Abstract
The Sundaic swamp clade of the genus Cyrtodactylus contains nine species that collectively range through Peninsular Malaysia and its associated land bridge islands, Singapore, Sumatra, Java, and Pulau Natuna Besar. Ancestral range reconstruction analyses using BioGeoBEARS based on an updated molecular phylogeny of the nine Sundaic swamp clade species of Cyrtodactylus demonstrated that this lineage evolved in Peninsular Malaysia, dispersed independently to Sumatra and Pulau Natuna Besar, Indonesia and most likely back into Peninsular Malaysia from Sumatra. This scenario is consistent with climate-driven, cyclical, ephemeral, geographic reconfigurations of Sundaic landmasses from at least the mid-Miocene to present.
References
Agarawal, I., Bauer, A.M., Jackman, T.R. & Karanth, K.P. (2014) Insights into Himalayan biogeography from geckos: a molecular phylogeny of Cyrtodactylus (Squamata: Gekkonidae). Molecular Phylogenetics and Evolution, 80, 145–155.
https://doi.org/10.1016/j.ympev.2014.07.018Brandley, M.C., Wang, Y., Guo, X., Nieto Montes de Oca, A., Feria-Ortiz, M., Hikida, T. & Ota, H. (2011) Accommodating locus-specific heterogeneity in molecular dating methods: an example using inter-continental dispersal of Plestiodon (Eumeces) lizards. Systematic Biology, 60, 3–15.
https://doi.org/10.1093/sysbio/syq045Cannon, C.H., Morley, R.J. & Bush, A.B.G. (2009) The current refugial rainforests of Sundaland are unrepresentative of their biogeographic past and highly vulnerable to disturbance. Proceedings of the National Academy of Sciences, 106, 11188–11193.
https://doi.org/10.1073/pnas.0809865106Carranza, S., Arnold, E.N., Mateo, J. & Lopez-Jurado, L. (2000) Long-distance colonization and radiation in gekkonid lizards, Tarentola (Reptilia: Gekkonidae), revealed by mitochondrial DNA sequences. Proceedings of the Royal Society B: Biological Sciences, 267, 637–649.
https://doi.org/10.1098/rspb.2000.1050de Bruyn, M., Rüber, L., Nylinder, S., Stelbrink, B., Lovejoy, N.R., Lavoué, S., Tan, H.H., Nugroho, E., Wowor, D., Ng, P.K.L., Siti Azizah, M.N., von Rintelen, T., Hall, R. & Carvalho, G.R. (2013) Paleo-drainage basin connectivity predicts evolutionary relationships across three Southeast Asian biodiversity hotspots. Systematic Biology, 62, 398–410.
https://doi.org/10.1093/sysbio/syt007de Bruyn, M., Stelbrink, B., Morley, R.J., Hall, R., Carvalho, G.R., Cannon, C.H., van den Bergh, G., Meijaard, E., MetcalfeI, R., Boitani, L., Maiorano, L., Shoup, R. & von Rintelen, T. (2014) Borneo and Indochina are major evolutionary hotspots for southeast Asian biodiversity. Systematic Biology, 63, 1–23.
https://doi.org/10.1093/sysbio/syu047Drummond, A.J., Suchard, M.A., Xie, D. & Rambaut, A. (2012) Bayesian phylogenetics with BEAUti and BEAST 1.7. Molecular Biology and Evolution, 29, 1969–1973.
https://doi.org/10.1093/molbev/mss075Gower, D., Johnson, K.G., Rosen, B.R., Richardson, J., Rüber, L. & Williams, S.T. (2012) Biotic evolution and environmental change in Southeast Asia. Cambridge University Press, Cambridge, 475 pp.
https://doi.org/10.1017/cbo9780511735882Grismer, L.L. & Grismer, J.L. (2017) A re-evaluation of the phylogenetic relationships of the Cyrtodactylus condorensis group (Squamata; Gekkonidae) and a suggested protocol for the characterization of rock-dwelling ecomorphology in Cyrtodactylus. Zootaxa, 4300 (4), 486–504.
https://doi.org/10.11646/zootaxa.4300.4.2Grismer, L.L., Wood Junior, P.L., Anuar, S., Davis, H.R., Cobos, A.J. & Murdoch, M.L. (2016) A new species of karst forest Bent-toed Gecko (genus Cyrtodactylus Gray) not yet threatened by foreign cement companies and a summary of Peninsular Malaysia’s endemic karst forest herpetofauna and the need for its conservation. Zootaxa, 4061 (1), 1–17.
https://doi.org/10.11646/zootaxa.4061.1.1Grismer, L.L., Wood Junior., P.L., Anuar, S., Quah, E.S.H., Muin, M.A., Chan, K.O., Sumarli, A.X. & Loredo, A.I. (2015) Repeated evolution of sympatric, paleoendemic species in closely related, co-distributed lineages of Hemiphyllodactylus Bleeker, 1860 (Squamata: Gekkonidae) across a sky-island archiplelago in Peninsular Malaysia. Zoological Journal of the Linnean Society, 174, 859–876.
https://doi.org/10.1111/zoj.12254Grismer, L.L., Wood, P.L. Jr. & Lim, K.K.P. (2012) Cyrtodactylus majulah, a new species of Bent-toed Gecko (Reptilia: Squamata: Gekkonidae) from Singapore and the Riau Archipelago. Raffles Bulletin of Zoology, 60, 487–499.
Harvey, M.B., O’Connell, K.A., Barraza, G., Riyanto, A., Kurniawan, N. & Smith, E.N. (2015) Two new species of Cyrtodactylus (Squamata: Gekkonidae) from the southern Bukit Barisan Range of Sumatra and an estimation of their phylogeny. Zootaxa, 4020 (3), 495–516.
https://doi.org/10.11646/zootaxa.4020.3.5
Heath, T.A., Hedtke, S.M. & Hillis, D.M. (2008) Taxon sampling and the accuracy of phylogenetic analyses. Journal of Systematics and Evolution, 46, 239–257.
https://doi.org/10.1080/10635150600697358Heinicke, M.P., Greenbaum, E., Jackman, T.R. & Bauer, A.M. (2011) Phylogeny of a trans-Wallacean radiation (Squamata, Gekkonidae, Gehyra) supports a single early colonization of Australia. Zoologica Scripta, 40, 584–602.
https://doi.org/10.1111/j.1463-6409.2011.00495.xHuelsenbeck, J.P., Ronquist, F., Nielsen, R. & Bollback, J.P. (2001) Bayesian inference of phylogeny and Its impact on evolutionary biology. Science, 294, 2310–2314.
https://doi.org/10.1126/science.1065889Landis, M., Matzke, N.J., Moore, B.R. & Huelsenbeck, J.P. (2013) Bayesian analysis of biogeography when the number of areas is large. Systematic Biology, 62, 789–804.
https://doi.org/10.1093/sysbio/syt040Lohman, D.J., de Bruyn, M. Page, T., von Rintelen, K., Hall, R., Ng, P.K.L., Shih, H.T., Carvalho, G.R. & von Rintelen, T. (2011) Biogeography of the Indo-Australian archipelago. Annual review of Evolution, Ecology and Systematics, 42, 205–226.
https://doi.org/10.1146/annurev-ecolsys-102710-145001Matzke, N.J. (2013) Probabilistic historical biogeography: New models for founder-event speciation, imperfect detection, and fossils allow improved accuracy and model-testing. Frontiers in Biogeography, 5, 242–248.
https://doi.org/10.1093/sysbio/syu056Matzke, N.J. (2014) Model selection in historical biogeography reveals that founder-effect speciation is a crucial process in island clades. Systematic Biology, 63, 1–21.
https://doi.org/10.1093/sysbio/syu056Matzke, N.J. (2017) BiGeoBEARS mistakes to avoid. Available from: http://phylo.wikidot.com/biogeobears-mistakes-to-avoid (accessed 13 August 2018)
Miller, M.A., Pfeiffer, W. & Schwartz, T. (2010) Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Proceedings of the Gateway Computing Environments Workshop (GCE), New Orleans, LA, 14 November 2010, pp. 1–8.
https://doi.org/10.1109/gce.2010.5676129Morley, R.J. (2000) Origin and evolution of tropical rain forests. John Wiley & Sons, Chichester, 362 pp.
Nielsen, S.V. & Oliver, P.M. (2017) Morphological and genetic evidence for a new karst specialist lizard from New Guinea (Cyrtodactylus: Gekkonidae). Royal Society Open Science, 4, 170781.
https://doi.org/10.1098/rsos.170781R Core Team. (2015) R: A language and environment for statistical computing. R Foundation for Statistical Computing. Vienna. http://www.R-project.org (accessed 29 December 2016)
Rambaut, A. & Drummond, A.J. (2013) TreeAnnotator v1.8.0 MCMC Output Analysis. Available from http://beast.bio.ed.ac.uk/ (accessed 13 August 2018)
Rambaut, A., Suchard, M.A., Xie, D. & Drummond, A.J. (2014) Tracer v1.6. Available from: http://tree.bio.ed.ac.uk/software/tracer/
Ree, R.H. & Sanmartín, I. (2018) Conceptual and statistical problems with the DEC+J model of founder-event speciation and its comparison with DEC via model selection. Journal of Biogeography, 45, 741–749.
https://doi.org/10.1111/jbi.13173Ree, R.H. & Smith, S.A. (2008) Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Systematic Biology, 57, 4–14.
https://doi.org/10.1080/10635150701883881Singham, G.V., Othman, A.S. & Lee, C.-Y.. (2017) Phylogeography of the termite Macrotermes gilvus and insight into ancient dispersal corridors in Pleistocene Southeast Asia. PLoS one, 12, e0186690.
https://doi.org/10.1371/journal.pone.0186690Uetz, P., Freed, P. & Hošek, J. (Eds.) (2018)The Reptile Database. Available from: http://www.reptile-database.org (accessed 13 August 2018)
Woodruff, D.S. (2010) Biogeography and conservation in Southeast Asia: how 2.7 million years of repeated environmental fluctuations affect today's patterns and the future of the remaining refugial-phase biodiversity. Biodiversity Conservation, 19, 919–941.
https://doi.org/10.1007/s10531-010-9783-3
Zamudio, K.R., Jones, K.B. & Ward, R.H. (1997) Molecular systematics of short-horned lizards: biogeography and taxonomy of a widespread species complex. Systematic Biology, 46, 284–305.
https://doi.org/10.1093/sysbio/46.2.284