Skip to main content Skip to main navigation menu Skip to site footer
Type: Article
Published: 2017-08-30
Page range: 449–470
Abstract views: 232
PDF downloaded: 9

Molecular phylogeny reveals strong biogeographic signal and two new species in a Cape Biodiversity Hotspot endemic mini-radiation, the pygmy geckos (Gekkonidae: Goggia)

Department of Natural Sciences, University of Michigan-Dearborn, 4901 Evergreen Road, Dearborn, Michigan 48128 USA
Department of Natural Sciences, University of Michigan-Dearborn, 4901 Evergreen Road, Dearborn, Michigan 48128 USA
Department of Biology, Villanova University, 800 Lancaster Avenue, Villanova, Pennsylvania 19085, USA
Reptilia allopatry Cape Fold Belt fynbos Karoo Namaqualand taxonomy

Abstract

The gekkonid genus Goggia includes eight described species of mostly small-bodied rock dwelling gecko endemic to the southwestern portion of southern Africa, in South Africa and extreme southern Namibia. Previous studies focused on Goggia have employed external morphology and allozyme electrophoresis, but no sequence-based molecular phylogeny of the group has been produced. We have generated a molecular phylogeny of Goggia including all named species and multiple individuals within each species, using sequences of the mitochondrial gene ND2 and nuclear genes RAG1 and PDC. The phylogeny depicts a basal divergence between eastern and western species of small-bodied Goggia, with additional divergences also showing structure strongly correlated with geography. Goggia lineata and G. rupicola are shown to be non-monophyletic, and examination of external morphology supports the distinctiveness of these lineages. We describe two new species to accommodate the southern lineages of “G. lineata” and “G. rupicola”: Goggia incognita sp. nov. and Goggia matzikamaensis sp. nov. Both new species are separated from their northern relatives by geographic barriers: the Knersvlakte plain for G. incognita sp. nov. and G. lineata, and the high Kamiesberg mountains for G. matzikamaensis sp. nov. and G. rupicola. The possible roles of geography, ecology, and climate in promoting diversification within Goggia are discussed.

 

References

  1. Alexander, G. & Marais, J. (2008) A Guide to the Reptiles of Southern Africa. Struik, Cape Town, 408 pp.

    Arévalo, E., Davis, S.K. & Sites, J.W. Jr. (1994) Mitochondrial DNA sequence divergence and phylogenetic relationships among eight chromosome races of the Sceloporus grammicus complex (Phrynosomatidae) in central Mexico. Systematic Biology, 43, 387–418.

    https://doi.org/10.1093/sysbio/43.3.387

    Bates, M.F., Branch, W.R., Bauer, A.M., Burger, M., Marais, J., Alexander, G.J. & de Villiers, M.S. (Eds.) (2014) Atlas and Red List of the Reptiles of South Africa, Lesotho, and Swaziland. SANBI, Pretoria, 464 pp.

    Bauer, A.M., de Silva, A., Greenbaum, E. & Jackman, T.R. (2007) A new species of day gecko from high elevation in Sri Lanka, with a preliminary phylogeny of Sri Lankan Cnemaspis (Reptilia: Squamata: Gekkonidae). Mitteilungen aus dem Museum für Naturkunde in Berlin. Zoologische Reihe, 83, 22–32.

    https://doi.org/10.1002/mmnz.200600022

    Bauer, A.M. (1999) Evolutionary scenarios in the Pachydactylus group geckos of southern Africa: new hypotheses. African Journal of Herpetology, 48, 53–62.

    https://doi.org/10.1080/21564574.1999.9651072

    Bauer, A.M., Branch, W.R. & Good, D.A. (1996) A new species of rock-dwelling Phyllodactylus (Squamata: Gekkonidae) from the Richtersveld, South Africa. Occasional Papers of the Museum of Natural Science, Louisiana State University, 71, 1–14.

    Bauer, A.M, Good, D.A. & Branch, W.R. (1997) The taxonomy of the southern African leaf-toed geckos (Squamata: Gekkonidae), with a review of Old World “Phyllodactylus” and the description of five new genera. Proceedings of the California Academy of Sciences, 49, 447–497.

    Boulenger, G.A. (1885) Catalogue of the Lizards in the British Museum (Natural History), Second Edition. Volume I. Geckonidae, Eublepharidae, Uroplatidae, Pygopodidae, Agamidae. British Museum, London, 497 pp.

    Branch, W.R. (1998) Field Guide to the Snakes and Other Reptiles of Southern Africa. Third Edition. Struik, Cape Town, 368 pp.

    Branch, W.R. & Bauer, A.M. (1995) The herpetofauna of the Little Karoo, Western Cape, South Africa. Herpetological Natural History, 3, 47–89.

    Branch, W.R. & Bauer, A.M. (1996) Notes on two poorly-known Phyllodactylus (Squamata: Gekkonidae) from South Africa. Herpetological Natural History, 4, 127–134.

    Branch, W.R., Bauer, A.M. & Good, D.A. (1995) Species limits in the Phyllodactylus lineatus complex (Reptilia: Gekkonidae), with the elevation of two taxa to specific status and the description of two new species. The Journal of the Herpetological Association of Africa, 44, 33–54.

    https://doi.org/10.1080/04416651.1995.9650390

    Branch, W.R., Bauer, A.M. & Good, D.A. (1996) A review of the Namaqua gecko, Pachydactylus namaquensis (Reptilia: Gekkonidae) from southern Africa, with the description of two new species. South African Journal of Zoology, 31, 53–69.

    https://doi.org/10.1080/02541858.1996.11448395

    Branch, W.R. & Braack, H.H. (1989) Reptiles and amphibians of the Karoo National Park: a surprising diversity. Journal of the Herpetological Association of Africa, 36, 26–35.

    https://doi.org/10.1080/04416651.1989.9650219

    Bytebier, B., Antonelli, A., Bellstedt, D.U. & Linder, H.P. (2011) Estimating the age of fire in the Cape flora of South Africa from an orchid phylogeny. Proceedings of the Royal Society of London B: Biological Sciences, 278, 188–195.

    https://doi.org/10.1098/rspb.2010.1035

    Cowling, R.M., Procheş, Ş. & Partridge, T.C. (2009) Explaining the uniqueness of the Cape flora: incorporating geomorphic evolution as a factor for explaining its diversification. Molecular Phylogenetics and Evolution, 51, 64–74.

    https://doi.org/10.1016/j.ympev.2008.05.034

    Daniels, S.R., Mouton, P.L.F.N. & Toit, D.A. (2004) Molecular data suggest that melanistic ectotherms at the south‐western tip of Africa are the products of Miocene climatic events: evidence from cordylid lizards. Journal of Zoology, 263, 373–383.

    https://doi.org/10.1017/S0952836904005424

    Daniels, S.R., Hofmeyr, M.D., Henen, B.T. & Baard, E.H.W. (2010) Systematics and phylogeography of a threatened tortoise, the speckled padloper. Animal Conservation, 13, 237–246.

    https://doi.org/10.1111/j.1469-1795.2009.00323.x

    Diedericks, G. & Daniels, S.R. (2014) Ain’t no mountain high enough, ain’t no valley low enough? Phylogeography of the rupicolous Cape girdled lizard (Cordylus cordylus) reveals a generalist pattern. Molecular Phylogenetics and Evolution, 71, 234–248.

    https://doi.org/10.1016/j.ympev.2013.10.015

    Dingle, R.V. & Hendry, Q.B. (1984) Late Mesozoic and Tertiary sediment supply to the eastern Cape Basin (SE Atlantic) and palaeo-drainage systems in southwestern Africa. Marine Geology, 56, 13–26.

    https://doi.org/10.1016/0025-3227(84)90003-3

    Dupont, L.M., Linder, H.P., Rommerskirchen, F. & Schefuß, E. (2011) Climate‐driven rampant speciation of the Cape flora. Journal of Biogeography, 38, 1059–1068.

    https://doi.org/10.1111/j.1365-2699.2011.02476.x

    FitzSimons, V.F.M. (1938) Transvaal Museum expedition to South-West Africa and Little Namaqualand, May to August 1937—reptiles and amphibians. Annals of the Transvaal Museum, 19, 153–209.

    FitzSimons, V.F.M. (1939) Descriptions of some new species and subspecies of lizards from South Africa. Annals of the Transvaal Museum, 20, 5–16.

    Foster, M.S. (2012) Preparing reptiles as voucher specimens. In: McDiarmid, R.W., Foster, M.S., Guyer, C., Gibbons, J.W. & Chernoff, N. (Eds.), Reptile Biodiversity: Standard Methods for Inventory and Monitoring. University of California Press, Berkeley, pp. 95–126.

    Gamble, T., Greenbaum, E., Russell, A.P., Jackman, T.R. & Bauer, A.M. (2012) Repeated origin and loss of toepads in geckos. PLoS ONE, 7 (6), e39429.
    https://doi.org/10.1371/journal.pone.0039429

    Good, R. (1974) The Geography of Flowering Plants. Fourth Edition. Longman, London, 574 pp.

    Good, D.A., Bauer, A.M. & Branch, W.R. (1996) A new species of Phyllodactylus (Squamata: Gekkonidae) from the Karoo National Park, South Africa. African Journal of Herpetology, 45, 49–58.

    https://doi.org/10.1080/21564574.1996.9649965

    Gray, J.E. (1838) A new species of lizard and land shells from South Africa. In: Alexander, J.E., An Expedition of Discovery into the Interior of Africa, through the Hitherto Undescribed Countries of the Great Namaquas, Boschmans, and Hill Damaras. Volume 2. Henry Colburn, London, pp. 268–269.

    Gray, J.E. (1845) Catalogue of the Specimens of Lizards in the Collection of the British Museum. British Museum, London, 289 pp.

    Greenbaum, E., Bauer, A.M., Jackman, T.R., Vences, M. & Glaw, F. (2007) A phylogeny of the enigmatic Madagascan geckos of the genus Uroplatus. Zootaxa, 1493, 41–51.

    Groth, J.G. & Barrowclough, G.F. (1999) Basal divergences in birds and the phylogenetic utility of the nuclear RAG-1 gene. Molecular Phylogenetics and Evolution, 12, 115–123.

    https://doi.org/10.1006/mpev.1998.0603

    Hall, T.A. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95–98.

    Heinicke, M.P., Daza, J.D., Greenbaum, E., Jackman, T.R. & Bauer, A.M. (2014) Phylogeny, taxonomy and biogeography of a circum-Indian Ocean clade of leaf-toed geckos (Reptilia: Gekkota), with a description of two new genera. Systematics and Biodiversity, 12, 23–42.

    https://doi.org/10.1080/14772000.2013.877999

    Heinicke, M.P., Jackman, T.R. & Bauer, A.M. (2017) The measure of success: geographic isolation promotes diversification in Pachydactylus geckos. BMC Evolutionary Biology, 17, 9.

    https://doi.org/10.1186/s12862-016-0846-2

    Hewitt, J. (1925) On some new species of reptiles and amphibians from South Africa. Records of the Albany Museum, 3, 343–370.

    Hewitt, J. (1937) Descriptions of South African lizards. Annals of the Natal Museum, 8, 199-–209.

    Jacobsen, N.H., Kuhn, A.L., Jackman, T.R. & Bauer, A.M. (2014) A phylogenetic analysis of the southern African gecko genus Afroedura Loveridge (Squamata: Gekkonidae), with the description of nine new species from Limpopo and Mpumalanga provinces of South Africa. Zootaxa, 3846 (4), 451–501.

    https://doi.org/10.11646/zootaxa.3846.4.1

    Katoh, K., Misawa, K., Kuma, K. & Miyata, T. (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30, 3059–3066.

    https://doi.org/10.1093/nar/gkf436

    Lamb, T. & Bauer, A.M. (2000) Relationships of the Pachydactylus rugosus group of geckos (Reptilia: Squamata: Gekkonidae). African Zoology, 35, 55–67.

    https://doi.org/10.1080/15627020.2000.11407192

    Lanfear, R., Calcott, B., Ho, S.Y.W. & Guindon, S. (2012) PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution, 29, 1695–1701.

    https://doi.org/10.1093/molbev/mss020

    Macey, J.R., Larson, A., Ananjeva, N.B., Feng, Z. & Papenfuss, T.J. (1997) Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Molecular Biology and Evolution, 14, 91-–104.

    https://doi.org/10.1093/oxfordjournals.molbev.a025706

    Matthee, C.A. & Flemming, A.F. (2002) Population fragmentation in the southern rock agama, Agama atra: more evidence for vicariance in Southern Africa. Molecular Ecology, 11, 465–471.

    https://doi.org/10.1046/j.0962-1083.2001.01458.x

    Metallinou, M., Cervenka, J., Crochet, P.A., Kratochvíl, L.,Wilms, T., Geniez, P., Shobrak, M.Y., Brito, J.C. & Carranza, S. (2015) Species on the rocks: Systematics and biogeography of the rock-dwelling Ptyodactylus geckos (Squamata: Phyllodactylidae) in North Africa and Arabia. Molecular Phylogenetics and Evolution, 85, 208–220.

    https://doi.org/10.1016/j.ympev.2015.02.010

    Myers, N., Mittermeier, R.A., Mittermeier, C.G., Da Fonseca, G.A. & Kent, J. (2000) Biodiversity hotspots for conservation priorities. Nature, 403, 853–858.

    https://doi.org/10.1038/35002501

    Nei, M. (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89, 583–590.

    Ogilby, W. (1838) On a collection of Mammalia procured by Captain Alexander during his journey into the country of the Damaras, on the south-west coast of Africa. Proceedings of the Zoological Society of London, 6, 5–6.

    Portik, D.M., Bauer, A.M. & Jackman, T.R. (2011) Bridging the gap: western rock skinks (Trachylepis sulcata) have a short history in South Africa. Molecular Ecology, 20, 1744–1758.

    https://doi.org/10.1111/j.1365-294X.2011.05047.x

    Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D.L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M. & Huelsenbeck, J.P. (2012) MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice across a Large Model Space. Systematic Biology, 61, 1–4.

    https://doi.org/10.1093/sysbio/sys029

    Sabaj, M.H. (2016) Standard symbolic codes for institutional resource collections in herpetology & ichthyology: an online reference. Version 6.5. Available from: http://www.asih.org (accessed 1 February 2017)

    Schnitzler, J., Barraclough, T.G., Boatwright, J.S., Goldblatt, P., Manning, J.C., Powell, M.P., Rebelo, T. & Savolainen, V. (2011) Causes of plant diversification in the Cape biodiversity hotspot of South Africa. Systematic Biology, 60, 343–357.

    https://doi.org/10.1093/sysbio/syr006

    Smit, H.A., Robinson, T.J. & Van Vuuren, B.J. (2007) Coalescence methods reveal the impact of vicariance on the spatial genetic structure of Elephantulus edwardii (Afrotheria, Macroscelidea). Molecular Ecology, 16, 2680–2692.

    Smith, A. (1849) Appendix. Illustrations of the Zoology of South Africa; Consisting Chiefly of Figures and Descriptions of the Objects of Natural History Collected During an Expedition into the Interior of South Africa, in the Years 1834, 1835, and 1836. Reptilia. Smith, Edler and Co., London, 28 pp.

    Stamatakis, A. (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30, 1312–1313.

    Swart, B.L., Tolley, K.A. & Matthee, C.A. (2009) Climate change drives speciation in the southern rock agama (Agama atra) in the Cape Floristic Region, South Africa. Journal of Biogeography, 36, 78–87.

    https://doi.org/10.1111/j.1365-2699.2008.01988.x

    Tolley, K.A., Burger, M., Turner, A.A. & Matthee, C.A. (2006) Biogeographic patterns and phylogeography of dwarf chameleons (Bradypodion) in an African biodiversity hotspot. Molecular Ecology, 15, 781–793.

    https://doi.org/10.1111/j.1365-294X.2006.02836.x

    Tolley, K.A., Chase, B.M. & Forest, F. (2008) Speciation and radiations track climate transitions since the Miocene Climatic Optimum: a case study of southern African chameleons. Journal of Biogeography, 35, 1402–1414.

    https://doi.org/10.1111/j.1365-2699.2008.01889.x

    Uetz, P., Fred., P. & Hošek, J. (2017) The Reptiles Database. Available from: http://www.reptiles-database.org (accessed 1 February 2017)