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.

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
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- 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.

24. cpDNA - ~25Kb
100
100
100
100
Bellardia
Parentucellia
Pseudoparentucellia
Neobartsia

25. 100
5 3
1
2
0

26. Neobartsia filiformis

27. -100 -90 -80 -70 -60 -50 -40
-60-40-20020
Neobartsia filiformis
0
1000
2000
3000
4000
5000
6000
Neobartsia filiformis

29. Neobartsia pedicularoides

30. −90 −80 −70 −60 −50 −40 −30
−60−40−20020
Neobartsia pedicularoides
0
1000
2000
3000
4000
5000
6000
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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

43. 20,000 BP Present

44. #nextgenerationproblems

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