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

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

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

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

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

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