Full Bayesian comparative biogeography of Philippine geckos challenges predictions of climate-driven vicariant speciation
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This document summarizes a presentation on a study that used full Bayesian comparative methods and RADseq genomic data to analyze the phylogeography of two genera of geckos in the Philippines, Cyrtodactylus and Gekko. The study found strong support for independent divergences of Cyrtodactylus populations across islands but weaker support for independent divergences in Gekko. This provides evidence against the "species pump" hypothesis that fragmentation of islands alone promoted diversification in these lizards. However, the study notes limitations including few island pairs analyzed and variation in fragmentation times among islands.
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Full Bayesian comparative biogeography of Philippine geckos challenges predictions of climate-driven vicariant speciation
- 1. 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
- 2. Comparative biogeography of geckos @jamoaks 2/16
- 3. Comparative biogeography of geckos @jamoaks 3/16
- 4. Did fragmentation of islands promote diversification? Comparative biogeography of geckos @jamoaks 3/16
- 5. 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
- 6. Comparative biogeography of geckos @jamoaks 4/16
- 7. Comparative biogeography of geckos @jamoaks 4/16
- 8. m1 m2 m3 m4 m5 Comparative biogeography of geckos @jamoaks 5/16
- 9. m1 m2 m3 m4 m5 We want to infer the model and divergence times given genetic data Comparative biogeography of geckos @jamoaks 5/16
- 10. 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 0 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
- 11. 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 0 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
- 12. 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 0 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
- 13. 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 0 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
- 14. Cyrtodactylus Gekko Latitude q q q q q q q q q q q q q q q q 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 q q q q q q q q q q q q q q q q 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
- 15. 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
- 16. 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
- 17. 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
- 18. 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
- 19. 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
- 20. 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) Estimatedtime(ˆt) J. R. Oaks et al. (2019). Evolution 73: 1151–1167 Comparative biogeography of geckos @jamoaks 9/16
- 21. Results: Simulations J. R. Oaks et al. (2019). Evolution 73: 1151–1167 Comparative biogeography of geckos @jamoaks 9/16
- 22. 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
- 23. 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
- 24. 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) Islandpair J. R. Oaks et al. (2019). Evolution 73: 1151–1167 Comparative biogeography of geckos @jamoaks 10/16
- 25. 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) Islandpair Strong support for independent divergences J. R. Oaks et al. (2019). Evolution 73: 1151–1167 Comparative biogeography of geckos @jamoaks 10/16
- 26. 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
- 27. 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) Islandpair J. R. Oaks et al. (2019). Evolution 73: 1151–1167 Comparative biogeography of geckos @jamoaks 11/16
- 28. 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) Islandpair Weak support for independent divergences J. R. Oaks et al. (2019). Evolution 73: 1151–1167 Comparative biogeography of geckos @jamoaks 11/16
- 29. Take home points Support against the “species-pump” hypothesis Comparative biogeography of geckos @jamoaks 12/16
- 30. 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
- 31. Caveats Too few island pairs to rule out climate-driven vicariant speciation Variation in fragmentation times among island pairs Variation in mutation rates Comparative biogeography of geckos @jamoaks 13/16
- 32. 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
- 33. 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
- 34. 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
- 35. Questions? joaks@auburn.edu phyletica.org c 2007 Boris Kulikov boris-kulikov.blogspot.com Comparative biogeography of geckos @jamoaks 16/16