Species level systematics of bartsia (orobanchaceae)- a multilocus approach with complete sampling and hundreds of individuals for a rapid and recent andean radiation
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Using microfluidic PCR and high-throughput sequencing technology, we analyzed the evolutionary relationships of the Andean plant genus Neobartsia. This is a presentation that I gave at the conference Botany2014 in Boise, Idaho, USA.
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Species level systematics of bartsia (orobanchaceae)- a multilocus approach with complete sampling and hundreds of individuals for a rapid and recent andean radiation
- 1. Species-level systematics of Bartsia (Orobanchaceae): a multilocus approach with complete sampling and hundreds of individuals for a rapid and recent Andean radiation Simon Uribe-Convers and David C. Tank University of Idaho www.simonuribe.com@uribe_convers
- 2. - Linnaeus - Herbs and shrubs - Hemiparasite - Alpine ecosystems - ca. 49 species
- 3. - 2 species in Africa - 1 species in Europe and northeastern North America - 1 species in the Mediterranean - ca. 45 species in South America high levels of sympatry
- 5. Molau, 1990 Back in 1990...
- 6. Back in 1990... Molau, 1990
- 8. Těšitel et al., 2010 Scheunert et al., 2012
- 9. Scheunert et al., 2012
- 10. Modified from Scheunert et al., 2012 Bellardia All. Bellardia trixago Bellardia viscosa Bellardia latifolia Bellardia canescens Bellardia mutica
- 11. 0.02 Odontites violaceus var brevifolius Rhinanthus freynii Bartsia santolinifolia Bartsia pedicularoides Melampyrum sylvaticum Bartsia sp 5 Tozzia alpina Euphrasia regelii Bartsia melampyroides Rhynchocorys maxima Hedbergia abyssinica var nykiensis Bartsia sericea Bartsia thiantha Odontites linkii ssp cyprius Bartsia decurva Rhynchocorys orientalis Melampyrum lineare Bartsia longiflora ssp longiflora Rhinanthus serotinus Bartsia alpina Bartsia trixago Euphrasia stricta Euphrasia mollis Rhynchocorys elephas Bartsia ramosa Hedbergia abyssinica var abyssinica Bartsia tenuis Bartsia crenoloba Bartsia laniflora Odontites corsicus Rhynchocorys stricta Odontites vulcanicus Melampyrum carstiense Rhinanthus kyrollae Bartsia sp 7 Bartsia pyricarpa Odontites vulgaris Bartsia laticrenata Euphrasia collina Parentucellia viscosa Euphrasia alsa Bartsia orthocarpiflora Rhynchocorys odontophylla Rhinanthus crista galli Rhynchocorys kurdica Hedbergia abyssinica var petitiana Bartsia stricta Bornmuellerantha aucheri Lathraea squamaria 1/100 1/93 1/100 1/93 0.98/- 1/100 1/98 0.92/- 1/92 1/100 1/93 0.98/99 1/83 1/100 1/100 1/100 1/100 1/100 1/100 1/83 0.98/- 0.99/73 0.94/80 1/88 1/100 1/100 1/100 1/100 1/100 1/100 1/100 1/98 1/100 1/100 1/100 1/100 1/1001/100 1/89 nrDNA: ITS, ETS cpDNA: rps16, trnT-F
- 12. MA0.05.010.015.020.025.030.035.040.0 South American Bartsia (45) Odontites (32) Euphrasia (350) Rhynchocorys (6) Rhinanthus (45) Melampyrum (35) Bellardia (3) Hedbergia Tozzia alpina (1) Lathraea (7) (3) Bartsia alpina (1) S.Am. Bartsia Background 0.1 0.2 0.3 0.4 051015 Net Diversification Rate Density ca. 2 Ma
- 13. MA0.05.010.015.020.025.030.0 South American Bartsia (45) Odontites (32) Euphrasia (350) Rhynchocorys (6) Rhinanthus (45) Melampyrum (35) Bellardia (3) Hedbergia Tozzia alpina (1) Lathraea (7) (3) Bartsia alpina (1) ca. 2 Ma S.Am. Bartsia Background 0.1 0.2 0.3 0.4 051015 Net Diversification Rate Density
- 14. http://goo.gl/l3DnHD http://goo.gl/ritOL4 Bellardia trixago (L.) All. http://goo.gl/o0e7Gs Bellardia viscosa (L.) Fisch. & C.A. Mey Bellardia latifolia (L.) Cuatrec. South American Bartsia
- 15. Modified from Scheunert et al., 2012 Bellardia All. Bellardia trixago Bellardia viscosa Bellardia latifolia Bellardia canescens Bellardia mutica MA0.05.010.015.020.025.030.035.040.0 South American Bartsia (45) Odontites (32) Euphrasia (350) Rhynchocorys (6) Rhinanthus (45) Melampyrum (35) Bellardia (3) Hedbergia Tozzia alpina (1) Lathraea (7) (3) Bartsia alpina (1) Bellardia
- 16. MA0.05.010.015.020.025.030.035.040.0 South American Bartsia (45) Odontites (32) Euphrasia (350) Rhynchocorys (6) Rhinanthus (45) Melampyrum (35) Bellardia (3) Hedbergia Tozzia alpina (1) Lathraea (7) (3) Bartsia alpina (1) Neobartsia Uribe-Convers & Tank Pseudoparentucellia viscosa Uribe-Convers & Tank Parentucellia latifolia Bellardia trixago Modified from Scheunert et al., 2012 Bellardia All. Bellardia trixago Bellardia viscosa Bellardia latifolia Bellardia canescens Bellardia mutica
- 17. South American Bartsia (45) Bellardia (3) Neobartsia Uribe-Convers & Tank
- 18. Schaal & Olsen, 2000Maddison, 1997
- 19. Multilocus dataset Yang & Rannala, 2010
- 20. −100 −80 −60 −40 −60−40−20020 0 1000 2000 3000 4000 5000 6000 ●●●● ●●● ●●●●●●●●● ● ● ●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●●●●●● ● ●●●●●●●●●●●●●●●●●●●●●● ●●● ●●●●●● ●●● ●●●● ● ●●●●●●●●●●●●●●●●●●●●● ●●●●●●● ●●●●●●●●●●●●● ●●●●●●●●●●●●●●●● ●●● ●●●●●●●●●● ●● ●●●● ● ● ● ● ●●●●●● ●●●● ●●● ●● ● ●●●●●●●●● ●●●●●●●● ●●●● ●●●●● ●● ●●●●●●● ●●●●●●●●●●●● ● ●●●●●●●●●●●●●●●● ●●●●●●● ● ●●●● ● ● ● ● ●● ● ● ●●● ● ● ● ● ●●● ●● ●● ● ●●●●●●●●●●●●●●●●●●●● ●●●●● ●●● ● ●●●●●●●●●●● ●●● ● ●●●●●●●●●●●●●●●●●●●●●●●● ●●● ●●●●●●●● ●●●● ●●●●●●●● ●●●●●●● ●●●●●●●●● ●●●●●● ●●●●●●●●● ● ●● ●●●●●● ●● ●●●● ●●●●●●● ●●●●●●●●●●●●●●●●● ●●●●● ●●●●●●●●●●●●● ●●● ●●●● ●● ●● ● ● ● ● - 505 samples Neobartsia - All species - Multiple individuals
- 21. Uribe-Convers et al., 2014
- 22. -48 chloroplast and 48 nuclear regions - ca. 50,000 bp -576 samples -Amplification of 24 microfluidic Fluidigm chips (55,296 PCRs!) -12 for the chloroplast and 12 for the nuclear genome -Sequencing in Illumina MiSeq (~21 million 300 bp paired-end reads)
- 23. Haploid or Diploid Homozygote Diploid Heterozygote p q Phylogenomics talk: Wed. 4:30 pm.
- 25. 100 5 3 1 2 0
- 27. -100 -90 -80 -70 -60 -50 -40 -60-40-20020 Neobartsia filiformis 0 1000 2000 3000 4000 5000 6000 Neobartsia filiformis
- 30. −90 −80 −70 −60 −50 −40 −30 −60−40−20020 Neobartsia pedicularoides 0 1000 2000 3000 4000 5000 6000 ●●●●●●●●● ● ●●●●● ●●● ●●●●●●●●● ●● ●● ●● ● ●●● ● ● ● ● Neobartsia pedicularoides
- 32. 100
- 33. A) B)
- 34. Coalescent-based methods with allelic information *BEAST MP-EST
- 35. Coalescent-based methods with allelic information *BEAST MP-EST 37.8 hours (~1.5 days) per million generation Not possible to run, exceeds memory
- 36. Coalescent-based methods with allelic information Reduced dataset - 3 individuals per species *BEAST MP-EST 3.5 hours per million generation ca. one month to finish
- 37. Species tree estimation - STAR Data without allelic information, ambiguity code instead
- 38. Species tree estimation - STAR Data without allelic information, ambiguity code instead
- 39. Data without allelic information, ambiguity code instead Traditional methods - Concatenated analysis of cpDNA and nuclear loci ~50kb
- 40. Data without allelic information, ambiguity code instead Traditional methods - Concatenated analysis of cpDNA and nuclear loci ~50kb
- 41. Data without allelic information, ambiguity code instead N. adenophylla N. serrata N. filiformis Traditional methods - Concatenated analysis of cpDNA and nuclear loci ~50kb
- 42. De Queiroz, 2007
- 45. Tank lab Diego Morales-Briones, Hannah Marx Sarah Jacobs, Maribeth Latvis ! Olmstead lab Dick Olmstead, John Chau, Laura Frost ! Nicolai Nürk Laura Kubatko Segundo Leyva, Mario Zapata ! Acknowledgments @uribe_convers