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Published December 31, 2017 | Version v1
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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

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Grismer, L. Lee, Grismer, Jesse 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, DOI: 10.11646/zootaxa.4300.4.2

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Cites
Publication: 10.1080/21564574.1996.9649959 (DOI)
Publication: 10.11646/zootaxa.3980.1.6 (DOI)
Publication: 10.1093/sysbio/syt069 (DOI)
Publication: 10.1111/j.1463-6409.2011.00495.x (DOI)
Publication: 10.1111/j.1095-8312.2001.tb01394.x (DOI)
Publication: 10.1093/bioinformatics/17.8.754 (DOI)
Publication: 10.1186/1471-2156-11-94 (DOI)
Publication: 10.1016/j.ympev.2013.09.005 (DOI)
Publication: 10.1111/j.1558-5646.1990.tb05225.x (DOI)
Publication: 10.1006/mpev.1999.0615 (DOI)
Publication: 10.1109/gce.2010.5676129 (DOI)
Publication: 10.1093/molbev/msu300 (DOI)
Publication: 10.1111/j.1461-0248.2004.00715.x (DOI)
Publication: 10.1016/S0169-5347(01)02198-X (DOI)
Publication: 10.1016/j.jseaes.2006.03.009 (DOI)
Publication: 10.1111/j.1095-8312.1975.tb00732.x (DOI)
Publication: 10.1046/j.1365-2435.2000.00430.x (DOI)
Publication: 10.1073/pnas.94.8.3828 (DOI)
Publication: 10.1016/j.ympev.2012.08.025 (DOI)
Has part
Figure: 10.5281/zenodo.839298 (DOI)
Figure: 10.5281/zenodo.839300 (DOI)
Figure: 10.5281/zenodo.839302 (DOI)
Figure: 10.5281/zenodo.839304 (DOI)
Figure: 10.5281/zenodo.839306 (DOI)
Figure: 10.5281/zenodo.839308 (DOI)
Figure: 10.5281/zenodo.839310 (DOI)
Figure: 10.5281/zenodo.839312 (DOI)
Figure: 10.5281/zenodo.839314 (DOI)

References

  • Bauer, A.M., Russell, A.P. & Powell, G.L. (1996) The evolution of locomotor morphology in Rhoptropus (Squamata: Gekkonidae): functional and phylogenetic consideration. African Journal of Herpetology, 45, 8-30. https://doi.org/10.1080/21564574.1996.9649959
  • Drummond, 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.
  • Goodman, B.A., Miles, D.B. & Schwarzkopf, L. (2008) Life on the rocks: habitat use drives morphological and performance evolution in lizards. Ecology, 89, 3462-3471.
  • Grismer, L.L., Belabut, D.M., Quah, E.S.H., Chan, K.O., Wood Jr., P.L. & Hashim, R. (2014a) A new species of karst forestadapted Bent-toed Gecko (genus Cyrtodactylus) belonging to the C. sworderi complex from a threatened karst forest in Perak, Peninsular Malaysia. Zootaxa, 3755, 434-466.
  • Grismer, L.L., Wood, Jr., P.L., Anuar S., Davis, H.R., Cobos, A.J. & Murdoch, M.L. (2016b) 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, 1-17.
  • Grismer, L.L., Wood, Jr., P.L., Anuar S., Grismer, M.S., Muin, M.A., Davis, H.R., Aguilar, C., Klaback, R., Cobos, A.J., Aowphol, A. & Sites Jr., J. (2016a) Two new Bent-toed Geckos of the Cyrtodactylus pulchellus complex from Peninsular Malaysia and multiple instances of convergent adaptation to limestone forest ecosystems. Zootaxa, 4105, 401-429.
  • Grismer, L.L., Wood, Jr., P.L., Chan, K.O., Anuar, S. & Muin, M.A. (2014b) Cyrts in the city: A new Bent-toed Gecko (Genus Cyrtodactylus) is the only endemic species of vertebrate from Batu Caves, Selangor, Peninsular Malaysia. Zootaxa, 3774, 381-394.
  • Grismer, L.L., Wood Jr., P.L., Anuar, S., Quah, E.S.H., Muin, M.A., Chan, K.O., Sumarli, A.X. & Loredo, A.I. (2015b) Repeated evolution of sympatric, paleoendemic species in closely related, co-distributed lineages of Hemiphyllodactylus Bleeker, 1860 (Squamata: Gekkonidae) across a sky-island archipellago in Peninsular Malaysia. Zoological Journal of the Linnean Society, 174, 859-876.
  • Grismer, L.L., Wood, Jr., P.L., Ngo, V.T. & Murdoch, M.L. (2015a) The systematics and independent evolution of cave ecomorphology in distantly related clades of Bent-toed Geckos (Genus Cyrtodactylus Gray, 1827) from the Mekong Delta and islands in the Gulf of Thailand. Zootaxa, 3980 (1), 106-126.
  • http://dx.doi.org/10.11646/zootaxa.3980.1.6
  • Grismer, L.L., Wood, Jr., Thura, M.K, Zin, T., Quah, E.S.H., Murdoch, M.L., Grismer, M.S., Lin, A., Kyaw, H. & Ngwe, L. (2017a) Twelve new species of Cyrtodactylus Gray (Squamata: Gekkonidae) from isolated limestone habitats in eastcentral and southern Myanmar demonstrate high localized diversity and unprecedented microendemism. ZoologicalJournal of the Linnean Society. [in press]
  • Grismer, L.L., Wood, Jr., Thura, M.K, Zin, T., Quah, E.S.H., Murdoch, M.L., Grismer, M.S., Lin, A., Kyaw, H. & Ngwe, L. (2017b) Phylogenetic taxonomy of Hemiphyllodactylus Bleeker, 1860 (Squamata: Gekkonidae) with descriptions of three new species from Myanmar. Journal of Natural History. [in press]
  • Grummer, J.A., Bryson, R.W. Jr. & Reeder, T.W. (2014) Species delimitation using Bayes factors: simulations and application to the Sceloporus scalaris species group (Squamata: Phrynosomatidae). Systematic Biology, 63, 119-133. https://doi.org/10.1093/sysbio/syt069
  • Heinicke, 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.x
  • Herrel, A., Meyers, J.J. & Vanhooydonck, B. (2001) Correlations between habitat use and body shape in a phrynosomatid lizard (Urosaurus ornatus): a population-level analysis. Biological Journal of the Linnean Society, 74, 305-314. https://doi.org/10.1111/j.1095-8312.2001.tb01394.x
  • Huelsenbeck, J.P., Bollback, J.P. & Levine, A.M. (2002) Inferring the root of a phylogenetic tree. Systematic Biology, 51, 332- 343.
  • Huelsenbeck, J. & Ronquist, F. (2001) MRBAYES: Bayesian inference of phylogeny. Bioinformatics, 17, 754-755. https://doi.org/10.1093/bioinformatics/17.8.754
  • Huelsenbeck, J.P., Ronquist, F., Nielsen, R. & Bollback, J.P. (2001) Bayesian Inference of phylogeny and its impact on evolutionary biology. Science, 294, 2310-2314.
  • Johnson, M.K., Russell, A.P. & Bauer, A.M. (2005) Locomoter morphometry of the Pachydactylus radiation of lizards (Gekkota: Gekkonidae): a phylogenetically and ecologically informed analysis. Canadian Journal of Zoology, 83, 1511- 1524.
  • Jombart, T., Devillard, S. & Balloux, F. (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics, 11, 94.
  • https://doi.org/10.1186/1471-2156-11-94
  • Kaiser, H.F. (1960) The application of electronic computers to factor analysis. Education and Psychological Measurement, 20, 141-151.
  • Kirchberger, P.C., Sefc, K.M., Sturmbauer, C. & Koblmuller, S. (2014) Outgroup effects the root position and tree toplogy in AFLP phylogeny of a rapidly radiating lineage of cichlid fish. Molecular Phylogenetics and Evolution, 70, 57-62. https://doi.org/10.1016/j.ympev.2013.09.005
  • Kiernan, K. (2011) Monadnaocks of the Mekong delt: character, caves, and evolution. Cave and Karst Science, 38, 71-80.
  • Lleonart, J., Salat, J. & Torres, G.J. (2000) Removing allometric effects of body size in morphological analysis. Journal of Theoretical Biology, 205, 85-93.
  • Losos, J.B. (1990) The evolution of form and function: morphology and locomotor performance in west Indian Anolis lizards. Evolution, 44, 1189-1203.
  • https://doi.org/10.1111/j.1558-5646.1990.tb05225.x
  • Luu, V.Q., Bonkowski, M., Nguyen, T.Q., Le, M.D., Schneider, N., Ngo, H.T. & Ziegler, T. (2016) Evolution in karst massifs: Cryptic diversity among bent-toed geckos along the Truong Son Range with descriptions of three new species and one new country record from Laos. Zootaxa, 4107 (2), 101-140.
  • Macey, J. & Schulte, J. (1999) Molecular Phylogenetics, Trna Evolution, and Historical Biogeography in Anguid Lizards and Related Taxonomic Families. Molecular Phylogenetics and Evolution, 12, 250-272. https://doi.org/10.1006/mpev.1999.0615
  • Minh, Q., Nguyen, M.A.T. & von Haeseler, A. (2013) Ultrafast approximation for phylogenetic bootstrap. Molecular Biology and Evolution, 30, 1188-1195.
  • 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), 2013, New Orleans, LA, pp. 1-8. https://doi.org/10.1109/gce.2010.5676129
  • Nguyen, VL, Ta, T.K.O. & Tateishi, M. (2000) Late Holocene depositional
  • Nguyen, L.-T., Schmidt, H.A., von Haeseler, A. & Minh, B.Q. (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Molecular Biology and Evolution, 32, 268-274. https://doi.org/10.1093/molbev/msu300
  • Nosil, P. (2012) Ecological Speciation. Oxford University Press, New York, 280 pp.
  • Rambaut, A. & Drummond, A.J. (2013) TreeAnnotator v1.8.0 MCMC Output Analysis. Available from: http:// beast.bio.ed.ac.uk/TreeAnnotator (accessed 28 June 2017)
  • Rambaut, A., Suchard, M.A., Xie, D. & Drummond, A.J. (2014) Tracer v1.6. Available from: http://beast.bio.ed.ac.uk/Tracer (accessed 28 June 2017)
  • Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D.L., Darling, A., Hohna, B., Larget, L., Liu, L., Suchard, M.A. & Huelsenbeck, J.P. (2012) Mr. Bayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice across a Large Model Space. Systematic Biology, 61, 539-542.
  • Rosenfeld, J.A., Payne, A. & DeSalle, R. (2012) Random roots and lineage sorting. Molecular Phylogenetics and Evolution, 64, 12-20.
  • Rota-Stabelli, O. & Telford, M.J. (2008) A multi-criterion approach for the selection of optimal outgrous in phylogeny: recovering some support for Mandibulata over Myriochelata using mitogenomics. Molecular Phylogenetics and Evolution, 48, 103-111.
  • Rundle, H.D. & Nosil, P. (2005) Ecological speciation. Ecology Letters, 8, 336-352. https://doi.org/10.1111/j.1461-0248.2004.00715.x
  • Schluter, D. (2001) Ecology and the origin of species. Trends In Ecology & Evolution 16, 372-380. https://doi.org/10.1016/S0169-5347(01)02198-X
  • Siler, C.D., Oaks, J.R., Esselstyn, J.A., Diesmos, A.C. & Brown, R.M. (2010) Phylogeny and biogeography of Philippine bent- toed geckos (Gekkonidae: Cyrtodactylus) contradict a prevailing model of Pleistocene diversification. Molecular Phylogenetics and Evolution, 55, 699-710.
  • Tamura, T., Saito, Y., Sieng, S., Ben, B., Kong, M., Choup, S. & Tsukawaki, S. (2007) Depositional facies and radiocarbon ages of a drill core from the Mekong River lowland near Phnom Penh, Cambodia: evidence for tidal sedimentation at the time of Holocene maximum flooding. Journal of Asian Earth Sciences, 29, 585-592. https://doi.org/10.1016/j.jseaes.2006.03.009
  • Thorpe, R.S. (1975) Quantitative handling of characters useful in snake systematics with particular reference to interspecific variation in the Ringed Snake Natrix natrix (L.). Biological Journal of the Linnean Society, 7, 27-43. https://doi.org/10.1111/j.1095-8312.1975.tb00732.x
  • Thorpe, R.S. (1983) A review of the numerical methods for recognized and analyzing racial differentiation. In: Felsenstein, J. (Ed.), Numerical Taxonomy. Springer-Verlag, Berlin, pp. 404-423.
  • Turan, C. (1999) A note on the examination of morphometric differentiation among fish populations: The Truss System. Turkish Journal of Zoology, 23, 259-263.
  • Uetz, P. & Hallermann, J. (2017) The Reptile Database. Electronic Database accessible. Available from: http://www.reptiledatabase.org (accessed 28 June 2017)
  • Vanhooydonck, B., Van Damme, R. & Aerts, P. (2000) Ecomorphological correlates of habitat partitioning in Corsican lacertid lizards. Funtional Ecology, 14, 358-368.
  • https://doi.org/10.1046/j.1365-2435.2000.00430.x
  • Vitt, L.J., Caldwell, J.P., Zani, P.A. & Titus, T.A. (1997) The role of habitat shift in the evolution of lizard morphology: evidence from tropical Tropidurus. Proceedings of the National Academy of Sciences, 94, 3828-3832. https://doi.org/10.1073/pnas.94.8.3828
  • Wheeler, W.C. (1990) Nucleic acid sequence phylogeny and random outgroups. Cladistics, 6, 363-367.
  • Wood, P.L. Jr., Heinicke, M.P., Jackman, T.R. & Bauer, A.M. (2012) Phylogeny of bent-toed geckos (Cyrtodactylus) reveals a west to east pattern of diversification. Molecular Phylogenetics and Evolution, 65, 992-1003. https://doi.org/10.1016/j.ympev.2012.08.025
  • Zaaf, A. & Van Dammer, R. (2001) Limb proportions in climbing and ground-dwelling geckos (Lepidosauria, Gekkonidae): a phylogenetically informed analysis. Zoomorphology, 121, 43-53.