Full Bayesian comparative biogeography of Philippine geckos - - PowerPoint PPT Presentation

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Full Bayesian comparative biogeography of Philippine geckos - - PowerPoint PPT Presentation

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Full Bayesian comparative biogeography of Philippine geckos challenges predictions of climate-driven vicariant speciation Evolution 2019 Jamie Oaks Auburn University Web: phyletica.org GitHub: joaks1 & phyletica Twitter: @jamoaks

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Full Bayesian comparative biogeography of Philippine geckos challenges predictions of climate-driven vicariant speciation

Evolution 2019

Jamie Oaks

Auburn University Web: phyletica.org GitHub: joaks1 & phyletica Twitter: @jamoaks Slides: phyletica.org/slides/evol2019.pdf

Cameron Siler Rafe Brown

University of Oklahoma University of Kansas Thanks to ASN, SSE, SSB, and all organizers!

Comparative biogeography of geckos @jamoaks 1/16

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Comparative biogeography of geckos @jamoaks 2/16

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Comparative biogeography of geckos @jamoaks 3/16

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Did fragmentation of islands promote diversification?

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Click here for a sea-level animation of SE Asia youtu.be/mLNLRdbu5W8 Did fragmentation of islands promote diversification?

Comparative biogeography of geckos @jamoaks 3/16

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Comparative biogeography of geckos @jamoaks 4/16

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Comparative biogeography of geckos @jamoaks 4/16

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m1 m2 m3 m4 m5

Comparative biogeography of geckos @jamoaks 5/16

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m1 m2 m3 m4 m5 We want to infer the model and divergence times given genetic data

Comparative biogeography of geckos @jamoaks 5/16

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Previous tests of “species-pump”

◮ Our previous attempts using ABC left little information in summary statistics to inform divergence times 1,2

0.00 0.05 0.10 0.15 0.20 1 2 3 4 5 6 7 8 9

Number of events Probability

Insulasaurus Ptenochirus Macroglossus Haplonycteris Gekko Dendrolaphis Cyrtodactylus Cynopterus Crocidura 5 10 15

Time Comparison 1 J. R. Oaks et al. (2013). Evolution 67: 991–1010. 2 J. R. Oaks (2014). BMC Evolutionary Biology 14: 150

Comparative biogeography of geckos @jamoaks 6/16

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Previous tests of “species-pump”

◮ Our previous attempts using ABC left little information in summary statistics to inform divergence times 1,2 What now?

0.00 0.05 0.10 0.15 0.20 1 2 3 4 5 6 7 8 9

Number of events Probability

Insulasaurus Ptenochirus Macroglossus Haplonycteris Gekko Dendrolaphis Cyrtodactylus Cynopterus Crocidura 5 10 15

Time Comparison 1 J. R. Oaks et al. (2013). Evolution 67: 991–1010. 2 J. R. Oaks (2014). BMC Evolutionary Biology 14: 150

Comparative biogeography of geckos @jamoaks 6/16

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Previous tests of “species-pump”

◮ Our previous attempts using ABC left little information in summary statistics to inform divergence times 1,2 What now? We need more data and/or a more efficient method

0.00 0.05 0.10 0.15 0.20 1 2 3 4 5 6 7 8 9

Number of events Probability

Insulasaurus Ptenochirus Macroglossus Haplonycteris Gekko Dendrolaphis Cyrtodactylus Cynopterus Crocidura 5 10 15

Time Comparison 1 J. R. Oaks et al. (2013). Evolution 67: 991–1010. 2 J. R. Oaks (2014). BMC Evolutionary Biology 14: 150

Comparative biogeography of geckos @jamoaks 6/16

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Previous tests of “species-pump”

◮ Our previous attempts using ABC left little information in summary statistics to inform divergence times 1,2 What now? We need more data and/or a more efficient method Our goal is to do both

0.00 0.05 0.10 0.15 0.20 1 2 3 4 5 6 7 8 9

Number of events Probability

Insulasaurus Ptenochirus Macroglossus Haplonycteris Gekko Dendrolaphis Cyrtodactylus Cynopterus Crocidura 5 10 15

Time Comparison 1 J. R. Oaks et al. (2013). Evolution 67: 991–1010. 2 J. R. Oaks (2014). BMC Evolutionary Biology 14: 150

Comparative biogeography of geckos @jamoaks 6/16

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Cyrtodactylus Gekko Latitude

  • Bohol

Palawan Samar Luzon 1 Luzon 2 Polillo Panay Sibuyan Camiguin Sur Borneo Leyte Babuyan Claro Camiguin Norte Luzon 3 Negros Tablas

Connected? Yes Maybe No

10 15 20 118 120 122 124 126

  • Babuyan Claro

North Gigante Lubang Masbate Negros Sabtang Romblon Camiguin Norte Calayan South Gigante Luzon Panay 1 Panay 2 Batan Tablas Dalupiri 10 15 20 118 120 122 124 126

Longitude

◮ Sampled 2–5 individuals from 8 pairs of populations for both Cyrtodactylus and Gekko ◮ Collected short DNA sequences (RADseq) from across genome of each individual

  • J. R. Oaks et al. (2019). Evolution 73: 1151–1167

Comparative biogeography of geckos @jamoaks 7/16

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Analyzed RADseq data with full-likelihood Bayesian comparative phylogeographic method1:

Ecoevolity: Estimating evolutionary coevality

1 J. R. Oaks (2019). Systematic Biology 68: 371–395 2 D. Bryant et al. (2012). Molecular Biology and Evolution 29: 1917–1932 Comparative biogeography of geckos @jamoaks 8/16

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Analyzed RADseq data with full-likelihood Bayesian comparative phylogeographic method1:

Ecoevolity: Estimating evolutionary coevality

◮ Analytically integrate over coalescent genealogies and mutational histories2 ◮ Dirichlet-process prior across divergence models

1 J. R. Oaks (2019). Systematic Biology 68: 371–395 2 D. Bryant et al. (2012). Molecular Biology and Evolution 29: 1917–1932 Comparative biogeography of geckos @jamoaks 8/16

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Analyzed RADseq data with full-likelihood Bayesian comparative phylogeographic method1:

Ecoevolity: Estimating evolutionary coevality

◮ Analytically integrate over coalescent genealogies and mutational histories2 ◮ Dirichlet-process prior across divergence models ◮ Goal: Fast, full-likelihood Bayesian method to infer patterns of co-diversification from genome-scale data

1 J. R. Oaks (2019). Systematic Biology 68: 371–395 2 D. Bryant et al. (2012). Molecular Biology and Evolution 29: 1917–1932 Comparative biogeography of geckos @jamoaks 8/16

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Analyzed RADseq data with full-likelihood Bayesian comparative phylogeographic method1:

Ecoevolity: Estimating evolutionary coevality

◮ Analytically integrate over coalescent genealogies and mutational histories2 ◮ Dirichlet-process prior across divergence models ◮ Goal: Fast, full-likelihood Bayesian method to infer patterns of co-diversification from genome-scale data ◮ Used simulations to assess how well ecoevolity works given the gekkonid RADseq data

1 J. R. Oaks (2019). Systematic Biology 68: 371–395 2 D. Bryant et al. (2012). Molecular Biology and Evolution 29: 1917–1932 Comparative biogeography of geckos @jamoaks 8/16

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Analyzed RADseq data with full-likelihood Bayesian comparative phylogeographic method1:

Ecoevolity: Estimating evolutionary coevality Want to learn more?

◮ Check out Kerry Cobb’s poster (Saturday at 5:30pm ExHallBC 18) ◮ I’ll be at the software bazaar (Sunday at 6:30pm)

1 J. R. Oaks (2019). Systematic Biology 68: 371–395 2 D. Bryant et al. (2012). Molecular Biology and Evolution 29: 1917–1932 Comparative biogeography of geckos @jamoaks 8/16

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Results: Simulations

0.00 0.02 0.04 0.00 0.01 0.02 0.03 0.04 Cyrtodactylus

p(t ∈ CI) = 0.873 RMSE = 1.11e-04

0.000 0.002 0.004 0.000 0.001 0.002 0.003 0.004 Gekko

p(t ∈ CI) = 0.895 RMSE = 1.66e-05

True divergence time (t) Estimated time (ˆ

t)

  • J. R. Oaks et al. (2019). Evolution 73: 1151–1167

Comparative biogeography of geckos @jamoaks 9/16

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Results: Simulations

  • J. R. Oaks et al. (2019). Evolution 73: 1151–1167

Comparative biogeography of geckos @jamoaks 9/16

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Results: Simulations Method performs well on simulated data

  • J. R. Oaks et al. (2019). Evolution 73: 1151–1167

Comparative biogeography of geckos @jamoaks 9/16

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Results: Cyrtodactylus

<0.0134 <0.00759 <0.00442 <0.00244 <0.00123 <0.000531 0.153 17.8 0.00 0.25 0.50 0.75 1.00 1 2 3 4 5 6 7 8

Number of events Probability

  • J. R. Oaks et al. (2019). Evolution 73: 1151–1167

Comparative biogeography of geckos @jamoaks 10/16

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Results: Cyrtodactylus

<0.0134 <0.00759 <0.00442 <0.00244 <0.00123 <0.000531 0.153 17.8 0.00 0.25 0.50 0.75 1.00 1 2 3 4 5 6 7 8

Number of events Probability

Sibuyan | Tablas Panay | Negros Polillo | Luzon 3 Luzon 2 | Camiguin Norte Luzon 1 | Babuyan Claro Samar | Leyte Bohol | Camiguin Sur 0.0000 0.0005 0.0010 0.0015 0.0020

Divergence time (substitutions/site) Island pair

  • J. R. Oaks et al. (2019). Evolution 73: 1151–1167

Comparative biogeography of geckos @jamoaks 10/16

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Results: Cyrtodactylus

<0.0134 <0.00759 <0.00442 <0.00244 <0.00123 <0.000531 0.153 17.8 0.00 0.25 0.50 0.75 1.00 1 2 3 4 5 6 7 8

Number of events Probability

Sibuyan | Tablas Panay | Negros Polillo | Luzon 3 Luzon 2 | Camiguin Norte Luzon 1 | Babuyan Claro Samar | Leyte Bohol | Camiguin Sur 0.0000 0.0005 0.0010 0.0015 0.0020

Divergence time (substitutions/site) Island pair

Strong support for independent divergences

  • J. R. Oaks et al. (2019). Evolution 73: 1151–1167

Comparative biogeography of geckos @jamoaks 10/16

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Results: Gekko

<0.0131 <0.0075 <0.00439 <0.00245 <0.00124 0.6 1.65 1.21 0.0 0.2 0.4 0.6 1 2 3 4 5 6 7 8

Number of events Probability

  • J. R. Oaks et al. (2019). Evolution 73: 1151–1167

Comparative biogeography of geckos @jamoaks 11/16

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Results: Gekko

<0.0131 <0.0075 <0.00439 <0.00245 <0.00124 0.6 1.65 1.21 0.0 0.2 0.4 0.6 1 2 3 4 5 6 7 8

Number of events Probability

Camiguin Norte | Dalupiri Romblon | Tablas Sabtang | Batan Negros | Panay 2 Panay 1 | Masbate Lubang | Luzon

  • S. Gigante | N. Gigante

Babuyan Claro | Calayan 0e+00 2e−04 4e−04 6e−04 8e−04

Divergence time (subsitutions/site) Island pair

  • J. R. Oaks et al. (2019). Evolution 73: 1151–1167

Comparative biogeography of geckos @jamoaks 11/16

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Results: Gekko

<0.0131 <0.0075 <0.00439 <0.00245 <0.00124 0.6 1.65 1.21 0.0 0.2 0.4 0.6 1 2 3 4 5 6 7 8

Number of events Probability

Camiguin Norte | Dalupiri Romblon | Tablas Sabtang | Batan Negros | Panay 2 Panay 1 | Masbate Lubang | Luzon

  • S. Gigante | N. Gigante

Babuyan Claro | Calayan 0e+00 2e−04 4e−04 6e−04 8e−04

Divergence time (subsitutions/site) Island pair

Weak support for independent divergences

  • J. R. Oaks et al. (2019). Evolution 73: 1151–1167

Comparative biogeography of geckos @jamoaks 11/16

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Take home points

◮ Support against the “species-pump” hypothesis

Comparative biogeography of geckos @jamoaks 12/16

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Take home points

◮ Support against the “species-pump” hypothesis ◮ Habitat heterogeniety and rare over-water dispersal via rafting on vegetation are likely more important

Comparative biogeography of geckos @jamoaks 12/16

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Caveats

◮ Too few island pairs to rule out climate-driven vicariant speciation ◮ Variation in fragmentation times among island pairs ◮ Variation in mutation rates

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Caveats

◮ Too few island pairs to rule out climate-driven vicariant speciation ◮ Variation in fragmentation times among island pairs ◮ Variation in mutation rates ◮ Seems safe to conclude that the “species-pump” is not the rule for Philippine gekkonids

Comparative biogeography of geckos @jamoaks 13/16

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Everything is on GitHub. . .

Software: ◮ Ecoevolity: https://github.com/phyletica/ecoevolity Open-Science Notebooks: ◮ Ecoevolity testing: https://github.com/phyletica/ecoevolity-experiments ◮ Gecko RADseq: https://github.com/phyletica/gekgo

Comparative biogeography of geckos @jamoaks 14/16

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Acknowledgments

Ideas and feedback: ◮ Phyletica Lab (the Phyleticians) ◮ David Bryant, Mark Holder, Adam Leach´ e, and Vladimir Minin; Editors Laura Kubatko, Mohamed Noor, and David Weisrock; and five anonymous Lab work: ◮ Patrick Monnahan and John Kelly for their help with the MSG libraries Computation: ◮ Alabama Supercomputer Authority ◮ Auburn University Hopper Cluster Funding: DEB 1656004 Photo credits: ◮ Rafe Brown and Cam Siler ◮ PhyloPic! Thanks to ASN, SSE, SSB, and all organizers of Evolution 2019!

Comparative biogeography of geckos @jamoaks 15/16

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Questions? joaks@auburn.edu phyletica.org

c 2007 Boris Kulikov boris-kulikov.blogspot.com Comparative biogeography of geckos @jamoaks 16/16