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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Did fragmentation of islands promote diversification? Comparative biogeography of geckos @jamoaks 3/16
Did fragmentation of islands promote diversification? Click here for a sea-level animation of SE Asia youtu.be/mLNLRdbu5W8 Comparative biogeography of geckos @jamoaks 3/16
Comparative biogeography of geckos @jamoaks 4/16
Comparative biogeography of geckos @jamoaks 4/16
m 1 m 2 m 3 m 4 m 5 Comparative biogeography of geckos @jamoaks 5/16
m 1 m 2 m 3 m 4 m 5 We want to infer the model and divergence times given genetic data Comparative biogeography of geckos @jamoaks 5/16
Previous tests of “species-pump” 0.20 ◮ Our previous attempts using ABC left 0.15 little information in summary statistics Probability 0.10 to inform divergence times 1 , 2 0.05 0.00 1 2 3 4 5 6 7 8 9 Number of events Comparison Crocidura Cynopterus Cyrtodactylus Dendrolaphis Gekko Haplonycteris Macroglossus Ptenochirus Insulasaurus 0 5 10 15 1 J. R. Oaks et al. (2013). Evolution 67: 991–1010. 2 J. R. Oaks (2014). BMC Evolutionary Biology 14: 150 Time Comparative biogeography of geckos @jamoaks 6/16
Previous tests of “species-pump” 0.20 ◮ Our previous attempts using ABC left 0.15 little information in summary statistics Probability 0.10 to inform divergence times 1 , 2 0.05 What now? 0.00 1 2 3 4 5 6 7 8 9 Number of events Comparison Crocidura Cynopterus Cyrtodactylus Dendrolaphis Gekko Haplonycteris Macroglossus Ptenochirus Insulasaurus 0 5 10 15 1 J. R. Oaks et al. (2013). Evolution 67: 991–1010. 2 J. R. Oaks (2014). BMC Evolutionary Biology 14: 150 Time Comparative biogeography of geckos @jamoaks 6/16
Previous tests of “species-pump” 0.20 ◮ Our previous attempts using ABC left 0.15 little information in summary statistics Probability 0.10 to inform divergence times 1 , 2 0.05 What now? 0.00 1 2 3 4 5 6 7 8 9 Number of events We need more data and/or a more efficient method Comparison Crocidura Cynopterus Cyrtodactylus Dendrolaphis Gekko Haplonycteris Macroglossus Ptenochirus Insulasaurus 0 5 10 15 1 J. R. Oaks et al. (2013). Evolution 67: 991–1010. 2 J. R. Oaks (2014). BMC Evolutionary Biology 14: 150 Time Comparative biogeography of geckos @jamoaks 6/16
Previous tests of “species-pump” 0.20 ◮ Our previous attempts using ABC left 0.15 little information in summary statistics Probability 0.10 to inform divergence times 1 , 2 0.05 What now? 0.00 1 2 3 4 5 6 7 8 9 Number of events We need more data and/or a more efficient method Our goal is to do both Comparison Crocidura Cynopterus Cyrtodactylus Dendrolaphis Gekko Haplonycteris Macroglossus Ptenochirus Insulasaurus 0 5 10 15 1 J. R. Oaks et al. (2013). Evolution 67: 991–1010. 2 J. R. Oaks (2014). BMC Evolutionary Biology 14: 150 Time Comparative biogeography of geckos @jamoaks 6/16
Cyrtodactylus Gekko Batan ● ● Sabtang 20 20 Babuyan Claro ● ● Babuyan Claro Calayan ● ● Camiguin Norte ● Dalupiri ● Camiguin Norte Luzon 2 ● ● Luzon 1 Connected? Yes Maybe No 15 15 ● Polillo Luzon Luzon 3 ● ● ● Latitude Lubang Romblon Tablas ● Tablas ● ● ● Sibuyan ● Masbate Samar Panay ● ● North Gigante ● ● Panay 1 ● South Gigante Panay 2 ● ● Leyte ● Negros 10 10 ● Negros Bohol ● ● Camiguin Sur ● Palawan ● Borneo 118 120 122 124 126 118 120 122 124 126 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
Analyzed RADseq data with full-likelihood Bayesian comparative phylogeographic method 1 : Ecoevolity : E stimating evo lutionary 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
Analyzed RADseq data with full-likelihood Bayesian comparative phylogeographic method 1 : Ecoevolity : E stimating evo lutionary coevality ◮ Analytically integrate over coalescent genealogies and mutational histories 2 ◮ 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
Analyzed RADseq data with full-likelihood Bayesian comparative phylogeographic method 1 : Ecoevolity : E stimating evo lutionary coevality ◮ Analytically integrate over coalescent genealogies and mutational histories 2 ◮ 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
Analyzed RADseq data with full-likelihood Bayesian comparative phylogeographic method 1 : Ecoevolity : E stimating evo lutionary coevality ◮ Analytically integrate over coalescent genealogies and mutational histories 2 ◮ 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
Analyzed RADseq data with full-likelihood Bayesian comparative phylogeographic method 1 : Ecoevolity : E stimating evo lutionary 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
Results: Simulations Cyrtodactylus Gekko 0.04 t ) p ( t ∈ CI ) = 0.873 p ( t ∈ CI ) = 0.895 Estimated time ( ˆ 0.004 RMSE = 1.11e-04 RMSE = 1.66e-05 0.03 0.003 0.02 0.002 0.01 0.001 0.00 0.000 0.00 0.02 0.04 0.000 0.002 0.004 True divergence time ( t ) J. R. Oaks et al. (2019). Evolution 73: 1151–1167 Comparative biogeography of geckos @jamoaks 9/16
Results: Simulations J. R. Oaks et al. (2019). Evolution 73: 1151–1167 Comparative biogeography of geckos @jamoaks 9/16
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
Results: Cyrtodactylus <0.0134 <0.00442 <0.00123 0.153 1.00 <0.00759 <0.00244 <0.000531 17.8 0.75 Probability 0.50 0.25 0.00 1 2 3 4 5 6 7 8 Number of events J. R. Oaks et al. (2019). Evolution 73: 1151–1167 Comparative biogeography of geckos @jamoaks 10/16
Results: Cyrtodactylus <0.0134 <0.00442 <0.00123 0.153 1.00 <0.00759 <0.00244 <0.000531 17.8 0.75 Probability Island pair 0.50 Bohol | Camiguin Sur Samar | Leyte Luzon 1 | Babuyan Claro 0.25 Luzon 2 | Camiguin Norte Polillo | Luzon 3 Panay | Negros 0.00 Sibuyan | Tablas 1 2 3 4 5 6 7 8 0.0000 0.0005 0.0010 0.0015 0.0020 Number of events Divergence time (substitutions/site) J. R. Oaks et al. (2019). Evolution 73: 1151–1167 Comparative biogeography of geckos @jamoaks 10/16
Results: Cyrtodactylus <0.0134 <0.00442 <0.00123 0.153 1.00 <0.00759 <0.00244 <0.000531 17.8 0.75 Probability Island pair 0.50 Bohol | Camiguin Sur Samar | Leyte Luzon 1 | Babuyan Claro 0.25 Luzon 2 | Camiguin Norte Polillo | Luzon 3 Panay | Negros 0.00 Sibuyan | Tablas 1 2 3 4 5 6 7 8 0.0000 0.0005 0.0010 0.0015 0.0020 Number of events Divergence time (substitutions/site) Strong support for independent divergences J. R. Oaks et al. (2019). Evolution 73: 1151–1167 Comparative biogeography of geckos @jamoaks 10/16
Results: Gekko <0.0131 <0.00439 <0.00124 1.65 0.6 <0.0075 <0.00245 0.6 1.21 0.4 Probability 0.2 0.0 1 2 3 4 5 6 7 8 Number of events J. R. Oaks et al. (2019). Evolution 73: 1151–1167 Comparative biogeography of geckos @jamoaks 11/16
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