15. To assess the extent to which the 2005 MEC and subsequent variants can provide costeffective, 

reliable means of assessing biodiversity at the scale of the Oceans 20/20 surveys. 

Completed. (Bowden et al. 2011b). 

16. Collating all information and analysis from all objectives, devise a series of statistically 

supported recommendations for surveying marine biodiversity in the future. This should 

include, but may not be limited to, statistical analyses and modelling. Bowden and Hewitt 

2011). 

ZBD2008-05 Macroalgal diversity associated with soft sediment habitats. 

Although macroalgae normally require hard substrata for attachment and occur less frequently 

in soft sediment environments they contribute to biodiversity in a range of soft sediment 

environments providing structural complexity, modifying flow and sediment regimes, and 

contributing to productivity. Soft sediment habitats where macroalgae are found are 

physically highly diverse, ranging from harbours and estuaries (with varying sediment types 

and sizes, freshwater influence, tidal flushing, current flows), to coarse stabilised sediments 

(shell fragments, cobbles, coarse gravels), and biogenic habitats such as worm tubes, horse 

mussel beds, brachiopod beds, mangrove forests, rhodolith (maerl) beds and seagrass 

meadows. 

The state of knowledge of macroalgal diversity, distribution and abundance is poor, and there 

are few examples of targeted collecting programmes for macroalgal assemblages, particularly 

in soft sediment habitats. This research conducted (a) a targeted collection programme across 

diverse soft sediment environments to develop a permanent reference collection of 

representative macroalgae, and (b) examined algal distribution in soft sediment habitats in 

relation to selected environmental variables. 

Macroalgal sampling trips to Kaipara (1), Whangarei (3) and Otago (4) Harbours were 

completed. Further sampling trips were planned for 2010, however, no further collections will 

be made in Kaipara Harbour. Approximately 2400 collections of algae were made from soft 

sediments in these harbours. In Whangarei and Otago Harbours, collections were made from a 

range of soft sediment habitats including mud, sand, shell gravel, sea grass, scallop, pipi and 

horse mussel beds. At each site algae were collected opportunistically, quantitatively (i.e. by 

quadrats), or by both methods. Standard ecological methods (e.g. species area curves, count 

frequencies) were used to assess the appropriateness of the methods. 

A database was developed for information about specimens and collection sites. Information 

was gathered on environmental variables within the target harbours. Identified algal 

distributions were analysed relative to these environmental variables. 

Collections were made from three harbours with the primary focus on Whangarei and Otago 

Harbours where seasonal sampling programmes were conducted in spring and in autumn. In 

the Kaipara Harbour sampling was conducted only in spring. Two hundred and forty four taxa 

sampled from intertidal and subtidal sites and a range of habitats: 146 (112 spring, 102 

autumn) from Whangarei, 43 Kaipara, 150 (107 spring, 115 autumn) from Otago. Diversity 

indices indicate that the collecting was not saturated and predict that there is higher diversity 

of macroalgae in these harbours than found in the samples obtained. 

The flora composition in the harbours was found to differ markedly e.g., only 67 taxa (45%) 

of the Whangarei flora were found to be in common with Otago Harbour collections; 17 taxa 

(39% ) of the Kaipara flora was in common with the Otahgo flora, in common (39% of K 

found in O); 27 taxa (63%) of the Kaipara flora was also found in Whangarei.19 nonindigenous 

species were found in the harbours, including two new records for the New 

254


Zealand algal flora (confirmed by sequence data), Hypnea cornuta and Polysiphonia 

morrowii. In Whangarei Harbour 8 non-indigenous species were found (4 new records for 

harbour including Hypnea), in Kaipara Harbour 4 species were found including 2 new records 

for the harbour, and in Otago Harbour 11 non-indigenous species were found including 1 new 

record as well as P. morrowii. More taxa were collected in the subtidal (107) in Whangarei 

Harbour than in the intertidal (84), compared with Otago where numbers of intertidal taxa 

(120) exceeded the subtidal taxa collected (83). 

Two methods were employed to enable high resolution sampling and these provided differing 

outcomes in the two main harbours sampled, clearly indicating that there was value in 

collecting by both methods in order to adequately sample the diversity: Whangarei Harbour 

90 taxa were collected in quadrat sampling compared with 118 taxa via opportunistic 

collections, and in the Otago Harbour 107 taxa were collected in quadrat sampling and 118 

taxa via opportunistic collections. 

ZBD2008-27 Review of deep-sea benthic biodiversity associated with trench, canyon and abyssal 

habitats below 1500 m depth in New Zealand waters 

The state of knowledge of benthic biodiversity and ecosystem functioning in deep-sea 

abyssal, canyon and trench habitats in the New Zealand Exclusive Economic Zone and the 

Ross Sea region, was summarised and recommendations for future deep-sea research in 

depths exceeding 1500 m were made. All biological information in scientific papers and 

reports from New Zealand below 1500 m was reviewed and an exhaustive search of multiple 

data sources was conducted. 

The area of the deep seafloor below 1500 m covers more than 65% of New Zealand‘s 

Exclusive Economic Zone. A total of 1489 benthic gear deployments have been conducted by 

New Zealand-based sampling initiatives since 1955, most of which were focused on obtaining 

geological samples. Less than 0.002 % of New Zealand‘s deep-sea environment (i.e. in terms 

of seabed area) below 1500 m has been sampled. All taxonomy-based studies of all taxa 

reported in New Zealand waters below 1500 m have been reviewed. To date, 8 species of 

Bacteria, 293 species of Protozoa, 785 species of invertebrates, and 56 fish species have been 

recorded from water depths greater than 1500 m. 

More than 8000 images are known to have been taken of the seafloor below 1500 m in the 

New Zealand region, covering an area of approximately 0.016 km2. Over 4000 of the images 

held at NIWA exist either as paper prints or negatives and ideally should be digitised for 

future storage and access for analyses. Analysis of these photographic images should yield 

considerable information about deep-sea biodiversity and ecosystem function in the New 

Zealand region and could be used to answer a number of research questions (especially 

around deep-sea benthic biodiversity). 

Recommendations on how to potentially further analyse existing data from images, databases 

and actual specimens were provided. The technical challenges, including gear requirements to 

sample deep-sea New Zealand benthos and potential future investments, were summarised. 

(see Coleman and Lörz 2010; Lörz 2011a, 2011b; Lörz et al. 2012a, 2012b). 

ZBD2008-50 Chatham Rise biodiversity hotspots. 

This survey covered the “Graveyard Seamount Complex” and “Andes Seamount Complex” 

on the Chatham Rise. Objectives were to monitor changes over time on Graveyard hills 

subject to differing management regimes (some open to fishing, some closed), as well as to 

compare seamount biodiversity between different regions of the Rise. It was linked to the 

CoML CenSeam programme, and the former FRST Seamounts research, now under the 

MBIE Vulnerable Deep-sea Communities project. The data from that survey are being 

255


worked up under the latter project (see Clark et al. 2009).). Analyses comparing the 3 surveys 

of the Graveyard complex between 2001 and 2009 indicate there are changes in some taxa 

following cessation of fishing operations on one of the features in 2001, but little sign of any 

recovery of stony coral species and associated benthic communities . Preliminary results were 

presented at the 2012 Deep Sea Biology Symposium (Clark et al. 2012). 

ZBD2009-03 The vulnerability of rhodoliths to environmental stressors and characterisation of 

associated biodiversity. 

Rhodoliths are free-living calcified red algae. They occur worldwide, forming structurally and 

functionally complex benthic marine habitats. Rhodolith beds form a unique ecosystem with a 

high benthic biodiversity supporting many species, including some that are rare and unusual. 

Recent international studies show that these fragile algae are at risk from the impacts of a range 

of human activities e.g., physical disruption, reduction in water quality, alterations to water 

movement, and aquaculture installations. Impacts of fragmentation may be critical in terms of 

biodiversity and abundance associated with rhodolith beds. 

The focus of this programme was to improve knowledge about the location, extent or ecosystem 

functioning of rhodolith beds in New Zealand. The ecology of subtidal rhodolith beds was 

been investigated for the first time in New Zealand, characterising two rhodolith species, 

Lithothamnion crispatum and Sporolithon durum, examining the structure and physical 

characteristics of beds at two locations and documenting their associated biodiversity. In 

addition the responses of these rhodolith species to environmental stressors were investigated 

for the first time. 

This study documented high biodiversity in two subtidal rhodolith beds sited in relatively 

close proximity in the coastal zone, with significant differences in biotic composition. The 

rhodolith beds studied (located in the Bay of Islands) differed significantly in terms of water 

motion, sediment characteristics and light levels. Biodiversity of the rhodolith beds was 

investigated sampling (1) invertebrates at three levels of association (epifauna, infauna, 

cryptofauna), (2) macroalgae, (3) fishes, as well as recording the biogenic and non-biogenic 

substrates: 

• a number of undescribed taxa were discovered as well as new records for the 

New Zealand region, and range extensions of species known elsewhere, 

• more than double the number of invertebrate taxa were present in the rhodolith 

beds than found outside the beds, 

• both rhodolith beds harboured high diversity of associated macroalgae and 

invertebrates but with markedly different species composition, 

• the floral and faunal composition differed significantly between sites. 

Both species of rhodolith were found to be vulnerable to the impacts of increasing 

temperature and decreasing pH. There was a significant difference between the effects of 

treatments on the two species and further statistical analysis showed significant interaction 

between temperature and pH level on growth. Overall the greatest effect on growth rate came 

with the combination of high temperature (25° C) and low pH (7.65) on Lithothamnion 

crispatum which showed negative growth, indicating probable dissolution. In experiments 

investigating other environmental stressors, temperature was found to be more important for 

the survival and growth of the rhodolith species examined than the effects of burial, light and 

fragmentation. 

The extent of rhodolith beds in other parts of the New Zealand region remain to be 

documented, including those in coastal areas (including intertidal beds) and subtidal beds on 

the shelf. 

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ZBD2010-40 Predictive modelling of the distribution of vulnerable marine ecosystems in the South 

Pacific Ocean region. 

In January 2010 New Zealand and the United States held their second Joint Commission 

meeting (JCM) on Scientific and Technological Cooperation. The meeting was to share 

knowledge about common interests and capabilities and identify areas for future 

collaboration. The JCM consisted of six workshops held simultaneously around the North 

Island and an officials meeting held in Wellington. One of the six workshops, ocean and 

marine sciences, identified an area of interest in a joint project in the South Pacific Regional 

Fisheries Management Organisation (SPRFMO) area to map and groundtruth vulnerable 

marine ecosystem (VME) distribution. 

The 3rd New Zealand and United States Joint Commission on Science and Technology 

Cooperation (JCM) met on 19 and 20 September 2012 in Washington. Building on several 

recommendations from the previous JCM (held in January 2010), and on the Marine 

Conservation Think Tank VME Workshop report 3: Science requirements for effective High 

Seas governance, held on 2-5 December 2011 (Lundquist et al 2012) 1, Topic 1 for the 

Oceans and Marine Workshop and the 3rd JCM meeting was again Vulnerable Marine 

Ecosystems (VMEs). Several actions were developed at the workshop and these included: 

‘Increase in situ deep-sea exploration and VME studies in regions of common interest by 

exploring options for NOAA/WHOI participation (including use of ROV/AUV technologies) 

in New Zealand funded initiative and voyage to explore and ground-truth VMEs in the South 

Pacific’ and ‘Facilitate U.S. researcher involvement in NIWA Louisville Ridge Exploration.’ 

There are relatively few data available on the distribution of VME species or taxa in the South 

Pacific Ocean (Parker et al. 2009) although studies have been conducted in Antarctica 

(Tracey et al. 2010, Parker et al. 2009) to use for the objective planning of spatial protection 

measures to protect those taxa, particularly in the SPRFMO Area. It is therefore becoming 

increasingly important to develop robust predictions of where VMEs are likely to occur, using 

habitat prediction and species distribution models. Such models have recently been developed 

and/or are in the process of being refined for certain VME taxa on a global scale (e.g. 

Actinaria, Guinotte et al. 2006; Scleractinia, Tittensor et al. 2009). However, the spatial 

resolution of existing models is coarse (larger than the scale of the topographic features 

typically targeted during demersal high seas fishing), and the level of uncertainty around the 

predictions is variable or still unknown. 

Phase 1 a project to use modelling to predict the location of VMEs in the SPRFMO area was 

initiated between the US and New Zealand (ZBD2010-40) and has now been completed. The 

objectives of the project were to: 

1. To develop and test spatial habitat modelling approaches for predicting distribution 

patterns of vulnerable marine ecosystems in the Convention Area of the South Pacific 

Regional Fisheries Management Organisation with agreed international partners. 

2. To collate data sets and evaluate modelling approaches which are likely to be useful 

to predict the distribution of vulnerable marine ecosystems in the South Pacific Ocean 

region. 

Data for ten Vulnerable Marine Ecosystems (VME) taxa were compiled from different data 

sources to produce a single groomed dataset for VME indicator taxa in the New Zealand 

region. Regional-tuned environmental data layers and global environmental data layers were 

obtained from available data sources. Using these data, three types of predictive models were 

made for each VME indicator taxon. Two models were made using regional-tuned 

environmental data layers, using maximum entropy analysis (MaxEnt) and boosted regression 

tree (BRT) techniques to provide a comparison of the different model approaches. The third 

type of model made used the MaxEnt approach, but using globally available environmental 

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data layers. Having a third model meant that model performance could be compared based on 

the use of different environmental data layers. Three model types for all VME taxa have been 

completed and the performance of the different modelling approaches and usefulness of the 

environmental data sets described. 

The next phases of the project will be undertaken as part of a MBIE-funded project that will 

revise models that predict the sites of Vulnerable Marine Ecosystems from existing data by 

conducting a ground truthing survey of benthic biodiversity on the Lewisville Ridge in 

2013/14 (Ministry of Business Innovation and Employment project code C01X1229). This 

will be used to inform New Zealand and South Pacific Regional Fisheries Management 

Organisation initiatives on spatial management in the South Pacific region, and potentially the 

New Zealand EEZ. 

Other research relevant or specifically linked to the projects above, is listed in Table 11.1. 

Table 11.1: Other research linked to Objective 1 habitat classification and characterisation. 

MPI HAB2007-01 Biogenic habitats as areas of particular significance for fisheries 

management 

ZBD2006-02 NABIS ongoing development 

Useful data related to defining potential VMEs are collected by MPI scientific fisheries 

observers working on NZ authorised fishing vessels that operate on the high seas in the 

South Pacific. 

CRI core C01X501 Coasts & oceans Centre (NIWA) ecosystem based management, habitat model 

purpose development with Auckland Regional Council 

funding C01X0907 Coastal Conservation Management (fish habitat classification) 

DOC 

(NIWA)C01X502 Biodiversity & Biosecurity (NIWA) 

C01X0508 Seamount fisheries (linking acoustic backscatter to habitat type and biota) 

(NIWA) 

CO1X0906 Vulnerable deep-sea communities (mapping and sampling a range of deep-sea 

habitats (seamounts, slope, canyons, seeps, vents) (NIWA) 

CO1X0702 Kermadec Arc minerals (mapping and sampling the biodiversity of several 

Kermadec Arc seamounts) (NIWA) 

MEC development and application to MPAs, Regional surveys 

OTHER University studies, Regional Council studies 

ZBD2010-40 Mapping VMEs in the SPRFMO area Part 1. Predictive modelling desktop study 

EMERGING ISSUES 

What portion of a given habitat type should remain intact to support sustainable ecosystems? 

What are the most effective predictive tools for predicting biodiversity in areas as yet unsampled? 

Can ecological mapping used in OS20/20 projects to date be extended to other areas of New Zealand? 

11.3.2. Progress on Science Objective 2. Ecosystem-scale research 

Marine ecosystems influence, and are influenced by, a wide array of oceanic, climatic, and ecological 

processes across a broad range of spatial and temporal scales. Marine communities are generally 

dynamic, can occur over large areas and have strong links to other communities through processes 

such as migration and long-distance physical transport (e.g. of larvae, nutrients, and biomass). 

Patterns observed on a small scale can interact with larger and longer-scale processes that in turn 

result in large scale patterns. Marine food webs are usually complex and dynamic over time (Link 

1999). To distinguish useful descriptors of long-term ecosystem change from short-term fluctuations 

requires innovative approaches to integrate broad-scale correlative studies from smaller scale 

manipulative experiments (Hewitt et al. 1998, 2007). 

Recent theoretical and technical advances show great promise toward the goal of understanding the 

role of biodiversity in ecosystems. Technologies for remote sensing and deepwater surveying, 

combined with powerful integrative and interpretive tools such as GIS, climate modelling, qualitative 

ecosystem modelling, and trophic ecosystem modelling, will contribute to the development of an 

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ecosystem-based approach to management (Thrush et al. 1997, 2000), with potential benefits for 

marine conservation and management. Ecosystem modelling of species distribution (and habitats) 

with respect to known and projected environmental parameters will improve predictability for both 

broad and fine-scale biodiversity distribution. This has already resulted in improved definition of 

environmental classifications addressing biodiversity assessment. It is also important to make 

progress in establishing the links between biodiversity and the long-term viability of fish stocks under 

various harvesting strategies. It is also important that modellers consider processes from all ecosystem 

function perspectives i.e., top-down effects such as predation (e.g. trophic modelling), bottom-up 

effects such as the environment (e.g., habitat classification based on environmental variable), and 

wasp-waisted systems where there are major effects in both directions. 

Projects 

ZBD2002-06A: Impacts of terrestrial run-off on the biodiversity of rocky reefs Completed. 

(Schwarz et al. 2006). 

ZBD2004-02: Ecosystem scale trophic relationships of fish on the Chatham Rise. Completed. 

(Connell et al. 2010, Dunn 2009, Dunn et al. in press, Dunn et al. 2010a, b, c, Eakin et al. 

2009, Forman and Dunn 2010, Horn et al. 2010, Stevens and Dunn 2010. Follow-up research 

on isotope signatures to improve the trophic data from ZBD2004-02 has been incorporated 

into the NIWA’s Coast and Ocean programme and trophic modelling is underway in this 

programme. 

ZBD2004-08 Sea-grass meadows as biodiversity and connectivity hotspots. 

This contract links closely with the MBIE project Coastal Conservation Management 

(CO1X0907). National scale sampling across North and South Island seagrass meadows in a 

range of estuarine and coastal settings has shown that seagrass meadows overall consistently 

supported higher species richness, biomass, and productivity of invertebrates (infaunal and 

epifaunal). Associated sampling of small fish assemblages found that while seagrass meadows 

provided a nursery function to a number of species, this function was most pronounced in 

northern New Zealand systems, where relatively high numbers of juvenile snapper, trevally, 

spotties, parore, and garfish/piper were caught. However, there was strongly spatial variation 

across different estuary and coast settings (MBIE91B). 

ZBD2004-19 Ecological function and critical trophic linkages in New Zealand softsediment 

habitats. Project completed. (see Lohrer et al. 2010.) 

ZBD2005-05 Effects of climate variation and human impacts on the structure and functioning of 

New Zealand shelf ecosystems. 

The project is a multidisciplinary study to utilise archeological, paleoecological, and historical 

data to retrospectively model ecosystem states during different historical and prehistoric time 

periods. The project is collaborating with the international History of Marine Animal 

Populations (HMAP) project, itself a part of the Census of Marine Life (CoML) programme. 

The data have been used as inputs to a mass balance model of the shelf ecosystem starting 

with the present day Hauraki Gulf. A short video about the NZ Taking Stock project was 

made by HMAP staff and is currently available on the HMAP website 

http://hmapcoml.org/projects/nz/. Several presentations have been made at NZ and 

international conferences as results have emerged. 

ZBD2008-01 Inshore biogenic habitats. 

Existing knowledge on biogenic habitat-formers in the


Over 600 targets of interest were identified and marked on marine charts, with more than 200 

of these targets being biogenic in nature. Fieldwork has been completed to verify and quantify 

biodiversity in biogenic habitats using Ocean Survey 20/20 vessel days on Tangaroa and a 

new MSI project to extend the survey potential of the project. New biogenic habitats have 

been identified, including extensive worm tube ‘meadows’ off the east coast of the South 

Island (“the Hay Paddock” and “Wire-weed”), with associated relatively high epi-faunal 

invertebrate diversity compared to adjacent bare sediments. Over 60 new species were also 

collected (dominated by sponges), along with range extensions of many other species. 

Analyses are underway for key selected areas included in the Tangaroa voyages, including 

offshore North Taranaki Bight, Ranfurly Bank, the polychaete meadows mentioned above, 

and the Otago Peninsula bryozoan fields. 

IPA2009-11. Trophic Review. 

This project publishes a report prepared on the feeding habits of New Zealand fishes 1960 to 

2000 (Stevens et al. 2011) 

Other research relevant or specifically linked to the projects above, is listed in Table 11.2. 

Table 11.2: Other research linked to ecosystem scale understanding of biodiversity in the marine environment. 

MPI ENV2006-04 Ecosystem indicators for New Zealand fisheries 

ENV2007-04 Climate and oceanographic trends relevant to New Zealand fisheries 

ENV2007-06 Trophic relationships of commercial middle depth species on the Chatham Rise 

CRI Core C01X501 coasts & oceans productivity plankton-mesopelagic fish trophic relations Chatham Rise 

purposes IO 2. Second Fisheries Oceanography voyage to Chatham Rise: mesopelagics and hyperbenthics 

OTHER AUT deepsea and subtidal food web dynamics; offshore & coastal biodiversity post graduate 

studies 

11.3.3. Progress on Science Objective 3. The role of biodiversity in 

the functional ecology of nearshore and offshore communities. 

An identified outcome of the Biodiversity Strategy is that by 2020 “New Zealand’s natural marine 

habitats and ecosystems are maintained in a healthy functioning state. Degraded marine habitats are 

recovering.” Sustaining ecosystem integrity in marine habitats requires a thorough understanding of 

the ecological and anthropogenic drivers affecting biodiversity and ecosystem function, and the ability 

to manage human impacts in marine environments. 

Near-shore environments range from wetlands to estuaries, coasts and continental shelf ecosystems, 

they contain a variety of habitats and often contain species that are particularly important, either for 

cultural, recreational, and commercial reasons, or because the species exerts disproportionate 

influence on community structure and ecosystem function. Near-shore ecosystems are the multi-use 

ecosystems most subjected to multiple stressors. Due to ocean-coast and land-coast interactions these 

ecosystems will be subjected to the greatest range of stresses associated with global warming. Nearshore 

environments may also contain habitats that are particularly important for biodiversity in other 

environments, for instance by providing larval/juvenile nursery areas or by exporting nutrients. The 

MPI Biodiversity Programme has directed funds into research examining the implications of 

environmental and human impacts on the functional ecology of these key species and habitats. 

Near-shore ecosystems are complex and changes in diversity and community composition may be 

driven by multiple variables. Interactions between variables are likely to be non-linear, with 

disturbance thresholds and the potential for multiple stable states. As a consequence, it is often 

difficult to distinguish ‘natural’ from ‘anthropogenic’ impacts affecting ecosystem dynamics. MPI 

260


BioInfo research seeks to help disentangle this complexity, recognising that there will be 

contributions to this from both biodiversity research and Fisheries Services research. 

Regional Councils and universities support some research projects and survey programmes in coastal 

and estuarine waters by investigating the effects of sedimentation, pollution, ocean outfalls, sand 

dredge spoils, sand mining and nutrient enrichment on the marine ecosystem 58 . Although this 

workstream applies to offshore areas as well as near-shore, research to date has focussed on the nearshore. 

Projects 

ZBD2005-09 Rocky reef ecosystems - how do they function? 

The draft report for this project has been submitted and reviewed (Beaumont et al. In press). 

The Hauraki Gulf in north-eastern New Zealand offers one of the best opportunities to 

investigate how rocky reef ecosystems function and what impact fishing and other human 

activities may have on them. This study took advantage of these circumstances to first review 

the extensive literature to set the parameters of a model of how north-eastern New Zealand reef 

ecosystems function. The study used the model to identify key species and interactions, and 

explore the impacts of fishing. Field work was then undertaken across the range of reefs within 

the Hauraki Gulf to test the model predictions, describe spatial variation in patterns of 

abundance of key species, determine trophic relationships and investigate the linkages of reefs 

to other habitats. 

A qualitative model of northeast New Zealand rocky reef ecosystems was developed to explore 

the complexity of interactions amongst New Zealand rocky reef species and the impacts of 

exploitation. This model was developed on the basis of a review and summary of interactions 

among reef components. A key modelling outcome was the highly predictive but opposite 

responses by small lobsters and large predatory invertebrates to changes in the abundance of a 

range of other groups. This suggests that these two groups are ideal candidates as variables for 

monitoring reef ecosystem responses to perturbations. The modelling agreed with a welldocumented 

example of responses to a perturbation in fishing pressure in the Leigh Marine 

Reserve. However, the predictability was low for all responses. This implies, for example, that 

the reduction of kina in the Leigh Marine Reserve and the subsequent increase in macro-algae 

consequent to an increase in lobster abundance may not necessarily occur in another area. 

Field sampling at ten rocky reef sites across the Hauraki Gulf revealed differences among sites 

in community structure of macroalgae and invertebrates within all habitat strata. Of the 

environmental factors available, depth followed by a measure of water clarity (mean secchi) 

explained the most variation in the dependent variables (invertebrate taxa) from the quadrat 

data. Fish abundance data showed a similar, though weaker, trend across sites with depth, 

distance across the Gulf, and water clarity being the most important factors. The strong 

association between depth and water clarity and abundances of key taxa was expected and is 

similar to that found in earlier studies. With the exception of crayfish, there was no apparent 

overall relationship between invertebrate and fish abundances and marine reserve status of 

study sites, though the baited underwater video data showed snapper to be significantly larger 

within marine reserve sites than at fished sites. 

Stable isotope analysis of tissue samples collected from key species from all study sites allowed 

insight into the functional relationships among species as well as dietary sources of carbon. 

Many of the study taxa, from the primary producers through to the predators, had the most 

depleted δ 13 C values at the furthest inshore and offshore sites (e.g. Poor Knights and Long Bay) 

58 See MFish Biodiversity Research Programme 2010: Part 4. Reference Materials and Other research 

261


and the highest δ 13 C values at the coastal sites (e.g. Leigh, Tawharanui and Kawau). Without 

direct modelling of end point source signatures we cannot definitively determine the percentage 

contribution of each carbon source. However, we suggest that the depleted δ 13 C of taxa from 

offshore sites is the result of a pelagic source of C and the enriched δ 13 C at coastal sites is the 

result of a more benthic input of C than at offshore sites, with sources including kelp detritus. 

Taxa at the inner gulf sites are also likely to be subjected to a proportion of benthicaly-derived 

enriched δ 13 C. There were no obvious effects of marine reserve status on the isotopic signatures 

of study taxa with the exception of slightly enriched δ 13 C of kina and snapper at Leigh, and of 

kina at Tawharanui. 

Otolith microchemistry results for parore and snapper indicate strong connectivity between reef 

and non-reef systems within the wider Hauraki Gulf ecosystem. The majority of fishes 

sampled (both species) were likely to have originated as juveniles from lower salinity water 

environments such as estuaries fringing the Gulf. For snapper, our data suggest that only a 

small percentage of juveniles derive from reefs themselves. However, greater sampling 

replication is now required across a range of reef sites to better define the ratio of reef- versus 

estuary-derived juveniles, given the low percentage of reef-derived snapper. 

A qualitative model of northeast New Zealand rocky reef ecosystems was developed to explore 

the complexity of interactions amongst New Zealand rocky reef species and the impacts of 

exploitation. This model was developed on the basis of a review and summary of interactions 

among reef components. A key modelling outcome was the highly predictive but opposite 

responses by small lobsters and large predatory invertebrates to changes in the abundance of a 

range of other groups. This suggests that these two groups are ideal candidates as variables for 

monitoring reef ecosystem responses to perturbations. The modelling agreed with a well 

documented example of responses to a perturbation in fishing pressure in the Leigh Marine 

Reserve. However, the predictability was low for all responses. This implies, for example, that 

the reduction of kina in the Leigh Marine Reserve and the subsequent increase in macro-algae 

consequent to an increase in lobster abundance may not necessarily occur in another area. 

Field sampling at ten rocky reef sites across the Hauraki Gulf revealed differences among sites 

in community structure of macroalgae and invertebrates within all habitat strata. Of the 

environmental factors available, depth followed by a measure of water clarity (mean secchi) 

explained the most variation in the dependent variables (invertebrate taxa) from the quadrat 

data. Fish abundance data showed a similar, though weaker, trend across sites with depth, 

distance across the Gulf, and water clarity being the most important factors. The strong 

association between depth and water clarity and abundances of key taxa was expected and is 

similar to that found in earlier studies. With the exception of crayfish, there was no apparent 

overall relationship between invertebrate and fish abundances and marine reserve status of 

study sites, though the baited underwater video data showed snapper to be significantly larger 

within marine reserve sites than at fished sites. 

Stable isotope analysis of tissue samples collected from key species from all study sites allowed 

insight into the functional relationships among species as well as dietary sources of carbon. 

Many of the study taxa, from the primary producers through to the predators, had the most 

depleted δ 13 C values at the furthest inshore and offshore sites (e.g. Poor Knights and Long Bay) 

and the highest δ 13 C values at the coastal sites (e.g. Leigh, Tawharanui and Kawau). Without 

direct modelling of end point source signatures we cannot definitively determine the percentage 

contribution of each carbon source. However, we suggest that the depleted δ 13 C of taxa from 

offshore sites is the result of a pelagic source of C and the enriched δ 13 C at coastal sites is the 

result of a more benthic input of C than at offshore sites, with sources including kelp detritus. 

Taxa at the inner gulf sites are also likely to be subjected to a proportion of benthicaly-derived 

enriched δ 13 C. There were no obvious effects of marine reserve status on the isotopic signatures 

of study taxa with the exception of slightly enriched δ 13 C of kina and snapper at Leigh, and of 

kina at Tawharanui. 

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Otolith microchemistry results for parore and snapper indicate strong connectivity between reef 

and non-reef systems within the wider Hauraki Gulf ecosystem. The majority of fishes 

sampled (both species) were likely to have originated as juveniles from lower salinity water 

environments such as estuaries fringing the Gulf. For snapper, our data suggest that only a 

small percentage of juveniles derive from reefs themselves. However, greater sampling 

replication is now required across a range of reef sites to better define the ratio of reef- versus 

estuary-derived juveniles, given the low percentage of reef-derived snapper. 

ZBD2008-07 Carbonate Sediments: The positive and negative effects of land-coast interactions on 

functional diversity (complete): 

Land-coast interactions can profoundly influence coastal biodiversity and ecosystem function. 

Estuarine primary productivity derived from phytoplankton, resuspended phytobenthos, aquatic 

vegetation and fringing habitat plant material is exported to the adjacent coast on outgoing tides 

and contributes to secondary production in the vicinity of the estuary mouth. However, landderived 

sediments and contaminants that are discharged from estuaries can also stress open 

coastal populations. The balance of these competing processes was evaluated using a 

combination of laboratory and field investigations. A survey of two coastal locations (outside 

Whangapoua and Tairua harbours on the Coromandel Peninsula, New Zealand) quantified 

shifts in community structure in mollusc-dominated habitats and demonstrated that both 

distance from the mouth of the estuary and the size and density of large shellfish living in the 

sediments affect the composition and functionality seafloor communities. Tracing the 

importance of different estuary-derived food resources (seagrass, mangrove, estuarine 

phytoplankton and phytobenthos) using stable isotopes emphasized the importance of estuarine 

productivity to coastal bivalve. The work in the field has been supplemented with laboratory 

feeding trials, with the goal of verifying isotopic uptake rates in bivalve body tissues in a 

carefully controlled experimental setting. Trophic connections have important effects on 

coastal biodiversity. Understanding ecosystem processes and dynamics and their implications 

for functional biodiversity emphasises the importance of shifting the management focus from 

exploitation to resilience. Enhancing or maintaining this biodiversity will require more 

integrative ecosystem-based management focused on maintaining the resilience of coastal 

ecosystems. 

Other research relevant or specifically linked to the projects above, are listed in Table 11.3. 

Table 11.3: Other research linked to investigation of the role of biodiversity in the functional ecology of nearshore 

and offshore marine communities. 

MPI ZBD2005-04 Information on benthic impacts in support of the Foveaux Strait Oyster Fishery 

Plan 

ZBD2005-15 Information on benthic impacts in support of the Coromandel Scallops Fishery 

Plan 

ENV2005-23 Monitoring recovery of the benthic community between North Cape and Cape 

Reinga 

BEN2007-01 Assessing the effects of fishing on soft sediment habitat, fauna, and processes 

CRI Core 

purpose 

HAB2007-01 Biogenic habitats as areas of particular significance for fisheries management 

C01X1005— Management Of Cumulative Effects Of Stressors On Aquatic Ecosystems ; 

CO1X0907 Coastal Conservation Management, Freshwater and Estuaries and Coasts and 

Oceans 

DOC Conservancy surveys 

BNZ Biosecurity surveys 

OTHER Universities 


Cumulative footprint of human activities; understanding cumulative impacts and risks; marine spatial planning 

Land-base effects on marine biodiversity and inshore/offshore habitats; pollution in offshore 

Ecosystem-based management and integrative governance 

Defining marine ecosystem services, linking them to ecosystem function and societal values 

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11.3.4. Progress on Science Objective 4. Marine genetic 

biodiversity 

Genetic biodiversity can be measured directly by measurement made at the genes and chromosomes 

scale or indirectly by measuring physical features at the organism scale (assuming they have a genetic 

basis). 

Genetic diversity is fundamental to the long-term survival, stability and success of a species. Central 

to this is the “metapopulation” concept where populations are sufficiently genetically distinct from 

each other to be identifiable as individual units. A low level of recruitment between populations 

counters the effects of random genetic drift and inbreeding depression of genetic diversity. 

Human activities can profoundly affect genetic diversity both within populations and between 

populations. For example, shipping activity (movement across the globe) and aquaculture practices 

(transfer of organisms to different areas) can increase population connectivity such that genetic 

biodiversity may decrease between populations. In extreme cases, populations can become the same 

genetically (homogeneous) although considerable within population diversity may remain. In the 

event of increased genetic connectivity, a species may become more susceptible to extinction through 

biological or catastrophic stochasticity. That is, in the absence of between population diversity there is 

insufficient genetic variance to adapt to the effects of climate change, disease epidemics and so on. 

In contrast, under the much more common scenario of habitat fragmentation caused by human 

activities (fishing, pollution), decreased connectivity between populations will result in greater 

between-population diversity, but a reduction of within-population diversity. This also results in a 

decrease in a species survival (fitness) because fragmented or isolated populations may become 

extinct through environmental and genetic stochasticity or localised depletion. Periodic fluctuations in 

annual temperature for example can lead to small scale population extinction, which in the absence of 

recruitment between populations will result, over time, in the demise of all populations. 

To reduce the risk of species loss information about the genetic diversity both within populations 

(population isolation) and between populations (population connectivity) is needed. Without such 

information, the effects of perturbation on a species persistence and survival cannot be predicted. 

Furthermore, the links between genetic diversity, the dispersal capacity (mode of reproduction and life 

history development) of a species and the minimum viable population (MVP) size required in the 

marine environment to ensure population persistence, are little understood. For example, the MVP 

size for a species with a large dispersal capacity is likely to be quite different from that of a species 

with a relatively restricted dispersal capacity. Examining the connectivity between populations in the 

marine environment is fundamental to resolving some of the central challenges in ecology and has 

almost been ignored in the management of New Zealand fisheries or protection of biodiversity. 

Projects 

ZBD2002-12 Molecular identification of cryptogenic/invasive marine species – gobies. 

Project complete. (Lavery et al. 2006.) 

ZBD2009/10 Multi-species analysis of coastal marine connectivity. 

An extensive literature review of published and unpublished information about connectivity 

of New Zealand coastal biota has been completed. Reviews were made of 58 studies of 42 

taxa to identify the taxon or taxa studied, the habitat where each study took place, and 

geographic location of sampling sites used by each study. From these data, gaps in knowledge 

about taxa, habitats and spatial coverage of sampling were identified. Recommendations 

about four species to be studied, habitats that they should be collected from, and location of 

sampling sites were made. Recommendations included a standardised collecting protocol and 

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for the development and application of microsatellite markers to quantify the population 

genetic structure and the coastal connectivity of these taxa (Gardner et al. 2010). 

Two PhD students are carrying out field work, genetic analyses, and writing up (in the form 

of two theses) of this research. Both studies are underway. Fieldwork has begun on two 

flatfish species and two species of shellfish. The project been extended to incorporate a 

subtidal species of shellfish. A new component of the coastal connectivity project has been 

added to include work on the New Zealand scallop, Pecten novaezelandiae. This work focuses 

on population genetic structure and genetic connectivity at two different spatial scales and 

uses microsatellite markers (consistent with the use of microsatellite markers for the 4 species 

already under investigation in the original ZBD2009-10 project). First, the extension work 

focusses on scallops in the Hauraki Gulf and Coromandel Peninsula region. Scallops have 

been collected from several populations in this region and further samples will be added in the 

next two years. Second, the extension work focuses on scallops across New Zealand (the full 

range of this species’ distribution). Samples have been sourced from several regions including 

the fiords, the far north, and central New Zealand. In both cases, genetic connectivity will be 

assessed to determine linkages among populations at the two different spatial scales. The 

smaller spatial scale information will be of particular relevance to the scallop fishery in the 

Hauraki Gulf and Coromandel Peninsula region, whereas the larger scale work will 

complement ongoing studies of coastal connectivity at the national scale already under 

examination as part of the project. A PhD student has been recruited for this work and a suite 

of microsatellite markers has been developed for the New Zealand scallop and testing of 

population genetic variation is underway 


Table 11.4: Other research linked to marine genetic biodiversity. 

MPI ENH2007-01 Stock enhancement of blackfoot paua 

GEN2007-01 Genetic population profile of blackfoot paua 

ENH2007-02 Outbreeding depression in invertebrate populations 

IPY2007-01 Objective 11. Barcode of life 

MBIE C01X0502 Biodiversity& Biosecurity 

MPI Base line surveys for non-indigenous species 

OTHER Universities [?] 

BRAG PROJECTS FOR 2011-12 

Extension to ZBD2009-10 to include subtidal shellfish 


Can genetics combined with hydrographic models usefully contribute to the identification of biodiversity hotspots 

and/or to source-sink relationships within ecosystems? 

11.3.5. Progress on Science Objective 5. Effects of climate change 

and variability on marine biodiversity 

Cyclical changes or trends in climate and oceanography and associated effects such as increased 

ocean acidification and how they affect the marine ecosystem as a whole have long-term implications 

for trophic interactions and biodiversity, as well as functional aspects of the system e.g. 

biogeochemical processes. With significant improvement in remote sensing tools and global 

monitoring of climate change, new patterns are emerging indicating that there are long-term cycles. 

Examples include the Interdecadal Pacific Oscillation as well as shorter periods of change in relation 

to the El Niño Southern Oscillation that affect ocean ecosystems. Further, physical phenomena such 

as the deep subtropical gyre ‘spin-up’ in the South Pacific which resulted in a warmer ocean around 

New Zealand from 1996–2002, can have flow-on effects on ecosystem functioning. 

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A new report was launched in 2010 by the United Nations on ocean acidification 59 Among other 

findings, the study shows that increasing ocean acidification will mean that by 2100 some 70% of 

cold water corals, (a key refuge and feeding ground for some commercial fish species), will be 

exposed to corrosive waters (see also Tracey et al. 2011). In addition, given the current greenhouse 

gas emission rates, it is predicted that the surface water of the highly productive Arctic Ocean will 

become under-saturated with respect to essential carbonate minerals by the year 2032, and the 

Southern Ocean by 2050 with disruptions to large components of the marine food source, in particular 

those calcifying species, such as foraminifera, pteropods, coccolithophores, which rely on calcium 

carbonate. 

Emerging research suggests that many of the effects of ocean acidification on marine organisms and 

ecosystems will be variable and complex and will affect different species in different ways. Evidence 

from naturally acidified locations confirms, however, that although some species may benefit, 

biological communities in acidified seawater conditions are less diverse and calcifying (calciumreliant) 

species are absent whereas algae tend to dominate. 

Many questions remain regarding the biological and biogeochemical consequences of ocean 

acidification for marine biodiversity and ecosystems, and the impacts of these changes on ecosystems 

and the services they provide, for example, in fisheries, coastal protection, tourism, carbon 

sequestration and climate regulation. 

Studies to predict changes in biodiversity in relation to climate change in more than a rudimentary 

way are beyond the state of current knowledge in New Zealand. Nevertheless, surveys of biodiversity 

that have occurred or are planned will provide a snapshot against which future research results or 

trends can be compared. 

Meeting the challenges of climate change and identifying crucial issues for marine biodiversity is an 

area of high political interest internationally 60 and has been identified as a gap in biodiversity research 

in New Zealand 61 

Projects 

ZBD2005-05 Long-term effects of climate variation and human impacts on the structure and 

functioning of New Zealand shelf ecosystems. 

This is a large scale project to investigate changes in shelf ecosystems over a 1000 year timescale 

to provide context and perspective on issues of natural variation versus human impacts on 

marine biodiversity. 

The project is a multidisciplinary study to collate and sythesise paleoecological, archaeological, 

historical, and contemporary data relating to changes in the structure and functioning of New 

Zealand shelf ecosystems since human arrival about 750 years ago. The data have been used to 

model present and four past states of the Hauraki Gulf ecosystem over the last 1000 years. 

The project is collaborating with the international History of Marine Animal Populations (HMAP) 

project, itself a part of the Census of Marine Life (CoML) programme. A short video about the 

NZ Taking Stock project was made by HMAP staff and is currently available on the HMAP 

website http://hmapcoml.org/projects/nz/. 

59 

http://www.un.org/apps/news/story.asp?NewsID=36941&Cr=emissions&Cr1 Downloadable Report The 

Environmental Consequences of Ocean Acidification 

60 

http://biodiversity-l.iisd.org/news/ungas-second-committee-considers-biodiversity-and-sustainabledevelopment/ 

61 

Green, W.; Clarkson, B. (2006). Review of the New Zealand Biodiversity Strategy Themes 

266


Fifteen reports stemming from this project have been submitted to the Ministry and are at various 

stages of review, acceptance and publication. Four reports are still to be delivered. The report 

most relevant to this section is Pinkerton (In press). Other reports published to date are Carroll et 

al. (In press); Jackson et al. (In Press); Lalas et al. (In Press) a; b; Lalas & MacDiarmid (In Press); 

Lorrey et al. (In Press); MacDiarmid et al. (In Press a; b); Maxwell & MacDiarmid (In Press); 

Neil et al. (In Press); Paul (2012); Parsons et al. (In Press); Smith (2011). 

ZBD2008-11 Predicting plankton biodiversity & productivity with ocean acidification. 

This multi-year project is inter-linked with the Coasts and Oceans OBI and has the following 

objectives: 

1. To document the spatial and inter-annual variability of coccolithophore abundance and 

biomass, and assess in terms of the phytoplankton abundance, biomass and community 

composition in sub-tropical and sub-Antarctic water. 

2. To document the seasonal and inter-annual variability of foraminifera and pteropod 

abundance and biomass at fixed locations in sub-tropical and sub-Antarctic water by analysis 

of sediment trap material from time-series data collection. 

3. To document the spatial and seasonal distribution of the key coccolithophore species, 

Emiliana huxleyi, using both archived and ongoing ingestion of satellite images of Ocean 

Colour, and ground-truth the reflectance algorithm for E huxleyi for future application in New 

Zealand waters 

4. To determine the sensitivity of, and response of E. huxleyi and other EEZ coccolithophores to 

pH under a range of realistic atmospheric CO2 concentrations in perturbation experiments, 

using monocultures and mixed populations from in situ sampling. 

5. To document the spatial variability of diazotrophs (nitrogen-fixing organisms) and associated 

nitrogen fixation rate, and assess in terms of phytoplankton abundance, biomass and 

community composition in sub-tropical waters north of New Zealand. 

6. To determine the sensitivity of diazotrophs to ocean acidification composition in sub-tropical 

waters north of New Zealand. 

The project is proceeding according to plan and is still primarily in the sample collection phase 

with some data analysis but limited interpretation to date. The biodiversity record of 

coccolithophore species in New Zealand waters has been extended, with a transect across the 

Tasman Sea and a number of transects across the Chatham Rise. A bloom of the coccolithophore 

Emiliana huxleyi on the Chatham Rise was extensively characterised in terms of surface water 

biogeochemistry, and subsequently successfully cultured in the lab. Seasonal and interannual 

variability of E. huxleyi blooms were further characterised by extending the true colour satellite 

image analysis of presence/absence of coccolithophore blooms in the New Zealand EEZ. This 

was augmented by sample collection for ground-truthing of published calcite algorithms (for 

satellite detection of coccolithophore blooms) and application of a published calcite algorithm to 

New Zealand waters for 2002-3. Coccolithophore acidification sensitivity experiments were run 

in the Tasman Sea and the Chatham Rise region, with preliminary analysis indicating a decline in 

coccolithophore abundance under high CO2, but not when accompanied by elevated temperature 

as predicted under future climate change scenarios. Analysis of sediment trap samples for 

pteropod and foraminifera identification and abundance was completed for 2000-2010, with 

significant interannual variability noted in both, but also some indication of a recent decline in 

pteropod abundance in Sub-Antarctic water. Sample analysis from the 2010 Tasman Sea voyage 

identified the presence of nitrogen-fixing unicellular cyanobacteria and significant nitrogen 

fixation south of the Tasman Front, in contrast to previous observations. In acidification 

sensitivity experiments on this voyage nitrogen fixation did not change or decreased under high 

CO2 concentrations, in contrast to published data. Outputs to date include Boyd et al. (in press). 

ZBD2009-13 Ocean acidification impact on key NZ molluscs. 

Ocean acidification associated with increased atmospheric CO2 levels is a pressing threat to 

coastal and oceanic ecosystems. The chemical reaction which occurs when this CO2 is dissolved 

in seawater results in a well documented decrease in seawater pH (and an increase in seawater 

267


acidity), which may physically dissolve CaCO3 shells and/or skeletons and affect the 

shell/skeleton generation, as well as influencing many other physiological processes. Flow on 

effects to the viability of populations and the economic benefit that can be derived from 

commercially important species are likely. There is very little information on how key NZ 

calcifying species will respond to this change. 

This project is using laboratory experiments to quantify responses of key New Zealand mollusc 

species (paua, Haliotus iris, cockles, Austrovenus stutchburyi, and oysters Tiostrea chiliensis) to 

levels of ocean CO2 saturation predicted to occur in NZ waters over the following decades. 

Results will be combined with information on the role of these key species in influencing 

ecosystem structure and function, to assess local and ecosystem-scale implications of acidification 

of NZ coastal waters expected in the following decades. 

ZBD2010-41. Potential effects of ocean acidification on habitat forming deep-sea corals in the New 

Zealand region. 

Specific Objectives of this research were to 1. Determine the carbonate mineralogy of selected 

deep-sea corals found in the New Zealand region, 2. Assess the distribution of deep-sea coral 

species in the region relative to improved knowledge of current and predicted aragonite (ASH) 

and calcite saturation horizons (CSH), and 3. Assess potential locations vulnerable to deepwater 

upwelling and areas of key deep-water fishery habitat. Through a literature search and analysis, 

the project aimed to determine the most appropriate tools to age corals and measure the effects of 

ocean acidification on deep-sea habitat-forming corals, and recommend the best approach for 

future assessments of the direct effects of declining ocean pH on these key fauna. 

Under Objective 1, new results of investigations into the carbonate mineralogy of selected deepsea 

corals found in the New Zealand region were presented, and previous work on coral 

mineralogy summarised. The mineralogy and trace element concentration (Sr and Mg) of the five 

branching stony coral species (Order: Scleractinia) Goniocorella dumosa, Solenosmilia 

variabilis, Enallopsammia rostrata, Madrepora oculata, and the endemic Oculina virgosa, and 

for the key habitat forming gorgonian coral species (Order: Alcyonacea) Keratoisis spp., 

Lepidisis spp., Paragorgia spp. and Primnoa sp., was ascertained. Stony branching corals are all 

aragonitic with high Sr and low Mg while most of the gorgonian corals are made of high Mg and 

low Sr, with high Mg calcite (>8 mol% Mg). The gorgonian sea fan, Primnoa sp., is aragonitic. 

Under Specific Objective 2, up to date position and depth data were used to produce distribution 

maps for the study species. Data compare well with previous publications from biodiversity 

research, research trawl, and observer sampling effort on wide regional distribution, but 

individual species display variations within the region. The peak depth distributions are unimodal 

at about 800-1000 m for most of the above species, but G. dumoas, E. rostrata, and Lepidisis 

spp. show bi-modal distributions and O. virgosa occurs primarily in shallow depths. In the 

second year of the project these distribution data will be compared with existing and predicted 

aragonite and calcite saturation horizons, particularly in areas of key deepwater fishery habitat. 

Also under Specific Objective 2, on-going opportunistic water sampling analyses are being 

carried out to determine alkalinity and dissolved inorganic carbon (DIC), and modelling to 

determine aragonite (ASH) and calcite saturation horizon (CSH) data is in progress. The aim is to 

compare water carbonate chemistry with regional biogeochemistry models and future scenarios 

to identify areas potentially at risk from ocean acidification. 

Under Specific Objective 3, at-sea sampling of live corals for aquarium studies has been carried 

out to investigate the feasibility of keeping the corals alive for growth and ocean acidification 

experiments. The corals collected in April, 2012 are still alive in the laboratory and include one 

small colony of S. variabilis. A literature search and analysis to determine the most appropriate 

tools to age and measure the effects of ocean acidification on deep-sea habitat-forming corals is 

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in progress. From these trials and reviews, recommendations on the best approach for future 

assessments of the direct effects of changes in ocean pH on these key fauna will be made. 


Table 11.5: Other research linked to effects of climate change and variability on marine biodiversity. 

MPI SAM2005-02 Effects of climate on commercial fish abundance 

ENV2007-04 Climate and oceanographic trends relevant to New Zealand fisheries 

MBIE C01X502 Coasts & Oceans Centre 

DOC Baseline surveys; protected deepsea corals (Tracey et al. 2011; Baird et al. 2012) 

OTHER University of Otago-NIWA shelf carbonate geochemistry and bryozoans 

Geomarine Services-foraminiferal record of human impact 

Regional Council monitoring programmes 

EMERGING ISSUES (this objective) 

What papers can be generated on the effects of climate change on marine biodiversity in NZ in time for 5 th 

IPCC report? 

How does climate change influence marine microbial diversity, species mix and biogeochemical roles? 

How will harmful toxic algal blooms be affected by warming seas? (e.g. Chang 2003, Chang et al. 2003) 

11.3.6. Progress on Science Objective 6. Biodiversity metrics and 

other indicators for monitoring change 

In the mid 1990s, monitoring of marine biodiversity and the marine environment was a topic of 

considerable discussion, yielding several reports on developing MfE indicators 62 However, since the 

publication of MfE’s indicators in 2001, a much reduced set of core indicators that relate to the 

marine environment have been reported on 63 . A new international initiative launched in 2010 

“Biodiversity Indicators Partnership 64 ” provides guidelines and examples of biodiversity indicators 

developed around the globe, however, Oceania does not appear to have any partnership identified. 

The link between this initiative and OECD environmental indicators is unclear. 

A serious gap identified by Green and Clarkson (2006) 65 in their review of progress on 

implementation of the NZBS was the lack of development of an integrated national monitoring system 

(see Biodiversity Research Programme 2010: Part 4). Efforts to respond to this gap within the 

Biodiversity Programme resulted in the immediate initiation of a 5-year Continuous Plankton 

Recorder project, and a series of workshops to determine how best to approach monitoring on a 

national scale (ZBD2008-14). [One objective of monitoring would be to test the effectiveness of 

management measures.] 

Projects 

ZBD2004-10 Development of bioindicators in coastal ecosystems. 

62 

Downloadable MfE reports Confirmed indicators for the marine environment 2001, ME398; An analysis of 

potential indicators for marine biodiversity 1998 TR44; Environmental Performance Indicators: an analysis of 

potential indicators for fishing impacts 1998 TR43; Environmental Performance Indicators: Summary of 

Proposed Indicators for the Marine Environment 1998, ME296; Environmental Performance Indicators: Marine 

environment potential indicators for physical and chemical processes, and human uses and values 1998 TR45; 

Potential coastal and estuarine indicators - a review of current research and data 1997 TR40; Monitoring and 

indicators of the coastal and estuarine environment - a literature review 1997 TR39 

63 

http://www.mfe.govt.nz/environmental-reporting/about/tools-guidelines/indicators/core-indicators.html 

64 

www.bipnational.net/IndicatorInitiatives 

65 

Green, W.; Clarkson, B. (2006). Review of the New Zealand Biodiversity Strategy Themes. 

269


Project complete (Savage 2009). Agricultural and urban development can increase run-off and lead 

to excessive nutrient loadings in fragile coastal environments that are nursery grounds for a diverse 

array of coastal and estuarine species, as well as other resident organisms. This project investigated 

the development of bioindicators to strengthen the ability of managers to detect and quantify 

changes in anthropogenic nitrogen inputs to coastal and estuarine ecosystems by comparing six 

study sites with different levels of development ranging from pristine through to fully urban. The 

results show a strong positive relationship between the percent agricultural land in surrounding 

catchments and total nitrogen (TN) loading to nearshore environments. 

These results also hint at differences in dissolved and particulate nitrogen source pools, and 

highlight the importance of using complementary components of food webs and high spatial 

replication to show linkages between watershed land use and chemical markers in biota. The 

effects of nutrient enrichment were transmitted up the food web, with growth of secondary 

consumers, Notolabrus celidotus (spotties) and Grahamina nigripenne (estuarine triplefins) 

generally enhanced in nutrient enriched coastal areas. Benthic prey dominated the diets of these 

fish species, with amphipods and brachyurans being the most important prey items for triplefins 

and spotties, respectively. However, there were site-specific differences in prey importance and 

diet diversity. Both triplefins and spotties consumed considerably more diverse prey items at 

pristine than nutrient-enriched coastal areas. Food web models based on stomach content analyses 

and dual isotope ratios suggest that there are shifts in the relative importance of the different 

organic matter sources supporting food structure among the different coastal ecosystems due to 

nutrient enhancement from land-based activities. [how might these results be used in a biodiversity 

management context?] 

ZBD2008-14 What and where should we monitor to detect long-term marine biodiversity and 

environmental changes? 

Two workshops and a follow up meeting were held with stakeholders in 2008/09 to discuss a 

marine environmental monitoring programme (MEMP) for New Zealand, to detect long-term 

changes in the marine environment, building on existing time series and data collection 

(Livingston 2009). The MEMP was formulated into a developmental project staged over 3 years 

and submitted to the former Ministry of Research Science and Technology’s Cross Departmental 

Research Pool (CDRP) for funding starting July 2010. Since that time, CDRP funding has been 

withdrawn. Instead a call for proposals taking a more modest approach to developing MEMP 

beginning with collation of all potential data series into a metadata database, a scientific evaluation 

of the existing time series as to their ‘fit to purpose’ for MEMP was made and tender evaluations 

are underway. 

Monitoring change in the marine environment is the only way we can measure long-term trends, 

mitigate risk and provide evidence of changes which may require policy or management practice 

response. DOC has since been developing an integrated approach to monitoring biodiversity 

particularly on the land but also in marine reserves 66 . 

ZBD2008-15 Continuous Plankton Recorder Project: implementation and identification. 

This project adopts the methods used in a long-term programme that has proved highly relevant to 

measuring biological changes in the ocean, i.e., the Continuous Plankton Recorder Programme in 

the North Atlantic (SAHFOS) and more recently the Southern Ocean 67 . This 5-year MPI project 

aims to map changes in the quantitative distribution of epipelagic plankton, including 

phytoplankton, zooplankton and euphausiid (krill) life stages annually when vessels depart and 

return from New Zealand on their journey to the Ross Sea toothfish fishery each year in 

November/December, and February/March traversing key water masses and ocean fronts in New 

66 The Department of Conservation Biodiversity Monitoring and Reporting System Fact Sheet July 2010 

67 Southern Ocean CPR programme http://data.aad.gov.au/aadc/cpr/ 

270


Zealand’s EEZ as well as south to the Ross Sea. Four years the transectshave been collected, staff 

have been trained in plankton ID work and over three years of samples analysed. 

ZBD2010-42 Marine Environmental Monitoring Programme. 

This project continues from ZBD2008-14. A starting point to the assessment and reporting of 

broad-scale changes in New Zealand’s marine environment is to define basic criteria and locate all 

existing and past time series of marine environmental data to improve awareness and access to 

these data. After this, these data can be evaluated as to their fitness-for-purpose for contributing 

towards a national Marine Environmental Monitoring Programme (MEMP). To date an online 

catalogue has been designed and a portal to this is available at http:\geodata.govt.nz. 

Questionnaires were developed to determine what marine environmental time series data were 

available within New Zealand. Information to date gives us 131 databases, 50% of these are listed 

as having ongoing funding (although not necessarily for all locations), and another 19% are listed 

as likely to continue. Over 70% are publically available. Most cover more than one location, 

although this is dependent on how the databases are constructed, e.g., DOC at present has a 

separate database for each marine reserve, while regional councils tend to have separate databases 

for different subjects (e.g., contaminant monitoring, ecological monitoring). Around 95estuaries 

and harbours are being sampled, which is not surprising given that the majority of the information 

comes from Regional Councils (Figure 1). There are 78 coastal locations and 33 marine reserves. 

The second phase, determining fitness-for-purpose, was begun at a workshop held at NIWA on 

11th June (see objective 3). Priority variables for inclusion in a national monitoring programme 

have been identified from responses to a questionnaire sent to scientific experts and central and 

regional government departments involved in monitoring and/or reporting. Core reference sites 

and major gaps in the spatial network are presently being determined and the requirements for 

spatial and temporal sampling determined. The project is due to be completed by June 2013. 


Table 11.6: Other research linked to biodiversity metrics and other indicators for monitoring change. 

MPI ENV2006-15: Database and fishing indicator on seamount habitats (Rowden et al 2008) 

BEN2009-02 (Tuck et al. 2010) 

ENV2006-04: Fisheries indicators from trawl surveys (Tuck 2009) 

DEE2010-05 

MBIE Core funding for Coasts and Oceans Centre 

DOC Conservancy projects-Hawke’s Bay; 

OTHER Regional Councils, Universities 


Monitoring coastal waters and New Zealand’s oceans to report on a national scale remains a major gap 

There is little longterm commitment to direct monitoring the marine environment 

11.3.7. Scientific Objective 7. Identifying threats and impacts to 

biodiversity and ecosystem functioning 

Many marine ecosystems in New Zealand have been modified in some way through the harvesting of 

marine biota, the selective reduction of certain species and size/age classes, modification of food 

webs, including the detrital components and habitat destruction. Benthic communities including 

seamount communities, volcanic vent communities, bryozoans, corals, hydroids and sponges are 

vulnerable to human disturbance. The mechanical disturbance of marine habitats that occurs with 

some activities such as trawling, dredging, dumping, and oil, gas and mineral exploration and 

extraction; can substantially change the structure and composition of benthic communities. The 

271


invasion of alien species into New Zealand waters is also a real threat, with evidence of nuisance 

species already well established 68 

A number of inshore marine ecosystems (especially estuaries and other sheltered waters) have been 

modified by sediment, contaminants and nutrients derived from human land use activities (Morrison 

et al. 2009). Coastal margin development has had a major impact on some inshore marine 

communities. 

A recent project commissioned by the MPI Aquatic Environment Programme, identifies key threats to 

the marine environment (BEN2007-05) is complete and has listed and ranked the top threats to New 

Zealand’s marine environment, as perceived by expert opinion. Relevant findings are that the highest 

ranking threats are ocean acidification, increasing sea water temperatures and bottom trawling (across 

all habitats) and that the most threatened habitats are intertidal reef systems in harbours and estuaries 

(MacDiarmid et al. 2012). Ecological risk assessment (ERA) methods have also been reviewed (under 

ENV200515, Rowden et al. 2008), and a trial Level 2+ assessment completed on Chatham Rise 

seamounts to estimate the relative risk to seamount benthic habitat from bottom trawling (under 

ENV200516, Clark et al. 2011). An MPI project (DEE2010-04) has resulted in a new ecological risk 

assessment being developed that is tailored for New Zealand deepwater fisheries (Clark et al. in 

press). 

Projects 

ZBD2009-25 Predicting impacts of increasing rates of disturbance on functional diversity in 

marine benthic ecosystems. The objectives of this project are to: 

1. Further develop landscape/seascapes ecological model of disturbance/recovery dynamics in 

marine benthic communities, incorporating habitat connectivity, based on existing model by 

Lundquist et al. (2010). 

2. Predict impacts of increasing rates of disturbance on rare species abundance, functional 

diversity, relative importance of biogenic habitat structure, and ecosystem productivity. 

3. Use literature and expert knowledge to quantify rare species abundance, biomass, functional 

diversity, habitat structure, and productivity of various successional community types in the 

model. 

4. Field test predictions of the model in appropriate marine benthic communities where 

historical rates of disturbance are known, and benthic communities have been sampled. 

The baseline model, incorporating connectivity, has been created in Matlab. Objective 2 

(predictions for functional biodiversity based on model) is underway. Some progress has been 

made on objective 3 (quantify functional biodiversity from existing data) through familiarisation 

of the programmers with the datasets of the Ocean Survey 2020 Chatham/Challenger project 

(ZBD2007-01) and biodiversity analyses to date for objective 8 of that project. Objective 4 is in 

process, with the majority of the field test funded by BEN2007-01. Researchers from both 

projects have met to discuss and modify the draft sampling design in order to best allocate 

sampling to test the predictions of the functional diversity model. The field testing took place in 

March-April 2010 in Tasman/Golden Bay. 


68 http://www.biosecurity.govt.nz/biosec/camp-acts/marine 

http://www.biosecurity.govt.nz/pests/salt-freshwater/saltwater 

http://www.biosecurity.govt.nz/about-us/our-publications/technical-papers 

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Table 11.7: Other research linked to threats to and impacts on biodiversity. 

MPI BEN2007-05 Assessment of anthropogenic threats to New Zealand marine habitats. MacDiarmid 

et al 2012 

DEE2010-04 

MBIE CO1X0906 Vulnerable deep-sea communities (mapping and sampling a range of deep-sea 

habitats (seamounts, slope, canyons, seeps, vents), and determining relative risk to their benthic 

communities from human activities 


The socio-economic valuation of biodiversity in NZ has not been adequately addressed. 

The cumulative footprint of anthropogenic activities on the NZ marine environment has not been assessed. 

Potential development of seabed mining makes this a priority in deepwater environments as well as coastal. 

11.3.8. Biodiversity in Antarctica: BioRoss Project Summaries and 

Progress 

The objectives of BioRoss are to improve understanding of the biodiversity and functional ecology of 

selected marine communities in the Ross Sea. These objectives are being achieved by commissioning 

directed research on the diversity and function of selected marine communities in the Ross Sea region. 

BioRoss is committed to linking with ongoing Ross Sea ecosystems research through the Antarctic 

Working Group, and supporting climate change related research, especially at high latitudes. 

Data acquisition from the Antarctic marine environment is logistically difficult and expensive. 

Nevertheless, the seven biodiversity Science Objectives listed above also drive BioRoss research 

projects. The BioRoss survey in 2004 and the Latitudinal Gradient Project ICECUBE have provided 

significant new information on biodiversity, species abundance and distribution that are now 

facilitating research into functional ecology and longer term monitoring programmes. This research 

has the potential to lead into other research on genetic diversity, climate variability and the 

development of indicators. The research results are also being used in the MPI Antarctic Research 

Programme projects on ecosystem modelling of the Ross Sea. 

The MPI Antarctic Research and BioRoss Programmes are also directly involved in supporting the 

development of protection measures around the Balleny Islands. In 2005 MPI scientists and Ministry 

of Foreign Affairs and Trade (MFAT) personnel prepared a paper for submission to CCAMLR 

justifying MPA designation around the islands to protect ecosystem processes occurring there that 

may be important for the stability and function of the wider Ross Sea regional ecosystem. 

To collect data in support of the MPA proposal, MPI BioRoss funded a targeted research voyage to 

the Balleny Islands in February 2006 (ZBD2005-01), and also provided supplementary funding to 

carry out opportunistic biological sampling at the Balleny Islands on a voyage to the Ross Sea that 

was primarily funded by LINZ to do bathymetric mapping. 

The field sampling of these projects were successful, both providing important data and specimens 

from the Balleny Islands area and supplementary information for the Antarctic Working Group 

Research Programme. The results will inform research planning for subsequent projects. Support for 

Ross Sea region biodiversity will remain a high priority for future research in the BioRoss 

Programme. 

In addition, BioRoss funded a further ICECUBE project to sample the Antarctic coastline during the 

summer season of 2006/07 (ZBD2006-03). ICECUBE is a key part of the international Latitudinal 

Gradient Project to explore hypotheses about environmental drivers of structure and function in subtidal 

ecosystems along the western Ross Sea coastline (Cummings et al. 2008 ). This project acquired 

funding for three seasons (2007/08, 08/09, 09/10) as part of the MBIE IPY contestable round (see also 

Cummings et al. 2011 and Thrush and Cummings 2011). Published reports and papers from the MPI 

273


Ross Sea coastal projects include Cummings et al. 2003, 2006, 2008, 2010, 2011. De Domenico et al. 

2006, Grotti et al, 2008, Guidetti et al. 2006, Norkko et al. 2002, 2004, 2005, 2007; Pinkerton et al. 

2006, Schwarz et al. 2003, 2005, Sharp et al. 2010, Sutherland 2008, Thrush et al. 2006, 2010 and in 

press. 

The New Zealand Government provided one-off funding for a Census of Antarctic Marine Life 

(CAML) survey to the Ross Sea from R.V. Tangaroa as part of New Zealand’s involvement in the 

2007-08 International Polar Year activities. The CAML Voyage was a large cooperative research 

effort under the banner of Ocean Survey 20/20 with considerable international collaboration, 

simultaneously utilising a number of different vessels with different strengths and capabilities. 

Progress on the two projects IPY2007-01 and IPY2007-02, is detailed below. 

Projects 

ZBD2002-02 Whose larvae is that? Molecular identification of planktonic larvae of the Ross Sea. 

Completed. (See Sewell et al. 2006, Sewell 2005, Sewell 2006.) 

ZBD2003-03 Biodiversity of deepwater invertebrates and fish communities of the north western 

Ross Sea. Completed. Two AEBR reports were produced by Rowden et al. (2012a, in press) and a 

Voyage Report, Mitchell and Clark 2004. A number of papers have also been published in the 

scientific literature using specimens or data from the 2004 biodiversity survey (e.g. De Domenico 

et al. 2006, Schiaparelli et al. 2006, Rehm et al. 2007, Kröger & Rowden 2008, Clark et al. 2010) 

ZBD2005-01 Balleny Islands Ecology Research, Tiama Voyage (2006). 

This voyage collected a large amount of new data from the Balleny Islands and surrounding waters 

using a range of methods, including bird and mammal observations, whale biopsy sampling, shorebased 

penguin colony surveys, SCUBA dive quadrats and transects, tissue collections for stable 

isotope analyses, and continuous acoustic/bathymetric data collection (Smith 2006). Some of the 

specimens and data have been used for other studies. 

ZBD2005-03 Opportunistic biological data during 2006 Ross Sea voyage utilising Tangaroa. 

This project is complete (MacDiarmid and Stewart 2012).In brief it proved feasible to assess 

demersal fish abundance using the camera and lights. Because sampling was restricted to areas 

outside the main fishery, no toothfish were observed. The camera system, (a predecessor to the deep 

towed imaging system (DTIS)) proved capable of characterizing the demersal fish habitat 

associations. Sampling using a variety of methods yielded specimens and tissue samples of a wide 

variety of benthic and pelagic organisms. The acoustic information collected on water column 

organisms was less useful than desired because of interference from the bottom profiling aspects of 

the voyage. Marine mammals and seabirds were routinely recorded and automated sampling of the 

surface waters using a continuous plankton recorder and instruments to record sea surface 

temperature, salinity and chlorophyll-a concentration was successful. 

ZBD2008-23 Macroalgae diversty and benthic community structure at the Balleny Islands. 

Project complete. As a result of this study, the known macroalgal flora of the Balleny Islands has 

increased from 13 to 27 species, and there are 2 new records for the Ross Sea in addition to the 3 

new records reported by Page et al. (2001). The biodiversity however remains poorly known, and 

detailed comparisons with other parts of the Antarctic region would be premature. A high 

proportion of the taxa reported here are known from only one collection, with a further group of 

taxa known from either two or three collections. Many of the taxa cannot be fully documented as 

there is insufficient mature material available. 

The samples collected as part of a benthic survey at Borradaile Island, one of the Balleny Islands 

group, during the 2006 Tiama expedition have been analysed to provide an assessment of benthic 

community structure. The Borradaile Island sites were located in a high energy environment, 

sediments had relatively high organic and chlorophyll a content, and considerably lower 

274


concentrations of degraded plant material (phaeophytin) than noted in previously surveyed 

southern Ross Sea locations. Borradaile Island macrofaunal diversity was within the range noted for 

the more southern sites; macrofaunal abundance however, was more variable. Epifaunal diversity 

was very low, with the seastar Odontaster validus the only large epifaunal taxon found. In contrast, 

the Borradaile Island dive sites had high macroalgal diversity. Although not observed at these dive 

sites, the Tiama voyage researchers noted shallow water areas with high diversities of encrusting 

organisms. This study has provided the first analysis of shallow water benthic communities of the 

Balleny Islands. While it has shown some interesting similarities and contrasts in benthic diversity 

with other coastal Ross Sea locations, this information from Borradaile Island may not be 

representative of the entire Balleny area, and further surveys from other sites within the Balleny 

group are recommended (Nelson et al. 2010). 

ZBD2008-20 Ross Sea Ecosystem function: predicting consequences of shifts in food supply. 

Project complete. Detailed information on the uptake and incorporation of different primary food 

sources to key epibenthic species help predict consequences of potential environmental change. Over 

a two year period, in situ investigations into responses to, and utilisation of, primary food sources by 

a common ophiuroid, were conducted at two contrasting coastal Ross Sea locations, Granite Harbour 

and New Harbour. At both locations, benthic net primary production was measured and the 

contributions of large macrobenthic organisms to ecosystem functions such as organic matter 

processing and nutrient recycling were quantified. Granite Harbour benthic soft-sediments supplied 

overlying waters with regenerated ammonium and phosphate, and the ophiuroid significantly 

increased the rates of nutrient release. Ultimately, the nutrients will be used by microalgae in the 

water column and under the ice. Detrital algae (phaeophytin) were present in sediments at greater 

concentrations than fresh microalgal material (chlorophyll a), and appears to be functionally 

important; it was a significant predictor of dissolved oxygen, phosphate, ammonium and nitrate-plusnitrite 

flux. Benthic organisms in predominantly ice covered Ross Sea locations such as Granite 

Harbour probably feed on degraded detrital algae for much of year, given the limited amount of fresh 

microalgae available due to the dimly lit environment, and the consequently low rates of in situ 

benthic primary production. Results of the New Harbour investigations contrast those of Granite 

Harbour, reflecting the very different ice conditions at these two locations (Cummings et al. 2010; 

Lohrer et al. 2012). 

IPY2007-01 NZ International Polar Year Census of Antarctic Marine Life 

Overall science objectives for the Project were developed by MPI, NIWA and other interested and 

participatory parties in discussions held through the Ocean Survey 20/20 Science Working Group. 

1. To measure and describe the relationships between patterns of marine organisms, their 

biodiversity and environmental variables between longitudes ~170°E and ~175°W, and 

depths down to ~3500-4000m in the Ross Sea region. 

2. To assess the trophic interrelationships of the major functional groups in the Ross Sea and 

regional ecosystem, with particular reference to improving inputs to ecosystem modelling. 

3. To obtain baseline measures of the marine environment and identify a suite of ecosystem or 

environmental indicators that could potentially be used to monitor change in response to 

environmental or anthropogenic forcing in the Ross Sea region 

All specific objectives apart from objective 2 have now been completed. 

Specific Objective 1: To measure seabed depth and rugosity using the multibeam system (whenever 

possible) to identify topographic features such as bottom type, iceberg scouring, seamounts etc and 

to determine areas for targeted benthic fauna sampling. (not funded in this project). Objective 

Completed. (Mitchell 2008, Hanchet et al. 2008) 

275


Specific Objective 2: To continue the analysis of opportunistic seabird and marine mammal 

distribution observations from this and previous BioRoss voyages and published records, and in 

relation to environmental variables. (Draft report completed.) 

The distributions of the seabird and marine mammal taxa reported from two RV Tangaroa voyages 

(TAN200602 and TAN200802) have been mapped. These represent the count data of seabirds 

recorded during the 2006 Ross Sea voyage and the locations of images of seabird taxa (recorded 

opportunistically) from the 2008 IPY-CAML voyage and records from observers from the 

toothfish fishery. The distributions include the presence data of taxa over waters south of about 60° 

S to the Ross Sea. Additional work to explain the distribution of the most common seabirds in 

relation to environmental variables has been proposed but has not yet started. 

Specific Objective 3: To identify and determine near-surface spatial distribution, diversity and 

abundance of phytoplankton, and zooplankton, based on Continuous Plankton Recorder samples 

collected during transit to and from the Ross Sea. 

The Continuous Plankton Recorder (CPR) was deployed during the IPY voyage, both during the 

transit to and from Wellington, and within the Ross Sea itself. CPR silks collected during transit 

were preserved in formalin and sent to Australian Antarctic Division where they were analyzed for 

zooplankton species composition and abundance. CPR silks collected within the Ross Sea were 

preserved in ethanol for the analysis of epipelagic meroplankon. In addition to the zooplankton, 

sampling, water samples were collected for phytoplankton analysis using the underway water 

sampling system from a depth of 7 m, corresponding to the approximate depth of CPR sampling. 

In addition to the work described above, ICOMM (International census of marine microbes) 

samples collected during the IPY-CAML survey (10 m depth x 4 stations) have been analysed by 

collaborators in the USA (Ghiglione et al. 2012). 

Specific Objective 4: To analyse underway and station data collected on salinity, temperature and 

chlorophyll a data, spot optical measurements with the SeaWiFS Profiling Multichannel 

Radiometer (SPMR), surface samples for chlorophyll a, nutrients and particle analysis as well as 

underway nutrient observations to allow ground-truthing of data collection from satellites and 

identify water masses (e.g. surface seawater temperature, and chlorophyll concentration). 

This objective addressed background physical and surface biological conditions at the time of the 

IPY-CAML survey. The objective was split into two parts 1. characterisation of the biological 

environment and bio-optical regime using continuous underway sampling, and 2. identification of 

thermohaline fronts using discrete and underway sampling of temperature, salinity and nutrient 

profiles. The combined dataset was used to validate satellite data of temperature and surface 

chlorophyll distributions, providing a synoptic overview of physical and biological conditions 

during the survey. 

Specific Objective 5: To identify and determine the spatial distribution, abundance (biomass), 

diversity, and size structure of epipelagic, mesopelagic (and possibly bathypelagic) species using 

acoustics data, target strength estimation techniques and net sampling. 

This objective addressed samples collected using the mesopelagic trawl and acoustic data collected 

from midwater marks using the ship’s echosounders. Results were presented at five conferences: 

1) CAML-IPY Symposium in Genoa, Italy, May 2009; 2) CCAMLR SG-ASAM meeting in 

Genoa, Italy, May 2009; 3) Antarctic New Zealand conference in Auckland, July 2009; New 

Zealand Marine Sciences’ Society conference in Stewart Island, July 2011; and International Polar 

Year Symposium, Montreal, Canada, April 2012. Results were also presented to the Ross Sea 

Bioregionalisation workshop in Wellington in June 2009 (see below) and were incorporated in the 

bioregionalisation reports prepared for CCAMLR (SC-CAMLR-XXIV-BG-25) and the Antarctic 

Treaty Consultative Meeting (ATCM). Reports include those by Koubbi et al. (2011), O’Driscoll 

(2009), O’Driscoll et al. (2009, 2011), Pinkerton et al. (in press), and Hanchet et al. (in press). 

276


Specific Objective 6: To identify and measure diversity, distribution and densities of 

mesozooplankton, macrozooplankton and meroplankton. 

This objective addressed the samples taken by Multiple Opening/Closing Net and Environmental 

Sampling System (MOCNESS) from the sea surface to the sea floor. The samples were 

quantitatively divided at sea to allow several complementary analyses to be performed. In terms of 

the mesozooplankton community in the Ross Sea, copepods were the dominant zooplankton 

collected in most samples, and this was primarily calanoids and cyclopoids (i.e., Oithona spp.). 

However, in certain cases pteropods (Limacina helacina antarctica) and salps (Salpa thompsoni) 

made important contributions to mesozooplankton abundance. Total water column 

mesozooplankton biomass ranged between 0.6-9.1 g C m -2 and was usually highest close to the 

surface. Mesozooplankton biomass in the Ross Sea was generally higher than expected, and can 

rival that of productive subantarctic regions (e.g., South Georgia). Salps were the main 

macrozooplankton species recorded in the MOCNESS samples and a paper describing the 

population ecology and distribution of Salpa thompsoni on the continental slope and around the 

seamounts to the north of the Ross Sea has been published by Pakhamov et al. (2011). 

Samples were also preserved in ethanol for the analysis of meroplankton species composition and 

DNA sequencing. Larvae from at least eight phyla were found, with a remarkable dominance of 

annelids in both abundance and diversity. Overall, larval abundances observed were lower than 

other Antarctic studies, likely attributable to the late summer sampling, months after Ross Sea’s 

phytoplankton bloom and the main trigger of spawning in many benthic invertebrates. Analysis of 

variation in meroplankton community composition showed significant differences among 

geographic regions (Shelf, Slope and waters of the Antarctic Circumpolar Current - ACC), among 

water masses (Shelf Water, Antarctic Surface Water, and Circumpolar Deep Water), and among 

depth strata (upper, midwater and bottom). Overall, near surface waters showed greater larval 

abundances, and these values decreased from the continental shelf to the slope, declining further in 

the deeper waters of the ACC. Differences between these locations were due not only to the 

presence or absence of certain taxa, but also a result of changes in OTU abundance. 

Specific Objective 7: To determine diversity, distribution and densities of viral, bacterial, 

phytoplankton and microzooplankton species in the water column. 

The full data sets have been completed and loaded into an MPI database and to the South western 

Pacific OBIS node (Gordon 2000). Phytoplankton and nanoplankton cell counts have revealed that 

there is a significant difference between shelf and abyssal site water column assemblages, both in 

terms of cell numbers, diversity and density. These data now have to be integrated with the water 

column data to help understand what may be driving the changes in these compositions. 

Specific Objective 8: To determine the spatial distribution, abundance (biomass), diversity, and size 

structure of shelf and slope demersal fish species and associated invertebrate species using a 

demersal survey. 

This objective had three key tasks; (i) to identify specimens, update the Ross Sea species list and 

determine biodiversity, (ii) to identify fish assemblages and relate them to environmental data, and 

(iii) to compare estimates of fish density and abundance between trawls, visual (video & still 

images) and acoustic sampling techniques. A fourth key task, to determine density and abundance 

of demersal fish using a bottom trawl survey, was funded under MPI project ANT2007-02. Results 

have been published as three scientific journal papers with an additional paper in review, and have 

been submitted to several CCAMLR working group meetings. 

A paper on the distribution and diversity of demersal and pelagic fish species in the Ross Sea 

region including results from both the BioRoss and IPY surveys and collections from the toothfish 

fishery will soon be published (Hanchet et al. in press). A diverse collection of over 2,500 fish 

277


specimens was obtained from the BioRoss and IPY-CAML surveys representing 110 species in 21 

families. When combined with previous documented material this gave a total species list of 175, 

of which 137 were from the Ross Sea shelf and slope (to the 2,000 m isobath). Demersal species 

richness, diversity and evenness indices all decreased going from the shelf to the slope and the 

seamounts. In contrast, indices for pelagic species were similar for the slope and seamounts/abyss 

but were much lower for the shelf. 

A paper on the variation of demersal fish assemblages in the western Ross Sea including results 

from both the BioRoss and IPY surveys has been published (Clark et al. 2010). The distribution 

and abundance of 96 species able to be identified to species level collected in these surveys were 

examined to determine if demersal fish communities varied throughout the area, and what 

environmental factors might influence this. Three broad assemblages were identified, in the 

southern Ross Sea (south of 74ºS), central–northern Ross Sea (between latitudes 71º–74ºS), and 

the seamounts further north (65º–68ºS) where some species more typical of sub-Antarctic latitudes 

were observed. Multivariate analyses indicated that environmental factors of seafloor rugosity 

(roughness), temperature, depth, and current speed were the main variables determining patterns in 

demersal fish communities. 

Acoustic data collected during the demersal survey suggest that there may be potential to use 

fisheries acoustic methods to obtain estimates of grenadier abundance (O’Driscoll et al. in press). 

The acoustic target strength distribution of single targets close to the bottom was very similar to 

that predicted based on the measured size range of grenadiers. There are also positive correlations 

between acoustic backscatter and trawl catches of grenadiers. 

Photographic data collected using NIWA’s Deep Towed Imaging System (DTIS) suggest that 

there may be potential to use photographic methods to obtain estimates of community structure 

and grenadier abundance (Bowden et al. in prep.). 

Twenty-three sites spanning the continental shelf, northern continental slope, abyssal plain, and 

two seamounts were sampled using the towed camera and either demersal trawl or beam trawl, 

allowing direct comparisons between sampling methods. Patterns of species turnover between sites 

were similar across all methods. Estimates of fish population densities from the towed camera and 

beam trawl data were also comparable but those from the demersal trawl were consistently lower 

than for the other methods. Macrourus spp. grenadiers were ca. eight times less abundant in the 

demersal trawl than the video data but more large individuals were sampled by the trawl than the 

video and biomass estimates were similar. 

Specific Objective 9: To determine the diversity, abundance/density, spatial distribution, and 

physical habitat associations of benthic assemblages across a body size spectrum from megafauna 

to bacteria, for shelf, slope, seamounts, and abyssal sites in the Ross Sea. 

Using cameras, corers, epibenthic sleds, and trawls, benthic bacteria, macro-infauna, macrohyperbenthic 

fauna, and mega-epifauna were sampled at sites on the continental shelf and 

previously unsampled areas on the northern continental slope of the Ross Sea, the abyssal plain, 

and seamounts to the north. Photographic data from seamounts in the northern Ross Sea region 

revealed a diverse and abundant fauna. Particularly striking were benthic communities comprised 

of stalked crinoids and brachiopods on Admiralty Seamount and the flanks of Scott Island which 

are reminiscent of an archaic fauna that may have survived through the isolation of these 

seamounts and reduced predator species (Bowden et al. 2010). 

Taxonomists in New Zealand and around the world identified more than 150,000 individual 

specimens representing more than 700 species, many undescribed, across sixteen phyla for the 

mega-epifauna groups alone (e.g. Lörz 2009, 2010, Eléaume et al. 2011). At least three genera and 

sixty-two species are new to science. All eukaryotic components of the benthic fauna showed 

similar broad-scale distributional trends across the study region. Total abundances and numbers of 

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taxa were orders of magnitude higher on the continental shelf than on the slope or abyss plain, and 

shelf, slope, and abyssal samples were distinct from each other in multivariate analyses. Diversity, 

however, was comparable between shelf and abyssal sites and lowest on the slope. Bacterial 

diversity was highest in abyssal and slope samples, but abundance, biomass, production, and 

activity of all enzymes except proteinase, which was highest in the abyss, were significantly higher 

in shelf samples. Benthic mega-epifaunal community composition was more strongly correlated 

with depth and seabed current speed than either water column productivity or seasonal ice cover, 

indicating that local hydrodynamics and their influence on advection of primary production are 

more important in determining distributions across the shelf than are local variations in production. 

Fauna on the seamounts were distinct from all other samples and were comprised of both Antarctic 

and Southern Ocean species, including remarkable populations of a new hyocrinid species on 

Admiralty seamount (Bowden et al. 2011, Eléaume et al. 2011). 

Published research to date has provided new insights into the distributions of several taxonomic 

groups (Lörz et al. 2009) , raised questions about the history of the northern seamount fauna over 

evolutionary time (Bowden et al. 2011), and contributed to a meta-analysis of the relationship 

between productivity and diversity in the deep sea (Leduc et al. 2012). In combination with 

molecular phylogenies and existing data from around Antarctica, results from this project represent 

a major contribution to knowledge of the Antarctic marine ecosystem. 

Specific Objective 10: To describe trophic/ecosystem relationships in the Ross Sea ecosystem 

(pelagic and benthic, fish and invertebrates). 

Progress has been made on obtaining data from which to elucidate trophic relationships between 

organisms in the Ross Sector of Antarctica collected on the IPY-CAML survey in February–March 

2008. Two methods have been used. First, 1081 stomachs from 22 species of Antarctic fish were 

examined and the contents of the full or partially-full stomachs (comprising 776 fish) were 

identified to 68 prey codes. Index of Relative Importance (IRI) has been calculated from these data 

and diet overlap between fish species is presented. Second, stable isotope and elemental 

composition analysis of samples were carried out for carbon and nitrogen. In total, nearly 2000 

samples were analysed. Samples include: 

• Fish (N=662 muscle, N=377 liver samples, 22 species); 

• Cephalopods (N=193); 

• Pelagic invertebrates (N=407); 

• Benthic sediments (N=36); 

• Phytoplankton (N=92); 

• Benthic invertebrates (N=200 completed, 95 pending analysis); 

Results have already been used to assist in parameterising and validating the quantitative model of 

the food web of the Ross Sea (paper accepted by CCAMLR Science). Research on the shrinkage of 

Antarctic silverfish carried out as part of this objective has contributed to a paper presented to the 

Ministry of Fisheries Antarctic Fisheries Working Group and accepted for submission to the 

CCAMLR working group on fisheries assessment in September 2010 (Pinkerton et al. 2007, 

2009a, 2009b). 

Specific Objective 11: Assess molecular taxonomy and population genetics of selected Antarctic 

fauna and flora to estimate evolutionary divergence within and among ocean basins in circumpolar 

species. Provide DNA barcoding for all fish and multi-cellular invertebrate species by sequencing 

reference specimens in conjunction with Canadian Barcoding Centre, for specimen identification 

in gut content, plankton, and in taxonomic and population genetic projects. 

DNA data sets generated for selected Ross Sea taxa were combined with parallel data sets 

generated by other Institutes in order to estimate divergence within and among regions in the 

Southern Ocean. High levels of divergence, indicative of cryptic speciation, were found in all 

279


major groups tested to date. Fishes: DNA sequencing of the COI gene revealed four well supported 

clades among the three recognized species of Macrourus in the Southern Ocean, indicating the 

presence of an undescribed species (Smith et al. 2011). A conclusion subsequently supported by 

meristic and morphometric examination of specimens with the description of a new species by 

McMillan et al. (2012). DNA barcodes also showed high sequence divergence among specimens 

of the slender codling Halargyreus johnsonii from New Zealand and the Southern Ocean, 

indicative of a cryptic species in this cosmopolitan species (Smith et al. 2011). A study of 

snailfishes collected during the IPY survey and from the toothfish fishery showed high species 

diversity with more than 34 Ross Sea liparid species in three genera; 18 of them new to science 

divergence (Stein 2012). 

Invertebrates: A combined NZ-BAS data set on the octopod genus Pareledone provided one of the 

largest barcoding studies on a Southern Ocean genus. Ross Sea specimens provisionally identified 

as Pareledone aequipapillae appeared in a discrete clade to specimens from the Antarctic 

Peninsula, with a barrier to gene flow to the west of the Antarctic Peninsula (Allcock et al. 2010). 

Large numbers of echinoderms have been tissue sampled and sequenced for COI and include the 

Asteroidea, Ophiuroidea, Echinoidea, Holothuroidea, and the crinoids (Dettai et al. in press). In the 

Ophiuroidea two dominant patterns emerged: a. widely distributed species showing shallow 

divergence by location and b. species with deeper divergence associated with location or depth, 

that represent cryptic species. A similar pattern emerged in the smaller set of Asteroid sequences, 

with deep divergences within some Ross Sea taxa. Preliminary results for the amphipod genus 

Rhacotropis showed 5 well supported clades, indicative of cryptic taxa; while for the genus 

Epimeria (27 specimens from the Ross Sea) there were two well supported clades for specimens 

identified as Epimeria robusta, and likewise for specimens identified as E. schiaparelli, indicative 

of cryptic taxa (Lörz 2009, 2010, Lörz et al. in press). These taxa show shallow morphological 

differences. 

IPY2007-02 NZ IPY-CAML Cephalopoda. 

This project will report on the diversity of Antarctic Cephalopoda (Octopus and Squid), including a 

complete inventory of taxa, and reports on ontogenetic and sexual variation in species, their 

systematics, diversity, distribution, life histories, and trophic importance. A MAppSc thesis has been 

completed as part of this project (Garcia 2010). 


Table 11.8: Other research linked to MPI Ross Sea Antarctica biodiversity programme. 

MPI 

ANT2011-01 Stock modelling, fishery effects and ecosystems of the Ross Sea 

MBIE C01X1001 Protecting Ross Sea Ecosystems. Comparative distribution and ecology of Macrourus 

caml and M. whitsoni in the Ross Sea region; feeding relationships of fish species in the Ross Sea 

region; Spatial processes, including spatial marine protection; Ecosystem modelling of the Ross 

Sea region).(Pinkerton et al. 2012a,b; Murphy et al. 2012) 

DOC Leigh Torres NIWA/Alison 

OTHER Universities NIWA;Lincoln, Canterbury, Otago, Auckland, Waikato 


Coastal research and functional ecology-ongoing need 

Taxonomic issues for fish and invertebrates (from IPY)ANT 2005-02 

Water samples from throughout water column to assess microbial content (from IPY) check with Els 

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11.4. Progress and re-alignment 

Given that the MPI Biodiversity programme has been running for 11+ years, and that a number of 

new strategic documents and directions are emerging across government, it is time to look both back 

and forward and review the programme to ensure its alignment with more recent strategic documents. 

In 2000, five strategic outcomes were built into the MPI Biodiversity Research Programme: 

That by 2010: 

i) the MPI Biodiversity programme will have become an integral part of the research effort 

devoted to understanding New Zealand’s marine environment. 

ii) research planning will benefit from close cooperative relationships within the Ministry of 

Fisheries, with other government agencies, and with external stakeholders. 

iii) mutually beneficial collaborative research projects will be carried out alongside other New 

Zealand and international research providers, especially for vessel-based research. 

iv) MPI Biodiversity projects will have contributed substantially to an improved understanding 

of New Zealand’s marine biodiversity and its role in marine ecosystem function, yielding 

scientifically rigorous outputs for a national and international professional audience. 

v) results generated by MPI Biodiversity projects will be incorporated into management 

policy, with clear benefits for the New Zealand marine environment. 

The Biodiversity Programme has been highly effective in delivering on the first 4 and part of the 5 th of 

the five outcomes. A missing element is some measure of “clear benefits for the New Zealand marine 

environment”. In recent years, significant all-of-government projects have been administered through 

the programme, and one-off funding applications made jointly with other stakeholders have been 

successful. The Programme has made a significant contribution to increasing understanding about 

biodiversity in the marine environment. Achievements in each outcome are addressed below. 

i) Has the Biodiversity Research Programme become integrated with New Zealand’s research effort 

to understand the marine environment? 

Seven science objectives were developed by multiple stakeholders through the Biodiversity Research 

Advisory Group. The agreed objectives include ecosystem-scale studies in the New Zealand marine 

environment, the classification and characterisation of the biodiversity of nearshore and offshore 

marine habitats, the role of biodiversity in the functional ecology of marine communities, connectivity 

and genetic marine biodiversity, the assessment of the effects of climate change and increased ocean 

acidification, identification of indicators of biodiversity that can be used to monitor change, 

identification of key threats to biodiversity, identification of threats and impacts to biodiversity and 

ecosystem functioning beyond natural environmental variation. 

Projects ranged from localised experiments on seabed communities of shellfish and echinoderms, to 

integrated studies of rocky reef systems and offshore fishery-scale trophic studies. The effects of 

ocean climate change (temperature, acidification) are being explored on shellfish, rhodolith 

communities, plankton productivity and the microbial productivity engines of polar waters. A major 

project to investigate shelf communities in relation to climate over the past 1000 years has resulted in 

the development of new methods and insights to past changes and human impact on New Zealand’s 

marine environment. 

A total of 55 projects were commissioned and managed within this 10 year period, yielding over 100 

final research reports, most of which have been published through MPI Publications (Marine 

Biosecurity and Biodiversity Reports and Aquatic Environment and Biodiversity Reports), books, 

Identification Guides and mainstream scientific literature. A number of other publications are still in 

preparation. In addition, several workshops have been run through the Programme, including 

qualitative modelling techniques, how to set up a marine monitoring programme and predictive 

281


modelling. A large number of science providers, including NIWA, Cawthron Institute, University of 

Auckland, Auckland University of Technology, University of Waikato, Victoria University of 

Wellington, University of Otago, University of Canterbury and Massey University have been directly 

commissioned or sub-contracted to take part in or conduct research projects through the Programme 

during the 10-year period. For some, the projects have provided critical synergies with MBIE funded 

OBIs or projects, while others have provided one-off opportunities for marine biodiversity 

investigation or opportunistic leveraging for research voyages. 

Research into the biodiversity of habitats such as seamounts has been completed and new methods to 

assess the vulnerability of seabed habitats have been developed. The land-sea interface is being 

investigated and projects have shown how land use in a given catchment can affect nutrient transfer 

and the living conditions and impact diversity and functioning of estuarine and coastal organisms. 

Publication and presentation of the results from these projects has resulted in widespread contribution 

to the development of Marine Science in New Zealand. Partnership with overseas researchers and 

presentations to international meetings and conferences has added to the growing global initiatives on 

marine biodiversity research questions. 

Feedback from stakeholders has indicated that the move to a 5 year research planning horizon was 

welcomed by research providers, but some stakeholders felt that Requests for Proposals should be at a 

higher level than individual projects to safeguard intellectual property on new ideas and methods. 

ii) Does research planning now benefit from close cooperative relationships within the Ministry 

of Fisheries, with other government agencies, and with external stakeholders? 

The Biodiversity Programme is very co-operative. Of 38 projects underway in the last 5 years, 14 

have formal collaborative components across government departments, with other stakeholders or 

multiple research providers and 10 have formal linkages to international research programmes. Within 

MPI and with other stakeholders (NGOs, industry, other government departments), the Biodiversity 

Projects have contributed to discussions about Marine Stewardship Council (MSC) certification, to 

decision papers on aspects of Antarctic management under CAMLR, fulfilling MPI commitments to 

the NZ Biodiversity Strategy, and to MPI progress towards recognising the role of the ecosystem in 

underpinning sustainable and healthy fisheries production. There are many other examples, e.g. the 

programme has towards DOC and MPI decisions on marine protected areas. The interaction at the 

research and policy advice stages of resource management feeds back into the BRAG planning for 

future research. 

There are close links with the MPI Aquatic Environment research programme, the National Aquatic 

Biodiversity Information System (NABIS), an MPI web-based interactive data access and mapping 

tool) and the MPI Antarctic Research programme. These and other links have enabled contributions 

resulting from progress on land-sea interface research, habitats of significance to fisheries 

management, trophic studies (MSC Certification), climate change (effects on shellfish) and habitat 

classification (fish optimised MEC, testing of MEC and BOMEC). The successful involvement of the 

Biodiversity Programme in major all-of-government projects such as Ocean Survey 20/20 and IPY- 

CAML, has also raised the profile of MPI and the research it has commissioned both across New 

Zealand and internationally. 

Datasets, voucher specimens and samples from all biodiversity research projects have resulted in a 

substantial amount of material that has been physically preserved and housed in the Te Papa Fish 

Collection and NIWA National Invertebrate Collection. All data are held in databases either at MPI, 

NIWA or Te Papa, and accessibility is being improved. The recent Bay of Islands Ocean Survey 

20/20 Portal was very well received and nominated for NZ Govt Open Source awards. It will also 

incorporate data access from Chatham Challenger and IPY projects. Data from a number of MPI 

biodiversity projects have also been entered into international biodiversity databases such as OBIS 

and from there into the Global Biodiversity Information Facility (GBIF). 

282


Biodiversity Research planning receives regular input from DOC, SeaFIC, MfE, Cawthron Institute, 

NIWA, GNS, LINZ, MAFBNZ, Te Papa, University of Auckland, AUT, University of Otago, 

MoRST, MFAT, Regional Councils and others. Research planning for 2011-12 and beyond will 

include a re-alignment of the current research programme to take account of new developments such 

as Fisheries 2030, MfE’s National Monitoring programme, DOC’s integrated coastal monitoring 

programme, Statistic New Zealand’s Environmental Domain Plan 69 , and international commitments 

such as the recent CBD COP10 Aichi-Nagoya Agreement. 

Feedback and support for projects by external stakeholders has shown that the Programme has been 

effective in promoting inter-agency collaboration. The Programme has also had close links with 

Research Data Management and the Observer Programme for certain projects (e.g trophic studies on 

the Chatham Rise, ZBD2004-02). With the former restructure of MPI and now the merger with MAF, 

and the move to Fisheries 2030 and Fisheries Plans, it important that the Programme develops strong 

relationships with the Fisheries Management and Strategy (International) groups within MPI and at 

MAF. 

iii) Have mutually beneficial collaborative research projects been carried out alongside other 

New Zealand and international research providers, especially for vessel-based research? 

As discussed above, collaborative research projects across government and among research providers 

have resulted in many mutually beneficial data and specimen collection, surveys of New Zealand 

marine biodiversity in NZ territorial seas, the EEZ and the Ross Sea, groundbreaking research into 

seamount biodiversity and the identification of VMEs, and research for international collaboration, 

particularly vessel based studies. Large scale vessel dependent oceanic research projects have made 

significant gains in baseline knowledge about the distribution and abundance of biodiversity in the 

EEZ/Ross Sea region. Vessel-based projects include: NORFANZ (Norfolk Island-Australia-New 

Zealand survey of biodiversity on Norfolk Ridge and Lord Howe Rise); BioRoss (MPI-LINZ, first NZ 

survey of biodiversity in the Ross Sea); Chatham-Challenger (LINZ-MPI-NIWA-DOC first Ocean 

Survey 20/20 project), NZ IPY-CAML (MPI-LINZ-NIWA (with international and NZ wide 

collaboration) survey of the Ross Sea as part of International Polar Year; Biodiversity of seamounts 

(MPI-NIWA-LINZ-MBIE voyages to the Kermadec Arc and on the Chatham Rise). These projects 

have generated huge geo-referenced datasets and thousands of specimens for Te Papa and National 

Invertebrate Collections. They have also resulted in the identification of new species, new genera and 

new families, as well as new records extending the known distribution of species. These surveys have 

contributed to habitat classification, identified areas of high biodiversity and challenged paradigms on 

the environmental drivers that determine biodiversity. More recently they have provided new 

information on the effects of ocean acidification on the productivity of polar seas, and in New Zealand 

waters. 

Vessel dependent coastal projects have also generated significant new understanding about the 

distribution of inshore biota, and the role they play in maintaining a healthy ecosystem. Experimental 

field work on the productivity of the seabed has been carried out in NZ waters (Fiordland, Otago, Bay 

of Islands, Hauraki Gulf, Kaipara and Manukau Harbours), and along the west coast of the Ross Sea. 

The impact of land practices on the land-sea interface has also highlighted real downstream effects on 

the productivity of the coastal environment. These projects have provided new insights into the 

connectivity between different species groups, and data are being used in a number of ways to assist 

with spatial planning by RMAs. 

Feedback from stakeholders has indicated that the collaborative voyages administered through the 

Programme have successfully created synergy and opportunity for New Zealand scientists as well as 

facilitating new international collaborations. 

69 http://www.stats.govt.nz/browse_for_stats/environment/natural_resources/environment-domain-plan- 

stocktake-paper.aspx 

283


iv) Have MPI [MFish] Biodiversity projects contributed substantially to an improved 

understanding of New Zealand’s marine biodiversity and its role in marine ecosystem function, 

yielding scientifically rigorous outputs for a national and international professional audience? 

In the early years, the Programme focussed primarily on taxonomy and the description of marine 

biodiversity. As the Programme matured, projects to address biodiversity roles in ecosystem function 

were introduced. Some were experimental and on a local scale while others were on a regional scale. 

Recent projects have addressed patterns of marine biodiversity in relation to environmental drivers 

with ecosystem function. This enabled modelling to predict the distribution of biodiversity in 

unsurveyed areas of ocean, and evaluation of the vulnerability of biodiversity to perturbations such as 

climate change, as well as the modelling of trophic interactions among key fish species. Presentations 

of research results have been made to numerous overseas and New Zealand science audiences, and 

publications in the mainstream literature have been encouraged. IPY, Chat chall, Alison s etc CBD- 

FAO Int seabed authority 

v) Have results generated by MPI [MFish] Biodiversity projects been incorporated into 

management policy, with clear benefits for the New Zealand marine environment? 

Examples of incorporation into management policy with clear benefits for the marine environment 

include the increased awareness of research topics initiated in the biodiversity programme by policy 

analysts to core Aquatic Environment research projects and Fishery Plans, (land-use effects, climate 

change in the ocean, habitat classification); links to the Antarctic research programme and uptake into 

CCAMLR (ecotrophic studies, ecosystem baselines, VME risk assessment, bioregionalisation), spatial 

management (seamount closures, BPAs, MPAs, RMAs), the need by MfE to report on the marine 

environment at a national scale (plankton recording programme, Marine Environmental Monitoring 

Programme). MPI biodiversity advice is frequently requested to contribute to cross-government 

initiatives including Ocean Survey 20/20, DOC Sub-Antarctic Islands Forum National Monitoring, 

Stats New Zealand Tier 1 statistic review and Environmental Domain Stocktake, International Year of 

Biodiversity, OECD and CBD reports, International Oceans Issues, SPRFMO, NRS marine issues 

paper, the Antarctic Science Framework, Ocean Fertilisation and IPCC Finally, the programme has 

contributed to New Zealand’s efforts in the international Census of Marine Life and an ongoing 

assessment of New Zealand’s progress in Marine Biodiversity has been proposed as a new Tier 1 

Environmental Statistic. However, the benefits to the marine environment are more inferred than 

demonstrated. There is substantially increased awareness within MPI and across government, that the 

health of fisheries and other valued uses of the sea depend on intact ecosystem services provided by 

the diversity of organisms, the diversity of habitats and the genetic diversity found in the marine 

environment. Statements of intent and long-term strategic documents such as Fisheries 2030 and Fish 

Plans have biodiversity protection and an ecosystem approach to fisheries management objectives 

explicitly stated. Future research questions will also need to address follow-up of management 

decisions to assess whether and to what extent the objectives have been achieved. 

In 2000, the concept of research on marine biodiversity was hotly debated among stakeholders and the 

benefit of the research (other than to scientists) was not widely accepted. In 2010, it is clear that much 

of the research in this biodiversity programme has been about defining and mapping the biological 

diversity of the sea, its roles in marine ecosystem function, threats to these roles and how best 

biodiversity and its successful protection can be measured. Huge advances have been made in 

providing new identification tools for major groups (e.g. Coralline algae …). Much progress has been 

made, and the programme has successfully raised the profile of biodiversity in coastal and ocean 

environmental management, in particular fisheries management, and biodiversity research uptake into 

policy and management decisions within MPI and across government. 

284

11.4.1. Concluding remarks 


New Zealand is moving into an era of unprecedented and increasing interest in the utilisation of 

marine resources. Mineral, petroleum and gas resources are estimated to be worth billions of dollars to 

the economy (Glasby and Wright 1990), and new environmental legislation has been drafted (the 

Exclusive Economic Zone and Continental Shelf (Environmental Effects) Act 2012). Changes inshore 

are also taking effect with the Environmental Protection Authority Act passed by Parliament on 11 

May 2011. This Act establishes a new Environmental Protection Authority (EPA) as a standalone 

crown agent from 1 July 2011. The newly released Coastal Policy statement and proposed Policy 

Statement on Indigenous Biodiversity demonstrates an awareness by Government that much of New 

Zealand’s primary production based economy is dependent on clean “green” policies supporting 

effective environmental management both on land, freshwater and in the sea. 

New Zealand is also a signatory to the CBD Aichi-Nagoya Agreement with a new International 

Decade for Biodiversity that runs 2011-2020 and New Zealand’s contribution to the identification of 

EBSAs in the SW Pacific, and to GOBI. Progress in our knowledge of the marine biodiversity and 

ecosystem services provided by the marine environment has clearly been made over the last decade. 

However, we need a more co-ordinated approach across government to link science to policy needs. 

For example, there is a compelling need for large-scale projects such as mapping seafloor habitats and 

establishing long-term nation-wide monitoring and reporting schemes to measure the effects of ocean 

climate change, regular assessment of the cumulative effects of anthropogenic activities and multiple 

stressors in the ocean and the effectiveness of their management. Without these, we face the risks that 

New Zealand’s “green” branding will be increasingly challenged, and that tipping points in the health 

of the aquatic environment may be reached too soon for evasive action to be taken. 

285



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294

11.6. Appendix 


Technical rationale for the goals and targets of the strategic plan for the period 2011- 

2020. UNEP/CBD/COP/10/9 18 July 2010. 

Strategic goal A. Address the underlying causes of biodiversity loss by mainstreaming biodiversity across 

government and society 

Strategic actions should be initiated immediately to address, over a longer term, the underlying causes of 

biodiversity loss. This requires policy coherence and the integration of biodiversity into all national 

development policies and strategies and economic sectors and at all levels of government. Approaches to 

achieve this include communication, education and public awareness, appropriate pricing and incentives, and 

the broader use of planning tools such as strategic environmental assessment. Stakeholders across all sectors of 

government, society and the economy, including business, will need to be engaged as partners to implement 

these actions. Consumers and citizens must also be mobilized to contribute to biodiversity conservation and 

sustainable use, to reduce their ecological footprints and to support action by Governments. 

[Note: Targets 1-5 not given here.] Targets 6-11 are directly quoted from the document. 

Target 6: By 2020, overfishing is ended, destructive fishing practices are eliminated, and all fisheries are 

managed sustainably.] or [By 2020, all exploited fish stocks and other living marine and aquatic resources 

are harvested sustainably [and restored], and the impact of fisheries on threatened species and vulnerable 

ecosystems are within safe ecological limits. 

Overexploitation is the main pressure on marine fisheries globally and the World Bank estimates that 

overexploitation represents a lost profitability of some $50 billion per year and puts at risk some 27 million jobs 

and the well-being of more than one billion people. Better fisheries management, which may include a reduction 

in fishing effort is needed to reduce pressure on ecosystems and to ensure the sustainable use of fish stocks. The 

specific target should be regarded as a step towards ensuring that all fisheries are sustainable while building 

upon existing initiatives such as the Code of Conduct for Responsible Fishing. Indicators to measure progress 

towards this target include the Marine Trophic Index, the proportion of products derived from sustainable 

sources and trends in abundance and distribution of selected species. Other possible indicators include the 

proportion of collapsed species, fisheries catch, catch per unit effort, and the proportion of stocks overexploited. 

Baseline information for several of these indicators is available from the Food and Agriculture Organization of 

the United Nations. 

Target 7: By 2020, areas under agriculture, aquaculture and forestry are managed sustainably, ensuring 

conservation of biodiversity. 

The increasing demand for food, fibre and fuel will lead to increasing losses of biodiversity and ecosystem 

services if management systems do not become increasingly sustainable with regard to the biodiversity. Criteria 

for sustainable forest management have been adopted by the forest sector and there are many efforts by 

Governments, indigenous and local communities, NGOs and the private sector to promote good agricultural, 

aquaculture and forestry practices. The application of the ecosystem approach would also assist with the 

implementation of this target. While, as yet, there are no universally agreed sustainability criteria, given the 

diversity of production systems and environmental conditions, each sector and many initiatives have developed 

their own criteria which could be used pending the development of a more common approach. Similarly, the use 

of certification and labelling systems or standards could be promoted as part of this target. Relevant indicators 

for this target include the area of forest, agricultural and aquaculture ecosystems under sustainable management, 

the proportion of products derived from sustainable sources and trends in genetic diversity of domesticated 

animals, cultivated plants and fish species of major socioeconomic importance. Existing sustainability 

certification schemes could provide baseline information for some ecosystems and sectors. 

UNEP/CBD/COP/10/9 Page 5 /... 

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Target 8: By 2020, pollution, including from excess nutrients, has been brought to levels that are not 

detrimental to ecosystem function and biodiversity. 

Pollution, including nutrient loading is a major and increasing cause of biodiversity loss and ecosystem 

dysfunction, particularly in wetland, coastal, marine and dryland areas. Humans have already more than doubled 

the amount of “reactive nitrogen” in the biosphere, and business-as-usual trends would suggest a further 

increase of the same magnitude by 2050. The better control of sources of pollution, including efficiency in 

fertilizer use and the better management of animal wastes, coupled with the use of wetlands as natural water 

treatment plants where appropriate, can be used to bring nutrient levels below levels that are critical for 

ecosystem functioning, without curtailing the application of fertilizer in areas where it is necessary to meet soil 

fertility and food security needs. Similarly, the development and application of national water quality guidelines 

could help to limit pollution and excess nutrients from entering freshwater and marine ecosystems. Relevant 

indicators include nitrogen deposition and water quality in freshwater ecosystems. Other possible indicators 

could be the ecological footprint and related concepts, total nutrient use, nutrient loading in freshwater and 

marine environments, and the incidence of hypoxic zones and algal blooms. Data which could provide baseline 

information already exists for several of these indicators, including the global aerial deposition of reactive 

nitrogen and the incidence of marine dead zones (an example of human-induced ecosystem failure). 

Target 9: By 2020, invasive alien species are identified, prioritized and controlled or eradicated and 

measures are in place to control pathways for the introduction and establishment of invasive alien species. 

Invasive alien species are a major threat to biodiversity and ecosystem services, and increasing trade and travel 

means that this threat is likely to increase unless additional action is taken. Pathways for the introduction of 

invasive alien species can be managed through improved border controls and quarantine, including through 

better coordination with national and regional bodies responsible for plant and animal health. While welldeveloped 

and, globally-applicable indicators are lacking, some basic methodologies do exist which can serve as 

a starting point for further monitoring or provide baseline information. Process indicators for this target could 

include the number of countries with national invasive species policies, strategies and action plans and the 

number of countries which have ratified international agreements and standards related to the prevention and 

control of invasive alien species. One outcome-oriented indicator is trends in invasive alien species while other 

possible indicators could include the status of alien species invasion, and the Red List Index for impacts of 

invasive alien species. 

Target 10: By [2020][2015], to have minimized the multiple pressures on coral reefs, and other vulnerable 

ecosystems impacted by climate change or ocean acidification, so as to maintain their integrity and 

functioning. 

Given the ecological inertias related to climate change and ocean acidification, it is important to urgently reduce 

other pressures on vulnerable ecosystems such as coral reefs so as to give vulnerable ecosystems time to cope 

with the pressures caused by climate change. This can be accomplished by addressing those pressures which are 

most amenable to rapid positive changes and would include activities such as reducing pollution and 

overexploitation and harvesting practices which have negative consequences on ecosystems. Indicators for this 

target include the extent of biomes ecosystems and habitats (% live coral, and coral bleaching), Marine Trophic 

Index, the incidence of human-induced ecosystem failure, and the health and well-being of communities who 

depend directly on local ecosystem goods and services, proportion of products derived from sustainable sources. 

UNEP/CBD/COP/10/9 Page 6 /... 

Strategic goal C: To improve the status of biodiversity by safeguarding ecosystems, species and genetic 

diversity 

Whilst longer term actions to reduce the underlying causes of biodiversity loss are taking effect, immediate 

actions, such as protected areas, species recovery programmes, land-use planning approaches, the restoration of 

degraded ecosystems and other targeted conservation interventions can help conserve biodiversity and critical 

ecosystems. These might focus on culturally-valued species and key ecosystem services, particularly those of 

importance to the poor, as well as on threatened species. For example, carefully sited protected areas could 

prevent the extinction of threatened species by protecting their habitats, allowing for future recovery. 

Target 11: By 2020, at least [15%][20%] of terrestrial, inland-water and [X%] of coastal and marine 

areas, especially areas of particular importance for biodiversity and ecosystem services, are conserved 

through comprehensive, ecologically representative and well-connected systems of effectively managed 

protected areas and other means, and integrated into the wider land- and seascape. 

Currently, some 13 per cent of terrestrial areas and 5 per cent of coastal areas are protected, while very little of 

the open oceans are protected. Therefore reaching the proposed target implies a modest increase in terrestrial 

protected areas globally, with an increased focus on representativity and management effectiveness, together 

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with major efforts to expand marine protected areas. Protected areas should be integrated into the wider land- 

and seascape, bearing in mind the importance of complementarity and spatial configuration. In doing so, the 

ecosystem approach should be applied taking into account ecological connectivity and the concept of ecological 

networks, including connectivity for migratory species. Protected areas should also be established and managed 

in close collaboration with, and through participatory and equitable processes that recognize and respect the 

rights of indigenous and local communities, and vulnerable populations. Other means of protection may also 

include restrictions on activities that impact on biodiversity, which would allow for the safeguarding of sites in 

areas beyond national jurisdiction in a manner consistent with the jurisdictional scope of the Convention as 

contained in Article 4. Relevant indicators to measure progress towards this target are the coverage of sites of 

biodiversity significance covered by protected areas and the connectivity/fragmentation of ecosystems. Other 

possible indicators include the overlay of protected areas with ecoregions, and the governance and management 

effectiveness of protected areas. Good baseline information already exists from sources such as the World 

Database of Protected Areas the Alliance for Zero Extinction, and the IUCN Red List of Threatened Species and 

the IUCN World Commission on Protected Areas. 

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12. Appendices 

AEBAR 2012: Appendices 

12.1. Terms of Reference for the Aquatic Environment 

Working Group in 2012 

Overall purpose 

For all New Zealand fisheries in the New Zealand TS and EEZ as well as other important fisheries in 

which New Zealand engages: 

to assess, based on scientific information, the effects of (and risks posed by) fishing, aquaculture, and 

enhancement on the aquatic environment, including: 

• bycatch and unobserved mortality of protected species (e.g. seabirds and marine 

mammals), fish, and other marine life, and consequent impacts on populations 

• effects of bottom fisheries on benthic biodiversity, species, and habitat 

• effects on biodiversity, including genetic diversity 

• changes to ecosystem structure and function from fishing, including trophic effects 

• effects of aquaculture and fishery enhancement on the environment and on fishing 

Where appropriate and feasible, such assessments should explore the implications of the effect, 

including with respect to government standards, other agreed reference points, or other relevant 

indicators of population or environmental status. Where possible, projections of future status under 

alternative management scenarios should be made. 

AEWG assesses the effects of fishing or environmental status, and may evaluate the consequences of 

alternative future management scenarios. AEWG does not make management recommendations or 

decisions (this responsibility lies with MPI fisheries managers and the Minister responsible for 

Fisheries). 

MPI also convenes a Biodiversity Research Advisory Group (BRAG) which has a similar review 

function to the AEWG. Projects reviewed by BRAG and AEWG have some commonalities in that 

they relate to aspects of the marine environment. However, the key focus of projects considered by 

BRAG is on marine issues related to the functionality of the marine ecosystem and its productivity, 

whereas projects considered by AEWG are more commonly focused on the direct effects of fishing. 

Preparatory tasks 

1. Prior to the beginning of AEWG meetings each year, MPI fisheries scientists will produce a 

list of issues for which new assessments or evaluations are likely to become available prior to 

the next scheduled sustainability round or decision process. AEWG Chairs will determine the 

final timetables and agendas. 

2. The Ministry’s research planning processes should identify most information needs well in 

advance but, if urgent issues arise, MPI-Fisheries or standards managers will alert MPI- 

Fisheries science managers and the Principal Advisor Fisheries Science, at least 3 months 

prior to the required AEWG meetings to other cases for which assessments or evaluations are 

urgently needed. 

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Technical objectives 


3. To review any new research information on fisheries impacts, including risks of impacts, and 

the relative or absolute sensitivity or susceptibility of potentially affected species, populations, 

habitats, and systems. 

4. To estimate appropriate reference points for determining population, system, or 

environmental status, noting any draft or published Standards. 

5. To conduct environmental assessments or evaluations for selected species, populations, 

habitats, or systems in order to determine their status relative to appropriate reference points 

and Standards, where such exist. 

6. In addition to determining the status of the species, populations, habitats, and systems relative 

to reference points, and particularly where the status is unknown, AEWG should explore the 

potential for using existing data and analyses to draw conclusions about likely future trends in 

fishing effects or status if current fishing methods, effort, catches, and catch limits are 

maintained, or if fishers or fisheries managers are considering modifying them in other ways. 

7. Where appropriate and practical, to conduct or request projections of likely future status using 

alternative management actions, based on input from AEWG, fisheries plan advisers and 

fisheries and standards managers, noting any draft or published Standards. 

8. For species or populations deemed to be depleted or endangered, to develop ideas for 

alternative rebuilding scenarios to levels that are likely to ensure long-term viability based on 

input from AEWG, fisheries managers, noting any draft or published Standards. 

9. For species, populations, habitats, or systems for which new assessments are not conducted in 

the current year, to review and update any existing Fisheries Assessment Plenary report text in 

order to determine whether the latest reported status summary is still relevant; else to revise 

the evaluations based on new data or analyses, or other relevant information. 

Working Group input to annual Aquatic Environment and Biodiversity Review 

10. To include in contributions to the environment analogue of the Fisheries Assessment Plenary 

Report (the Aquatic Environment and Biodiversity Review, AEBAR) summaries of 

information on selected issues that may relate to species, populations, habitats, or systems that 

may be affected by fishing. These contributions are analogous to Working Group Reports 

from the Fisheries Assessment Working Groups. 

11. To provide information and scientific advice on management considerations (e.g. area 

boundaries, by-catch issues, effects of fishing on habitat, other sources of mortality, and input 

controls such as mesh sizes and minimum legal sizes) that may be relevant for setting 

sustainability measures. 

12. To summarise the assessment methods and results, along with estimates of relevant standards, 

references points, or other metrics that may be used as benchmarks or to identify risks to the 

aquatic environment. 

13. It is desirable that full agreement among technical experts is achieved on the text of 

contributions to the AEBAR. If full agreement among technical experts cannot be reached, 

the Chair will determine how this will be depicted in the AEBAR, will document the extent to 

which agreement or consensus was achieved, and record and attribute any residual 

disagreement in the meeting notes. 

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14. To advise the Principal Advisor Fisheries Science, about issues of particular importance that 

may require review by a plenary meeting or summarising in the AEBAR, and issues that are 

not believed to warrant such review. The general criterion for determining which issues 

should be discussed by a wider group or summarised in the AEBAR is that new data or 

analyses have become available that alter the previous assessment of an issue, particularly 

assessments of population status or projection results. Such information could include: 

• New or revised estimates of environmental reference points, recent or current population 

status, trend, or projections 

• The development of a major trend in bycatch rates or amount 

• Any new studies or data that extend understanding of population, system, or 

environmental susceptibility to an effect or its recoverability, fishing patterns, or 

mitigation measures that have a substantial implications for a population, system, or 

environment or identify risks associated with fishing activity 

• Consistent performance outside accepted reference points or Standards 

Membership and Protocols for all Science Working Groups (paragraph numbers 

consistent with those in Terms of Reference for Fisheries Assessment Working Groups) 

Working Group chairs 

17. The Ministry will select and appoint the Chairs for Working Groups. The Chair will be a MPI 

fisheries scientist who is an active participant in the Working Group, providing technical 

input, rather than simply being a facilitator. Working Group Chairs will be responsible for: 

* ensuring that Working Group participants are aware of the Terms of Reference for the 

working group, and that the Terms of Reference are adhered to by all participants. 

* setting the rules of engagement, facilitating constructive questioning, and focussing on 

relevant issues. 

* ensuring that all peer review processes are conducted in accordance with the Research and 

Science Information Standard for New Zealand Fisheries 110 (the Research Standard), and that 

research and science information is reviewed by the Working Group against the P R I O R 

principles for science information quality (page 6) and the criteria for peer review (pages 12- 

16) in the Standard. 

* requesting and documenting the affiliations of participants at each Working Group meeting 

that have the potential to be, or to be perceived to be, a conflict of interest of relevance to the 

research under review (refer to page 15 of the Research Standard). Chairs are responsible for 

managing conflicts of interest, and ensuring that fisheries management implications do not 

jeopardise the objectivity of the review or result in biased interpretation of results. 

* ensuring that the quality of information that is intended or likely to inform fisheries 

management decisions is ranked in accordance with the information ranking guidelines in the 

Research Standard (page 21-23), and that resulting information quality ranks are 

appropriately documented in Working Group reports and, where appropriate, in Status of 

Stock summary tables. 

* striving for consensus while ensuring the transparency and integrity of research analyses, 

results, conclusions and final reports. 

* reporting on Working Group recommendations, conclusions and action items; and ensuring 

follow-up and communication with the MPI Principal Advisor Fisheries Science, relevant 

MPI fisheries management staff, and other key stakeholders. 

110 Link to the Research Standard: http://www.fish.govt.nz/ennz/Publications/Research+and+Science+Information+Standard.htm 

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Working Group members 


18. Working Groups will consist of the following participants: 

* MPI fisheries science chair – required 

* Research providers – required (may be the primary researcher, or a designated substitute 

capable of presenting and discussing the agenda item) 

* Other scientists not conducting analytical assessments to act in a peer review capacity 

* Representatives of relevant MPI fisheries management teams 

* Any interested party who agrees to the standards of participation below. 

19. Working Group participants must commit to: 

* participating in the discussion 

* resolving issues 

* following up on agreements and tasks 

* maintaining confidentiality of Working Group discussions and deliberations (unless otherwise 

agreed in advance, and subject to the constraints of the Official Information Act) 

* adopting a constructive approach 

* avoiding repetition of earlier deliberations, particularly where agreement has already been 

reached 

* facilitating an atmosphere of honesty, openness and trust 

* respecting the role of the Chair 

* listening to the views of others, and treating them with respect 

20. Participants in Working Group meetings will be expected to declare their sector affiliations 

and contractual relationships to the research under review, and to declare any substantial 

conflicts of interest related to any particular issue or scientific conclusion. 

21. Working Group participants are expected to adhere to the requirements of independence, 

impartiality and objectivity listed under the Peer Review Criteria in the Research Standard 

(pages 12-16). It is understood that Working Group participants will often be representing 

particular sectors and interest groups, and will be expressing the views of those groups. 

However, when reviewing the quality of science information, representatives are expected to 

step aside from their sector affiliations, and to ensure that individual and sector views do not 

result in bias in the science information and conclusions. 

Information Quality Ranking: 

22. Science Working Groups are required to rank the quality of research and science 

information that is intended or likely to inform fisheries management decisions, in 

accordance with the science information quality ranking guidelines in the Research 

Standard (pages 21-23). This information quality ranking must be documented in 

Working Group reports and, where appropriate, in Status of Stock summary tables. 

* Working Groups are not required to rank all research projects and analyses, but key pieces of 

information that are expected or likely to inform fisheries management decisions should 

receive a quality ranking. 

* Explanations substantiating the quality rankings must be included in Working Group reports. 

In particular, the quality shortcomings and concerns for moderate/mixed and low quality 

information must be documented. 

* The Chair, working with participants, will determine which pieces of information require a 

quality ranking. Not all information resulting from a particular research project would be 

expected to achieve the same quality rank, and different quality ranks may be assigned to 

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different components, conclusions or pieces of information resulting from a particular piece 

of research. 

Working Group papers: 

23. Working group papers will be posted on the MPI-Fisheries website prior to meetings if 

they are available. As a general guide, Powerpoint presentations and draft or discussion 

papers should be available at least 2 working days before a meeting, and near-final 

papers should be available at least 5 working days before a meeting if the Working 

Group is expected to agree to the paper. However, it is also likely that many papers will 

be tabled during the meeting due to time constraints. If a paper is not available for 

sufficient time before the meeting, the Chair may provide for additional time for written 

comments from Working Group members. 

24. Working Group papers are “works in progress” whose role is to facilitate the discussion 

of the Working Groups. They often contain preliminary results that are receiving peer 

review for the first time and, as such, may contain errors or preliminary analyses that will 

be superseded by more rigorous work. For these reasons, no-one may release the 

papers or any information contained in these papers to external parties. In general, 

Working Group papers should never be cited. Exceptions may be made in rare 

instances by obtaining permission in writing from the Principal Advisor Fisheries 

Science, and the authors of the paper. 

25. Participants who use Working Group papers inappropriately, or who do not adhere to the 

standards of participation, may be requested by the Chair to leave a particular meeting or, 

in more serious instances, to refrain from attending one or more future meetings. 

26. Meetings will take place as required, generally January-April and July-November for FAWGs 

and throughout the year for other working groups (AEWG, BRAG, Marine Amateur Fisheries 

and Antarctic Working Groups). 

27. A quorum will be reached when the Chair, the designated presenter, and three or more other 

technical experts are present. In the absence of a quorum, the Chair may decide to proceed as 

a sub-group, with outcomes being taken forward to the next meeting at which a quorum is 

formed. 

28. The Chair is responsible for deciding, with input from the entire Working Group, but 

focussing primarily on the technical discussion and the views of technical expert members: 

* The quality and acceptability of the information and analyses under review 

* The way forward to address any deficiencies 

* The need for any additional analyses 

* Contents of Working Group reports 

* Choice of base case models and sensitivity analyses to be presented 

* The status of the stocks, or the status/performance in relation to any relevant environmental 

standards or targets 

29. The Chair is responsible for facilitating a consultative and collaborative discussion. 

30. Working Group meetings will be run formally, with agendas pre-circulated, and formal 

records kept of recommendations, conclusions and action items. 

31. A record of recommendations, conclusions and action items will be posted on the MPI- 

Fisheries website after each meeting has taken place. 

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32. Data upon which analyses presented to the Working Groups are based must be provided to 

MPI in the appropriate format and level of detail in a timely manner (i.e. the data must be 

available and accessible to MPI; however, data confidentiality concerns mean that such data 

are not necessarily available to Working Group members) 

33. The outcome of each Working Group round will be evaluated, with a view to identifying 

opportunities to improve the Working Group process. The Terms of Reference may be 

updated as part of this review. 

34. MPI fisheries scientists and science officers will provide administrative support to the 

Working Groups. 

Record-keeping 

35. The overall responsibility for record-keeping rests with the Chair of the Working Group, and 

includes: 

* keeping notes on recommendations, conclusions and follow-up actions for all Working Group 

meetings, and to ensure that these are available to all members of the Working Group and the 

Principal Advisor Fisheries Science in a timely manner. If full agreement on the 

recommendations or conclusions cannot readily be reached amongst technical experts, then 

the Chair will document the extent to which agreement or consensus was achieved, and record 

and attribute any residual disagreement in the meeting notes. 

* compiling a list of generic assessment issues and specific research needs for each Fishstock or 

species or environmental issue under the purview of the Working Group, for use in 

subsequent research planning processes. 

12.2. AEWG Membership 2012 

Convenors: Martin Cryer (protected species) and Rich Ford (other issues) 

Members: Blake Abernethy, Ed Abraham, Owen Anderson, William Arlidge, Chris Baigent, 

Karen Baird, Suze Baird, Barry Baker, Michael Batson, Michelle Beritzhoff, Jenny 

Black, Tiffany Bock, Laura Boren, Yoland Bosiger, Paul Breen, Stephen Brouwer, 

Martin Cawthorn, Simon Childerhouse, Louise Chilvers, Tom Clarke, Malcolm 

Clark, Deanna Clement, George Clement, Owen Cox, Rohan Currey, Igor Debski, Ian 

Doonan, Alastair Dunn, Charles Edwards, Ursula Ellenburg, Jack Fenaughty, Chris 

Francis, Malcolm Francis, Kevin Hackwell, Judi Hewitt, Rosie Hurst, Aaron Irving, 

Catherine Jones, Dan Kluza, Craig Lawson, Mary Livingston, Dave Lundquist, Greg 

Lydon, Warrick Lyon, Pamela Mace, Darryl Mackenzie, Rob Mattlin, Tania 

McPherson, Sarah Meadows, David Middleton, Laura Mitchell, Sophie Mormede, 

Mark Morrison, Richard O’Driscoll, Tracey Osborne, Milena Palka, Johanna Pierre, 

Irene Pohl, Kris Ramm, Vicky Reeve, Pat Reid, Yvan Richard, Jim Roberts, Ashley 

Rowden, Carol Scott, Ben Sharp, Liz Slooten, Paul Starr, Kevin Stokes, Katrina 

Subedar, John Taunton-Clarke, Alex Thompson, David Thompson, Finlay Thompson, 

Geoff Tingley, Ian Tuck, Dee Wallace, Barry Weeber, Richard Wells, Francene 

Wineti, Ray Wood, Bob Zuur. 

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12.3. Terms of Reference for the Biodiversity Research 

Advisory Group (BRAG) 2012 


Since 2000, the objectives of the Biodiversity Research Programme have been drawn directly from 

MFish commitments to Theme 3 of the New Zealand Biodiversity Strategy. Within this framework, 

the Biodiversity Medium Term Research Plan has been adapted over time as new issues emerge, to 

build on synergies with other research programmes and work where biodiversity is under greatest 

threat from fishing or other anthropogenic activity. 

Within the constraints of the overall purpose of the Programme, 

“To improve our understanding of New Zealand marine ecosystems in terms of species 

diversity, marine habitat diversity, and the processes that lead to healthy ecosystem 

functioning, and the role that biodiversity has for such key processes111;” 

and the NZBS definition of biodiversity (the variability among living organisms from all sources 

including inter alia, terrestrial, marine and other aquatic ecosystems and the ecological complexes of 

which they are a part; this includes diversity within species, between species and of ecosystem) the 

science currently commissioned broadly aims to: 

• Describe and characterise the distribution and abundance of fauna and flora, as expressed 

through measures of biodiversity, and improving understanding about the drivers of the 

spatial and temporal patterns observed; 

• determine the functional role of different organisms or groups of organisms in marine 

ecosystems, and assess the role of marine biodiversity in mitigating the impacts of 

anthropogenic disturbance on healthy ecosystem functioning; 

• identify which components of biodiversity must be protected to ensure the sustainability of a 

healthy marine ecosystem as well as to meet societal values on biodiversity. 

MPI also convenes an Aquatic Environment Working Group (AEWG) which has a similar review 

function to the BRAG. Projects reviewed by BRAG and AEWG have some commonalities in that 

they relate to aspects of the marine environment. However, the key focus of projects considered by 

BRAG is on marine issues related to the functionality of the marine ecosystem and its productivity, 

whereas projects considered by AEWG are more commonly focused on the direct effects of fishing. 

BRAG may identify natural resource management issues that extend beyond fisheries management 

and make recommendations on priority areas of research that will inform MPI or other government 

departments of emerging science results that require the attention of managers, policymakers and 

decision-makers in the marine sector. BRAG does not make management recommendations or 

decisions (this responsibility lies with the MPI Fisheries Management Group and the Minister of 

Primary Industry). 

Preparatory tasks 

1. Prior to the beginning of BRAG meetings each year, MPI fisheries scientists will produce a 

list of issues for which new research projects are likely to required in the forthcoming 

financial year. The BRAG Chair will determine the final timetables and agendas. 

111 See MFish Biodiversity Research Programme 2010: Part 1. Context and Purpose 

304


2. The Ministry’s research planning processes should identify most information needs well in 

advance but, if urgent issues arise, MPI fisheries managers will alert the Aquatic Environment 

and Biodiversity Science Manager and the Principal Advisor Fisheries Science at least three 

months prior to the required meetings where possible. 

BRAG Technical objectives 

3. To review, discuss and convey views on the results of marine biodiversity research projects 

contracted by Ministry for Primary Industries MPI (formerly Ministry of Fisheries). 

It is the responsibility of the BRAG to review, discuss, and convey views on the results of marine 

biodiversity research projects contracted by MPI and the former Ministry of Fisheries. The review 

process is an evaluation of how existing research results can be built upon to address emerging 

research issues and needs. It is essentially an evaluation of "what we already know" and how this can 

be used to obtain "what we need to know”. This information should be used by the BRAG to identify 

gaps in our knowledge and for developing research plans to address these gaps. 

4. Discuss, evaluate, make recommendations and convey views on a 3 to 5 year Medium Term 

Research Plan. 

It is the responsibility of BRAG participants to discuss, evaluate, make recommendations and convey 

views on a 3 to 5 year Medium Term Research Plan for its particular research area as required. 

Individual related projects on a species or fishery or research topic need to be integrated into Medium 

Term Research Plans. The Medium Term Research Plans should encompass research needs and 

directions for at least the next 3 to 5 years. 

The Biodiversity Medium Term Research Plan is aligned to relevant strategic and policy directions 

such as the "MPI Statement of Intent" and any Strategic Research Plan (Fisheries 2030, Deepwater 10 

year research plan) and fisheries plans developed for the appropriate species/fishery or research area, 

including biodiversity. 

The recommendations on project proposals for the next financial year will be submitted via the Chair 

of BRAG to the Principal Science Advisor Fisheries (MPI). 

5. The Biodiversity Research Programme includes research in New Zealand’s TS, EEZ, 

Extended Continental Shelf, the South Pacific Region and the Ross Sea region and has seven 

scientific work streams as follows: 

• To develop ecosystem-scale understanding of biodiversity in the New 

Zealand marine environment 

• To classify and characterise the biodiversity, including the description and 

documentation of biota, associated with nearshore and offshore marine 

habitats in New Zealand 

• To investigate the role of biodiversity in the functional ecology of nearshore 

and offshore marine communities. 

• To assess developments in all aspects of biodiversity, including genetic 

marine biodiversity and identify key topics for research 

• To determine the effects of climate change and increased ocean acidification 

on marine biodiversity, as well as effects of incursions of non-indigenous 

species, and other threats and impacts. 

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• To develop appropriate diversity metrics and other indicators of biodiversity 

that can be used to monitor change 

• To identify threats and impacts to biodiversity and ecosystem functioning 

beyond natural environmental variation 

BRAG input to MPI “Aquatic Environment and Biodiversity Annual Review” 

6. To contribute to and summarise progress on biodiversity research in the Aquatic Environment 

and Biodiversity Annual Review. This contribution is analogous to Working Group Reports 

from the Fishery Assessment Working Groups. 

7. To summarise the assessment methods and results, along with estimates of relevant standards, 

references points, or other metrics that may be relevant to biodiversity objectives by MPI, the 

Biodiversity Strategy and international obligations. 

8. It is desirable that full agreement among technical experts is achieved on the text of these 

contributions. If full agreement among technical experts cannot be reached, the Chair will 

determine how this will be depicted in the Aquatic Environment and Biodiversity Annual 

Review, will document the extent to which agreement or consensus was achieved, and record 


9. To advise the Principal Science Advisor Fisheries (MPI), about issues of particular 

importance that may require review by a plenary meeting or summarising in the Aquatic 

Environment and Biodiversity Annual Review. The general criterion for determining which 

issues should be discussed by a wider group include: 

• Emerging issues, recent or current biodiversity status assessments, trends, or 

projections 

• The development of a major trend in the marine environment that will impact on 

marine productivity or ecosystem resilience to stressors 

• Any new studies or data that impact on international obligations 

Membership and Protocols for all Science Working Groups (NOTE: paragraph 

numbers consistent with those in Terms of Reference for Fisheries Assessment Working 

Groups) 

Working Group chairs 

17. The Ministry will select and appoint the Chairs for Working Groups. The Chair will be a MPI 

fisheries scientist who is an active participant in the Working Group, providing technical 

input, rather than simply being a facilitator. Working Group Chairs will be responsible for: 

* ensuring that Working Group participants are aware of the Terms of Reference for the 

working group, and that the Terms of Reference are adhered to by all participants. 

* setting the rules of engagement, facilitating constructive questioning, and focussing on 

relevant issues. 

* ensuring that all peer review processes are conducted in accordance with the Research and 

Science Information Standard for New Zealand Fisheries 112 (the Research Standard), and that 

112 Link to the Research Standard: http://www.fish.govt.nz/ennz/Publications/Research+and+Science+Information+Standard.htm 

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research and science information is reviewed by the Working Group against the P R I O R 

principles for science information quality (page 6) and the criteria for peer review (pages 12- 

16) in the Standard. 

* requesting and documenting the affiliations of participants at each Working Group meeting 

that have the potential to be, or to be perceived to be, a conflict of interest of relevance to the 

research under review (refer to page 15 of the Research Standard). Chairs are responsible for 

managing conflicts of interest, and ensuring that fisheries management implications do not 

jeopardise the objectivity of the review or result in biased interpretation of results. 

* ensuring that the quality of information that is intended or likely to inform fisheries 

management decisions is ranked in accordance with the information ranking guidelines in the 

Research Standard (page 21-23), and that resulting information quality ranks are 

appropriately documented in Working Group reports and, where appropriate, in Status of 

Stock summary tables. 

* striving for consensus while ensuring the transparency and integrity of research analyses, 

results, conclusions and final reports. 

* reporting on Working Group recommendations, conclusions and action items; and ensuring 

follow-up and communication with the MPI Principal Advisor Fisheries Science, relevant 

MPI fisheries management staff, and other key stakeholders. 

Working Group members 

18. Working Groups will consist of the following participants: 

* MPI fisheries science chair – required 

* Research providers – required (may be the primary researcher, or a designated substitute 

capable of presenting and discussing the agenda item) 

* Other scientists not conducting analytical assessments to act in a peer review capacity 

* Representatives of relevant MPI fisheries management teams 

* Any interested party who agrees to the standards of participation below. 

19. Working Group participants must commit to: 

* participating in the discussion 

* resolving issues 

* following up on agreements and tasks 

* maintaining confidentiality of Working Group discussions and deliberations (unless otherwise 

agreed in advance, and subject to the constraints of the Official Information Act) 

* adopting a constructive approach 

* avoiding repetition of earlier deliberations, particularly where agreement has already been 

reached 

* facilitating an atmosphere of honesty, openness and trust 

* respecting the role of the Chair 

* listening to the views of others, and treating them with respect 

20. Participants in Working Group meetings will be expected to declare their sector affiliations 

and contractual relationships to the research under review, and to declare any substantial 

conflicts of interest related to any particular issue or scientific conclusion. 

21. Working Group participants are expected to adhere to the requirements of independence, 

impartiality and objectivity listed under the Peer Review Criteria in the Research Standard 

(pages 12-16). It is understood that Working Group participants will often be representing 

particular sectors and interest groups, and will be expressing the views of those groups. 

However, when reviewing the quality of science information, representatives are expected to 

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step aside from their sector affiliations, and to ensure that individual and sector views do not 

result in bias in the science information and conclusions. 

Information Quality Ranking: 

22. Science Working Groups are required to rank the quality of research and science 

information that is intended or likely to inform fisheries management decisions, in 

accordance with the science information quality ranking guidelines in the Research 

Standard (pages 21-23). This information quality ranking must be documented in 

Working Group reports and, where appropriate, in Status of Stock summary tables. 

* Working Groups are not required to rank all research projects and analyses, but key pieces of 

information that are expected or likely to inform fisheries management decisions should 

receive a quality ranking. 

* Explanations substantiating the quality rankings must be included in Working Group reports. 

In particular, the quality shortcomings and concerns for moderate/mixed and low quality 

information must be documented. 

* The Chair, working with participants, will determine which pieces of information require a 

quality ranking. Not all information resulting from a particular research project would be 

expected to achieve the same quality rank, and different quality ranks may be assigned to 

different components, conclusions or pieces of information resulting from a particular piece 

of research. 

Working Group papers: 

23. Working group papers will be posted on the MPI-Fisheries website prior to meetings if 

they are available. As a general guide, Powerpoint presentations and draft or discussion 

papers should be available at least 2 working days before a meeting, and near-final 

papers should be available at least 5 working days before a meeting if the Working 

Group is expected to agree to the paper. However, it is also likely that many papers will 

be tabled during the meeting due to time constraints. If a paper is not available for 

sufficient time before the meeting, the Chair may provide for additional time for written 

comments from Working Group members. 

24. Working Group papers are “works in progress” whose role is to facilitate the discussion 

of the Working Groups. They often contain preliminary results that are receiving peer 

review for the first time and, as such, may contain errors or preliminary analyses that will 

be superseded by more rigorous work. For these reasons, no-one may release the 

papers or any information contained in these papers to external parties. In general, 

Working Group papers should never be cited. Exceptions may be made in rare 

instances by obtaining permission in writing from the Principal Advisor Fisheries 

Science, and the authors of the paper. 

25. Participants who use Working Group papers inappropriately, or who do not adhere to the 

standards of participation, may be requested by the Chair to leave a particular meeting or, 

in more serious instances, to refrain from attending one or more future meetings. 

26. Meetings will take place as required, generally January-April and July-November for FAWGs 

and throughout the year for other working groups (AEWG, BRAG, Marine Amateur Fisheries 

and Antarctic Working Groups). 

27. A quorum will be reached when the Chair, the designated presenter, and three or more other 

technical experts are present. In the absence of a quorum, the Chair may decide to proceed as 

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a sub-group, with outcomes being taken forward to the next meeting at which a quorum is 

formed. 

28. The Chair is responsible for deciding, with input from the entire Working Group, but 

focussing primarily on the technical discussion and the views of technical expert members: 

* The quality and acceptability of the information and analyses under review 

* The way forward to address any deficiencies 

* The need for any additional analyses 

* Contents of Working Group reports 

* Choice of base case models and sensitivity analyses to be presented 

* The status of the stocks, or the status/performance in relation to any relevant environmental 

standards or targets 

29. The Chair is responsible for facilitating a consultative and collaborative discussion. 

30. Working Group meetings will be run formally, with agendas pre-circulated, and formal 

records kept of recommendations, conclusions and action items. 

31. A record of recommendations, conclusions and action items will be posted on the MPI- 

Fisheries website after each meeting has taken place. 

32. Data upon which analyses presented to the Working Groups are based must be provided to 

MPI in the appropriate format and level of detail in a timely manner (i.e. the data must be 

available and accessible to MPI; however, data confidentiality concerns mean that such data 

are not necessarily available to Working Group members) 

33. The outcome of each Working Group round will be evaluated, with a view to identifying 

opportunities to improve the Working Group process. The Terms of Reference may be 

updated as part of this review. 

34. MPI fisheries scientists and science officers will provide administrative support to the 

Working Groups. 

Record-keeping 

35. The overall responsibility for record-keeping rests with the Chair of the Working Group, and 

includes: 

* keeping notes on recommendations, conclusions and follow-up actions for all Working Group 

meetings, and to ensure that these are available to all members of the Working Group and the 

Principal Advisor Fisheries Science in a timely manner. If full agreement on the 

recommendations or conclusions cannot readily be reached amongst technical experts, then 

the Chair will document the extent to which agreement or consensus was achieved, and record 


* compiling a list of generic assessment issues and specific research needs for each Fishstock or 

species or environmental issue under the purview of the Working Group, for use in 

subsequent research planning processes. 

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12.4. BRAG attendance 2011-2012 

Convenor: Mary Livingston (MPI chair), 

Members: Malcolm Clark, Mark Morrison, Wendy Nelson, Cliff Law, Di Tracey, Dennis 

Gordon, Anne-Nina Lorz, Stuart Hanchet, Richard O’Driscoll, Jonathon Gardner, 

Simon Thrush, David Bowden, Matt Pinkerton, Els Maas, Ashley Rowden, Carolyn 

Lundquist, Judi Hewitt, Drew Lohrer, Alison MacDiarmid, Julie Hall, Vonda 

Cummings, Kate Neill, Tracy Farr, Di Tracey, Barb Hayden (all NIWA), Richard 

Wells, Greg Lydon (SeaFIC), Rich Ford (MPI), Shane Lavery, Mark Costello 

(Auckland University) 

12.5. Generic Terms of Reference for Research Advisory 

Groups (Sept 2010) 


1. The purpose of the Research Advisory Groups (RAGs) is to develop research proposals to 

meet management information needs and support standards development. 

Context 

2. To assist RAG members with their work this section outlines the wider process that RAGs 

will operate within. 

Fisheries Plans will guide the management of fisheries 

3. From 1 July 2011 the Ministry of Fisheries (MFish) will be using Fisheries Plans in the 

following five areas to guide the management of fisheries: 

• Deepwater 

• Highly Migratory Species 

• Inshore – Finfish 

• Inshore – Freshwater 

• Inshore – Shellfish 

4. In each of those five areas there will be: 

• A Fisheries Plan that sets out management objectives over a 5 year period. 

• An Annual Operational Plan that sets out what will be done in a financial year to help 

meet those objectives, including in the areas of science research, compliance and observer 

coverage (i.e., the Annual Operational Plan will be where priorities are set each year). 

Note that external stakeholders will have an opportunity to provide comment on 

prioritisation through draft Annual Operational Plans. 

• An Annual Review Report that will assess progress made against the management 

objectives, and help identify gaps to be considered in setting the next set of priorities. 

RAGs will largely be aligned to the Fisheries Plan areas 

5. There will be a RAG for each of the five Fisheries Plan areas above. 

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6. In addition there will be a RAG for Aquatic Environment (Standards), for research needed to 

support standards development, and another for Antarctic research. (Note that biodiversity 

research is dealt with through a separate process that has more of a cross-agency focus.) 

RAGs will develop research proposals to be considered as part of a subsequent 

prioritisation process 

7. As part of the process for developing the Annual Operational Plans, the identification and 

prioritisation of science research will broadly occur as follows: 

i. MFish fisheries managers will identify the fisheries management objectives and 

information needs that they want the relevant RAG to consider. This will be done in 

conjunction with MFish scientists, and will draw on the following: 

• The relevant Annual Review Report discussed above 

• Existing research plans 

• Science Assessment Working Groups’ feedback arising from research that has been 

evaluated previously 

• Ad-hoc issues as they arise 

• Initial indications of the available budget 

ii. The RAGs will then develop proposals for scientific research to meet those management 

and information needs. 

iii. MFish fisheries managers will then run a process for prioritising the research proposals 

that have been developed and updating multi-year research plans, in conjunction with 

MFish scientists. This will be part of the wider process for developing Annual 

Operational Plans. 

8. In the Aquatic Environment (Standards) and Antarctic areas a similar process will be 

followed to that above, involving relevant MFish managers. 

9. In practice, these processes are likely to iterate between the above steps, e.g., when 

prioritising research proposals fisheries managers may identify additional questions that they 

want a RAG to consider. 

10. RAGs will only be convened when necessary. If, for example, all of the research for the 

coming year under review has previously been approved as part of a multi-year funding 

package for an area, and no additional management needs have emerged, the relevant RAG 

will not be convened. 

11. During 2010-11 RAGs will be used, as required, in all areas except Inshore, given that the 

three Inshore Fisheries Plans are still being developed through the year. For the Inshore areas 

a transitional process will be used, with RAGs commencing during 2011-12. 

Research proposals 

12. RAGs will provide recommendations to fisheries managers on research to meet management 

needs. This section provides more detail on the research proposals that the RAGs will 

produce. 

13. The RAGs will produce an initial set of project proposals to meet the management and 

information needs provided to the RAG, for consideration in the subsequent prioritisation 

process. 

14. The proposals may be in the form of multi-year projects where appropriate. 

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15. While the prioritisation of research is outside the scope of the work of the RAGs, the 

proposals will include information on potential cost and feasibility to guide decisions on 

prioritisation. Cost estimates should be specified as ranges so as to not unduly influence 

subsequent research provider costings. 

16. Where the RAG identifies more than one desirable option for scientific research to meet 

management and information needs, the RAG’s proposals will cover those options, their 

relative pros and cons, their respective potential costs, and the RAG’s recommendation as to 

the preferred option. 

17. Once prioritisation decisions have been made on the initial set of research proposals, the RAG 

may be asked to produce more fully developed project proposals for inclusion in the relevant 

Annual Operational Plan, and for the purposes of cost recovery consultation and tendering. 

Membership 

18. Membership of RAGs is expertise-based. 

19. Membership will be by invitation from MFish only. 

20. A RAG will consist of a core group of one MFish scientist and one manager from the relevant 

Fisheries Plan or Standards team, with the option to “call in” relevant technical expertise 

(internal and/or external) as needed. 

21. External participants will be paid for their time. This will include preparing for and attending 

RAG meetings, and any time spent writing proposals. 

Protocols 

22. All RAG members will commit to: 

• participating in the discussion in an objective and unbiased manner; 

• resolving issues; 

• following up on agreements and tasks; 

• adopting a constructive approach; 

• facilitating an atmosphere of honesty, openness and trust; 

• having respect for the role of the Chair; and 

• listening to the views of others, and treating them with respect. 

23. RAG meetings will be run formally with agendas pre-circulated and formal records kept of 

recommendations, conclusions and action items. 

24. Participants who do not adhere to the standards of participation may be requested by the Chair 

to leave a particular meeting or, in more serious instances, will be excluded from the RAG. 

Chairpersons 

25. The Chair of each RAG will be a MFish scientist with appropriate expertise. 

26. The Chair commits to undertaking the following roles: 

• The Chair is an active participant in RAGs, who also provides technical input, rather than 

simply being a facilitator. 

• The Chair is responsible for: setting the rules of engagement; promoting full participation 

by all members; facilitating constructive questioning; focussing on relevant issues; 

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reporting on RAG recommendations, conclusions and action items, and ensuring followup; 

and communicating with relevant MFish managers. 

27. The Chair is responsible for facilitating consultative and collaborative discussions. 

Decision-making 

28. The Chair is responsible for working towards an agreed view of the RAG members on their 

recommendations to the fisheries manager, but where that proves not to be possible then the 

Chair is responsible for determining the final recommendation. Minority views should be 

clearly represented in proposals in those cases. 

29. A record of recommendations, conclusions and action items will be circulated by e-mail after 

each meeting by the Chair. 

30. Each RAG round will be evaluated by MFish, with a view to identifying opportunities to 

improve the process. The Terms of Reference may be updated as part of this review. 

Non-disclosure agreements 

31. Participants may be asked to sign a Non-Disclosure Agreement relating to documents that 

disclose cost details. 

Conflicts of Interest 

32. New Zealand is a small country and fisheries research is a relatively limited market, even 

internationally. People with the necessary skills and knowledge to participate in this advisory 

process may also have close working relationships with industry, research providers and other 

stakeholders. This will apply to nearly all external members of a RAG. 

33. Participants will be asked to declare any “actual, perceived or likely conflicts of interest” 

before involvement in a RAG is approved, and any new conflicts that arise during the process 

should be declared immediately. These will be clearly documented by the Chair. 

34. Management of conflicts of interest will be determined by the Chair in consultation with 

Fisheries Managers, and approved by the Deputy Chief Executive, Fisheries Management 

prior to meetings commencing. 

Frequency of Meetings 

35. Relevant MFish managers, in consultation with the Chair of the RAG, will decide on the 

frequency and timing of RAG meetings. 

Documents and record-keeping 

36. Unless signalled by the Chair, all RAG documents (papers, agendas, formal records of 

recommendations, conclusions and action items) will be available to all interested parties 

through the Ministry of fisheries website (www.fish.govt.nz), except where confidentiality is 

required for reasons of commercial sensitivity (e.g. cost estimates). 

37. RAG documents will be distributed securely. 

38. Participants who use RAG papers inappropriately may not be invited to subsequent RAG 

meetings. 

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39. The overall responsibility for record-keeping rests with the Chair and includes: 

• Records of recommendations, conclusions and follow-up actions for all RAG meetings 

and to ensure that these are available in a timely manner. 

• If full agreement on the recommendations or conclusions cannot readily be reached 

amongst technical experts, then the Chair will document the extent to which agreement or 

consensus was achieved, and record and attribute any residual disagreement in the 

meeting notes. 

12.6. Fisheries 2030 

Use outcome – Fisheries resources are used in a manner that provides the greatest overall economic, 

social, and cultural benefit. This means having: 

• An internationally competitive and profitable seafood industry that makes a significant 

contribution to our economy 

• High-quality amateur fisheries that contribute to the social, cultural, and economic well-being 

of all New Zealanders 

• Thriving customary fisheries, managed in accordance with kaitiakitanga, supporting the 

cultural well-being of iwi and hapū 

• Healthy fisheries resources in their aquatic environment that reflect and provide for intrinsic 

and amenity value. 

Governance conditions – Fundamental to achieving our goal is the recognition that our approach 

must be based on sound governance. This means having arrangements that lead to: 

• The Treaty partnership being realised through the Crown and Māori clearly defining their 

respective rights and responsibilities in terms of governance and management of fisheries 

resources 

• The public having confidence and trust in the effectiveness and integrity of the fisheries and 

aquaculture management regimes 

• All stakeholders having rights and responsibilities related to the use and management of 

fisheries resources that are understood and for which people can be held individually and 

collectively accountable 

• Having an enabling framework that allows stakeholders to create optimal economic, social, 

and cultural value from their rights and interests 

• An accountable, responsive, dynamic, and transparent system of management. 

Fisheries 2030 draws on a number of values and principles. These seek to outline the behaviour and 

approach that should be used to undertake the actions, make decisions, and achieve the goal for New 

Zealand fisheries. 

Values 

• Tikanga: the Mäori way of doing things; correct procedure, custom, habit, lore, method, 

manner, rule, way, code, meaning, reason, plan, practice, convention. It is derived from the 

word tika meaning ‘right’ or ‘correct’. 

• Kaitiakitanga: The root word in kaitiakitanga is tiaki, which includes aspects of guardianship, 

care, and wise management. Kaitiakitanga is the broad notion applied in different situations. 

• Kotahitanga: Collective action and unity. 

• Manaakitanga: Manaakitanga implies a duty to care for others, in the knowledge that at some 

time others will care for you. This can also be translated in modern Treaty terms as “create no 

further grievances in the settlement of current claims”. 

• Integrity: Be honest and straightforward in our dealings with one another. If we agree to do 

something we will carry it out. 

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• Respect: Treat each other with courtesy. We will respect each other’s right to have different 

values and hold different opinions. 

• Constructive relationship: Strive to build and maintain constructive ways of working with 

each other, which can endure. 

• Achieving results: Focus on producing a solution rather than just discussing the problem. 

Principles 

• Ecosystem-based approach: We apply an ecosystem-based approach to fisheries management 

decision-making. 

• Conserve biodiversity: Use should not compromise the existence of the full range of genetic 

diversity within and between species. 

• Environmental bottom lines: Biological standards define the limits of extraction and impact 

on the aquatic environment. 

• Precautionary approach: Particular care will be taken to ensure environmental sustainability 

where information is uncertain, unreliable, or inadequate. 

• Address externalities: Those accessing resources and space should address the impacts their 

activities have on the environment and other users. 

• Meet Settlement obligations: Act in ways that are consistent with the Treaty of Waitangi 

principles and deliver settlement obligations. 

• Responsible international citizen: Manage in the context of international rights, obligations, 

and our strategic interests. 

• Inter-generational equity: Current use is achieved in a manner that does not unduly 

compromise the opportunities for future generations. 

• Best available information: Decisions need to be based on the best available and credible 

biological, economic, social, and cultural information from a range of sources. 

• Respect rights and interests: Policies should be formulated and implemented to respect 

established rights and interests. 

• Effective management and services: Use least-cost policy tools to achieve objectives where 

intervention is necessary and ensure services are delivered efficiently. 

• Recover management costs for the reasonable expenses of efficiently provided management 

and services, from those who benefit from use, and those who cause the risk or adverse effect. 

• Dynamic efficiency: Frameworks should be established to allow resources to be allocated to 

those who value them most. 

Fisheries 2030 includes a “plan of action” for the five years from 2009, including: improving the 

management framework; supporting aquaculture and international objectives; ensuring sustainability 

of fish stocks; improving fisheries information; building sector leadership and capacity; meeting 

obligations to Māori; and enabling collective management responsibility. The key components 

guiding this document are ensuring sustainability of fish stocks and improving fisheries information: 

Ensuring sustainability of fish stocks 

• Setting and implementing fisheries harvest strategy standards 

• Setting and monitoring environmental standards, including for threatened and protected 

species and seabed impacts 

• Enhancing the framework for fisheries management planning, including the use of decision 

rules to adjust harvest levels over time 

Improving fisheries information 

• Determining best options for information collection on catch from amateur fisheries, 

including the implementation of charter boat reporting 

• Improving our knowledge of fish stocks and the environmental impacts of fishing through 

long-term research plans 

• Gaining access to increased research and development funding 

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12.7. OUR STRATEGY 2030: Growing and protecting New 

Zealand 

Also available at: http://www.mpi.govt.nz/Portals/0/Documents/about-maf/strategy.pdf 

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AEBAR 2012: Appendices: Past projects 

12.8. Other strategic policy documents 

12.8.1. Biodiversity Strategy 

New Zealand’s Biodiversity Strategy was launched in 2000 in response to the decline of New 

Zealand’s indigenous biodiversity — described in the State of New Zealand’s Environment report as 

our “most pervasive environmental issue”. It can be found on the government’s biodiversity website 

at: 

(http://www.biodiversity.govt.nz/picture/doing/nzbs/contents.html) 

The Strategy also reflects New Zealand’s commitment, through ratification of the international 

Convention on Biological Diversity, to help stem the loss of biodiversity worldwide. Strategic Priority 

7 of the strategy was “To manage the marine environment to sustain biodiversity”. Fishing practices, 

the effects of activities on land, and biosecurity threats are identified as constituting the areas of 

greatest risk to marine biodiversity. Pertinent objectives and summarised actions from the strategy are 

as follows: 

Objective 3.1: Improving our knowledge of coastal and marine ecosystems (Substantially increase 

our knowledge of coastal and marine ecosystems and the effects of human activities on them, 

especially assessing the importance of, and threats facing, marine biodiversity, and establishing 

environmental monitoring capabilities to assess the effectiveness of measures to avoid, remedy or 

mitigate impacts on marine biodiversity). 

Objective 3.4: Sustainable marine resource use practices (Protect biodiversity in coastal and 

marine waters from the adverse effects of fishing and other coastal and marine resource uses, 

especially maintaining harvested species at sustainable levels, integrating marine biodiversity 

protection into an ecosystem approach, applying a precautionary approach, identifying marine species 

and habitats most sensitive to disturbance, and integrating environmental impact assessments into 

fisheries management decision making.) 

Objective 3.6: Protecting marine habitats and ecosystems (Protect a full range of natural marine 

habitats and ecosystems to effectively conserve marine biodiversity, using a range of appropriate 

mechanisms, including legal protection, especially establishing a network of areas that protect marine 

biodiversity.) 

Objective 3.7: Threatened marine and coastal species management (Protect and enhance 

populations of marine and coastal species threatened with extinction, and prevent additional species 

and ecological communities from becoming threatened.) 

In addition to its annual reviews (http://www.biodiversity.govt.nz/news/publications/index.html), the 

Biodiversity Strategy was reviewed by Green and Clarkson at the end of its 5-year term. This review 

was published in 2006 (http://www.biodiversity.govt.nz/pdfs/nzbs-5-year-review-synthesis-report.pdf). Most 

relevant to this synopsis were their findings on Objective 3.4 (Sustainable marine resource use) where 

they cited “Moderate progress”. “The policy move towards adopting a more ecosystem approach to 

fisheries management should be encouraged and strengthened. We acknowledge, however, the 

difficulties associated with obtaining the necessary information to make this approach effective. There 

are links to Objective 3.1 and the need for a more coordinated approach to identifying priority areas 

for marine research.” 

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12.8.2. Biosecurity Strategy 

In its 2003 Biosecurity Strategy, The Ministry of Agriculture and Forestry’s Biosecurity NZ defined 

biosecurity as “the exclusion, eradication or effective management of risks posed by pests and 

diseases to the economy, environment and human health”. New Zealand is highly dependent on 

effective biosecurity measures because our indigenous flora, fauna, biodiversity, and, consequently, 

our primary production industries, including fisheries are uniquely at risk from invasive species. 

Information can be found on the Biosecurity New Zealand website at: 

(http://www.biosecurity.govt.nz/biosec/sys/strategy/biostrategy/biostrategynz 

A complementary Biosecurity Science Strategy for New Zealand was developed in 2007 to address 

the science expectations of the Biosecurity Strategy. The science strategy identified the need to: 

• prioritise science needs; 

• minimise biosecurity risks at the earliest stage possible by increasing focus on research that is 

strategic and proactive; 

• improve planning, integration and communication in the delivery of science; 

• ensure research outputs can be used effectively to improve biosecurity operations and 

decision making. 

12.8.3. Marine Protected Areas Policy 

The Marine Protected Areas (MPA) Policy and Implementation Plan was released for consultation in 

December 2005 jointly by the Ministry of Fisheries and Department of Conservation. It confirmed 

Government’s commitment to ensuring that New Zealand’s marine biodiversity was protected, and 

established MPA Policy as a key component of that commitment. The MPA Policy objective is to 

protect marine biodiversity by establishing a network of Marine Protected Areas that is 

comprehensive and representative of New Zealand’s marine habitats and ecosystems. The Policy 

involved a four-stage approach to implementation: 

Stage 1: Development of the approach to classification, formulation of a standard of protection, 

and mapping of existing protected areas and/or mechanisms. Scientific workshops 

will be used to assist with the process, and the results will be put on the website for 

comment 

Stage 2: Development of the MPA inventory, identification of gaps in the MPA network, and 

prioritisation of new MPAs 

Stage 3: Establishment of new MPAs to meet gaps in the network. This will be undertaken at a 

regional level and a national process will be followed for offshore MPAs 

Stage 4: Evaluation and monitoring. 

Stage 1 and the inventory specified for Stage 2 are complete and regional forums were established for 

the Subantarctic and West Coast bioregions. In June 2009, these planning forums released 

consultation documents on implementation of the MPA Policy in their bioregions: 

Consultation Document - Implementation of the Marine Protected Areas Policy in the Territorial Seas 

of the Subantarctic Biogeographic Region of New Zealand: 

http://www.biodiversity.govt.nz/pdfs/seas/subantarctics-mpa-policy-consultation-document.pdf 

Proposed Marine Protected Areas for the South Island’s West Coast Te Tai o Poutini: A public 

consultation document: 

http://www.westmarine.org.nz/documents/ProposedMPAsWestCoastSubmissiondocumentwebresv2.pdf 

The MPA Classification, Protection Standard, Implementation Guidelines, together with a summary 

of subsequent consultation processes around implementing the policy can be found on the 

Government Biodiversity website at: 

http://www.biodiversity.govt.nz/seas/biodiversity/protected/mpa_consultation.html 

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12.8.4. Revised Coastal Policy Statement 

The revised New Zealand Coastal Policy Statement (NZCPS) came into force in December 2010, 

replacing the original 1994 NZCPS. The statement is to be applied, as required by the Resource 

Management Act 1991 (RMA), by persons exercising functions and powers under that Act. The 

documentation can be read on the Department of Conservation’s website at: 

http://www.doc.govt.nz/publications/conservation/marine-and-coastal/new-zealand-coastal-policystatement/new-zealand-coastal-policy-statement-2010/ 

The NZCPS does not directly apply to fisheries management decision-making, although the Minister 

of Fisheries is required to have regard to the Statement when making decisions on sustainability 

measures under section 11 of the Fisheries Act. In addition, this synopsis include chapters on land use 

issues and habitats of particular significance for fisheries management for which the main threats are 

managed under the RMA (e.g., land use practices could increase sedimentation and affect the 

estuarine nursery grounds of important fishstocks). In other areas, management of effects under the 

RMA can complement management of the effects of fishing (e.g., complementary management of the 

habitat and bycatch of a protected species). The following objectives and policies are considered 

relevant (numbering as per NZCPS, text in parentheses summarises subheadings in the Statement of 

most relevance to fisheries values): 

Objective 1: To safeguard the integrity, form, functioning and resilience of the coastal 

environment and sustain its ecosystems, including marine and intertidal areas, estuaries, dunes 

and land (especially by maintaining or enhancing natural biological and physical processes in the 

coastal environment). 

Objective 6: To enable people and communities to provide for their social, economic, and 

cultural wellbeing and their health and safety, through subdivision, use, and development 

(especially by recognising that the protection of habitats of living marine resources contributes to 

social, economic and cultural wellbeing and that the potential to utilise coastal marine natural 

resources should not be compromised by activities on land). 

Policy 5: Land or waters managed or held under other Acts (especially to consider effects on 

coastal areas held or managed under other Acts with conservation or protection purposes and to avoid, 

remedy or mitigate adverse effects of activities in relation to those purposes). 

Policy 8: Aquaculture: Recognise the significant existing and potential contribution of 

aquaculture to the social, economic and cultural well-being of people and communities 

(especially by taking account of the social and economic benefits of aquaculture, recognising the need 

for high water quality, and including provision for aquaculture in the coastal environment). 

Policy 11: Indigenous biodiversity: To protect indigenous biological diversity in the coastal 

environment (especially by avoiding, remedying or mitigating adverse effects on: habitats that are 

important during the vulnerable life stages of indigenous species; ecosystems and habitats that are 

particularly vulnerable to modification; and habitats of indigenous species that are important for 

recreational, commercial, traditional or cultural purposes). 

Policy: 21 Enhancement of water quality: Where the quality of water in the coastal environment 

has deteriorated so that it is having a significant adverse effect on ecosystems, natural habitats, 

or water based recreational activities, or is restricting existing uses, such as aquaculture, 

shellfish gathering, and cultural activities, give priority to improving that quality. 

Policy 22: Sedimentation (especially with respect to impacts on the coastal environment). 

319


Policy 23: Discharge of contaminants (especially with respect to impacts on ecosystems and 

habitats). 

12.8.5. Management of Activities in the EEZ 

In August 2007 the Ministry for the Environment (MfE) released a discussion paper “Improving 

regulation of environmental effects in New Zealand’s Exclusive Economic Zone” seeking comment on 

a preferred legislative option for managing the impacts of activities in the EEZ. The discussion paper 

stated that environmental effects in the EEZ were, at that time, managed by sector-specific legislation, 

which creates the following problems: 

• gaps and inconsistencies in the operational control of environmental effects 

• unclear environmental outcomes against which activities and their effects should be assessed 

• uncertainty for investors about the regulatory environment 

• uncertainty about how the effects of activities on each other should be managed. 

The MfE website (http://www.mfe.govt.nz/issues/oceans/current-work/index.html) states that EEZ 

legislation is a priority for the current government. In response to the Gulf of Mexico oil spill, the 

Ministry of Economic Development is commissioning an independent study on New Zealand's health, 

safety and environmental provisions around minerals activities such as deep sea drilling. This report, 

along with the proposed legislation developed by the last government, will be considered by Ministers 

before making final policy and timeline decisions for EEZ legislation. 

Proposals for EEZ legislation to manage effects other than those caused by fishing do not directly 

apply to fisheries management decision-making under the Fisheries Act. However, there are issues 

around the management of cumulative effects (e.g., of more than one activity on benthic 

communities) and around effects of any proposed new activities in the EEZ on fishing activity already 

occurring. Some projects already completed or currently underway are likely to be useful for these 

processes (e.g., detailed maps of fishing effort produced under ENV2001/07 and BEN2006/01 and 

enhancements of the Marine Environment Classification produced under ZBD2005-02 for demersal 

fishes and BEN2006/01A for benthic invertebrates). 

12.8.6. Ministry for Research Science and Technology 

Roadmaps 

The Ministry for Science Research and Technology (MRST, now a component of the Ministry of 

Business, Innovation and Employment, MBIE) stated in its 2006 overview “Science for New Zealand” 

that our science system aims to set long-term direction for RS&T, but allows flexibility to alter 

direction as needs and opportunities change. Recent direction setting has replaced periodic national 

processes with a range of continuous processes, often focused on particular areas or topics including: 

• Government-led strategy processes around particular areas of national need or opportunity. 

The Biodiversity Strategy and Biosecurity Strategy are recent examples that have led to 

changes in institutional arrangements, policies, and funding in RS&T. 

• More focused processes by research organisations and or user communities around how a 

particular area of science could better support national needs, or may be needed to retain or 

build new capability. These may be endorsed by Ministers or implemented directly by 

research organisations. 

• ‘Roadmaps for Science’, led by MRST, aimed at developing and coordinating RS&T 

directions and bringing a stronger RS&T perspective to other Government strategies. 

Roadmaps describe New Zealand’s current research activity, interpret Government’s 

objectives and strategies in the area, and provide guidance to public research investment 

agencies as well as other participants in the science system. 

320


Roadmaps for Science were published by MRST for Energy Research (December 2006), Nanoscience 

& Nanotechnologies (February 2007), Biotechnology Research (March 2007), and Environment 

Research (June 2007). Probably the most relevant of these is that for Environment Research which 

can be found at MRST’s website at: 

http://www.msi.govt.nz/update-me/archive/publications-archive/ 

(if you would like to request a copy of this publication, please email info@msi.govt.nz). 

It is important to note that these roadmaps relate primarily to research funded by the erstwhile 

Foundation for Research Science and Technology (FRST, now also part of MBIE) and much less to 

applied, operational research purchased by the Ministry of Fisheries and some other government 

departments. However, the Environmental Roadmap for Science noted that environmental 

management decisions increasingly require an understanding of whole system processes and a multidimensional 

approach. More integrated and systems-based approaches can offer environmental 

managers and decision-makers answers to many of the questions they are facing. A crucial task then 

becomes one of creating a New Zealand science environment within which systems-based approaches 

can develop and flourish, acknowledging that small-scale studies remain important to underpin these 

approaches. MRST identified three overarching themes that require additional focus: systems 

understanding and integration (e.g., ecosystem aspects of fisheries management); transfer and uptake 

(including adaptive management to advance scientific understanding); and information systems 

(including management of databases and collections. 

From a suite of six key research areas (global environmental change, land, water and coasts, including 

the coastal marine area, urban design and hazards, biosecurity, biodiversity, and oceanic systems), 

MRST identified five key research directions, two of which are of most relevance to fisheries 

interests: 

Direction 4: Over the next few years, the government will give priority to developing more integrated 

multidisciplinary approaches, and to improving transfer, uptake and information systems in the 

following areas: 

• global environmental change – with a focus on providing the knowledge for integrated 

ecological, physical and socio-economic modelling of climate change impacts on water and 

soil resources, land use, biosecurity, biodiversity and potential global impacts; 

• land, water and coasts – with a focus on sustainable land and coastal aquatic use, including 

the impacts of land use on freshwater and the impacts of freshwater, land management and 

aquatic production on coastal marine environments; 

• biosecurity – reflecting the directions set in the Biosecurity Science Research and Technology 

Strategy. 

Direction 5: Over the longer-term, the government will focus on more integrated multidisciplinary 

approaches, and improved transfer and uptake, and information systems in the biodiversity and 

oceanic systems areas. 

MRST believes that the Environmental Science Roadmap will make a difference by: 

• Equipping environmental managers with integrated research results and tools which will help 

them avoid, remedy or mitigate future environmental problems. 

• Enhancing New Zealand’s potential as a test bed and world leader for new innovations and 

business developments in environmental technologies. 

• Improved predictions of and responses to natural hazards events. 

• Improved responses to climate change. 

321


12.8.7. National Plan of Action to Reduce the Incidental 

Catch of Seabirds in New Zealand Fisheries 

The National Plan of Action (NPOA) to Reduce the Incidental Catch of Seabirds in New Zealand 

Fisheries came into action in April 2004. The NPOA-Seabirds provides a framework to inform the 

management of seabird/fisheries interactions. It also sets a number of time-bound objectives to be 

reached by partnering with the fishing industry to reduce the incidental catch of seabirds. 

The document is available online at: 

http://www.doc.govt.nz/documents/conservation/native-animals/birds/npoa.pdf 

A revised version of this document is currently under consultation, with a draft version available 

online through the consultations page of the Fisheries website of the Ministry for Primary Industries 

at: 

http://www.fish.govt.nz/en-nz/Consultations/default.htm?wbc_purpose=bas 

Note that these links are likely to change due to the current revision. The revised document will be available 

early in 2013. 

12.8.8. New Zealand National Plan of Action for the 

Conservation and Management of Sharks 

The New Zealand National Plan of Action (NPOA) for the Conservation and Management of Sharks 

was approved by the Minister of Fisheries on 13 October 2008. The purpose of the NPOA-Sharks is 

to ensure the conservation and management of sharks and their long-term sustainable use. It also 

contains a set of actions in order to meet this purpose. The document is available online at: 

http://www.fish.govt.nz/NR/rdonlyres/F0530841-CD61-4C3E- 

9E50153A281A4180/0/NPOAsharks.pdf 

Note that the NPOA-Sharks is currently under review with a revised edition due in 2013. 

322


12.9. Appendix of Aquatic Environment and Biodiversity 

funded and related projects 

The following listing of projects are those relevant to aquatic environment research that have been 

through research planning and subsequently been funded by the Ministry of Fisheries (MFish), the 

Ministry for Primary Industries (MPI) or the fishing industry. These projects have been ordered by the 

research themes: 

1. Protected species 

2. Non-protected bycatch 

3. Benthic impacts 

4. Ecosystem effects 

5. Biodiversity 

Within these themes projects are ordered chronologically (from the most recent to the oldest). A list of 

references cited within the table is included at the end of this appendix. 

Each project or row of the table is described by a project number (used by MFish/MPI), a project title, 

specific objectives (where there are many objectives and some are clearly not relevant to aquatic 

environment research they may not be listed), project status and any relevant citations from the 

project. 

Citations listed below can be accessed differently depending upon the type of output. Finalised FARs 

(Fisheries Assessment Reports) and AEBRs (Aquatic Environment and Biodiversity Reports), 

historical FARDs (Fisheries Assessment Research Documents) and MMBRs (Marine Biodiversity 

and Biosecurity Reports), and some FRRs (final Research Reports) can be found at: 

http://fs.fish.govt.nz/Page.aspx?pk=61&tk=209. Increasingly, reports will be available from the MPI 

website at: http://www.mpi.govt.nz/news-resources/publications. For unpublished documents or those not 

available on either of these websites please contact Science.Officer@mpi.govt.nz. Every attempt has 

been made to make this table comprehensive and correct, but if any errors are found please send 

suggested corrections or additions through to Science.Officer@mpi.govt.nz. 

323

PROTECTED SPECIES 


Project 

Code 

Project Title Specific Objectives Status Citation/s 

PRO2012-02 Assessment of the risk to 1. To scope the risk assessment, including producing an agreed list of Approved but 

marine mammal 

marine mammal populations (in concert with MAF and DOC). 

not contracted 

populations from New 2. To review the literature, compile the required information and evaluate the 

Zealand commercial appropriate level of risk assessment for the marine mammal populations 

fisheries 

identified in objective 1. 

3. To conduct a risk assessment for the marine mammal populations 

identified in objective 1 using, where possible, a risk index reflecting the ratio 

of fisheries-related mortality to the level of potential biological removal. 

4. To refine the results of the risk assessment for priority marine mammal 

populations by incorporating spatially and temporally-explicit abundance, 

distribution and capture information. 

PRO2012-07 Cryptic mortality of 

seabirds in trawl and 

longline fisheries 

1. To review available information from international literature and 

unpublished sources to characterize and inform estimation of cryptic 

mortality and live releases for at-risk seabirds in New Zealand trawl and 

longline fisheries 

2. To review the extent to which fisheries observer data informing current 

estimates of seabird captures may be used to also estimate cryptic 

mortalities in different fishery groups in the seabird risk assessment, and 

identify key assumptions and associated uncertainty in the estimation of 

cryptic mortalities. 

3. To identify those species and/or fishery groups for which current 

uncertainty regarding cryptic mortality contributes most strongly to high risk 

scores for at-risk seabird species, and recommend options to improve 

estimation of cryptic mortality for those species / fishery group combinations. 

324 

Approved but 

not contracted

PROTECTED SPECIES continued 


Project 

Code 


PRO2012-08 Improved estimation of 1. To generate seabird distribution map layers for seabird species which the Approved but 

spatio-temporal overlap existing level 1 risk assessment identifies as being at-risk, but for which no not contracted 

with fisheries for at-risk level 2 assessment has been completed. 2. To modify seabird distribution 

seabird species 

layers used in the current level 2 risk assessment, for those species that the 

L2 assessment identifies as at-risk and for which: i) spatial distributions used 

in the current L2 assessment are known to be wrong, or ii) improved spatial 

distribution layers are readily available (e.g. from new satellite telemetry 

data). 3. To seasonally disaggregate seabird spatial distribution data layers 

for those at-risk seabird species with a strongly seasonal abundance and/or 

distribution in the New Zealand EEZ4. To utilize updated spatial/seasonal 

seabird distribution layers to generate improved estimates of spatio-temporal 

overlap with fisheries, for integration into the existing level 2 seabird risk 

assessment framework. 

PRO2012-09 Improvements to key 1. To improve estimates of the population size of specified seabirds where Approved but 

information gaps for this will substantially reduce uncertainty in the risk ratio estimated in the not contracted 

highest risk seabird Level 2 seabird risk assessment. 

populations TBC 

2. To improve estimates of the age at first breeding for specified seabird 

populations where this will substantially reduce uncertainty in the risk ratio 

estimated in the Level 2 seabird risk assessment. 

3. To improve estimates of the average adult survival rate for specified 

seabird populations where this will substantially reduce uncertainty in the risk 

ratio estimated in the Level 2 seabird risk assessment. 

PRO2012-10 Level 3 risk assessment for 

Antipodean albatross TBC 

ENV2011-01 NPOA-sharks science 

reivew 

1. Develop an Antipodean albatross population model 

2. Assess the effect of fisheries mortality on population viability 

3. As information permits, assess the effect of alternative management 

strategies 

1. To collate and summarise information in support of a review of the 

National Plan of Action for the Conservation and Management of Sharks 

(NPOA-sharks). 

2. To identify research gaps from objective 1 and suggest cost-effective 

ways these could be addressed. 

325 

Approved but 


Completed Francis & Lyon 2012



Project Code Project Title Specific Objectives Status Citation/s 

No project 

number 

A risk assessment of 

threats to Maui’s dolphins 

SRP2011-03 Probabilistic modelling of 

sea lion interactions 

To evaluate of the risks posed to Maui’s dolphin to support the review of the 

TMP. 

1. Estimate the probability that a sea lion suffers mild head trauma following a 

collision with a SLED grid 

326 

Completed Currey et al. 2012 

Completed Abraham 2011 

SRP2011-04 HSL Modelling 1. Revise Breen-Fu-Gilbert sea lion model Completed Breen et al. 2010 

DEE2010-03 Development of a 

methodology to estimate 

crypticmortalities to ETP 

species from DW fishing 

activity 

No project 

number 

A risk assessment 

framework for incidental 

seabird mortality 

associated with New 

Zealand fishing in the New 

Zealand EEZ 

PRO2010-01 Estimating the nature and 

extent of incidental 

captures of seabirds, 

marine mammals and 

turtles in New Zealand 

commercial fisheries 

PRO2010-02 Research into key areas of 

uncertainty or 

development of mitigation 

techniques for the revised 

npoa-seabirds 

1. To conduct a review of existing national and international techniques to 

estimate cryptic mortality of endangered, threatened and protected species 

caused by deepwater fishing activities 

2. To develop one or more approaches to estimating cryptic mortality of 

endangered, threatened and protected species caused by deepwater fishing 

activities 

3. To field test one or more approaches to estimating cryptic mortality of 

endangered, threatened and protected species caused by deepwater fishing 

activities 

To describe the conceptual and methodological framework of this risk 

assessment approach to guide the completion of similar risk assessments 

elsewhere. 

1. To estimate the nature and extent of captures of seabirds, marine mammals 

and turtles, and the warp strikes of seabirds in New Zealand fisheries for the 

fishing years 2009/10, 2010/11 and 2011/12. 

1.To provide the information necessary to underpin the revised NPOA-seabirds 

or develop mitigation techniques to reduce risk identified via the revised NPOAseabirds. 

Ongoing 

analysis 

Completed Sharp et al. 2011 

Ongoing 

analysis 

Ongoing 

analysis 

Thompson et al. 2011




SRP2010-03 Fur Seal interactions with 

a SED excluder device 

SRP2010-05 Fur seal interaction with 

an SLED excluder device 

IPA2009-09 Sea Lion bioenergetics 

modelling 

IPA2009-16 Preliminary impact 

assessment of NZ sea lion 

interaction with SLEDS 

IPA2009- 

19/20 

No project 

number 

Level 2 seabird risk 

assessment rerun 

External review of NZ sea 

lion bycatch necropsy data 

and methods 

PRO2009-01A Abundance & distribution 

of Hector's & 

maui'sdolphins (5 year 

project) 

1. Fur seal interactions with SED excluder device (Dr J Lyle) Completed Lyle 2011 

• Using a series of 10-15 impact tests at a maximum collision speed of 5 or 6 ms- 

1, develop a “HIC map” for the SLED grid to enable the consequences of 

collisions with different parts of the grid by sea lions of different head masses to 

be predicted (scaling values (for eq 3) will include -1/3, -2/3, and -3/4) 

• Using a small number of collision tests, verify that the HIC for a glancing blow 

can be predicted with sufficient accuracy by resolving vectors 

• Calculate the maximum possible sensitivity to different boundary conditions 

using the relative masses of the SLED grid and sea lion heads 

• Clarify in the final research report that undertaking tests in air (as opposed to 

underwater) should not affect the results 

1. To review and collate data on growth, metabolism, diet and reproductive 

parameters of NZ sea lions or, if data are inexistent, of other sea lions species 

2. To analyse the energy density of various NZ sea lion prey items 

3. To incorporate the data acquired in objectives 1. and 2. into a bioenergetics 

model to estimate the energy and food requirements of NZ sea lions 

1. Preliminary impact assessment of New Zealand sea lion interactions with 

SLEDs 

1. To examine the risk of incidental mortality from commercial fishing for 64 

seabird species in New Zealand trawl and longline fisheries 

The primary purposes of this review were to determine whether, in the opinion of 

a group of independent experts: 

- the interpretation of necropsy findings and trauma classification system used by 

Dr Wendi Roe are valid 

- sea lions recovered from trawl nets have sustained clinically significant trauma 

- some or all of the sea lions exiting through SLEDs are likely to survive 

1. To estimate the distribution of the South Coast South Island Hector’s dolphin 

sub-population in both winter and summer. 

2. The work for this sub-project was subsequently extended to include data 

collection necessary to estimate abundance. 

327 

Completed Ponte et al. 2011 

Completed Meynier 2010 

Completed Ponte et al. 2010 

Completed Richard et al. 2011 

Completed Roe 2010a 

Completed Clement & Mattlin 2010


Project 

Code 

PRO2009- 

01B 

PRO2009- 

04 



Abundance, distribution, and productivity of 

Hector’s (and Maui’s) dolphins 

Development and efficacy of seabird mitigation 

measures 

ENV2008-03 Bycatch of basking sharks in New Zealand 

fisheries 

PRO2008- 

01 

Risk assessment of protected species bycatch in 

NZ fisheries 

1. To estimate the likely precision of abundance estimates 

from summer aerial surveys for Hector’s dolphins along the 

East Coast South Island (ECSI; from Farewell Spit to 

Nugget Point) under different levels of sampling intensity 

and stratification. 

2. To estimate the likely precision of abundance estimates 

and the likely quality of distribution information from winter 

aerial surveys for Hector’s dolphins along the ECSI under 

different levels of sampling intensity and stratification. 

3. To identify and quantify trade-offs between the precision 

of abundance estimates and the quality of distribution 

information as well as between overall precision and likely 

cost (e.g., based on the number of flying hours required). 

4. To identify key areas and times for which it would be 

particularly useful to have information on Hector’s dolphin 

distribution (e.g., where risk may come from overlap with 

particular fisheries) and quantify trade-offs between the 

precision of ECSI-wide surveys and collecting such finescale 

information. 

5. Assess the extent to which two-phase or adaptive 

approaches would be useful to improve the surveys’ utility 

for assessing dolphin distribution, particularly the seaward 

limit. 

1. To test the efficacy of a variety of configurations of 

mitigation techniques at reducing seabird mortality (or 

appropriate proxies for mortality) in longline fisheries 

1. To review the productivity of basking sharks 

2. To describe the nature and extent of fishery-induced 

mortality of basking sharks in New Zealand waters and 

recommend methods of reducing the overall catch. 

1. To provide an assessment of the risk posed by different 

fisheries to the viability of New Zealand protected species, 

and to assign a risk category to all New Zealand fishing 

operations. 

328 

Ongoing 

analysis 

Completed No reports specified 

as required output 

Completed Francis & Smith 2010 

Completed Waugh et al. 2009




SAP2008-14 Sea lion population 

modelling, additional 

Deepwater 

Group 

Necropsy of marine 

mammals captured in New 

Zealand fisheries in the 

2007-08 fishing year 

IPA2007-09 Protected species risk 

assessment 



captures of seabirds in 

New Zealand commercial 

fisheries 





fisheries 

1. To assess the likely performance of different bycatch control rules for the 

SQU6T fishery. 

2. To correct and update the Breen-Fu-Gilbert (2008) sea lion model- including 

assessment of the performance of 200-series and 300-series management 

control rules. 

3. To document the development of the model- including all four objectives of 

project IPA2006/09 and objective 1 of this project- in a single report suitable for 

an international review. 

Necropsy of marine mammals captured in New Zealand fisheries in the 2007-08 

fishing year 

To provide an asessment of the risk posed by different fisheroes to the viability of 

NZ protected species- and to assign a risk category to all NZ fishing operations 

1. Estimate capture rates per unit effort and total captures of seabirds for the 

New Zealand EEZ and in selected fisheries by method, area, target fishery, in 

relation to mitigation methods in use, and, where possible, by seabird species for 

the fishing year 2006/07, 2007/08 and 2008/09. 

2. Examine the incidence of seabird warp strike in trawl fisheries where these 

data are available from fisheries observers, and estimate the rate of incidents 

(birds affected per hour) and total number of seabirds affected by fishery, area 

and method. Examine the factors (fishery, environmental, seasonal, mitigation, 

area) that influence the probability of warp-strike occurring. 

1. Estimate capture rates per unit effort and total captures of seabirds for the 

New Zealand EEZ and in selected fisheries by method, area, target fishery, in 

relation to mitigation methods in use, and, where possible, by seabird species for 

the fishing year 2006/07, 2007/08 and 2008/09. 

2. Examine the incidence of seabird warp strike in trawl fisheries where these 

data are available from fisheries observers, and estimate the rate of incidents 

(birds affected per hour) and total number of seabirds affected by fishery, area 

and method. Examine the factors (fishery, environmental, seasonal, mitigation, 

area) that influence the probability of warp-strike occurring. 

329 

Completed Breen et al. 2010 

Completed Roe 2009a 

Completed Waugh et al. 2008 

Completed Abraham 2010; Abraham & 

Thompson 2009a; 2010; 

2011a; b; Thompson & 

Abraham 2009a; Abraham et 

al. 2010b 

Completed Abraham et al. 2010a; 

Thompson & Abraham 

2009a; 2009b; 2009c; 2010; 

2011; Thompson et al. 

2010a; 2010b




ENV2006-05 The use of electronic 

monitoring technology in 

New Zealand longline 

fisheries 

IPA2006-02 The efficacy of warp strike 

mitigation devices: trials in 

the 2006 squid fishery 

IPA2006-09 Modelling interactions 

between trawl fisheries 

and New Zealand Sea lion 

interactions 

1. Trial the deployment of electronic monitoring systems in selected longline 

fisheries, monitoring 

incidental take of protected species. 

2. Evaluate the efficacy of electronic monitoring in allowing enumeration and 

identification of 

protected species captures. 

3. Recommend options for data management and information transfer arising 

from the deployment 

of electronic monitoring in selected fisheries. 

1. Groom the mitigation trial data and produce a summary of the data (100%) 

2. Examine strike rates and capture rates on warps and mitigation devices 

(100% ) 

3. Determine the relative efficacy of mitigation devices tested in the trial (100%) 

4. Make recommendations regarding future trials (100%) 

5. Compare seabird warp strike data for 2005 and 2006 (100%) 

6. Work with SeaFIC and the mitigation trials TAG to produce analyses and 

outputs (100%) 

1. Model the New Zealand sea lion population and explore alternative 

management procedures for controlling New Zealand sea lion bycatch in the 

SQU 6T fishery 

2. Collate and review all available sea lion biological data- fisheries data- and 

sea lion bycatch data relevant to a population model and management strategy 

evaluation for the Auckland Islands sea lion population 

3. Update and improve the existing Breen and Kim sea lion population model 

(2003) to incorporate all relevant data and address model uncertainties including 

but not necessarily limited to those identified by the AEWG 

4. Fit the revised model to all available data and test sensitivity including but not 

necessarily limited to runs identified by the AEWG 

5. Test a range of management procedures (rules) with the model to determine if 

they meet agreed management criteria 

330 

Completed McElderry et al. 2008 

Completed Middleton & Abraham 2007 

Completed Breen 2008




IPA2006-13 Identification of Marine 

Mammals Captured in 

New Zealand Fisheries 

PRO2006-01 Data collection of 

demographic, 

distributional and trophic 

information on selected 

seabird species to allow 

estimation of effects of 

fishing on population 

viability 

PRO2006-02 Modelling of the effects of 

fishing on the population 

viability of selected 

seabirds 

PRO2006-04 Estimation of the nature 

and extent of incidental 



fisheries 


extent of marine mammal 

captures in New Zealand 

commercial fisheries 

1. To determine, through examination of returned marine mammal carcasses, 

the species, sex, reproductive status, and age-class of marine mammals 

returned from New Zealand fisheries. 

2. To detail any injuries and, where possible, the cause of mortality of marine 

mammals returned from New Zealand fisheries, and examine relationships 

between injuries and body condition, breeding status, and other associated 

demographic characteristics. 

1 To gather demographic, distributional and dietary information on selected 

seabird species to allow assessment of effects of fishing on population viability. 

1. Model the effects of fisheries mortalities on population viability compared with 

other sources of mortality or trophic effects of fishing 

2. Examine the overlap of fishing activity with species distribution at sea for 

different stages of the breeding and life-cycle and for different sexes, and assess 

the likely risk to species or populations from fisheries (by target species fisheries, 

fishing methods, area and season) in the New Zealand EEZ 

1. To estimate the nature and extent of captures and warp-strikes of seabirds 

in New Zealand fisheries for the fishing year 2005/06. 

1. To estimate and report the total numbers, releases and deaths of marine 

mammals where possible by species, fishery and fishing method, caught in 

commercial fisheries for the years 1990 to the end of the fishing year 2005/06. 

2. To analyse factors affecting the probability of fur seal captures for the years 

1990 to the end of the fishing year 2005/06. 

3. To classify fishing areas, seasons and fishing methods into different risk 

categories in relation to the probability of marine mammal incidental captures for 

the years from 1990 through to the end of the fishing year 2005/06. 

331 

Completed Roe 2009b 

Completed Sagar & Thompson 2008; 

Sagar et al. 2009a; b; 2010a; 

b; c; Baker et al. 2008; 2009; 

2010 

Completed Francis & Bell 2010; Francis 


Completed Baird & Smith 2008 

Completed Mormede et al. 2008; Baird 

2008a; 2008b; Smith & Baird 

2009; Smith & Baird 2011; 

Baird 2011.




PRO2006-07 Characterise noncommercial 

fisheries 

interactions 

ENV2005-06 Estimation of protected 

species captures in 

longline fisheries using 

electronic monitoring 

ENV2005-01 Estimation of the nature 

and extent of incidental 


New Zealand fisheries 

ENV2005-02 Estimation of the nature 

and extent of marine 

mamal captures in New 

Zealand fisheries 

ENV2005-04 Identification of marine 

mammals captured in New 


1. To characterise non-commercial fisheries interactions with seabirds and 

marine mammals 

2. Characterise non-commercial fisheries risk to seabirds and marine mammals 

by area and method 

Recommend mitigation measures appropriate for uptake in non-commercial 

fisheries in which seabird or marine mammal captures occur 

1. To provide estimates of seabird and marine mammal mortalities from longline 

fisheries in New Zealand using electronic monitoring systems and to recommend 

deployment and data management options for ongoing use of these systems for 

estimation of protected species incidental take. 

1. To estimate the nature and extent of captures of seabirds in selected New 

Zealand fisheries for the fishing year 2004/05. 

To examine the nature and extent of the captures of marine mammals in New 

Zealand fisheries, for the whole New Zealand EEZ, by Fishery Management 

Area and fishing season, and by smaller metric as appropriate for the fishing 

year 2004/05. 

2. Examine alternative methods for estimating sea lion captures and recommend 

one or more alternative standardised methods for describing and estimating sea 

lion captures in the SQU 6T fishery. 

1. To determine the species- sex- and where possible- age and reproductive 

status of marine mammals captured in New Zealand fisheries. 

2. To necropsy marine mammals captured incidentally to New Zealand fishing 

operations to determine life-history characteristics and the likely cause of 

mortality. 

3. To determine- through examination of returned marine mammal carcasses- 

the taxon to species-level- sex- and reproductive status- and age-class of marine 

mammals captured in New Zealand fisheries. 

4. To detail the injuries and where possible the cause of mortality of marine 

mammals returned from New Zealand fisheries- along with their body condition 

and breeding status- and other associated demographic characteristics. 

5. To detail the protocol used for the necropsy of marine mammals- to provide a 

standardised procedure for autopsy to determine species- age- sex and 

associated demographic characteristics for fishery-killed specimens. 

332 

Completed Abraham et al. 2010a; 

Thompson & Abraham 

2009a; 2009b; 2009c; 2010; 

2011; Thompson et al. 

2010a; b; c 

Completed McElderry et al. 2007 

Completed Baird & Smith 2007a; Baird & 

Gibbert 2010 

Completed Abraham 2008; Baird 2007; 

Smith & Baird 2007b; Baird & 

Smith 2007b 

Completed Roe 2007




ENV2005-09 Data collection to estimate 

key performance 

indicators in the Chatham 

albatross, Diomedea 

eremita. 

ENV2005-13 Assessment of risk to 

yellow-eyed penguin 

Megady-ptes antipodes 

from fisheries incidental 

mortality 

ENV2004-04 Characterisation of 

seabird captures in New 


ENV2004-05 Modelling of impacts of 

fishing-related mortality on 

New Zealand seabird 

populations 

1. To gather data on key population parameters for Chatham albatross 

Diomedea eremita- to enable population viability to be assessed- and the 

responses of key parameters to fisheries mortality and fisheries management 

activities to mitigate fisheries related risk 

2. To undertake field research to collect data on population growth rates- adult 

survival- inter-breeding season survival- mortality due to predation at the colonyfecundity 

and associated parameters for Chatham Albatross- following the study 

design project 

3. To undertake field research to determine the range and extent foraging 

movements of Chatham albatrosses within New Zealand fishing waters- and 

examine the nature and extent of any association between Chatham albatrosses 

and fishing activities. 

1. To review existing data on yellow-eyed penguin M. antipodes population 

performance and fisheries information and provide an analysis of the potential 

effect of fishing mortality and other factors on population viability. 

2. To recommend data collection requirements and protocols for the assessment 

of the effects of fishing on yellow-eyed penguins. 

333 

Completed No reports specified as 

required output 

Completed Maunder 2007 

1. Characterisation of seabird captures in New Zealand fisheries. Completed Mackenzie & Fletcher 2006 

1. To examine and identify modelling approaches to analyse seabird 

demographic impacts that may be occurring as a result of fisheries mortality. 

2. To compile databases of available demographic and distributional data on 

selected seabirds affected by fisheries mortality and New Zealand fisheries and 

estimate key population parameters and seasonal distribution for each species. 

3. To estimate rates of removals related to fishing activities in New Zealand for 

selected seabird species, where possible by age class and sex. 

4. To describe the spatial overlap of seabird distributions at sea, with fisheries 

where the risk of incidental mortality has been demonstrated to be moderate to 

high. 

5. To examine the potential for factors other than fisheries removals within the 


zone to influence the population dynamics of the selected study species. 

6. To characterise selected seabird populations’ abilities to sustain removals 

related to fishing operations within the New Zealand EEZ, and to recommend, 

where possible environmental standards for assessing the sustainability of 

selected fishing operations in relation to impacts on seabird populations. 

Completed Fletcher et al. 2008




ENV2004-02 Estimation of New 

Zealand sea lion incidental 


Fisheries 

1. To estimate the level of New Zealand sea lion (Phocartos hookeri) incidental 

capture in New Zealand fisheries 

334 

Completed Smith & Baird 2007a 

ENV2004-06 Maui's dolphin study 1. To quantify and compare summer and winter distribution of maui's dolphin Completed Slooten et al. 2005 

IPA2004-14 Seabird warp strike in the 

southern squid trawl 

fishery 

ENV2003-05 Review of the Current 

Threat Status of 

Associatedor Dependent 

Species 

No project 

number 

QMA SQU6T New 


catch and necropsy data 

for the fishing years 2000- 

01, 2001-02 and 2002-03 

MOF2002-03L Exploring alternative 

management procedures 

for controlling bycatch of 

Hooker’s sea lions in the 

SQU 6T squid fishery 

ENV2001-01 Estimation of seabird 

incidental captures in New 


ENV2001-02 Incidental capture of 

Phocarctos hookeri (New 

Zealand sea lions) in 


fisheries, 2001-02. 

ENV2001-03 Estimation of 

Arctocephalus forsteri 

(New Zealand fur seal) 

incidental captures in New 


1. To document seabird warp strike in the southern squid trawl fishery, 2004-05 Completed Abraham & Kennedy 2008 

1. To assess the current threat status of selected associated or dependent 

species. 

Completed Baird et al. 2010 

Objectives unknown Completed Mattlin 2004 

Objectives unknown Completed Breen & Kim 2006 

1. To estimate the level of seabird incidental capture in New Zealand fisheries. 

2. To recommend appropriate levels of observer coverage for estimation of 

seabird incidental capture in New Zealand fisheries. 

1. To estimate and report the total numbers of captures, releases, and deaths of 

Phocarctos hookeri caught in fishing operations, including separate estimates for 

SQU 6T and other areas, as appropriate, during the 2001102 fishing year, 

including confidence limits and an investigation of any statistical bias in the 

estimate. 

1. To estimate the level of Arctocephalus forsteri incidental capture in New 

Zealand fisheries. 


Arctocephalus forsteri incidental capture in New Zealand fisheries. 

Completed Baird 2004a; b; c; Smith & 

Baird 2008b 

Completed Baird 2005a; b; c; Baird & 

Doonan 2005 

Completed Smith & Baird 2008a; Baird 

2005d; e; f




ENV2000-01 Protected species bycatch 1. To estimate the total numbers of captures, releases, and deaths of seabirds 

and marine mammals - by species -caught in fishing operations during the 1999- 

2000 fishing year. 

ENV2000-02 Estimation of incidental 

mortality of New Zealand 

sea lions in New Zealand 

fisheries 

ENV99-01 Incidental capture of 

seabirds, marine 

mammals and sealions in 

commercial fisheries in 

New Zealand waters 

ENV98-01 Estimation of nonfish 

bycatch in commercial 

fisheries in New Zealand 

waters, 1997–98 

No project 

number 

Annual review of bycatch 

in southern bluefin and 

related tuna longline 

fisheries in the New 

Zealand 200 n. mile 

Exclusive Economic Zone 

SANF01 Report on the incidental 

capture of nonfish species 

during fishing operations 

in New Zealand waters 

No project 

number 

No project 

number 

No project 

number 

Nonfish Species and 

Fisheries Interactions 



Incidental catch of 

Hooker's sea lion in the 

southern trawl fishery for 

squid, summer 1994 

1. To examine the factors that may influence the level of incidental mortality of 

New Zealand sea lion in New Zealand fisheries 


incidental mortality of New Zealand sea lion in New Zealand sea lion fisheries 

335 

Completed Baird 2003 

Completed Doonan 2001; Bradford 

2002; Smith & Baird 2005a; b 

Objectives unknown Completed Baird 2001; Doonan 2000 

Objectives unknown Completed Baird 1999b; Baird & 

Bradford 1999 

Objectives unknown Completed Baird et al. 1998 

Objectives unknown Completed Baird 1997 



Objectives unknown Completed Doonan 1995




No project 

number 

No project 

number 

No project 

number 

Analyses of factors which 

influence seabird bycatch 

in the Japanese southern 

bluefin tuna longline 

fishery in New Zealand 

waters, 1989-93 



Incidental catch of fur 

seals in the west coast 

South Island hoki trawl 

fishery, 1989-92 

1. to assess the inhence that 15 monitored environmental and fishery related 

factors had on seabird bycatch rates, and to gauge the effectiveness of various 

mitigation measures 

336 

Completed Duckworth 1995 


Objectives unknown Completed Mattlin 1993


NON-PROTECTED BYCATCH 


No project 

number 

Incidental catch of non-fish 

species by setnets in New 

Zealand waters 

DAE2010-02 Bycatch monitoring & 

quantication for scampi 

bottom trawl 

ENV2009-02 Bycatch and discards in 

oreo and orange roughy 


IDG2009-01 Finfish field identification 

guide 

ENV2008-01 Fish and invertebrate 

bycatch and discards in 

southern blue whiting 

fisheries 

ENV2008-02 Estimation of non-target 

fish catch and both target 

and non-target fish 

discards in hoki, hake and 

ling trawl fisheries 

ENV2008-04 Productivity of deepwater 

sharks 

Objectives unknown Completed Taylor 1992 

1. To estimate the quantity of non-target fish species caught, and the target and 

non-target fish species discarded in the specified fishery, for the fishing years 

since the last review, using data from Ministry of Fisheries Observers and 

commercial fishing returns. 

2. To compare estimated rates and amounts of bycatch and discards from this 

study with previous projects on bycatch in the specified fishery. 

3. To compare any trends apparent in bycatch rates in the specifiedfishery with 

relevant fishery independent trawl surveys. 

4. To provide annual estimates of bycatch for nine Tier 1 species fisheries and 

incorporate into the Aquatic Environment and Biodiversity Report specified in 

Objective 3 for SQU, SCI, HAK, HOK, JMA, ORH, OEO, LIN, SBW 


non-target fish species discarded, in the trawl fisheries for oreos for the fishing 

years 2002/03 to 2008/09 using data from Scientific Observers and commercial 

fishing returns. 


non-target fish species discarded, in the trawl fisheries for orange roughy for the 

fishing years 2004/05 to 2008/09 using data from Scientific Observers and 


1. To complement the field identification guide under IDG2006/01 with the 

remaining 120 fish species caught by commercial fishers in New Zealand waters 


non-target fish species discarded, in the trawl fisheries for southern blue whiting 

for the fishing years 2002/03 to 2006/07 using data from Scientific Observers 

and commercial fishing returns. 

Estimates of the catch of non-target fish species, and the discards of target and 

non-target fish species in the hoki (Macruronus novaezelandiae), hake 

(Merluccius australis), and ling (Genypterus 

blacodes) trawl fisheries for the fishing years 2003–04 to 2006–07 using data 

from Scientific Observers and commercial fishing returns 

1. To determine the growth rate, age at maturity, longevity and natural mortality 

rate of shovelnose dogfish (Deania calcea) and leafscale gulper shark 

(Centrophorus squamosus). 

337 

Completed Anderson 2012 

Completed Anderson 2011 

Completed McMillan 2011 a;b;c 

Completed Anderson 2009b 

Completed Ballara et al. 2010 

In the process 

of publication 

Parker & Francis 2012


NON-PROTECTED BYCATCH continued 


ENV2007-03 Productivity and Trends in 

Rattail Bycatch Species 

DEE2006-03 Monitoring the abundance 

of deepwater sharks 

ENV2006-01 Bycatch and discards in 

ling longline fisheries 

IDG2006-01 Finfish field indentification 

guide 

TUN2006-02 Estimation of non-target 

fish catches in the tuna 

longline fishery 

TUN2004-01 Estimation of non-target 

fish catches in the tuna 




discards in jack mackerel 


1. To estimate growth, longevity, rate of natural mortality, and length at maturity 

of four key rattail bycatch species in New Zealand trawl fisheries. 

2. To examine data from trawl surveys and other data sources for trends in catch 

rates or indices of relative abundance for species in Objective 1. 

1. To monitor the abundance of deepwater sharks taken by commercial trawl 

fisheries 

To estimate the quantity of non-target fish species caught, and the target and 

non-target fish species discarded, in the longline fisheries for ling for the fishing 

years 1998/99 to 2005/06 using data from MFish Observers and commercial 

fishing returns. 

1. To produce a field guide for fish species in New Zealand 

2. To produce a field identification guide for all QMS and other fish species 

commonly caught in commercial and non-commercial fisheries 

1. To estimate the catches, catch rates, and discards of non-target fish in tuna 

longline fisheries data from the Observer Programme and commercial fishing 

returns for the 2005/06 fishing year. 

2. To describe bycatch trends in tuna longline fisheries using data from this 

project and the results of previous similar projects. 

To estimate the catch rates of non-target fish in the 10ngline fisheries for tuna 

using data from the Observer Programme and commercial fishing returns for the 

2002/03, 2003/04 and 2004/05 fishing years. 

2. To estimate the quantities of non-target fish caught in the longline fisheries for 

tuna using data from the Observer Programme and commercial fishing returns 

for the 2002/03, 2003/04 and 2004/05 fishing years. 

3. To estimate the discards of non-target fish caught in the longline fisheries for 

tuna using data from the Observer Programme and commercial fishing returns 

for the 2002/03, 2003/04 and 2004/05 fishing years. 

4. To describe trends in the non-target fish catches in the tuna longline fisheries 

using data from this project and the results of previous similar projects. 


non-target fish species discarded, in the trawl fisheries for jack mackerel for the 

fishing years 20011/2002 to 2004/05 using data from Mfish observers and 


338 

Completed Stevens et al. 2010 

Completed Blackwell 2010 


Completed McMillan 2011 a;b;c 

Completed Griggs et al. 2008 

Completed Griggs et al. 2007 

Completed Anderson 2007a







discards in orange roughy 



catches in the hoki fishery 




discards for the tuna 


ENV2001-04 Non-target fish catch and 

discards in selected New 


ENV2001-05 To assess the productivity 

and relative abundance of 

deepwater sharks 

ENV2001-07 Reducing bycatch in 

scampi trawl fisheries 





1. To estimate the catch rates, quantity and discards of non-target fish catches 

and the discards of target fish catches in trawl fisheries for hoki, using data from 

the Observer Programme and commercial fishing returns for the 1999/00 to 

2002/03 fishing years. 

2. To compare and contrast the estimates from the four years of data in Specific 

Objective 1 above with the 1990/91 through 1998/99 series previously reported. 

1.To estimate the catch rates, quantity and discards of non-target fish, 

particularly oceanic shark species, broadbill swordfish and marlin species, 

caught in the longline fisheries for tuna, using data from Scientific Observers and 

commercial fishing returns for the 2000/01 and 2001/02 fishing years. 

To generate estimates of the catch of non-target fish species, and the discards 

of target and non-target fish species in three important New Zealand trawl 

fisheries: arrow squid (Nototodarus sloani & N. gouldi), jack mackerel (Trachurus 

declivis, T. novaezelandiae, & T. symmetricus murphyi) and scampi 

(Metanephrops challengeri) 

1. To review the relative abundance, distribution and catch composition of the 

most commonly caught deepwater shark species: shovelnose dogfish (Deania 

catcea), Baxter's dogfish (Etmopterus baxten), Owston's dogfish 

(Cenhoscymnus owstoni), longnosed velvet dogfish (Centroscymnus crepidater), 

leafscale gulper shark (Cenhophom quamosus), and the seal shark (Dalatias 

ticha). 

1. Collate and review the international literature on methods of reducing bycatch 

in crustacean trawl fisheries. 

2. Review and analyse the data from New Zealand studies. 

3. Develop recommendations on future approaches to reducing bycatch in the 

New Zealand scampi fishery, including some general thoughts on the 

experimental design of field trials. 

339 

Completed Anderson 2009a 

Completed Anderson & Smith 2005 

Completed Ayers et al. 2004 


Completed Balckwell & Stevenson 2003 

Completed Hartill et al. 2006




PAT2000-01 Review of rattail and skate 

bycatch, and analysis of 

rattail standardised CPUE 

from the Ross Sea 

toothfish fishery in 

Subarea 88.1, from 1997- 

1998 to 2001-02 




discards in selected New 


ENV98-02 Pelagic shark bycatch in 

the New Zealand tuna 


No project 

number 

Fish bycatch in New 

Zealand tuna longline 

fisheries 

ENV97-01 Estimation of nonfish 

bycatch in New Zealand 

fisheries 

Objectives unknown Completed Feanaughty et al. 2003; 

Marriot et al. 2003 

1. To estimate the quantity of non-target fish species caught in the trawl fisheries 

for hoki and orange roughy for the fishing years 1990-91 to 1998-99 using data 

from Scientific Observers, commercial fishing returns and from research trawl 

surveys. 

2. To estimate the quantity of target and non-target fish species discarded in the 

trawl fisheries for hoki and orange roughy for the fishing years 1990-91 to 1998- 

99 using data from Scientific Observers, commercial fishing returns and from 

research trawl surveys. 

3. To explore the effects of various factors on the total catch of non-target fish 

species and the discards of target and non-target fish species in the trawl 

fisheries for hoki and orange roughy for the fishing years 1990-91 to 1998-99. 

4. To recommend appropriate levels of observer coverage for estimation of nontarget 

fish catch and discards of target and non-target fish species in the hoki 

and orange roughy fisheries. 

Completed Anderson et al. 2001 

To determine pelagic shark bycatch in the New Zealand tuna longline fishery Completed Francis et al. 2001 

Objectives unknown Completed Francis et al. 1999; 2000 

1. Unknown 

2. To provide weekly within season estimates of total captures, releases, and 

deaths by sex and area for New Zealand sea lions taken in the southern squid 

trawl fishery beginning two (2) weeks after the start of the fishery until 15 May 

1998. Estimates of the confidence intervals and coefficient of variation of the 

point estimates must also be provided. 

3. Unknown 

340 

Completed Doonan 1998; Baird 1999a; 

Baird et al. 1999




SCI97-01 Scampi stock assessment 

for 1998 and an analysis 

of the fish and invertebrate 

bycatch of 

scampi trawlers 

1. To summarise catch, effort, observer, and research information for scampi 

fisheries in QMAs 1,2,3,4 (east and western portions), and 6A in 1998 

341 

Completed Cryer et al. 1999


BENTHIC IMPACTS 


BEN2012-02 

Spatial overlap of mobile 

bottom fishing methods 

and coastal benthic 

habitats 

DAE2010-04 Monitoring the trawl 

footprint for deepwater 

fisheries 

DEE2010-06 Design a camera / transect 

study 

BEN2009-02 Monitoring recovery of 

benthic communities in 

Spirits Bay 

Internally 

funded 1 

Internally 

funded 2 

Internally 

funded 3 

Internally 

funded 4 

1. To use existing information and classifications to describe the distribution of 

benthic habitats throughout New Zealand’s coastal zone (0–200 m depth). 

2. To rank the vulnerability to fishing disturbance of habitat classes from 

Objective 1. 

3. To describe the spatial pattern of fishing using bottom trawls, Danish seine 

nets, and shellfish dredges and assess overlap with each of the habitat classes 

developed in Objective 1. 

1. To estimate the 2009/10 trawl footprint and map the spatial and temporal 

distribution of bottom contact trawling throughout the EEZ between 1989/90 and 

2009/10. 

2. To produce summary statistics, for major deepwater fisheries and the 

aggregate of all deepwater fisheries, of the spatial extent and frequency of 

fishing by year, by depth zone, by fishable area, and by habitat class, and to 

identify any trends or changes. 

1. To design and provide indicative costs for a programme to monitor trends in 

deepwater benthic habitats and communities. 

2. To explore the feasibility of using existing trawl and acoustic surveys to 

capture data relevant to monitoring trends in deepwater benthic habitats and 

communities. 

1. To survey Spirits Bay and Tom Bowling Bay benthic invertebrate communities 

according to the monitoring programme designed in ENV2005/23. 

2. To assess changes in benthic communities inside and outside the closed area 

since 1997. 

SPRFMO 1. To develop detection criteria for measuring trawl impacts on vulnerable marine 

ecosystems in high sea fisheries of the South Pacific Ocean 

SPRFMO 1. To document protection measures implemented by New Zealand for 

vulnerable marine ecosystems in the South Pacific Ocean 

CCAMLR 1. An Impact Assessment Framework for Bottom Fishing Methods in the 

CCAMLR Convention Area 

SPRFMO 1. to develop a bottom Fishery Impact Assessment: Bottom Fishing Activities by 

New Zealand Vessels Fishing in the High Seas in the SPRFMO Area during 

2008 and 2009 

342 

Approved but 


Ongoing 

analysis 

Ongoing 

analysis 



Black et al. In Press 

Tuck & Hewitt In Press 

Completed Parker et al. 2009a 

Completed Penney et al. 2009 

Completed Sharp et al. 2009 

Completed Ministry of Fisheries 2008


BENTHIC IMPACTS continued 


IFA2008-04 Guide for the rapid 

identification of material in 

the process of managing 

Vulnerable Marine 

Ecosystems 

IFA2007-02 Development of a Draft 

New Zealand High-Seas 

Bottom Trawling Benthic 

Assessment Standard 

BEN2007-01 Assessing the effects of 

fishing on soft sediment 

habitat, fauna, and 

processes 

BEN2006-01 Mapping the spatial and 

temporal extent of fishing 

in the EEZ 

To produce a guide for the rapid identification of material in the process of 

managing Vulnerable Marine Ecosystems 

1. To generate data summaries and maps of New Zealand’s recent historic highseas 

bottom trawling catch and effort in the proposed convention area of the 

South Pacific Regional Fisheries Management Organization (SPRFMO). 

2. To map vulnerable marine ecosystems (VMEs) in the SPRFMO area. 

3. To develop a draft standard for assessment of benthic impacts of high-seas 

bottom trawling on VMEs in the proposed SPRFMO convention area. 

1. To design and test sampling and analytical strategies for broad-scale 

assessments of habitat and faunal spatial structure and variation across a variety 

of seafloor habitats. 

2. To design and carry out experiments to assess the effects of bottom trawling 

and dredging on benthic communities and ecological processes important to the 

sustainability of fishing at scales of relevance to fishery managers. 

1. To update maps and develop GIS layers of fishing effort from project 

ENV2000/05 to show the spatial and temporal distribution of mobile bottom 

fishing throughout the EEZ between 1989/90 and 2004/05. 

2. To produce summary statistics of major fisheries and the aggregate of all 

bottom impacting fisheries in terms of the extent and frequency of fishing by 

year, by depth zone, by fishable area, and, to the extent possible, by habitat 

type. 

3. To identify and document any major trends or changes in fishing effort or 

fishing behaviour. 

4. To identify, discuss the implications of, and make recommendations on data 

quality and other problems with current reporting systems that complicate 

characterisation and quantification of bottom fishing effort. 

5. To integrate information on the distribution, frequency, and magnitude of 

fishing disturbance with habitat characteristics throughout the EEZ, using 

information stored in national databases, expert opinion, and the MEC. 

343 

Completed Tracey et al. 2008 

Completed Parker 2008 

Ongoing 

analysis 

Completed Baird et al. 2009; 2011; Baird 

& Wood 2010; Leathwick et 

al. 2010; 2012




ENV2005-15 Information for managing 

the Effects of Fishing on 

Physical Features of the 

Deep-sea Environment 

ENV2005-16 Investigate the Effects of 

Fishing on Physical 

Features of the Deep-sea 

Environment 




discards in jack mackerel 





discards in orange roughy 


1. To provide an updated database that identifies all known seamounts in the 

“New Zealand region”, encompassing the area from 24o00’ – 57o30’S, 157o00’E 

– 167o00’W. The database will catalogue relevant data (e.g. physical, biological, 

location, fishing effort) for individual seamounts. 

2. To identify indicators and measures suitable for the assessment of risk 

pertaining to the effects of fishing disturbance on the benthic biota of seamounts, 

and review suitable ecological risk assessment methods, that can be derived or 

utilise information contained within the seamount database. 

1. To monitor changes in fauna and habitats over time on selected UTFs in the 

Chatham Rise area that have a range of fishing histories. 

2. To continue development of the risk assessment model to predict the effects 

of fishing, and provide options for the management of UTF ecosystems. 


non-target fish species discarded, in the trawl fisheries for jack mackerel for the 

fishing years 20011/2002 to 2004/05 using data from Mfish observers and 






344 

Completed Rowden et al. 2008; Clark et 

al. 2010b 

Completed Clark et al. 2010a; b; c; 2011 

Completed Anderson 2007a 

Completed Anderson 2009a




ENV2005-20 Benthic invertebrate 

sampling and species 

identification in trawl 

fisheries 

ENV2005-23 Monitoring recovery of the 

benthic community 

between North Cape and 

Cape Reinga 

ZBD2005-04 Information on benthic 

impacts in support of the 

Foveaux Strait Oyster 

Fishery Plan 

1. To produce identification guides for benthic invertebrate species encountered 

in the catches of commercial and research trawlers. 

1. To design a monitoring programme that will provide the following quantitative 

estimates: 

i) Estimates of the nature and extent of past fishing impacts on the benthic 

community between North Cape and Cape Reinga; 

ii) Estimates of change over time in areas previously fished but subsequently 

closed to fishing. Estimated parameters will include indices representing 

biodiversity, community composition, and biogenic structure; 

iii) Estimates of change over time in areas environmentally comparable to those 

assessed in (ii), above, but subject to ongoing fishing impacts; and 

iv) Estimates of change over time in areas comparable to those above, but not 

impacted by fishing (if any such areas can be found). 

1. To assess the distribution- vulnerability to disturbance- and ecological 

importance of habitats in Foveaux Strait- and describe the spatial distribution of 

the Foveaux Strait oyster fishery relative to those habitats. 

2. To assemble and collate existing information on the Foveaux Strait system 

between the Solander Islands and Ruapuke Island or other area to be agreed 

with MFish. 

3. To map- using best available information- substrate type- bathymetry- wave 

energy- and tidal flow in this area. 

4. To assess the extent to which these data can be used to define useful 

functional categories that might serve as habitat classes. 

5. To rank the vulnerability to fishing disturbance of habitat classes developed in 

Objective 3 using approximate regeneration times. 

6. To describe the functional role and ecosystem services provided by each 

habitat class developed in Objective 3- including an assessment of the relative 

importance of each to overall ecosystem function and productivity. 

7. To describe the spatial pattern and intensity of dredge fishing for Foveaux 

Strait oysters over the past 10 fishing years and relate this to natural disturbance 

regimes and habitat classes developed in Objective 3. 

8. To carry out a qualitative video survey of benthic habitats in Foveaux Strait- 

both within the established commercial oyster fishery area and areas outside the 

fishery area but within OYU 5. 

345 

Completed Tracey et al. 2007; Williams 

et al. 2010; Clark et al. 2009 

Completed Tuck et al. 2010 

Completed Michael et al. 2006






Coromandel Scallops 

Fishery Plan 



Southern Blue Whiting 

Fishery Plan 

ENV2004-02 Estimation of New 



Fisheries 

ENV2003-03 Determining the spatial 

extent, nature and effect of 

mobile bottom fishing 

methods 

1. To assemble and collate existing information on the coromandel Scallop 

Fishery between cape Rodney and Town Point or other, wider area to be agreed 

with Mfish. 

2. To map, using best available information, substrate type, bathymetry, wave 

energy, and tidal flow in this area. 

3. To assess the extent to which data can be used to define useful functional 

categories that might serves as habitat classes. 

4. To rank the vulnerability of fishing disturbance of habitat classes developed in 



habitat class developed in Objective 3, including an assessment of the relative 


6. To describe the spatial pattern and intensity of dredge and trawl fishing within 

the Coromandel scallop fishery over the past 15 fishing years and relate this to 

natural disturbance regimes and habitat classes developed in Objective 3. 

1. To assemble and collate existing information on the Southern Blue Whiting 

fishery in SBW6A, SBW6B, SBW6I, and SBW6R or other wider area to be 

agreed with MFish 

2. To map, using best available information, substratum type, bathymetry, wave 

energy, tides, and ocean currents in these areas 

3. To assess the extent to which these data can be used to define useful 

functional categories that might serve as habitat categories. 

4. To rank the vulnerability to fishing disturbance of habitat classes developed in 



habitat class developed in Objective 3, including an assessment of the relative 


6. To describe the spatial pattern and intensity of trawl fishing within the 

Southern Blue Whiting fishery over the past 10 fishing years and relate this to 

natural disturbance regimes and habitat classes developed in Objective 3. 

1. To estimate the level of New Zealand sea lion (Phocartos hookeri) incidental 

capture in New Zealand fisheries 

1. To determine the spatial extent, nature and time between disturbances of 

mobile bottom fishing methods in the Chatham Rise trawl fisheries. 

346 

Completed Tuck et al. 2006a; b 

Completed Cole et al. 2007 

Completed Smith & Baird 2007a 

Completed Baird et al. 2006




ENV2002-04 Benthic invertebrate 

sampling and specific 


fisheries 

ENV2001-07 Reducing bycatch in 

scampi trawl fisheries 

ENV2001-09 The effects of mobile 

bottom fishing gear on 

bentho-pelagic coupling 

ENV2001-15 The effects of bottom 

impacting trawling on 

seamounts 

OYS2001-01 Foveaux Strait oyster 

stock assessment 

ENV2000-05 Spatial extent, nature and 

impact of mobile bottom 

fishing methods in the 

New Zealand EEZ 

ENV2000-06 Review of technologies 

and practices to reduce 

bottom trawl bycatch and 

seafloor disturbance in 


1. To quantify and map the benthic invertebrate species incidental catch in 

commercial and research trawling throughout the New Zealand EEZ 

1. Collate and review the international literature on methods of reducing bycatch 

in crustacean trawl fisheries. 

2. Review and analyse the data from New Zealand studies. 

3. Develop recommendations on future approaches to reducing bycatch in the 

New Zealand scampi fishery, including some general thoughts on the 

experimental design of field trials. 

To describe any effects of fishing that might modify bentho-pelagic coupling (a 

complex, interlinked suite of processes transferring energy, oxygen, carbon, and 

nutrients between pelagic and benthic systems), to consider the scale of such 

possible effects, and to put the summary in a New Zealand context. 

1. To design a programme in New Zealand waters previously trawled and now 

closed to trawling to monitor the rate of regeneration of benthic communities on 

seamounts. 

1. To carry out a survey and determine the distribution and absolute abundance 

of pre-recruit and recruited oysters in both non-commercial and commercial 

areas of Foveaux Strait. The target coefficient of variation (c.v.) of the estimate 

of absolute recruited abundance is 20%. 

2. To estimate the sustainable yield for the areas of the commercial oyster 

fishery in Foveaux Strait for the year 2002 oyster season. 

3. To identify and count benthic macro-biota collected during the dredge survey. 

1. To determine the spatial extent, nature and impact of mobile bottom fishing 

methods within the New Zealand EEZ. 

347 

Completed Tracey et al. 2005 

Completed Hartill et al. 2006 

Completed Cryer et al. 2004 

Completed Clark & O'Driscoll 2003; 

Clark & Rowden 2009 

Completed Rowden et al. 2007 

Completed Cryer and Hartill 2002; Baird 

et al. 2002 

Objectives unknown Completed Booth et al. 2002; Beentjes 

& Baird 2004




ENV98-05 The effects of fishing on 

the benthic community 

structure between North 

Cape and Cape Reinga 

1. To determine the effects of fishing on the benthic community structure 

between North Cape and Cape Reinga. 

348 

Completed Cryer et al. 2000


ECOSYSTEM EFFECTS 


ENV2012-01 A literature review of 

Nitrogen levels and 

adverse ecological effects 

in embayments in 

temperate regions. 

ZBD2012-06 Ocean status: trends in NZ 

marine environment and 

Tier 1 statistic 

1. To complete a literature review of Nitrogen levels and adverse ecological 

impacts from temperate embayments in order to assist aquaculture consenting 

authorities in determining at what concentration of Nitrogen adverse effects may 

be expected. 

1. To provide an up to date overview of climatic trends and cycles and how they 

affect New Zealand oceanographic conditions, and highlight key changes since 

the previous assessment. 

2. To identify candidate oceanographic variables for potential development as 

part of the proposed Tier 1 Statistic, Atmospheric and Ocean Climate Change 

ANT2011-01 Antarctic fisheries 1. To develop, implement and refine approaches for assessing the stock status 

of toothfish (Dissostichus spp.) in the Ross Sea region. 

2. To develop, implement and refine approaches for assessing and monitoring 

the status of non-target fish species, and dependent and related species. 

3. To develop, implement and refine approaches for understanding and 

managing the ecological relationships between the toothfish (Dissostichus spp.) 

fishery and the Ross Sea ecosystem. 

DAE2010-01 Taxonomic identification of 

benthic specimens 

DAE2010-03 Ecological risk 

assessment for deepwater 

stocks 

DEE2010-04 Development of a 

methodology for 

Environmental Risk 

Assessments for 

deepwater fisheries 

DEE2010-05 Development of a suite of 

environmental indicators 

for deepwater fisheries 

ENV2010-03 Habitats of particular 

significance for inshore 

finfish fisheries 

management 

1. To identify benthic invertebrates in samples taken during research trawls and 

by Observers on fishing vessels. 

2. To update relevant databases recording the catch of invertebrates in research 

trawls and commercial fishing. 

1. To undertake a qualitative (level 1) risk assessment for tier 3 fishstocks within 

the deepwater fisheries plan. 

To review approaches to Ecological Risk Assessments (ERA) and methods 

available for deepwater fisheries both QMS and non-QMS. 

2. To develop and recommend a generic, cost effective, method for ERA in 

deepwater fisheries by using or modifying methods identified in Objective 1. 

1. To review the literature and hold a workshop to recommend a suite of 

ecosystem and environmental indicators that will contribute to assessing the 

performance of deepwater fisheries within an environmental context. 

2. To examine available data and design a data collection programme to enable 

future calculation of the indicators identified in Specific Objective 1. 

1. To review the literature to determine the most important juvenile or 

reproductive (spawning, pupping or egg-laying) areas for inshore finfish target 

species. 

2. To use a gap analysis to prioritize areas for future research concerning the 

important juvenile or reproductive (spawning, pupping or egg-laying) areas for 

target inshore finfish fisheries 

349 

Approved but 


Approved but 


Ongoing 

analysis 

Ongoing 

analysis 

Ongoing 

analysis 

Completed Clark et al. In Press 

Ongoing 

analysis 

Ongoing 

analysis


ECOSYSTEM EFFECTS continued 


ENV2010- 

05A&B and 

SEA 2010-15 

Habitats of particular 

significance for fisheries 

management: shark 

nursery areas 

ZBD2010-42 Development of a National 

Marine Environment 

Monitoring Programme 

1. Identify, from the literature, important nursery grounds for rig in estuaries 

around mainland New Zealand. 

2. Design and carry out a survey of selected estuaries and harbours around New 

Zealand to quantify the relative importance of nursery ground areas. 

3. Identify threats to these nursery ground areas and recommend mitigation 

measures. 

1. To design a Marine Evnironment Monitoring Programme (MEMP) to track the 

physical, chemical and biological changes taking place across New Zealand's 

marine environment over the long term 

2. To prepare an online inventory (metadatabase) of repeated (time series) 

biological and abiotic marine observations/datasets in New Zealand 

3. To review, evaluate fitness for purpose, and identify gaps in the utility and 

interoperability of these datasets for inclusion in MEMP from both science and 

policy perspectives 

4. To design a MEMP that includes relevant existing data collection and 

proposed new time series 

ANT2009-01 Antarctic fisheries 1. To explore the biology of fishes captured in the toothfish fishery to underpin 

future stock assessment and ecosystem modelling research 

2. To develop and refine stock assessment approaches for toothfish in the Ross 

Sea 

3. To assess the status of toothfish stocks in the Ross Sea 

4. To explore the Ross Sea toothfish fishery at an ecosystem level 

5. To review and further develop procedures for the ageing of Antarctic toothfish 

(Dissostichus mawsoni) and Patagonian toothfish (D. eleginoides). 

6. To review and update the species profiles for toothfish 

7. To characterise the toothfish fishery in the Ross Sea up to 2009/10 

8. To further develop toothfish biological and modelling parameters 

9. To assess the status of the Ross Sea toothfish stock(s) with respect to 

CCAMLR performance measures 

10. To further develop approaches to assessing the status of skates in the Ross 

Sea region with respect to CCAMLR performance measures 

11. Further develop the SPM approach 

12. To develop new approaches and refine existing approaches to understanding 

the impacts of fishing on potential VMEs 

13. To further develop ecosystem monitoring through the analysis of the diet of 

toothfish in the north and slope fisheries. 

14. To refine the draft data collection plan for the Ross Sea region fisheries and 

undertake associated preliminary reviews of fishery and observer performance 

against targets immediately post-season 

350 



Ongoing 

analysis 

Francis et al. 2012; Jones et 

al. In Press 

Completed Parker & Bowden 2010; 

Parker et al. 2009c; Tracey 

et al. 2010




ENV2009-04 Trends in relative 

mesopelagic biomass 

using time series of 

acoustic backscatter data 

from trawl surveys 

ENV2009-07 Habitats of particular 

significance for 

fisheriesmanagement: 

kaipara harbour 

GMU2009-01 Spatial Mixing of GMU1 

using Otolith 

Microchemistry 

IPA2009-11 Trophic studies publication 

of review 

ANT2008-03 Ecosystem effects of 

fishing in the Ross Sea 

AQE2008-02 Review of ecological 

effects of farming shellfish 

and other species 

1. To evaluate relative changes in abundance of mesopelagic fish and other 

biological components from acoustic records collected during Chatham Rise and 

Sub-Antarctic trawl surveys. 

2. To explore links between trends in mesopelagic biomass and climate variables 

and variations, and condition indices of commercial species in the Chatham Rise 

and Sub-Antarctic areas. 

1. Collate and review information on the role and spatial distribution of habitats in 

the Kaipara Harbour that support fisheries production. 

2. Assess historical, current, and potential anthropogenic threats to these 

habitats that could affect fisheries values, including fishing and land-based 

threats. 

3. Design and implement cost-effective habitat mapping and monitoring surveys 

of habitats of particular significance for fisheries management in the Kaipara 

Harbour. 

1. To determine the level of spatial mixing and connectivity of grey mullet (Mugil 

cephalus) populations using otolith microchemistry. 

2. To collect and analyse the chemical composition of grey mullet otoliths. 

3. To analyse the otoliths collected under Objective 1 to determine if the samples 

can be spatially separated. 

1. To publish the comprehensive review of New Zealand-wide trophic studies 

completed in 2000 that was prepared by NIWA. 

To evaluate the VMEIO classification accuracy of observers, identify potential 

causes for taxonomic confusion, and make recommendations for improvements 

in the classification guide, observer training, and in the data collection protocols 

1. To collate and review information on the ecological effects of farming mussels 

(Perna canaliculus), including offshore mussel farming and spat catching, in the 

New Zealand marine environment. 

2. To collate and review information on the ecological effects of farming oysters 

in the New Zealand marine environment. 

3. To collate and review information on the ecological effects of farming species 

other than mussels (Perna canaliculus), oysters, and finfish, in the New Zealand 

marine environment. 

351 

Completed O'Driscoll et al. 2011 

Ongoing 

analysis 

Ongoing 

analysis 

Completed Stevens et al. 2011 

Completed Parker et al. 2009b; 2010 

Completed Keeley et al. 2009




TOH2008-01 Distribution and 

abundance of Toheroa 

IFA2008-08 Inputs to the Ross Sea 

bioregionalisation 

ANT2007-01 Biology of fishes in the 

toothfish fishery 

BEN2007-01 Assessing the effects of 

fishing on soft sediment 

habitat, fauna, and 

processes 

BEN2007-05 Risk assessment 

framework for assessing 

fishing &other 

anthropogenic effects on 

coastal fisheries 

ENH2007-01 Stock enhancement of 

blackfoot paua 

1. To estimate the size structure and absolute abundance of toheroa on Oreti 

Beach, during February 2009. The target c.v. for the estimate of absolute 

abundance of legal sized toheroa ( 100 mm shell length) is 20%. 

2. To describe changes in the size structure and absolute abundance of toheroa 

on Oreti Beach by comparing the results from this work with those from previous 

surveys. 

3. To estimate the size structure and absolute abundance of toheroa on 

Bluecliffs Beach, during February 2009. The target c.v. for the estimate of 

absolute abundance of legal sized toheroa ( 100 mm shell length) is 20%. 

4. To describe changes in the size structure and absolute abundance of toheroa 

on Bluecliffs Beach by comparing the results from this work with those from 

previous surveys. 

1. To produce one or more benthic invertebrate classifications of the Ross Sea 

region; 

2. To use fishery catch data to examine spatial distributions of major demersal 

fish species; 

3. To prepare other biological or environmental spatial data layers for use in the 

Ross Sea workshop. 

3. To develop an identification guide for observers of benthic invertebrate 

species (especially sponges, corals etc) caught in the Ross Sea region fisheries. 

1. To design and test sampling and analytical strategies for broad-scale 

assessments of habitat and faunal spatial structure and variation across a variety 

of seafloor habitats. 

2. To design and carry out experiments to assess the effects of bottom trawling 

and dredging on benthic communities and ecological processes important to the 

sustainability of fishing at scales of relevance to fishery managers. 

1. To collate existing information on the distribution, intensity, and frequency of 

anthropogenic disturbances in the coastal zone that could be used in a risk 

assessment model to estimate their likely aggregate effect on ecosystem 

function across habitats and over different scales of ecosystem functioning and 

biological organization. 

2. To develop a risk assessment framework in conjunction with a variety of 

stakeholders and environmental scientists. 

1. To assess the survival rate of enhanced paua from introduction into the wild 

through to harvest. 

2. To assess the genetic diversity of hatchery spawned juvenile paua bred for 

enhancement purposes. 

3. To assess interactions between introduced and wild paua populations and to 

recommend research and monitoring to quantify those impacts that are 

potentially adverse. 

352 

Completed Beentjes 2010 

Completed Pinkerton et al. 2009a 

Completed Parker et al. 2008 

Ongoing 

analysis 

Completed MacDiarmid et al. 2012 

Ongoing 

analysis




ENV2007-04 Climate and 

Oceanographic Trends 

Relevant to New Zealand 

Fisheries 

ENV2007-06 Trophic Relationships of 

Commercial Middle Depth 

Species on the Chatham 

Rise 

HAB2007-01 Biogenic habitats as areas 

of particular significance 

for fisheries management 

1. To summarise, for fisheries managers, climatic and oceanographic 

fluctuations and cycles that affect productivity, fish distribution and fish 

abundance in New Zealand. 

1. To quantify the inter-annual variability in the diets of hoki, hake and ling on the 

Chatham Rise 1992–2007 

2.To quantify seasonal dietary cycles for hoki, hake and ling that have been 

collected from the commercial fleet throughout the year 

1. To collate and review available information on the location, value, functioning, 

threats to, and past and current status of biogenic habitats that may be important 

for fisheries production in the New Zealand marine environment. 

2. To identify information gaps, in the New Zealand context, and recommend 

measures to address those important to an ecosystem approach to fisheries 

management 

1. To review and collate scientific knowledge and research on the impacts of 

IPA2007-07 Land Based Effects on 

Costal Fisheries 

land-based activities on coastal fisheries and biodiversity 

TOH2007-03 Toheroa Abundance 1. To investigate variations in the abundance of toheroa. 

2. To investigate sources of mortality of toheroa and factors affecting the 

recruitment of toheroa 

ENV2006-04 Ecosystem indicators for 1. To carry out a literature review of potential fish-based ecosystem indicators 

New Zealand fisheries and identify a suite of indicators to be tested in Objective 2 

2. To test a suite of fish-based ecosystem indicators (identified by Objective 1) 

on existing trawl survey time series in New Zealand. The utility of these 

indicators for monitoring the effects of fishing in New Zealand should also be 

evaluated 

GBD2006-01 DNA database for 

1. To collect DNA sequences for vouchered specimens of commercially 

commercial marine fish important marine fishes and submit the DNA data to the international Barcode of 

and invertebrates 

Life Database (BOLD). 

2. To collect DNA sequences for vouchered specimens of commercially 

important marine invertebrates and submit the DNA data to the international 

Barcode of Life Database (BOLD). 

Note: The funding was limited to $60 000 for this Objective. Therefore MFish 

agreed to omit the invertebrate species (Objective 2) from this project and 

reduce the number of fish species sequenced from 100 to 80 (up to 5 specimens 

per species). During the course of the project MFish staff asked NIWA to identify 

smoked eel product, suspect shark fillets, and possible paua slime with DNA 

markers, consequently the project was modified to accommodate these requests 

353 

Completed Hurst et al. 2012 

Completed Horn & Dunn 2010 

Ongoing 

analysis 

Completed Morrisson et al. 2009 

Ongoing 

analysis 

Williams et al. In Press 

Completed Tuck et al. 2009 

Completed No reports specified as 

required output




SAP2006-06 West coast south island 

review 

IPA2006-08 Review of the Ecological 

Effects of Marine Finfish 

aquaculture: Final Report 

ANT2005-02 Aspects of the biology of 

fishes in the toothfish 

fishery 

ANT2005-04 Ecosystem modelling of 

the Ross Sea 

ENV2005-08 Experimental design of a 

programme of indicators 

SAM2005-02 Effects of climate on 

commercial fish 

abundance 

1. To publish a review document summarising oceanic and environmental 

research information particularly relevant to hoki- but also other fisheries- that 

spawn off Westland in winter 

2. Update the draft chapters prepared in 2004 by oceanographers- modellers 

and scientists towards the overall objective 

3. Incorporate a section on other west coast spawning fisheries 

1. Summarise and review existing information on ecological effects of finfish 

farming on the marine environment in New Zealand and overseas 

1. Estimate length and age at maturity for Antarctic toothfish in the Ross Sea 

2. Examine TOA length at age by depth and area 

3. Estimate biological parameters for TOA (M, growth rates corrected for 

selectivity, h, r) 

4. Determine stock structure of TOA based on parasite data 

5. Determine length-weight relationships, diet, reproduction, age and growth of 

C.dewitti 

6. ID and speciation of Antarctic skates 

7. Develop an ID guide for scientific Observers of fish in the Ross Sea fishery 

8. Identify heavy metal contents of selected fish species in the Ross Sea fishery 

1. Carry out stable isotope analysis of TOA and 3 key fish prey to determine 

trophic links 

2. Determine squid diet by analysis of squid beaks for stable isotope analysis 

3. Participate in the design of an IPY survey 

4. Participate in EMM as required 

1. To assess the utility/feasibility of using demographic information to assess the 

effects of 

fishing on seabird populations. 

2. To identify population indicators and to provide sampling protocols and 

experimental 

design for selected high to medium priority seabird populations. 

3. To recommend experimental protocols for sampling of selected seabird 

populations in New Zealand 

influenced by fisheries mortality, employing robust-design methodology and 

including 

recommendations for inclusions of data into Ministry of Fisheries databases. 

To examine the possible effects of climate on fishery yields and abundance 

indices for commercial fisheries around New Zealand 

354 

Completed Bradford-Grieve & Livingston 

2011 

Completed Forrest et al. 2007 

Completed McMillan et al. 2007; Smith 

et al. 2007; Sutton et al. 2006 

Completed Pinkerton et al. 2007b 

Completed MacKenzie & Fletcher 2010 

Completed Dunn et al. 2009




ANT2004-01 Characterisation of the 

toothfish fishery 

ANT2004-05 Modelling of the 

ecosystem effects of 

fishing in the Ross Sea 

HOK2004-01 Hoki Population modelling 

and stock assessment 

AQE2003-01 Effects of aquaculture and 

enhancement stock 

sources on wild fisheries 

resources and the marine 

environment. 

EEL2003-01 Non-fishing mortality of 

freshwater eels 

MOF2003-01 The implications of marine 

reserves for fisheries 

resources and 

management in the New 

Zealand context 

ENV2002-03 Beach cast seaweed 

review 

1. update descriptive analysis of toothfish fishery in the Ross Sea to 04/05 

2. analyse age, LF and sex ratio for toothfish and rattails for 04/05 

3. update and refine the CPUE for TOA in Ross Sea for 04/05 

4. determine diet of sub-adult TOA in the Ross Sea 

5. review the TOA parasite collection protocol 

6. document TOA tagging protocol 

7. review approaches to monitoring and assessing rattails and skates in the Ross 

Sea 

8. descriptive analysis of stake tagging programme in the Ross Sea 

9. determine factors affecting bycatch of rattails and skates between vessels 

10. carry out risk assessment for M. whitsoni and A. georgina in the Ross Sea 

1. develop an effects of fishing model based around toothfish fishery 

2. investigate possible consequences of different management strategies 

3. make recommendations for future research to decrease uncertainty in the 

model 

2. To investigate the prediction of year class strength from environmental 

variables. 

355 

Completed Smith & Notman 2005; 

Stevens 2006 

Completed Pinkerton et al. 2005; 2006 

Completed Francis et al. 2005 

1. To identify, discuss the effects and qualitatively assess the risks of 

aquaculture and enhancement stocks improved by hatchery technology on New 

Zealand’s wild fisheries resources and the marine environment. 

2. To identify, discuss the effects and qualitatively assess the risks associated 

with the translocation of aquaculture and enhancement stocks on New Zealand’s 

wild fisheries resources and the marine environment. 

3. To make recommendations on priority issues, risks, or research to be 

undertaken, as a result of information discussed and evaluated in objectives 1-2. 

Completed Speed 2005 

1. To undertake a feasibility study on establishing an estimate of the mortality of 

eels caused by hydroelectric turbines and other point sources of mortality caused 

by human activity. 

Completed Bentjees et al. 2005 

Objectives unknown Completed Speed et al. 2006 

1. To collate existing information on the role of beach-cast seaweed in coastal 

ecosystems to assess the nature and extent of the impacts that the removal of 

beach cast seaweed may have on the marine environment. 

2. On the basis of the review in Specific Objective 1 above, to identify key 

research gaps related to any marine environment impacts that the removal of 

beach cast seaweed may have. 

Completed Zemke-White et al. 2005




ENV2002-07 Energetics and trophic 

relationships of important 

fish and invertebrate 

species 

CRA2000-01 Rock lobster stock 

assessment 

ENV2000-04 Identification of areas of 

habitat of particular 


management within the 

New Zealand EEZ 

MOF2000- 

02A 

Future research 

requirements for the Ross 

Sea Antarctic toothfish 

(Dissostichus mawsoni) 

fishery. 

ENV99-03 Identification of areas of 

habitat of particular 


management within the 

NZ EEZ. 

ENV99-04 A framework for evaluating 

spatial closures as a 

fisheries management tool 

No project 

number 

The fishery for freshwater 

eels (Anguilla spp.) in New 


1. To quantify food webs supporting important fish and invertebrate species Completed Livingston 2004 

Objective 11: To conduct a desktop study to identifi and explore data needs 

associated with 

managing the effects of rock lobsterfishing on the environment. 

Completed Breen 2005 

1. To review literature and existing data for all significant fish species, including 

all QMS species, encountered from the 200 1500 m contour within the New 

Zealand EEZ to: 

a) determine areas of important juvenile fish habitat; 

b) determine areas of importance to spawning fish populations; and 

c) determine areas of importance for shark populations for pupping or egg laying. 

2. To review literature and existing data for all significant pelagic fish species 

(excluding highly migratory species) encountered within the New Zealand EEZ 

to: 

a) determine areas of important juvenile fish habitat; 

b) determine areas of importance to spawning fish populations; and 

c) determine areas of importance for shark populations for pupping or egg laying 

3. To review literature and existing data for all significant marine invertebrate 

species encountered within the New Zealand EEZ to: 

a) determine areas of important juvenile habitat; and 

b) determine areas of importance to spawning populations 

Completed O'Driscoll et al. 2003 

Objectives unknown Completed Hanchet 2000 

1. To determine areas of habitat of importance to fisheries management within 

the New Zealand EEZ for selected fish species in selected areas 

356 

Completed Hurst et al. 2000 

Unknown Completed Bentley et al. 2004 

Objectives unknown Completed Jellyman 1994


BIODIVERSITY 


SRP2011-02 IDG 2009-01 field guide 

completion 

ZBD2010-39 Improved benthic 

invertebrate species 


fisheries 

ZBD2010-40 Predictive modelling of the 

distribution of vulnerable 

marine ecosystems in the 

South Pacific Ocean 

region. 

ZBD2010-41 Ocean acidification in 

fisheries habitat 

IPA2009-14 Bryozoan identificaiton 

guides 

ZBD2009-03 To evaluate the 

vulnerability of New 

Zealand rhodolith species 

to environmental stressors 

and to characterise 

diversity of rhodolith beds. 

1. IDG 2009-01 field guide completion Completed McMillan 2011 a;b;c 

1. To revise and update the document “A guide to common deepsea 

invertebrates in New Zealand waters (second edition)” to allow a third edition of 

this guide to be printed 

1. To develop & test spatial habitat modelling approaches for predicting 

distribution patterns of vulnerable marine ecosystmes in the convention Area of 

the South Pacific Regional Fisheries Management Organisation with agreed 

international partners. 

2. To collate datasets and evaluate modelling approaches which are likely to be 

useful to predict the distribtuion of vulnerable marine ecosystmes in the South 

pacific Ocean region. 

1. To assess the risks of ocean acidification to deep sea corals and deepwater 

fishery habitat 

2. To determine the carbonate mineralogy of selected deep sea corals found in 

the New Zealand region 

3. To assess the distribution of deep sea coral species in the New Zealand 

region relative to improved knowledge of current and predicted aragonite and 

calcite saturation horizons, assessment of potential locations vulnerable to deep 

water upwelling 

4. Through a literature search and analysis, determine the most appropriate tools 

to age and measure the effects of ocean acidification on deep sea habitatforming 

corals, and recommend the best approach for future assessments of the 

direct effects 

1. For each of ~50 species of common bryozoans, provide photos and text to 

allow for identification. Provide information on distribution and habitat (as far as 

is known) and further references for each species and on bryozoans as a whole. 

2. Submit these data for publication in the Ministry of Fisheries series New 

Zealand Aquatic Environment and Biodiversity Research. 

1. To characterise the distribution and physical characteristics of two New 

Zealand rhodolith beds and characterise the associated biodiversity. 

2. To measure the growth rates and evaluate the vulnerability of New Zealand 

species of rhodoliths to environmental stressors. 

357 

Completed Tracey et al. 2011a 

Ongoing 

analysis 

Ongoing 

analysis 

Tracey et al. 2011b 

Completed Smith & Gordon 2011 

Completed Nelson et al. 2012


BIODIVERSITY continued 


ZBD2009-10 Multi-species analysis of 

coastal marine 

connectivity 

ZBD2009-13 Ocean acidification impact 

on key nz molluscs 

ZBD2009-25 Predicting impacts of 

increasing rates of 

disturbance on functional 

diversity in marine benthic 

ecosystems 

1. Determine overall patterns of regional connectivity in a broad range of NZ 

coastal marine organisms to define the geographic units of genetic diversity for 

protection and the dispersal processes that maintain this diversity. 

2. Review previous studies of marine connectivity and population genetics in NZ 

coastal organisms to determine the preliminary range of patterns observed and 

the principal gaps (taxonomic geographic and ecological) in our understanding. 

3. In a range of invertebrate and vertebrate marine organisms determine 

geographic patterns of genetic variation using standardised sampling and 

molecular techniques. 

4. Analyse data across past and present studies to reveal both common and 

unique patterns of connectivity around the NZ coastline and the locations of 

common barriers to dispersal. 

1. Controlled laboratory experiments will be used to determine the effect of pCO2 

levels that are predicted to occur in NZ waters over the next few decades on 

appropriate life history stages of at least two key NZ mollusc species. A number 

of response variables will be assessed. 

2. Implications of these responses to the local and broader ecosystems will be 

assessed. 

1. Further develop the landscape ecological model of disturbance/recovery 

dynamics in marine benthic communities, incorporating habitat connectivity, 

based on existing model by Lundquist, Thrush, and Hewitt. 

2. Predict impacts of increasing rates of disturbance on rare species abundance, 

functional diversity, relative importance of biogenic habitat structure, and 

ecosystem productivity. 

3. Use literature and expert knowledge to quantify rare species abundance, 

biomass, functional diversity, habitat structure, and productivity of various 

successional community types in the model. 

4.Field test predictions of the model in appropriate marine benthic communities 

where historical rates of disturbance are known, and benthic communities have 

been sampled. 

358 

Completed Gardner et al. 2010 

Ongoing 

analysis 

Ongoing 

analysis 

Cummings 2011; Cummings 

et al. 2011b 

Lundquist et al. 2010




ZBD2008-01 Biogenic large–habitat– 

former hotspots in the 

near-shore coastal zone 

(50–250 m); quantifying 

their location, identity, 

function, threats and 

protection 

ZBD2008-05 Macroalgal diversity 

associated with soft 

sediment habitats 

ZBD2008-07 Carbonate sediments: the 

positive and negative 

effects of land-coast 

interactions on functional 

diversity 

1. To collect and integrate existing knowledge on biogenic habitat-formers in the 




ZBD2008-11 Predicting changes in 

plankton biodiversity and 

productivity of the EEZ in 

response to climate 

change induced ocean 

acidification 

ZBD2008-14 What and where should 

we monitor to detect longterm 

marine biodiversity 

and environmental 

changes-remote sensing, 

biota, context, inshore 

offshore workshop 

1. To document the spatial and inter-annual variability of coccolithophore 

abundance and biomass- and assess in terms of the phytoplankton abundancebiomass 

and community composition in sub-tropical and sub-Antarctic water. 

2. To document the seasonal and inter-annual variability of foraminifera and 

pteropod abundance and biomass at fixed locations in sub-tropical and sub- 

Antarctic water by analysis of sediment trap material from time-series data 

collection. 

3. To document the spatial and seasonal distribution of the key coccolithophore 

species- Emiliana huxleyi- using both archived and ongoing ingestion of satellite 

images of Ocean Colour- and ground-truth the reflectance. 

4. To determine the sensitivity of- and response of E. huxleyi and other EEZ 

coccolithophores to pH under a range of realistic atmospheric CO2 

concentrations in perturbation experiments- using monocultures and mixed 

populations from in situ sampling. 

5. To document the spatial variability of diazotrophs (nitrogen-fixing organisms) 

and associated nitrogen fixation rate- and assess in terms of phytoplankton 

abundancebiomass and community composition in sub-tropical waters north of 

the STF. 

7. To determine the sensitivity of- and response of Trichodesmium spp. and 

other diazotrophs to pH under a range of realistic atmospheric CO2 

concentrations in perturbation experiments using monocultures 

1. Identify the key questions to be addressed by long-term monitoring of marine 

biodiversity and environment. 

2. Identify appropriate monitoring indices, how they should be spatially 

distributed and their sampling frequency. 

3. Identify relevant existing monitoring programmes across the range of New 

Zealand agencies and science providers and identify gaps. 

4. Provide those agencies setting environmental goals/ standards or research 

needs (MoRST, FRST, MFish, DoC, MfE, Commissioner for the Environment) 

with a thorough situational analysis, including a list of priority monitoring 

projects/plans. 

360 

Ongoing 

analysis 

Ongoing 

analysis 

Law et al. 2012: Boyd & Law 

2011 

Livingston 2009




ZBD2008-15 Continuous plankton 

recorder project: 

implementation and 

identification 

ZBD2008-20 Ross sea benthic 

ecosystem function: 

predicting consequences 

of shifts in food supply 

ZBD2008-22 Acidification and 

ecosystem impacts in NZ 

and southern ocean 

waters (data collected 

during IPY). 

ZBD2008-23 Macroalgae diversty and 

benthic community 

structure at the Balleny 


1. To set up a time series of annual CPR data collection by deployment from a 

toothfish vessel on the annual summer transit between New Zealand and the 

Ross Sea. 

2. To identify phytoplankton and zooplankton according to strict observation 

protocols determined by the SAHFOS[1] CPR Survey and SO-CPR[2]. 

3. To enter species data, frequency and location along the transect into a 

spreadsheet that will allow spatial mapping of the plankton density and 

distribution. 

4. To analyse the full dataset after 5 years of data collection to: (a) determine 

trends in the dataset and (b) compare results with Australian datasets available 

through SO-CPR. 

5. To evaluate the continuation of the programme 

1. To increase understanding of Ross Sea coastal benthic ecosystem function 

2. Conduct in situ investigations into responses to and utilisation of primary food 

sources by key species, at two contrasting coastal Ross Sea locations 

1. To assess the response of cocolithophorids, and their replacement by noncalcifying 

organisms during incubation under a range of dissolved CO2 

concentrations. 

2. To describe and characterise changes in abundance and biodiversity of 

microbial components of the samples incubated at sea under a range of 

dissolved CO2 concentrations. 

3.To predict the likely impacts of higher acidity on foodwebs and on carbon 

fixation under scenarios to be encountered in the Southern Ocean under 

forecasted trends associated with climate change. 

1. To describe and characterise macroalgae diversity from the Balleny Islands 

and the Western Ross Sea. 

2. To describe and quantify benthic community structure from one location at the 

Balleny Islands 

3. To complete anatomical and morphological investigations & molecular 

sequencing required for the identification of macroalgae samples from the 

Balleny Islands & western Ross Sea coastline to describe & characterise 

macroalgae diversity in Balleny Isds 

4. To process and analyse samples collected at the Balleny Islands- to analyse 

them using ICECUBE methodology- and compare results with those from other 

ICECUBE sampling locations along the Ross Sea coastline 

361 

Ongoing 

analysis 

Completed Cummings & Lohrer 2011; 

Cummings et al. 2011a; 

Lohrer et al. 2012 

Completed Maas et al. 2010b 

Completed Nelson et al. 2010




ZBD2008-27 Scoping investigation into 

New Zealand abyss and 

trench biodiversity 

ZBD2008-50 OS2020 Chatham Rise 

Biodiversity Hotspots 

IPY2007-02 International polar year 

census of antarctic marine 

life post-voyage 

analysis:Ross Sea - 

Southern Ocean 

Biodiversity 

1. Review what is already known of abyssal, canyon and trench faunas in NZ. 

2. Review what is already known of abyssal, canyon and trench faunas around 

the world. 

3. Prioritise science questions and locations for exploration. 

4. Assess NZ capacity to sample at the required depths; identify sampling 

equipment needs. 

5. Design a suitable vessel-based sampling programme 

1. To improve understanding of the effects of trawl fishing in New Zealand on the 

biodiversity of seamounts- knolls and hills. 

2. To describe differences in benthic biodiversity between northwestern and 

eastern regions of the Chatham Rise 

3. To continue the time series of observations in the NW Chatham Rise to 

demonstrate recovery in terms of biodiversity 

4. To extend the observations on fished-unfished contrasts and recovery of 

fauna on protected seamounts to an oceanographically distinct location 

1. To measure and describe key elements of species distribution- abundance 

(density or biomass) & biodiversity for the Ross Sea and Southern Ocean for 

main habitats and key functional ecosystem roles- for major groups- virusesbacteria- 

archaea........ 

2. To report on the diversity of Antarctic Cephalopoda (Octopus and Squid)including 

a complete inventory of taxa- & reports on ontogenetic & sexual 

variation in species- their systematics- diversity- distribution- life histories- & 

trophic importance. 

3. To Beak/Biomass Regression Equations 

4. Life cycle determination 

362 

Completed Lörz et al. 2012 

Completed Clark et al. 2009 

Completed Garcia 2010




IPY2007-01 International polar year 

census of antarctic marine 

life post-voyage 

analysis:Ross Sea - 

Southern Ocean 

Biodiversity 

1. To measure seabed depth and rugosity using the multibeam system to identify 

topographic features such as bottom type, iceberg scouring, seamounts etc and 

to determine areas for targeted benthic faunal sampling. 

2. To continue the analysis of opportunistic seabird and marine mammal 

distribution observations from this and previous BioRoss voyages and published 

records, and in relation to environmental variables. 

3. To identify and determine near-surface spatial distribution, diversity and 

abundance of phytoplankton, and zooplankton, based on Continuous Plankton 

Recorder samples collected during transit to and from the Ross Sea. 

4. To collect & analyse data collected both underway, & at stations for salinity, 

temperature nutrient and chlorophyll a data, spot optical measurements with the 

SeaWiFS. 

5. To identify and determine the spatial distribution, abundance (biomass), 

diversity, and size structure of epipelagic, mesopelagic (and possibly 

bathypelagic) species using acoustics and net sampling. 

6. To identify and measure diversity, distribution & densities of mesozooplankton, 

macrozooplankton & meroplankton (as collected by all plankton sampling 

methods except transit CPR samples). 

7. To determine diversity, distribution & densities of viral, bacterial, phytoplankton 

& microzooplankton species in the water column. 

8. To determine the spatial distribution, abundance (biomass), diversity, and size 

structure of shelf and slope demersal fish species and associated invertebrate 

species using a demersal survey. 

9. To determine the diversity, abundance/density, spatial distribution, and 

physical habitat associations of benthic assemblages across a body size 

spectrum from megafauna to bacteria, for shelf, slope, seamounts, and abyssal 

sites in Ross Sea. 

10. To describe trophic/ecosystem relationships in the Ross Sea ecosystem 

(pelagic and benthic, fish and invertebrates). 

11. Assess molecular taxonomy and population genetics of selected Antarctic 

fauna and flora to estimate evolutionary divergence within and among ocean 

basins in circumpolar species. Provide DNA barcoding. 

363 

Completed Allcock et al. 2009; 2010; 

Submitted; Alvaro et al. 

2011; Bowden et al. 2011a; 

In Prep; Clark et al. 2010a; 

Dettai et al. 2011; Eakin et al. 

2009; Eleaume et al. 2011; In 

Prep; Ghiglione et al. 2012; 

Gordon 2000; Grotti et al. 

2008; Hanchet et al. 2008a; 

2008b; 2008c; 2008d; 

Hanchet 2009; 2010; 

Hanchet et al. In Press; 

Heimeier et al. 2010; Hemery 

et al. In prep; Koubbi et al. 

2011; Leduc et al. 2012a; b; 

Linse et al. 2007; Lörz 2009; 

Lörz 2010a; 2010b; 2010c; 

Lörz & Coleman 2009; Lörz 

et al. 2007; 2009; 2012a; b; 

In Press; In Prep; Maas et al. 

2010a; McMillan et al. 2012.; 

Mitchell 2008; Nielsen et al. 

2009; Norkko et al. 2005; 

O'Driscoll 2009; O'Driscoll et 

al. 2009; 2010; O’Driscoll et 

al. In Press; O'Loughlin et al. 

2011; Pakhomov et al. 2011; 

Pinkerton et al. 2007a; 

Pinkerton et al. 2009a; b; 

Pinkerton et al. In review; In 

press; Schiaparelli et al. 

2006; 2008; 2010; Smith et 

al. 2011a; b; Stein 2012; 

Strugnell et al. Submitted




ZBD2007-01 Chatham-Challenger 

Oceans 20/20 Post- 

Voyage 

1. To quantify in an ecological manner- the biological composition and function of 

the seabed at varying scales of resolution- on the Chatham Rise and Challenger 

Plateau 

2. To elucidate the relative importance of environmental drivers- including 

fishing- in determining sea bed community composition and structure. 

3. To determine if remote-sensed data (e.g. acoustic) and environmentally 

derived classification schemes (e.g. marine environmental classification system) 

can be utilized to predict bottom community composition- function and diversity 

4. To count- measure- and identify to species-level (where possible- otherwise to 

genus) all macro invertebrates (> 2 mm) and fish collected during Oceans 20/20 

voyages. 

5. To count- measure and identify to species-level (where possible- otherwise to 

genus or family) all meiofauna (> 2 mm) from multicore samples collected during 

the Oceans 20/20 voyages. 

6. To count- measure and identify to species- level (where possible- otherwise to 

genus or family) all fauna collected by hyper-benthic sled during the Oceans 

20/20 voyages. 

7. To count- measure- and identify to species-level all macrofauna observed on 

DTIS images collected during the Oceans 20/20 voyages. The number of 

biogenic features (burrows/mounds) and habitat (spatial) complexity should also 

be estimated. 

8. To count- measure- and identify to species-level (where possible- otherwise to 

genus or family) all macrofauna observed on DTIS video footage collected during 

the Oceans 20/20 voyages. 

9. To calculate and compare the performance of a suite of diversity measures 

(species and taxonomic-based) at varying levels of resolution. 

10. To estimate particle size composition and organic content of sediment 

samples. Sediment samples should be aggregated over the top 5 cm of 

sediment. 

11. To measure the bacterial biomass (top 2 cm) of the sediment and in the 

sediment surface water samples- collected during the Oceans 20/20 voyages 

12. To elucidate the relationships- patterns and contrasts in species composition- 

assemblages- habitats- biodiversity and biomass (abundance) both within and 

between stations- strata and areas. 

13. To define habitats (biotic) encountered during the survey and assess their 

relative sensitivity to modification by physical disturbance- their recoverability 

and their importance to ecosystem function / production. 

14. To quantify the productivity- energy flow (trophic networks) and the energetic 

coupling (bentho pelagic or otherwise) of the area surveyed areas at various 

levels of resolution. 

364 

Completed Bowden 2011; Bowden et al. 

2011 ; In press; Bowden & 

Hewitt 2012; Compton et al. 

2012; Coleman and Lörz 

2010; Hewitt et al. 2011a; 

2011b; Lörz 2011a; 2011b; 

Nodder et al. 2012; Floerl et 

al. 2012


15. To assess the extent to which patterns of species distributions and 

communities can be predicted using environmental data (including fishing) 

collected during the Ocean 20/20 voyages or held in other databases. 

16. To provide an interactive- high resolution mapping facility for displaying & 

plotting all data collected & derived indices. Includes environmental data- the 

abundance of species- indices of biomass or diversity- and statistically derived 

groupings 

17. To assess the extent to which acoustic- environmental- or other remotesensed 

data can provide cost-effective- reliable means of assessing biodiversity 

at the scale of the Oceans 20/20 surveys. 

18. To assess the extent to which the 2005 MEC and subsequent variants can 

provide cost-effective- reliable means of assessing biodiversity at the scale of the 

Oceans 20/20 surveys. 

19. Collating all information and analysis from all objectives- devise a series of 

statistically supported recommendations for surveying marine biodiversity in the 

future. Including- but may not be limited to- statistical analyses and modelling. 



ZBD2006-02 Ongoing NABIS 

development 

As part of NABIS, users will be able to identify spatial information relating to the 

annual distribution (average distribution over the period of a year) of particular 

species within the waters around New Zealand and in the terrestrial environment 

(including off shore islands) of New Zealand. Users will also be able to 

interrogate metadata and attribute data related to the information layers 

presented. Users will employ NABIS to identify where a particular species is 

found, to identify what species are found within an area of interest, and be able 

to compare the spatial distribution of a particular species with other information 

layers. 

2. Some species may have notable changes in their spatial distribution 

throughout a year. For such species, users of NABIS will be able to view spatial 

information relating to the seasonal distribution of particular species within the 

waters around New Zealand and in the terrestrial environment (including offshore 

islands) of New Zealand. Users will also be able to interrogate metadata and 

attribute data related to the information layers presented. For species with a 

seasonal component to their biological distribution, users will employ NABIS to 

identify where a particular species is found within the waters around New 

Zealand and in the terrestrial environment (including off shore islands) of New 

Zealand at a particular time of the year, to identify what species are found within 

an area of interest at a particular time of year, or be able to compare the 

distribution of a particular species at a particular time of year, with other 

information layers. 

3. To provide analysis of the data used in determining the hotspot distribution. 

365 

Completed Anderson 2007b




ZBD2006-03 Antarctic coastal marine 

systems 

ZBD2006-04 Chatham/challenger 

oceans 20/20 

ZBD2005-02 Marine Environment 

Classification Project 

ZBD2005-09 Rocky reef ecosystems - 

how do they function? 

Integrating the roles of 

primary and secondary 

production, biodiversity 

and connectivity across 

coastal habitats 

1. Quantify patterns in benthic community structure and function at two coastal 

Ross Sea locations (Terra Nova Bay and Cape Evans). 

2. Quantify benthic community structure and function at selected locations in 

Terra Nova Bay and Cape Evans. 

1. To collect seabed fauna, sediment samples and photographic images along 

transects in the Chatham Rise and the Challenger Plateau, as determined by the 

sampling protocol described in the Voyage Programmes for Voyages 2 and 3 of 

the project. Multibeam data should be collected opportunistically as time allows. 

2. To describe the distribution of broad macro epifauna groups (I.D. level to be 

determined at sea during Surveys 2 & 3), their relative abundance, the substrate 

and habitat types, including representative photographic images of each sea-bed 

habitat and associated fauna along transects in the survey areas. 

3. To provide a description of the observed evidence of fishing along transects. 

4. To provide indicative measures of alpha biodiversity (richness, number of 

taxonomic groups) at appropriate scales within and between transects, and 

between the Chatham Rise and the Challenger Plateau. 

5. To determine broad scale variability in sea-bed habitats and associated 

biodiversity within and between MEC classes at 20 class level. 

6. To process and archive biological samples and data into databases and 

collections for future analysis in meeting the Overall Objectives above. 

1. Co-fund the Marine Environment Classification Project (being done by NIWA) 

with the Department of Conservation. 

1. To develop a qualitative numerical model of how New Zealand’s rocky reef 

systems are functionally structured 

2. To quantify the effects of human predation, and environmental degradation 

across reef gradients – top-down, or bottom-up functioning? 

3. To advance our understanding of how subtidal reef systems are fuelled 

through primary and secondary production (from a range of sources), the role 

that biodiversity plays, and how this varies across different reef settings. 

4. To quantify how subtidal reef systems are linked with other habitats and 

ecosystems at broader spatial scales, including the connectivity of MPAs with 

other habitats and areas. 

366 

Completed Cummings et al. 2003; 

2006b; 2008; Thrush & 

Cummings 2011; Thrush et 

al. 2010 

Completed Nodder 2008; Nodder et al. 

2011 

Completed Snelder et al. 2005; 2006; 

Leathwick et al. 2006a; b; c 

In the process MacDiarmid et al. In Press c 

of publication




ZBD2005-03 Tangaroa ross sea voyage 1. To test the feasibility of obtaining estimates of demersal fish relative 

abundance using cameras with and without flood lights in areas of high 

importance for the Ross Sea toothfish fishery (principally 800-1200 m). 

2. To utilise deepwater camera transects, supported by other direct sampling 

methods, to characterise the relative abundance, distribution, and diversity of 

demersal fish species (assuming Objective 1 yields satisfactory results) and of 

benthic macro-invertebrates, and to examine relationships between demersal 

fishes and benthic habitats/communities. Camera transects will be deployed 

opportunistically, with focus on the following high-priority areas (in order of high 

to low priority) wherever possible: 

i) Areas of the continental shelf break at depths of high importance for the 

toothfish fishery (principally 800-1200 m but also 600-800m & 1200-1500 m if 

time permits), 

ii) Shallow (50-200 m) water in the immediate vicinity of the Balleny Islands; 

iii) Deeper water in the vicinity of the Balleny Islands; iv) seamounts around and 

between Scott Island and the Balleny Islands; and v) at other locations (< 600 m) 

as opportunity arises (e.g. around Scott Island, western Ross Sea, south-eastern 

Ross Sea). 

3. To collect specimens/tissues of selected benthic and pelagic organisms with 

priority in the vicinity of the Balleny Islands (and to the east/southeast, for pelagic 

specimens especially Antarctic krill species) and deliver specimens to other 

projects for stable isotope analysis in order to contribute to understanding of 

trophic relationships. 

4. To acquire a continuous acoustic survey of the water column, opportunistically 

undertake species verification of acoustic marks, integrate the acoustic marks 

and produce a GIS map of verified and unverified distributions of functionally 

important mesopelagic species (e.g. krill, Antarctic silverfish). 

5. To undertake routine identification and abundance estimates of marine 

mammal and seabird species and deliver raw and GIS summarised data to other 

related projects in order to generate spatially and temporally explicit population 

biomass and foraging distribution estimates for top air-breathing predators in the 

Ross Sea. 

6. To undertake automated water sampling in order to monitor the identities and 

spatial and temporal distributions of plankton in the Ross Sea region and to allow 

ground-truthing of data collection from satellites (e.g. surface seawater 

temperature, and chlorophyll-a concentration). 

367 



MacDiarmid & Stewart In 

Press; Mitchell & MacDiarmid 

2006




ZBD2005-01 Balleny Islands Ecology 

Research, Tiama Voyage 

(2006) 

1. To characterise shallow benthic communities across a range of habitat 

settings around the Balleny Islands, utilising a range of data collection 

methodologies (including SCUBA-based rock-wall suspension feeder photo 

quadrats, SCUBA-based linear video transects, and drop camera photography), 

and to analyse community patterns with reference to possible 

physical/oceanographic, biological, and/or biogeographic influences on 

community structure. 

2. To characterise aspects of the marine food web of the Balleny Islands area, 

using stable isotope analysis of specimens from important functional groups, and 

to make inferences about factors affecting ecosystem-scale trophodynamics in 

the Balleny Islands area and potential implications for the function of the wider 

ecosystem. 

3. To characterise the spatial and temporal distributions of higher-level consumer 

species (birds, seals and whales) and of dominant pelagic prey (i.e. krill swarms) 

by opportunistically recording all at-sea sightings, and by systematic observation 

of landbased top predators (birds and seals) while sailing along the coast of the 

islands. 

4. To collect and photograph and/or retain fish specimens from shallow benthic 

environments using a range of fishing methods, including food-baited fish traps, 

lightbaited fish traps, rotenone sampling, and/or baited lines. 

5. To continuously collect bathymetric data and water-column acoustic data (i.e. 

mesopelagic acoustic marks) throughout the voyage, using an acoustic sounder. 

6. To opportunistically collect a variety of data/materials during shore-based 

landings, including wherever possible: i) breast feathers from living penguins; ii) 

tissue samples/feathers/bones from dead seals/penguins/other sea birds; iii) seal 

scats; iv) visual estimates of adult and juvenile penguin numbers; v) visual 

assessments of penguin colony status; vi) photographs of penguin colonies; vii) 

sediment excavations of occupied and abandoned colonies. (Where appropriate 

these data will contribute to Objective 2). 

368 

Terminated Smith 2006




ZBD2005-05 Long-term effects of 

climate variation and 

human impacts on the 

structure and functioning 

of New Zealand shelf 

ecosystems 

ZBD2004-01 Baseline information on 

the diversity and function 

of marine ecosystems 

ZBD2004-02 Ecosystem-scale trophic 

relationships: diet 

composition and guild 

structure of middle-depth 

fish on the chatham rise 

1. To estimate changes in marine productivity via fluctuations in ocean climate 

and terrestrial nutrient input over the last 1000 years. 

2. To assess and collate ex isting archaeological, historical and contemporary 

data (including catch records and stock assessments) on relevant components of 

the marine ecosystem to provide a detailed description of change in the shelf 

marine ecosystem in two areas of contrasting human occupation over last 1000 

years. 

3. To collect additional oral histories from Maori and non-Maori fishers and 

shellfish gathers regarding the distribution, sizes and relative abundance 

(compared to present availability) of key fish and invertebrate stocks in both 

regions during the first half of the 20th century before the start of widespread 

modern industrial fishing. 

4. To build mass-balance ecosystem models (e.g. Ecopath) of the coastal and 

shelf ecosystem in each area for five critical time periods: now, 60 years BP 

(before modern industrial fishing), 250 years BP (before European whaling and 

sealing), 600 y BP (early Maori phase) and 1000 years BP (before human 

settlement). 

5. To use qualitative modelling techniques to determine the critical interactions 

amongst species and other ecosystem components in order to identify those that 

should be a priority for future research. 

1. To quantify, and compare, the macro-invertebrate assemblage composition of 

a number of 

seamounts at the southernmost end of the Kermadec volcanic arc. 

2. To compare the macro-invertebrate diversity of the southernmost end of the 

Kermadec 

volcanic arc with that of seamounts already sampled and reported on. 

1. To quantitatively characterise the diets of abundant middle-depth fish species 

on the Chatham Rise, by analysis of fish stomach contents collected from the 

January 2005, January 2006 and January 2007 Chatham Rise middle-depths 

trawl surveys. 

2. To quantitatively characterise Chatham Rise fish diets throughout the year, for 

a period of 24 months, by analysis of fish stomach contents collected 

opportunistically aboard industry vessels. 

3. To describe and examine patterns of diet variation within each fish species as 

a function of spatial, temporal, and environmental variables, and of fish size. 

4. To define and characterise trophic guilds for abundant fish species on the 

Chatham Rise, using multivariate analysis of fish diet data, and to analyse the 

nature and relative strength of potential trophic interactions between guilds. 

5. To create and populate a diets database to store all of the dietary information 

collected under Objectives 1 and 2, and for use in subsequent dietary studies. 

369 



Carroll et al. In Press; 

Jackson et al. In Press; Lalas 

et al. In Press a; b; Lalas & 

MacDiarmid In Press; Lorrey 

et al. In Press; MacDiarmid 

et al. In Press a; b; Maxwell 

& MacDiarmid In Press; Neil 

et al. In Press; Paul 2012; 

Parsons et al. In Press; 

Pinkerton In Press; Smith 

2011 

Completed Rowden & Clark 2010; Smith 

et al. 2008 

Completed Connell et al. 2010; Dunn 

2009; Dunn et al. 2010a; b; 

c; Dunn et al. In press; 

Forman & Dunn 2010; Horn 

et al. 2010; Stevens & Dunn 

2010;




ZBD2004-05 Assessment and definition 

of the biodiversity of 

coralline algae of northern 


ZBD2004-10 Development of 

bioindicators in coastal 

ecosystems 

ZBD2004-19 Ecological function and 

critical trophic linkages in 

New Zealand softsediment 

habitats 

ZBD2003-02 Biodiversity of Coastal 

Benthic Communities of 

the North Western Ross 

Sea. 

ZBD2003-03 Biodiversity of deepwater 

invertebrates and fish 

communities of the north 

western Ross Sea 

1. To assess and define the biodiversity of coralline algae in northern New 

Zealand. 

2. To develop rapid identification tools for coralline algae using molecular 

sequencing data. 

3. To contribute representative material to the national Coralline Algal 

Collections. 

4. To produce ID guides to common coralline algae of northern New Zealand. 

1. Investigate linkages between land use patterns in catchments and nitrogen 

loading to recipient 

estuaries and coastal ecosystems 

2. Characterise isotopic signatures of selected bioindicator organisms in relation 

to different 

terrestrial nutrient loads; and 

3. Validate the use of bioindicators using controlled laboratory and field 

experiments. 

1. Define the interactive effects of two functionally important benthic species in 

maintaining critical trophic linkages in soft-sediment systems from a series of 

integrated field experiments. 

2. Quantify effects of heart urchins (Echinocardium australe) on sediment 

properties- benthic primary production- and macrofaunal diversity through 

manipulative field experiments in Mahurangi Harbour. 

3. Test for interactions between pinnid bivalves (Atrina zelandica) and heart 

urchins (Echinocardium australe) in field experiments- and measure their 

respective and combined contributions to sediment properties- benthic primary 

production- and macrofau na 

4. Determine the dependence of results from objectives 1 and 2 (functional 

contributions of Echinocardium and Atrina) in an environmental context by 

conducting experiments along an estuarine-coastal gradient. 

1. Quantify patterns in biodiversity and community structure in the coastal Ross 

Sea region 

2. Quantify biodiversity in benthic communities at selected locations in the Ross 

sea north of Terra Nova Bay 

3. Describe ecosystem function at selected locations in the Ross Sea north of 

Terra Nova Bay. 

1. To describe, and quantify the diversity of, the benthic macroinvertebrates and 

fish assemblages of the Balleny Islands and adjacent seamounts, and to 

determine the importance of certain environmental variables influencing 

assemblage composition. 

370 

Completed Farr et al. 2009 

Completed Savage 2009 

Completed Lohrer et al. 2010 

Completed Cummings et al. 2003; 

2006a; 2010; De Domenico 

et al. 2006; Guidetti et al. 

2006; Norkko et al. 2004 

Completed Rowden et al. 2012a; In 

Press; Mitchell & Clark 2004




ZBD2003-04 Fiordland Biodiversity 

Research Cruise 

ZBD2003-09 Macquarie Ridge 

Complex Research 

Review 

ZBD2002-01 Ecology of Coastal 

Benthic Communities in 

Antarctica 

ZBD2002-02 Whose larvae is that? 

Molecular identification of 

planktonic larvae of the 

Ross Sea. 

ZBD2002-06A Impacts of terrestrial runoff 

on the biodiversity of 

rocky reefs 

1. How can ecotone boundaries be defined? 

2. If you have an ecotone boundary defining the edge of a commercial exclusion 

zone how wide is the transition zone across the boundary? 

3. If you have an area delineated as a marine protected area or a commercial 

exclusion zone, does it adequately represent the different habitats or biodiversity 

of the whole region? 

To review and summarise both biological and physical research carried out on or 

around the section of the Macquarie Ridge Complex that lies between New 

Zealand and Macquarie Island 

371 

Completed Wing 2005 

Completed Grayling 2004 

Objectives unknown Completed Schwarz et al. 2003; 2005; 

Thrush et al. 2006; Thrush & 

Cummings 2011; Cummings 

et al. 2003; Sharp et al. 

2010; Sutherland 2008 

1. To use molecular sequencing tools in the taxonomic identification of 

cryptic/invasive marine 

2. To provide a molecular description and characterisation of gobies that are 

introduced (Arenigobius bifrenatus and Acentrogobius pflaumii) cryptogenic 

(Parioglossus marginalis) or native (eg.Favonigobius lentiginosus and F. 

expuisitus). 

3. To describe the molecular diversity of the above species throughout their 

native and introduced distributions- and characterise a range of the greatest 

potential invasive gobioid and blennioid species from the Australasian region. 

4. To develop molecular criteria to rapidly identify invasive or cryptogenic gobioid 

and blennioid fish 

1. Conduct field and laboratory experiments to determine relationships between 

sediment loading, epifaunal assemblages, and mortality of filter feeding 

invertebrates. 

2. Conduct field and laboratory experiments to identify the influence of sediment 

on early life stages of key grazers. 

3. Determine photosynthetic characteristics and survival of large brown 

seaweeds and understorey algal species in relation to a sediment gradient. 

Completed Sewell 2005; 2006; Sewell et 

al. 2006 

Completed Schwarz et al. 2006




ZBD2002-12 Molecular identification of 

cryptogenic/invasive 

marine species – gobies. 

ZBD2002-16 Joint New Zealand and 

Australian Norfolk Ridge 

ZBD2002-18 Quantitative survey of the 

intertidal benthos of 

Farewell Spit Golden Bay 

ZBD2001-02 Documentation of New 

Zealand Seaweed 

ZBD2001-03 Ecology and biodiversity of 

coastal benthic 

communities in Antarctica. 

1. To use molecular sequencing tools in the taxonomic identification of 

cryptic/invasive marine species 

2. To provide a molecular description and characterisation of gobies that are 

introduced (Arenigobius bifrenatus and Acentrogobius pflaumii) cryptogenic 

(Parioglossus marginalis) or native (eg.Favonigobius lentiginosus and F. 

expuisitus). 

3. To describe the molecular diversity of the above species throughout their 

native and introduced distributions- and characterise a range of the greatest 

potential invasive gobioid and blennioid species from the Australasian region. 

4. To develop molecular criteria to rapidly identify invasive or cryptogenic gobioid 

and blennioid fish. 

1. To describe the marine biodiversity of the Norfolk Ridge and Lord Howe Rise 

seamount communities. 

2. To survey- sample and document the marine biodiversity and environmental 

data from seamounts on the Norfolk Ridge and Lord Howe Rise to a depth of at 

least 1-000m depth. (b) To preserve samples of fishes and invertebrates and 

hold these in ac... 

1. To undertake a baseline survey of intertidal macrobenthic organisms at 

Farewell Spit Nature Reserve and adjacent flats. 

2. To undertake an initial field survey of Zostera distribution at Farewell Spit 

Nature Reserve and adjacent intertidal flats. 

3. To undertake a preliminary survey of sediment characteristics of the intertidal 

flats at Farewell Spit Nature Reserve and adjacent flats. 

1. To publish a regional algal flora of Fiordland based on voucher herbarium 

specimens. 

2. To assemble a database of references and to review the current state of 

knowledge about New Zealand macroalgae. 

1. To develop sampling protocols for estimating the relative abundance of algae 

and benthic invertebrates 

2. To quantify patterns in biodiversity and benthic community structure at two 

locations in McMurdo Sound 

3. To analyse Ross Island Sea-Level data. 

372 

Completed Lavery et al. 2006 

Completed Clark & Roberts 2008 

Completed Battley et al. 2005 

Completed Nelson et al. 2002 

Completed Norkko et al 2002 

ZBD2001-04 “Deep Sea New Zealand” To help publish the book "Deep Sea New Zealand" Completed Batson 2003 

ZBD2001-05 Crustose coralline algae of 


1. To assess the biodiversity of crustose coralline algae in NZ using modern 

taxonomic methods and molecular sequence tools. 

2. To establish the NZ National Coralline Algal Collection. 

3. To produce identification guides to NZ species. 

Completed Harvey et al. 2005; Farr et 

al. 2009; Broom et al 2008




ZBD2001-06 Biodiversity of New 

Zealand’s soft-sediment 

communities 

ZBD2001-10 Additional Research on 

Biodiversity of Seamounts 

MOF2000-01 Bryozoan thickets off 

Otago Peninsula 

ZBD2000-01 A review of current 

knowledge describing the 

biodiversity of the Ross 

Sea region 

ZBD2000-02 Exploration and 

description of the 

biodiversity, in particular 

the benthic macrofauna, of 

the western Ross Sea 

1. To review the current knowledge of the biodiversity of macroinvertebrates and 

macrophytes living in and on soft-sediment substrates in New Zealand“s 

harbours- estuaries- beaches and to 1000 m water depth. 

2. To review existing published and unpublished sources of information on softsediment 

marine assemblages around New Zealand. 

3. Using the results of Objective 1- identify gaps in the knowledge- hotspots of 

biodiversity- areas of particular vulnerability- and make recommendations on 

areas or assemblages that could be the subject of directed research in future 

years. 

Completed Rowden et al. 2012b 

1. To determine the macro-invertebrate assemblage composition on Cavalii 

seamount, and adjacent seamount W1, by photographic transects and 

epibenthic sled sampling. 

2. To determine the distniution of macro-invertebrate assemblages on the 

seamounts. 

3. To compare the macro-invertebrate species diversity of neighbouring 

seamounts. 

4. To evaluate and collect samples fiom suitable macro-invertebrate species for 

genetic analysis. 

5. To map bathymetry and habitat characteristics of the seamounts. 

6. To compare macro-invertebrate assemblage composition of the seamounts 

with nearby hard bottom low relief (under 100 m) on the slope, if suitable areas 

can be located. 

Completed Rowden et. al 2004 

Objectives unknown Completed Batson & Probert 2000 

1. To review and document existing published and unpublished information 

describing the biodiversity of the Ross Sea region. 

2. To identify and document Ross Sea region marine communities that are under 

high pressure or likely to come under high pressure from human activities in the 

near future. 

1. To utilise sampling opportunities provided by the presence of RV Tangaroa in 

the western Ross Sea in February / March 2001 to make collections of 

(primarily) benthic organisms as a contribution to the understanding of 

biodiversity in the region. 

2. To identify and document the organisms collected and provide for their proper 

storage in national collections. 

3. To describe the logistic constraints of working in the Ross Sea region, and 

make recommendations for future research to improve understanding of 

biodiversity in the Ross Sea. 

373 

Completed Bradford-Grieve & Fenwick 

2001a; 2001b; Fenwick & 

Bradford-Grieve 2002a; 

2002b; Bradford-Grieve & 

Fenwick 2002; Varian 2005 

Completed Page et al. 2001




ZBD2000-03 The spatial extent and 

nature of the 

bryozoan communities at 

Separation 

Point, Tasman Bay 

ZBD2000-04 Supplementary Research 

on Biodiversity of 

Seamounts 

ZBD2000-06 “The Living Reef: The 

Ecology of New Zealand's 

Rocky Reefs” 

ZBD2000-08 A review of current 

knowledge describing New 

Zealand’s Deepwater 

Benthic Biodiversity 

1. To assess the present state and extent of bryozoan communities around 

Separation Point. 

2. To characterise the bryozoan communities around Separation Point. 

1. To determine the biodiversity of seamounts of the southern Kermadec 

volcanic arc (Rumble V, Rumble 111, Brothers). 

2. To describe the distribution of fauna, with an emphasis on mapping the nature 

and extent, of biodiversity associated with hydrothermal vents. 

3. To compare the biodiversity of the thee seamounts, and adjacent slope. 

4. To collect samples from near the vent sources (if possible, as these are 

thought to be very localised) to measure chemical and thermal aspects of the 

environment 

374 

Completed Grange et al. 2003 

Completed Rowden et al. 2002 and 

2003; Clark & O'Driscoll 2003 

1. Funding to support the publication of this book. Completed Andrew & Francis (Eds.) 

2003 

1. To review and document existing published and unpublished reports and data 

describing New Zealand’s deepwater benthic biodiversity. 

2. To make recommendations on representative communities and potentially 

impacted communities that could be the subject of directed research. 

Completed Key 2002 

ZBD2000-09 Antarctic fish taxonomy 1. Ross Sea fishes processing and identification Completed Roberts & Stewart & 2001

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