species level systematics of bartsia (orobanchaceae)- a multilocus approach with complete sampling...

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. TankUniversity of Idaho

www.simonuribe.com@uribe_convers

- Linnaeus - Herbs and shrubs - Hemiparasite - Alpine ecosystems - ca. 49 species

- 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

Molau, 1990

Back in 1990...

Back in 1990...

Molau, 1990

Těšitel et al., 2010 Scheunert et al., 2012

Scheunert et al., 2012

Modified from Scheunert et al., 2012

Bellardia All.

Bellardia trixago

Bellardia viscosa

Bellardia latifolia

Bellardia canescens

Bellardia mutica

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 7Bartsia 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

1/1001/100

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

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. BartsiaBackground

0.1 0.2 0.3 0.4

05

1015

Net Diversification Rate

Dens

ityca. 2 Ma

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. BartsiaBackground

0.1 0.2 0.3 0.4

05

1015

Net Diversification RateDe

nsity

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Bellardia trixago (L.) All.

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Bellardia viscosa (L.) Fisch. & C.A. Mey

Bellardia latifolia (L.) Cuatrec. South American Bartsia

Modified from Scheunert et al., 2012

Bellardia All. Bellardia trixagoBellardia viscosa

Bellardia latifoliaBellardia canescensBellardia 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

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 & TankParentucellia latifolia

Bellardia trixago

Modified from Scheunert et al., 2012

Bellardia All. Bellardia trixagoBellardia viscosa

Bellardia latifoliaBellardia canescensBellardia mutica

South American Bartsia (45)

Bellardia (3)

Neobartsia Uribe-Convers & Tank

Schaal & Olsen, 2000Maddison, 1997

Multilocus dataset

Yang & Rannala, 2010

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- 505 samples Neobartsia - All species - Multiple individuals

Uribe-Convers et al., 2014

-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)

Haploid or Diploid Homozygote

Diploid Heterozygote

pq

Phylogenomics talk: Wed. 4:30 pm.

cpDNA - ~25Kb

100

100

100

100

Bellardia

ParentucelliaPseudoparentucellia

Neobartsia

100

5 3

1

2

0

Neobartsia filiformis

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Neobartsia filiformis

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Neobartsia filiformis

Neobartsia pedicularoides

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Neobartsia pedicularoides

100

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B)

Coalescent-based methods with allelic information

*BEAST

MP-EST

Coalescent-based methods with allelic information

*BEAST

MP-EST

37.8 hours (~1.5 days) per million generation

Not possible to run, exceeds memory

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

Species tree estimation - STARData without allelic information, ambiguity code instead

Species tree estimation - STARData without allelic information, ambiguity code instead

Data without allelic information, ambiguity code insteadTraditional methods - Concatenated analysis

of cpDNA and nuclear loci ~50kb

Data without allelic information, ambiguity code insteadTraditional methods - Concatenated analysis

of cpDNA and nuclear loci ~50kb

Data without allelic information, ambiguity code instead

N. adenophylla

N. serrata

N. filiformis

Traditional methods - Concatenated analysis of cpDNA and nuclear loci ~50kb

De Queiroz, 2007

20,000 BP Present

#nextgenerationproblems

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