286
Views
3
CrossRef citations to date
0
Altmetric
Articles

A contribution to the phylogeny and taxonomy of the Pachydactylus weberi group (Squamata: Gekkonidae): a case of intraspecific colour polymorphism confounding taxonomy

, , , , , & show all

References

  • Aljanabi, S.M. & Martinez, I. 1997. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res. 25: 4692–4693. doi: 10.1093/nar/25.22.4692
  • Bates, M.F., Branch, W., Bauer, A., Burger, M., Marais, J., Alexander, G. & de Villiers, M. 2014. Atlas and red list of the reptiles of South Africa, Lesotho and Swaziland. South African National Biodiversity Institute, Pretoria, South Africa.
  • Bauer, A. & Branch, W. 1995. Geographic variation in western populations of the Pachydactylus punctatus complex (Reptilia Gekkonidae). TroP. Zool. 8: 69–84. doi: 10.1080/03946975.1995.10539273
  • Bauer, A., Heinicke, M., Jackman, T. & Branch, W. 2011. Systematics of the Pachydactylus mariquensis group of geckos (Reptilia: Squamata: Gekkonidae): status of P. mariquensis latirostris, P. m. macrolepis and P. amoenus. Navorsinge van die Nasionale Museum Bloemfontein 27: 85–107.
  • Bauer, A.M. 2010. A new species of Pachydactylus (Squamata: Gekkonidae) from the Otavi Highlands of northern Namibia. Bonn Zool. Bull. 57: 257–266.
  • Bauer, A.M. 2014a. Pachydactylus goodi. In Bates, M.F., Branch, W.R., Bauer, A.M., Burger, M., Marais, J., Alexander, G.J. & de Villiers, M.S. (Eds), Atlas and Red List of Reptiles of South Africa, Lesotho and Swaziland. South African National Biodiversity Institute, Pretoria, South Africa.
  • Bauer, A.M. 2014b. Pachydactylus atorquatus. In Bates, M.F., Branch, W.R., Bauer, A.M., Burger, M., Marais, J., Alexander, G.J. & de Villiers, M.S. (Eds), Atlas and Red List of Reptiles of South Africa, Lesotho and Swaziland. South African National Biodiversity Institute, Pretoria, South Africa.
  • Bauer, A.M., Barts, M. & Hulbert, F. 2006a. A new species of the Pachydactylus weberi group (Reptilia: Squamata: Gekkonidae) from the Orange River, with comments on its natural history. Salamandra 42: 83–92.
  • Bauer, A.M., Lamb, T. & Branch, W.R. 2002. A revision of Pachydactylus scutatus (Reptilia: Squamata: Gekkonidae) with the description of a new species from Northern Namibia. Proc. Calif. Acad. Sci. 53:23–36.
  • Bauer, A.M. & Lamb, T. 2002. Phylogenetic relationships among members of the Pachydactylus capensis group of southern African geckos. Afr. Zool. 37: 209–220. doi: 10.1080/15627020.2002.11657176
  • Bauer, A.M. & Lamb, T. 2003. A new species of the Pachydactylus weberi-group (Reptilia: Squamata: Gekkonidae) from the Waterberg Plateau, Namibia. Cimbebasia 19: 1–12.
  • Bauer, A.M. & Lamb, T. 2005. Phylogenetic relationships of southern African geckos in the Pachydactylus Group (Squamata: Gekkonidae). Afr. J. Herpetol. 54: 105–129. doi: 10.1080/21564574.2005.9635525
  • Bauer, A.M., Lamb, T. & Branch, W.R. 2006b. A revision of the Pachydactylus serval and P. weberi groups (Reptilia: Gekkota: Gekkonidae) of Southern Africa, and with the description of eight new species. Proc. Cal. Acad. Sci. 57: 595–709.
  • Branch, W.R., Bauer, A.M., Jackman, T.R. & Heinicke, M. 2011. A new species of the Pachydactylus weberi complex (Reptilia: Squamata: Gekkonidae) from the Namibrand Reserve, southern Namibia. Breviora 524: 1–15. doi: 10.3099/0006-9698-524.1.1
  • Burbrink, F.T., Lawson, R. & Slowinski, J.B. 2000. Mitochondrial DNA phylogeography of the polytypic North American rat snake (Elaphe obsoleta): a critique of the subspecies concept. Evolution 54: 2107–2118. doi: 10.1111/j.0014-3820.2000.tb01253.x
  • Carstens, B.C., Pelletier, T.A., Reid, N.M. & Satler, J.D. 2013. How to fail at species delimitation. Mol. Ecol. 22: 4369–4383. doi: 10.1111/mec.12413
  • Castresana, J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17: 540–552. doi: 10.1093/oxfordjournals.molbev.a026334
  • Chapple, D.G., Hutchinson, M.N., Maryan, B., Plivelich, M., Moore, J.A. & Keogh, J.S. 2008. Evolution and maintenance of colour pattern polymorphism in Liopholis (Squamata: Scincidae). Austr. J. Zool. 56: 103–115. doi: 10.1071/ZO08040
  • Corl, A., Davis, A.R., Kuchta, S.R. & Sinervo, B. 2010. Selective loss of polymorphic mating types is associated with rapid phenotypic evolution during morphic speciation. PNAS 107: 4254–4259. doi: 10.1073/pnas.0909480107
  • De Queiroz, K. 1998. The general lineage concept of species, species criteria, and the process of speciation: A conceptual unification and terminological recommendations. Endless forms: Species and speciation. Oxford University Press, New York.
  • De Queiroz, K. 2007. Species concepts and species delimitation. Syst. Biol. 56.6: 879–886. doi: 10.1080/10635150701701083
  • Drummond, A. & Rambaut, A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7: 214. doi: 10.1186/1471-2148-7-214
  • Drummond, A.J., Suchard, M.A., Xie, D. & Rambaut, A. 2012. Bayesian Phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol 29: 1969–1973. doi: 10.1093/molbev/mss075
  • FitzSimons, V. 1941. Descriptions of some new lizards from South Africa and a frog from Southern Rhodesia. Annals of the Transvaal Museum 20: 273–281.
  • Flecks, M., Schmitz, A., Böhme, W., Henkel, W.F. & Ineich, I. 2012. A new species of Gehyra Gray, 1834 (Squamata, Gekkonidae) from the Loyalty Islands and Vanuatu, and phylogenetic relationships in the genus Gehyra in Melanesia. Zoosystema 34: 203–221. doi: 10.5252/z2012n2a1
  • Gamble, T., Bauer, A.M., Greenbaum, E. & Jackman, T.R. 2008. Evidence for Gondwanan vicariance in an ancient clade of gecko lizards. J. Biogeogr. 35: 88–104.
  • Groth, J.G. & Barrowclough, G.F. 1999. Basal divergences in birds and the phylogenetic utility of the nuclear RAG-1 gene. Mol. Phylogenet. Evol. 12: 115–123. doi: 10.1006/mpev.1998.0603
  • Heinicke, M.P., Adderly, L.M., Bauer, A.M. & Jackman, T.R. 2011. A long-known new species of gecko allied to Pachydactylus bicolor (Squamata: Gekkonidae) from the central Namibian coast. Afr. J. HerP. 60: 113–129. doi: 10.1080/21564574.2011.613952
  • Heinicke, M.P., Jackman, T.R. & Bauer, A.M. 2017. The measure of success: geographic isolation promotes diversification in Pachydactylus geckos. BMC Evol. Biol. 17: 9. doi: 10.1186/s12862-016-0846-2
  • Huyghe, K., Husak, J.F., Herrel, A., Tadić, Z., Moore, I.T., Van Damme, R. & Vanhooydonck, B. 2009. Relationships between hormones, physiological performance and immunocompetence in a color-polymorphic lizard species, Podarcis melisellensis. Horm. Behav. 55: 488–494. doi: 10.1016/j.yhbeh.2009.02.005
  • Katoh, K. & Standley, D.M. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30: 772–780. doi: 10.1093/molbev/mst010
  • Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S. & Duran, C. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28: 1647–1649. doi: 10.1093/bioinformatics/bts199
  • Knowles, L.L. & Carstens, B.C. 2007. Delimiting species without monophyletic gene trees. Syst. Biol. 56: 887–895. doi: 10.1080/10635150701701091
  • Kocher, T.D., Thomas, W.K., Meyer, A., Edwards, S.V., Pääbo, S., Villablanca, F.X. & Wilson, A.C. 1989. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. PNAS 86: 6196–6200. doi: 10.1073/pnas.86.16.6196
  • Lamb, T. & Bauer, A.M. 2002. Phylogenetic relationships of the large-bodied members of the African lizard genus Pachydactylus (Reptilia: Gekkonidae). Copeia 2002: 586–596. doi: 10.1643/0045-8511(2002)002[0586:PROTLB]2.0.CO;2
  • Lanfear, R., Calcott, B., Ho, S.Y.W. & Guindon, S. 2012. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol. Biol. Evol. 29: 1695–1701. doi: 10.1093/molbev/mss020
  • Macey, J.R., Larson, A., Ananjeva, N.B., Fang, Z. & Papenfuss, T.J. 1997. Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Mol. Biol. Evol. 14: 91–104. doi: 10.1093/oxfordjournals.molbev.a025706
  • McLean, C.A. & Stuart-Fox, D. 2014. Geographic variation in animal colour polymorphisms and its role in speciation. Biol. Rev. 89: 860–873. doi: 10.1111/brv.12083
  • Miller, M., 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). IEE, New Orleans.
  • Olsson, M., Stuart-Fox, D. & Ballen, C. 2013. Genetics and evolution of colour patterns in reptiles. Semin. Cell Dev. Biol. 24: 529–541. doi: 10.1016/j.semcdb.2013.04.001
  • Ota, H., Fisher, R.N., Ineich, I. & Case, T.J. 1995. Geckos of the genus Lepidodactylus (Squamata: Reptilia) in Micronesia: description of a new species and reevaluation of the status of Gecko moestus Peters, 1867. Copeia 1995, 183–195.
  • Palumbi, S. 1996. Nucleic acids II: the polymerase chain reaction. In Hillis, D.M., Moritz, C. & Mable, B.K. (Eds), Molecular systematics, 2nd edn. Sinauer Associates, Sunderland, USA.
  • Pizzatto, L. & Dubey, S. 2012. Colour-polymorphic snake species are older. Biol. J. Linn. Soc. 107: 210–218. doi: 10.1111/j.1095-8312.2012.01936.x
  • Pons, J., Barraclough, T.G., Gomez-Zurita, J., Cardoso, A., Duran, D.P., Hazell, S., Kamoun, S., Sumlin, W.D. & Vogler, A.P. 2006. Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst. Biol. 55: 595–609. doi: 10.1080/10635150600852011
  • R Development Core Team 2014. R: A language and environment for statistical computing. The R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/.
  • Rambaut, A. & Drummond, A. 2007. Tracer v1.4. Available from http://beast.bio.ed.ac.uk/Tracer.
  • Rösler, H., Ineich, I., Wilms, T.M. & Böhme, W. 2012. Studies on the taxonomy of the Gekko vittatus Houttuyn, 1782 complex (Squamata: Gekkonidae) I. On the variability of G. vittatus Houttuyn, 1782 sensu lato, with the description of a new species from Palau Islands, Micronesia. Bonn Zool. Bull. 61: 241–254.
  • Shimodaira, H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51: 492–508. doi: 10.1080/10635150290069913
  • Shimodaira, H. & Hasegawa, M. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16: 1114–1116. doi: 10.1093/oxfordjournals.molbev.a026201
  • Shimodaira, H. & Hasegawa, M. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17: 1246–1247. doi: 10.1093/bioinformatics/17.12.1246
  • Stamatakis, A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688–2690. doi: 10.1093/bioinformatics/btl446
  • Tamura K., Stecher G., Peterson D., Filipski A. & Kumar S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30:2725–2729. doi: 10.1093/molbev/mst197
  • Teasdale, L., Stevens, M. & Stuart-Fox, D. 2013. Discrete colour polymorphism in the tawny dragon lizard (Ctenophorus decresii) and differences in signal conspicuousness among morphs. J. Evolution. Biol. 26: 1035–1046. doi: 10.1111/jeb.12115
  • Tonini, J.F.R., Beard, K.H., Ferreira, R.B., Jetz, W. & Pyron, R.A. 2016. Fully-sampled phylogenies of squamates reveal evolutionary patterns in threat status. Biol. Conserv. 204: 23–31. doi: 10.1016/j.biocon.2016.03.039
  • Uetz, P., Freed, P. & Hošek, J. 2016. The Reptile database. http://www.reptile-database.org/.
  • Vane-Wright, R. 2003. Indifferent philosophy versus almighty authority: on consistency, consensus and unitary taxonomy. Syst. Biodivers. 1: 3–11. doi: 10.1017/S1477200003001063
  • Yang, Z. & Rannala, B. 2010. Bayesian species delimitation using multilocus sequence data. PNAS 107: 9264–9269. doi: 10.1073/pnas.0913022107
  • Zhang, J., Kapli, P., Pavlidis, P. & Stamatakis, A. 2013. A general species delimitation method with applications to phylogenetic placements. Bioinformatics 29: 2869–2876. doi: 10.1093/bioinformatics/btt499

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.