Biodiversity Literature Repository
Published December 31, 2016 | Version v1
Journal article Restricted

Applying n-dimensional hypervolumes for species delimitation: unexpected molecular, morphological, and ecological diversity in the Leaf-Toed Gecko Phyllodactylus reissii Peters, 1862 (Squamata: Phyllodactylidae) from northern Peru

Creators

Description

Koch, Claudia, Flecks, Morris, Venegas, Pablo J., Bialke, Patrick, Valverde, Sebastian, Rödder, Dennis (2016): Applying n-dimensional hypervolumes for species delimitation: unexpected molecular, morphological, and ecological diversity in the Leaf-Toed Gecko Phyllodactylus reissii Peters, 1862 (Squamata: Phyllodactylidae) from northern Peru. Zootaxa 4161 (1): 41-80, DOI: 10.11646/zootaxa.4161.1.2

Files

Restricted

The record is publicly accessible, but files are restricted to users with access.

Linked records

Additional details

Cites
Publication: 10.3897/zookeys.364.6109 (DOI)
Publication: 10.11606/issn.2316-9079.v14i1p53-62 (DOI)
Publication: 10.1111/j.1095-8312.2012.01903.x (DOI)
Publication: 10.1111/j.1096-3642.2007.00251.x (DOI)
Publication: 10.1016/j.tree.2006.11.004 (DOI)
Publication: 10.1016/j.ympev.2015.01.003 (DOI)
Publication: 10.1111/geb.12146 (DOI)
Publication: 10.1093/oxfordjournals.molbev.a026334 (DOI)
Publication: 10.1111/j.1095-8312.2005.00503.x (DOI)
Publication: 10.1016/j.ympev.2014.07.022 (DOI)
Publication: 10.1093/nar/gkh340 (DOI)
Publication: 10.1371/journal.pone.0035126 (DOI)
Publication: 10.1016/j.ympev.2012.07.012 (DOI)
Publication: 10.1093/sysbio/syt033 (DOI)
Publication: 10.1098/rspb.2011.1653 (DOI)
Publication: 10.1016/j.ympev.2011.11.033 (DOI)
Publication: 10.1111/zoj.12064 (DOI)
Publication: 10.1002/joc.1276 (DOI)
Publication: 10.1007/978-1-59745-251-9_3 (DOI)
Publication: 10.11646/zootaxa.3964.2.4 (DOI)
Publication: 10.3897/zookeys.141.1678 (DOI)
Publication: 10.11646/zootaxa.3745.2.6 (DOI)
Publication: 10.1007/s13127-012-0098-y (DOI)
Publication: 10.11646/zootaxa.3694.1.3 (DOI)
Publication: 10.11646/zootaxa.3856.4.3 (DOI)
Publication: 10.1111/zsc.12052 (DOI)
Publication: 10.1016/j.ympev.2010.12.007 (DOI)
Publication: 10.1111/j.1749-6632.1920.tb55353.x (DOI)
Publication: 10.1186/1471-2148-10-386 (DOI)
Publication: 10.1111/j.1096-3642.2008.00424.x (DOI)
Publication: 10.1186/1742-9994-7-16 (DOI)
Publication: 10.1016/j.ympev.2011.08.012 (DOI)
Publication: 10.1093/bioinformatics/14.9.817 (DOI)
Publication: 10.1111/j.1365-294x.2011.05239.x (DOI)
Publication: 10.1093/sysbio/sys029 (DOI)
Publication: 10.1093/bioinformatics/btq706 (DOI)
Publication: 10.1016/j.ympev.2013.09.014 (DOI)
Publication: 10.1111/jbi.12375 (DOI)
Publication: 10.1670/12-017 (DOI)
Publication: 10.1670/07-1341.1 (DOI)
Publication: 10.1093/bioinformatics/btt499 (DOI)
Has part
Taxonomic treatment: 10.5281/zenodo.5632194 (DOI)
Taxonomic treatment: http://treatment.plazi.org/id/B44087EDCE6CFFD3FF7F4902F19BFC7B (URL)
Taxonomic treatment: 10.5281/zenodo.5632196 (DOI)
Taxonomic treatment: http://treatment.plazi.org/id/B44087EDCE68FFD0FF7F4F4AF3FAFF44 (URL)
Taxonomic treatment: 10.5281/zenodo.5632198 (DOI)
Taxonomic treatment: http://treatment.plazi.org/id/B44087EDCE6BFFCFFF7F4A0EF25EFE48 (URL)
Figure: 10.5281/zenodo.256498 (DOI)
Figure: 10.5281/zenodo.256499 (DOI)
Figure: 10.5281/zenodo.256500 (DOI)
Dataset: http://table.plazi.org/id/68966673CE62FFD9FF7F4D79F5C3F928 (URL)
Dataset: http://table.plazi.org/id/68966673CE63FFD8FF7F4BDCF31EFF53 (URL)
Figure: 10.5281/zenodo.256501 (DOI)
Figure: 10.5281/zenodo.256502 (DOI)
Figure: 10.5281/zenodo.256503 (DOI)
Dataset: http://table.plazi.org/id/68966673CE6FFFD4FF7F4BDCF462FF53 (URL)
Is source of
Dataset: http://www.gbif.org/dataset/4de18441-9329-474b-a4a0-dea3aaf1e1ee (URL)

References

  • Aguilar, C., Wood, P., Cusi, J.C., Guzman, A., Huari, F., Lundberg, M., Mortensen, E., Ramirez, C., Robles, D., Suarez, J., Ticona, A., Vargas, V., Venegas, P.J. & Sites, J. (2013) Integrative taxonomy and preliminary assessment of species limits in the Liolaemus walkeri complex (Squamata, Liolaemidae) with descriptions of three new species from Peru. ZooKeys, 364, 47-91.
  • http://dx.doi.org/10.3897/zookeys.364.6109
  • Aurich, J., Koch, C. & Bohme, W. (2011) Ecology of a unique gecko assemblage (Phyllodactylidae: Squamata) from northern Peru. Northwestern Journal of Zoology, 7 (2), 310-317.
  • Aurich, J., Koch, C. & Bohme, W. (2015) Reproduction of a gecko assemblage (Squamata: Phyllodactylidae) in the Maranon Region (Peru) and comments on the largest gekkonid in the New World. Phyllomedusa, 14 (1), 53-62. http://dx.doi.org/10.11606/issn.2316-9079.v14i1p53-62
  • Barata, M., Perera, A., Martinez-Freiria, F. & Harris, D.H. (2012) Cryptic diversity within the Moroccan endemic day geckos Quedenfeldtia (Squamata: Gekkonidae): a multidisciplinary approach using genetic, morphological and ecological data. Biological Journal of the Linnean Society, 106 (4), 828-850.
  • http://dx.doi.org/10.1111/j.1095-8312.2012.01903.x
  • Bergmann, P.J. & Russell, A.P. (2007) Systematics and biogeography of the widespread Neotropical gekkonid genus Thecadactylus (Squamata), with the description of a new cryptic species. Zoological Journal of the Linnean Society, 149, 339-370.
  • http://dx.doi.org/10.1111/j.1096-3642.2007.00251.x
  • Bickford, D., Lohman, D.J., Navjot, S.S., Ng, P.K.L., Meier, R., Winker, K., Ingram, K.K. & Das, I. (2006) Cryptic species as a window on diversity and conservation. Trends in Ecology and Evolution, 22, 148-155. http://dx.doi.org/10.1016/j.tree.2006.11.004
  • Blair, C., Mendez de la Cruz, F.R., Law, C. & Murphy, R.W. (2015) Molecular phylogenetics and species delimitation of leaftoed geckos (Phyllodactylidae: Phyllodactylus) throughout the Mexican tropical dry forest. Molecular Phylogenetics and Evolution, 84, 254-265.
  • http://dx.doi.org/10.1016/j.ympev.2015.01.003
  • Blair, C., Mendez de la Cruz, F.R., Ngo, A., Lindell, J., Lathrop, A. & Murphy, R.W. (2009) Molecular phylogenetics and taxonomy of leaf-toed geckos (Phyllodactylidae: Phyllodactylus) inhabiting the peninsula of Baja California. Zootaxa, 2027, 28-42.
  • Blonder, B., Lamanna C., Violle C. & Enquist, B.J. (2014) The n-dimesional hypervolume. Global Ecology and Biogeography, 23, 595-609.
  • http://dx.doi.org/10.1111/geb.12146
  • Bridgewater, S., Pennington, R.T., Reynel, C.A., Daza, A. & Pennington, T.D. (2003) A preliminary floristic and phytogeographic analysis of the woody flora of seasonally dry forests in northern Peru. Candollea, 58, 129-141.
  • Castresana, J. (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution, 17, 540-552.
  • http://dx.doi.org/10.1093/oxfordjournals.molbev.a026334
  • Dayrat, B. (2005) Towards integrative taxonomy. Biological Journal of the Linnean Society, 85, 407-415. http://dx.doi.org/10.1111/j.1095-8312.2005.00503.x
  • Domingos, F.M., Bosque, R.J., Cassimiro, J., Colli, G.R., Rodrigues, M.T., Santos, M.G. & Beheregaray, L.B. (2014) Out of the deep: cryptic speciation in a Neotropical gecko (Squamata, Phyllodactylidae) revealed by species delimitation methods. Molecular Phylogenetics and Evolution, 80, 113-124.
  • http://dx.doi.org/10.1016/j.ympev.2014.07.022
  • Dixon, J.R. (1964) The systematics and distribution of lizards of the genus Phyllodactylus in North and Central America. New Mexico State University Research Center Scientific Bulletin, 64, 1-139.
  • Dixon, J.R. & Huey, R.B. (1970) Systematics of the lizards of the gekkonid genus Phyllodactylus of mainland South America. Los Angeles County Museum Contributions in Science, 192, 1-78.
  • Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32 (5), 1792-1797.
  • http://dx.doi.org/10.1093/nar/gkh340
  • Finer, M. & Jenkins, C.N. (2012) Proliferation of Hydroelectric Dams in the Andean Amazon and Implications for Andes- Amazon Connectivity. PLoS ONE, 7 (4), e35126.
  • http://dx.doi.org/10.1371/journal.pone.0035126
  • Fouquet, A., Loebmann, D., Castroviejo-Fisher, S., Padial, J.M., Orrico, V.G.D., Lyra, M.L., Joventino Roberto, I., Kok, P.J.R., Haddad, C.F.B. & Rodrigues, M.T. (2012) From Amazonia to the Atlantic forest: Molecular phylogeny of Phyzelaphryninae frogs reveals unexpected diversity and a striking biogeographic pattern emphasizing conservation challenges. Molecular Phylogenetics and Evolution, 65, 547-561.
  • http://dx.doi.org/10.1016/j.ympev.2012.07.012
  • Fujisawa, T. & Barraclough, T.G. (2013) Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent (GMYC) approach: a revised method and evaluation on simulated datasets. Systematic Biology, 62, 707-724. http://dx.doi.org/10.1093/sysbio/syt033
  • Funk, W.C., Caminer, M. & Ron, S.R. (2012) High levels of cryptic species diversity uncovered in Amazonian frogs. Proceedings of the Royal Society of London B, 279 (1734), 1806-1814.
  • http://dx.doi.org/10.1098/rspb.2011.1653
  • Gamble, T., Colli, G.R., Rodrigues, M.T., Werneck, F.P. & Simons, A.M. (2012) Phylogeny and cryptic diversity in geckos (Phyllopezus; Phyllodactylidae; Gekkota) from South America's open biomes. Molecular Phylogenetics and Evolution, 62 (3), 943-953.
  • http://dx.doi.org/10.1016/j.ympev.2011.11.033
  • Grismer, L.L., Wood, Jr, P.L., Anuar, S., Muin, M.A., Quah, E.S.H., Mcguire, J.A., Brown, R.M., Van Tri, N. & Thai, P.H. (2013) Integrative taxonomy uncovers high levels of cryptic species diversity in Hemiphyllodactylus Bleeker, 1860 (Squamata: Gekkonidae) and the description of a new species from Peninsular Malaysia. Zoological Journal of the Linnean Society, 169, 849-880.
  • http://dx.doi.org/10.1111/zoj.12064
  • Hijmans, R.J., Cameron, S.E., Parra, J.L., Jones, P.G. & Jarvis, A. (2005) Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology, 25, 1965-1978.
  • http://dx.doi.org/10.1002/joc.1276
  • Hoogmoed, M.S. (1989) Introduced geckos in Puerto Ayora, Santa Cruz, with remarks on other areas. Noticias de Galapagos, 47, 12-16.
  • IUCN & UNEP-WCMC (2016) The World Database on Protected Areas (WDPA) [On-line]. UK: UNEP-WCMC, Cambridge. Available from: www.protectedplanet.net (accessed 4 April 2016)
  • Katoh, K., Asimenos, G. & Toh, H. (2009) Multiple Alignment of DNA Sequences with MAFFT. Methods in Molecular Biology, 537, 39-64.
  • http://dx.doi.org/10.1007/978-1-59745-251-9_3
  • Koch, C. & Beraun, A.M. (2011) Squamata, Phyllodactylidae, Phyllodactylus thompsoni Venegas, Townsend, Koch and Bohme 2008 and Phyllodactylus delsolari Venegas, Townsend, Koch and Bohme 2008: Latitudinal and altitudinal distribution extension and geographic distribution map. Check List, 7 (3), 272-275.
  • Koch, C., Venegas, P.J. & Bohme, W. (2006) A remarkable discovery: Description of a big-growing new gecko (Squamata: Gekkonidae: Phyllopezus) from northwestern Peru. Salamandra, 42 (2/3), 145-150.
  • Koch, C., Venegas, P.J. & Bohme, W. (2015) Three new endemic species of Epictia Gray, 1845 (Serpentes: Leptotyphlopidae) from the dry forest of northwestern Peru. Zootaxa, 3964 (2), 228-244.
  • http://dx.doi.org/10.11646/zootaxa.3964.2.4
  • Koch, C., Venegas, P.J., Garcia-Bravo, A. & Bohme, W. (2011) A new bush anole (Iguanidae: Polychrotinae: Polychrus) from the upper Maranon basin, Peru, with a redescription of Polychrus peruvianus (Noble, 1924) and additional information on P. gutturosus Berthold, 1845. Zookeys, 141, 79-107.
  • http://dx.doi.org/10.3897/zookeys.141.1678
  • Koch, C., Venegas, P.J., Rodder, D., Flecks, M. & Bohme, W. (2013) Two new endemic species of Ameiva (Squamata: Teiidae) from the dry forest of northwestern Peru and additional information on Ameiva concolor Ruthven, 1924. Zootaxa, 3745 (2), 263-295.
  • http://dx.doi.org/10.11646/zootaxa.3745.2.6
  • Lemme, I., Erbacher, M., Kaffenberger, N., Vences M. & Kohler, J. (2013) Molecules and morphology suggest cryptic species diversity and an overall complex taxonomy of fish scale geckos, genus Geckolepis. Organisms Diversity & Evolution, 13, 87-95.
  • http://dx.doi.org/10.1007/s13127-012-0098-y
  • Makhubo, B.G., Tolley, K.A. & Bates, M.F. (2015) Molecular phylogeny of the Afroedura nivaria (Reptilia: Gekkonidae) species complex in South Africa provides insight on cryptic speciation. Molecular Phylogenetics and Evolution 82, Part A, 31-42.
  • McCranie, J.R. & Hedges, S.B. (2013) A new species of Phyllodactylus (Reptilia, Squamata, Gekkonoidea, Phyllodactylidae) from Isla de Guanaja in the Honduran Bay Islands. Zootaxa, 3694 (1), 51-58.
  • http://dx.doi.org/10.11646/zootaxa.3694.1.3
  • Minoli, I., Morando, M. & Avila, L.J. (2014) Integrative taxonomy in the Liolaemus fitzingerii complex (Squamata: Liolaemini) based on morphological analyses and niche modeling. Zootaxa, 3856 (4), 501-528. http://dx.doi.org/10.11646/zootaxa.3856.4.3
  • Morando, M., Medina, C.D., Avila, L.J., Perez, C.H.F., Buxton, A. & Sites, J.W. Jr. (2014) Molecular phylogeny of the New World gecko genus Homonota (Squamata: Phyllodactylidae). Zoological Scripta, 43 (3), 249-260. http://dx.doi.org/10.1111/zsc.12052
  • Myers, N., Mittermeier, R.A., Mittermeier, C.G., da Fonseca, G.A.B. & Kent, J. (2000) Biodiversity hotspots for conservation priorities. Nature, 403, 853-858.
  • Nielsen, S.V., Bauer, A.M., Jackman, T.R., Hitchmough, R.A. & Daugherty, C.H. (2011) New Zealand geckos (Diplodactylidae): cryptic diversity in a post-Gondwanan lineage with trans-Tasman affinities. Molecular Phylogenetics and Evolution, 59 (1), 1-22.
  • http://dx.doi.org/10.1016/j.ympev.2010.12.007
  • Noble, G.K. (1921) Some new lizards from northwestern Peru. Annals of the New York Academy of Sciences, 29, 133-139. http://dx.doi.org/10.1111/j.1749-6632.1920.tb55353.x
  • Noble, G.K. (1924) New lizards from northwestern Peru. Boston Society of Natural History, 5, 107-113.
  • Oliver, P.M., Adams, M. & Doughty, P. (2010) Molecular evidence for ten species and Oligo-Miocene vicariance within a nominal Australian gecko species (Crenadactylus ocellatus, Diplodactylidae). BMC Evolutionary Biology, 10 (386), 1-11. http://dx.doi.org/10.1186/1471-2148-10-386
  • Padial, J.M. & De la Riva, I. (2009) Integrative taxonomy reveals cryptic Amazonian species of Pristimantis (Anura: Strabomantidae). Zoological Journal of the Linnean Society, 155, 97-122.
  • http://dx.doi.org/10.1111/j.1096-3642.2008.00424.x
  • Padial, J.M., Miralles, A., De la Riva, I. & Vences, M. (2010) The integrative future of taxonomy. Frontiers in Zoology, 7, 16. http://dx.doi.org/10.1186/1742-9994-7-16
  • Pepper, M., Doughty, P., Hutchinson, M.N. & Keogh, J.S. (2011) Ancient drainages divide cryptic species in Australia's arid zone: Morphological and multi-gene evidence for four new species of Beaked Geckos (Rhynchoedura). Molecular Phylogenetics and Evolution, 61 (3), 810-822.
  • http://dx.doi.org/10.1016/j.ympev.2011.08.012
  • Peters, W.C.H. (1862) Uber einen neuen Phyllodactylus aus Guayaquil. Monatsberichte der koniglichen Preussischen Akademie der Wissenschaften zu Berlin, 1862 (November), 626-627.
  • Posada, D. & Crandall, K.A. (1998) Modeltest: testing the model of DNA substitution. Bioinformatics, 14, 817-818. http://dx.doi.org/10.1093/bioinformatics/14.9.817
  • Puillandre, N., Lambert, A., Brouillet, S. & Achaz, G. (2012) ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Molecular Ecology, 21, 1864-1877.
  • http://dx.doi.org/10.1111/j.1365-294x.2011.05239.x
  • Q&V Ingenieros SAC (2007) Elaboracion de resumenes ejecutivos y fichas de estudio de las centrales hidroelectricas con potencial para exportacion a Brasil. Ministerio de Energia y Minas, Direccion General de Electricidad, 79 pp.
  • Rambaut, A., Suchard, M.A., Xie, D. & Drummond, A.J. (2014) Tracer v1.6, Available from http://beast.bio.ed.ac.uk/Tracer (accessed 1 Sept. 2016)
  • Rios, N.E. (2014) Geolocate, a platform for georeferencing legacy collection data. In: 2014 GSA Annual Meeting in Vancouver, British Columbia.
  • Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D.L., Darling, A., Hohna, S., Larget, B., Liu, L., Suchard, M.A. & Huelsenbeck, J.P. (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61, 539-542.
  • http://dx.doi.org/10.1093/sysbio/sys029
  • Sarkinen, T.E., Marcelo-Pena, J.L., Yomona, A.D., Simon, M.F., Pennington, R.T. & Hughes, C.E. (2011) Underestimated endemic species diversity in the dry inter-Andean valley of the Rio Maranon, northern Peru: An example from Mimosa (Leguminosae, Mimosoideae). Taxon, 60 (1), 139-150.
  • Schliep, K.P. (2011) phangorn: phylogenetic analysis in R. Bioinformatics, 27 (4), 592-593. http://dx.doi.org/10.1093/bioinformatics/btq706
  • Siler, C.D., Dececchi , T.A., Merkord, C.L., Davis, D.R. , Christiani, T.J. & Brown, R.M. (2014) Cryptic diversity and population genetic structure in the rare, endemic, forest-obligate, slender geckos of the Philippines. Molecular Phylogenetics and Evolution, 70, 204-209.
  • http://dx.doi.org/10.1016/j.ympev.2013.09.014
  • Stattersfield, A.J., Crosby, M.J., Long, A.J. & Wege, D. (1998) Endemic Birds Areas of the World. Priorities for biodiversity conservation. BirdLife International, Cambridge, UK, 860 pp.
  • Torres-Carvajal, O., Barnes, C.W., Pozo-Andrade, M.J., Tapia, W. & Nicholls, G. (2014) Older than the islands: origin and diversification of Galapagos leaf-toed geckos (Phyllodactylidae: Phyllodactylus) by multiple colonizations.. Journal of Biogeography, 41 (10), 1883-1894.
  • http://dx.doi.org/10.1111/jbi.12375
  • Torres-Carvajal, O., Carvajal-Campos, A., Barnes, C.W., Nicholls, G . & Pozo-Andrade, M.J. (2013) A New Andean Species of Leaf-toed Gecko (Phyllodactylidae: Phyllodactylus) from Ecuador. Journal of Herpetology, 47 (2), 384-390. http://dx.doi.org/10.1670/12-017
  • Torres-Carvajal, O. & Tapia, W. (2011) First record of the common house gecko Hemidactylus frenatus Schlegel, 1836 and distribution extension of Phyllodactylus reissii Peters, 1862 in the Galapagos. Check List, 7 (4), 470-472.
  • Uetz, P. & Hosek, J. (2016) The Reptile Database. Available from http://www.reptile-database.org (accessed 4 April 2016)
  • Venegas, P.J. (2005) Herpetofauna del bosque seco Ecuatorial de Peru: taxonomia, ecologia y biogeografia. Zonas Aridas, 9, 9- 26.
  • Venegas, P.J., Townsend, J.H., Koch, C. & Bohme, W. (2008) Two new sympatric species of leaf-toed geckos (Gekkonidae: Phyllodactylus) from the Balsas region of the upper Maranon Valley, Peru. Journal of Herpetology, 42 (2), 386-396. http://dx.doi.org/10.1670/07-1341.1
  • Wagner, P., Leache, A.D. & Fujita, M.K. (2014) Description of four new West African forest geckos of the Hemidactylus fasciatus Gray, 1842 complex, revealed by coalescent species delimitation. Bonn Zoological Bulletin, 63 (1), 1-14.
  • Werner, F. (1900 [1901]) Reptilien und Batrachier aus Peru und Bolivien. Abhandlungen und Berichte des Koniglichen Zoologischen und Anthropologisch-Ethnographischen Museums zu Dresden, 9 (2), 1-14.
  • Werner, F. (1910 [1909]) Uber neue oder seltene Reptilien des Naturhistorischen Museums in Hamburg. II. Eidechsen. Mitteilungen aus dem Naturhistorischen Museum in Hamburg, 15. Jahrgang, 2. Beiheft, 1-46.
  • Werner, F. (1912) Neue oder seltene Reptilien und Frosche des Naturhistorischen Museums in Hamburg. Mitteilungen aus dem Naturhistorischen Museum in Hamburg, 17. Jahrgang, 2. Beiheft, 1-51.
  • Zhang, J., Kapli, P., Pavlidis, P. & Stamatakis, A. (2013) A general species delimitation method with applications to phylogenetic placements. Bioinformatics, 29, 2869-2876.
  • http://dx.doi.org/10.1093/bioinformatics/btt499