species level systematics of bartsia (orobanchaceae)- a multilocus approach with complete sampling...
DESCRIPTION
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.TRANSCRIPT
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
http
://g
oo.g
l/l3
DnH
D
http
://g
oo.g
l/rit
OL4
Bellardia trixago (L.) All.
http
://g
oo.g
l/o0
e7G
s
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
−100 −80 −60 −40
−60
−40
−20
020
0
1000
2000
3000
4000
5000
6000
●●●●●●●●●●●●●●●●●
●
●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●
●●●●●●
●
●●●●●●●●●●●●●●●●●●●●●●
●●●
●●●●●●
●●●
●●●●●
●●●●●●●●●●●●●●●●●●●●●●●●●●●●
●●●●●●●●●●●●●
●●●●●●●●●●●●●●●●●●●
●●●●●●●●●●
●●●●●●●●
●●
●●●●●●●●●●●●●●●
●
●●●●●●●●●●●●●●●●●●●●●
●●●●●●●
●●●●●●●●●●●●●●●●●●●
●
●●●●●●●●●●●●●●●●
●●●●●●●
●
●●●●
●
●
●
●
●●●
●
●●●
●
●
●
● ●●●●●
●●●
●●●●●●●●●●●●●●●●●●●●●●●●●
●●●
●
●●●●●●●●●●●
●●●
●
●●●●●●●●●●●●●●●●●●●●●●●●
●●●
●●●●●●●●●●●●●●●●●●●●
●●●●●●●●●●●●●●●●
●●●●●●●●●●●●●●●
●
●●
●●●●●●
●●
●●●●
●●●●●●●
●●●●●●●●●●●●●●●●●●●●●●
●●●●●●●●●●●●●
●●●●●●●●●●●
●
●
●
●
- 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
-100 -90 -80 -70 -60 -50 -40
-60
-40
-20
020
Neobartsia filiformis
0
1000
2000
3000
4000
5000
6000
Neobartsia filiformis
Neobartsia pedicularoides
−90 −80 −70 −60 −50 −40 −30
−60
−40
−20
020
Neobartsia pedicularoides
0
1000
2000
3000
4000
5000
6000●●●●●●●●●
●
●●●●●●●●
●●●●●●●●●●●
●●
●●
●
●●● ●●
●
●
Neobartsia pedicularoides
100
A)
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