Evolutionary relationships amongst polymorphic direct-developing frogs in the Craugastor rhodopis Species Group (Anura: Craugastoridae)

References

• Arenas-Monroy, J.C., González-Saucedo, Z.Y., Carbajal-Márquez, R.A. & Rodríguez, J.J. 2012. Geographic Distribution: Craugastor occidentalis. Herpetological Review 43, 298.
   Google Scholar
• Barbour, T. 1922. Three new neotropical Salientia. Proceedings of the Biological Society of Washington 35, 111–114.
   Google Scholar
• Bauer, A.M., Parham, J.F., Brown, R.M., Stuart, B.L., Grismer, L., Papenfuss, T.J., Böhme, W., Savage, J.M., Carranza, S., Grismer, J.L., Wagner, P., Schmitz, A., Ananjeva, N.B. & Inger, R.F. 2011. Availability of new Bayesian-delimited gecko names and the importance of character-based descriptions. Proceedings of the Royal Society B 278, 490–492.
   Google Scholar
• Boulenger, G.A. 1898. Fourth report on additions to the batrachian collection in the Natural-History Museum. Proceedings of the Zoological Society of London 1898, 473–482.
   Google Scholar
• Boulenger, G.A. 1903. Descriptions of new batrachians in the British Museum. Annals and Magazine of Natural History, Series 7 12, 552–557.
   Google Scholar
• Bryson, R.W. & Riddle, B.R. 2011. Tracing the origins of widespread highland species: a case of Neogene diversification across the Mexican sierras in an endemic lizard. Biological Journal of the Linnean Society 105, 382–394.
   Web of Science ®Google Scholar
• Bryson, R.W., García-Vázquez, O. & Riddle, B.R. 2011a. Relative roles of Neogene vicariance and Quaternary climate change on the historical diversification of bunchgrass lizards (Sceloporus scalaris group) in Mexico. Molecular Phylogenetics and Evolution 62, 447–457.
   PubMed Web of Science ®Google Scholar
• Bryson, R.W., García-Vázquez, O. & Riddle, B.R. 2011b. Diversification in the Mexican horned lizard Phrynosoma obiculare across a dynamic landscape. Molecular Phylogenetics and Evolution 62, 87–96.
   PubMed Web of Science ®Google Scholar
• Bryson, R.W., García-Vázquez, O. & Riddle, B.R. 2011c. Phylogeography of Middle American gophersnakes: mixed responses to biogeographical barriers across the Mexican Transition Zone. Journal of Biogeography 38, 1570–1584.
   Web of Science ®Google Scholar
• Bryson, R.W., Nieto-Montes De Oca, A., Jaeger, J.R. & Riddle, B.R. 2010. Elucidation of cryptic diversity in a widespread Nearctic treefrog reveals episodes of mitochondrial gene capture as frogs diversified across a dynamic landscape. Evolution 64, 2315–2330.
   PubMed Web of Science ®Google Scholar
• Campbell, J.A. 1998. Amphibians and reptiles of northern Guatemala, the Yucatan, and Belize. The University of Oklahoma Press, USA, pp. 380.
   Google Scholar
• Carapelli, A., Soto-Adames, F.N., Simon, C., Frati, F., Nardi, F. & Dallai, R. 2004. Secondary structure, high variability and conserved motifs for domain III of 12S rRNA in the Arthopleona (Hexapoda; Collembola). Insect Molecular Biology 13, 659–670.
   PubMed Web of Science ®Google Scholar
• Castoe, T.A., Daza, J.M., Smith, E.N., Sasa, M.M., Kuch, U., Campbell, J.A., Chippindale, P.T. & Parkinson, C.L. 2009. Comparative phylogeography of pitvipers suggests a consensus of ancient Middle American highland biogeography. Journal of Biogeography 36, 88–103.
   Web of Science ®Google Scholar
• 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). Australian Journal of Zoology 56, 103–115.
   Web of Science ®Google Scholar
• Chen, S.H. 2005. Chromosomal variation in the rhodopis group of the southern Central American eleutherodactyline frogs (Leptodactylidae: Eleutherodactylus). In: Donnelly, M.A., Ed., Ecology and Evolution in the Tropics: A Herpetological Perspective. The University of Chicago Press, USA, pp. 102–144.
   Google Scholar
• Cope, E.D. 1867 “1866”. Fifth contribution to the herpetology of tropical America. Proceedings of the Academy of Natural Sciences of Philadelphia 18, 317–323.
   Google Scholar
• Cox, C.L. & Davis-Rabosky, A.R. 2013. Spatial and temporal drivers of phenotypic diversity in polymorphic snakes. The American Naturalist 182, E40–E57.
   PubMed Web of Science ®Google Scholar
• Cox, C.L, Streicher, J.W., Sheehy III, C.M., Campbell, J.A. & Chippindale, P.T. 2012a. Patterns of genetic differentiation among populations of Smilisca fodiens. Herpetologica 68, 226–235.
   Web of Science ®Google Scholar
• Cox, C.L., Davis Rabosky A.R., Reyes-Velasco, J., Ponce-Campos, P., Smith, E.N., Flores-Villela, O. & Campbell, J.A. 2012b. Molecular systematics of the genus Sonora (Squamata: Colubridae) in central and western Mexico. Systematics and Biodiversity 10, 93–108.
   Web of Science ®Google Scholar
• Crawford, A.J. 2003a. Huge populations and old species of Costa Rican and Panamanian dirt frogs inferred from mitochondrial and nuclear gene sequences. Molecular Ecology 12, 2525–2540.
   PubMed Web of Science ®Google Scholar
• Crawford, A.J. 2003b. Relative rates of nucleotide substitution in frogs. Journal of Molecular Evolution 57, 366–641.
   Google Scholar
• Crawford, A.J. & Smith, E.N. 2005. Cenozoic biogeography and evolution in direct-developing frogs of Central America (Leptodactylidae: Eleutherodactylus) as inferred from a phylogenetic analysis of nuclear and mitochondrial genes. Molecular Phylogenetics and Evolution 35, 536–555.
   PubMed Web of Science ®Google Scholar
• Crawford, A.J., Bermingham, E. & Polanía, C. 2007. The role of tropical dry forest as a long-term barrier to dispersal: A comparative phylogeographic analysis of dry forest tolerant and intolerant frogs. Molecular Ecology 16, 4789–4807.
   PubMed Web of Science ®Google Scholar
• Devitt, T.J. 2006. Phylogeography of the western lyresnake (Trimorphodon biscutatus): testing aridland biogeographical hypotheses across the Neartic-Neotropical transition. Molecular Ecology 15, 4387–4407.
   PubMed Web of Science ®Google Scholar
• Dixon, M.T. & Hillis, D.M. 1993. Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis. Molecular Biology and Evolution 10, 256–267.
   PubMed Web of Science ®Google Scholar
• Duellman, W.E. 1960. A distributional study of the amphibians of the Isthmus of Tehuantepec, Mexico. University of Kansas Publications Museum of Natural History 13, 19–72.
   Google Scholar
• Duellman, W.E. 1961. The amphibians and reptiles of Michoacán, México. University of Kansas Publications Museum of Natural History 15, 1–148.
   Google Scholar
• Firschein, I.L. & H.M. Smith. 1956. A New Fringe-Limbed Hyla (Amphibia: Anura) from a New Faunal District of Mexico. Herpetologica, 12, 17–21.
   Google Scholar
• Frost, D.R. 2013. Amphibian species of the world: an online reference. Version 5.6 (9 January 2013). American Museum of Natural History, New York, USA.
   Google Scholar
• Frost, D.R., Grant, T., Faivovich, J., Bain, R.H., Haas, A., Haddad, C.F.B., De Sá, R.O., Channing, A., Wilkinson, M., Donnellan S.C., Raxworthy, C.J., Campbell, J.A., Blotto, B.L., Moler, P.E., Drewes, R.C., Nussbaum, R.A., Lynch, J.D., Green, D.M. & Wheeler, W.C. 2006. The amphibian tree of life. Bulletin of the American Museum of Natural History 297, 1–370.
   Web of Science ®Google Scholar
• Galeotti, P., Rubolini, D., Dunn, P.O. & Fasola, M. 2003. Colour polymorphism in birds: causes and functions. Journal of Evolutionary Biology 16, 635–646.
   PubMed Web of Science ®Google Scholar
• García, A. & Ceballos, G. 1994. Guía de campo de los reptiles y anfibios de la costa de Jalisco, México. Fundación Ecológica de Cuixmala, A.C. Instituto de Bilogía, U.N.A.M., Mexico, pp. 184.
   Google Scholar
• García-Vázquez, U.O., Canseco-Márquez, L., Aguilar-López, J.L., Solano-Zavaleta, I. & Maceda-Cruz, R.J. 2009. Noteworthy records of amphibians and reptiles from Puebla, México. Herpetological Review 40, 467–470.
   Google Scholar
• Günther, A.C.L.G. 1869 “1868”. First account of species of tailless batrachians added to the collection of the British Museum. Proceedings of the Zoological Society of London 1868, 478–490.
   Google Scholar
• Günther, A.C.L.G. 1900. Reptilia and Batrachia. Part 157. In: Salvin, O. & Godman, F.D., Eds., Biologia Centrali Americana, Vol. 7. pp. 229–236. R. H. Porter and Dulau & Co. London. UK.
   Google Scholar
• Hancock, J.M., Diethard, T. & Dover, G.A. 1988. Evolution of the secondary structures and compensatory mutations of the ribosomal RNAs of Drosophila melanogastor. Molecular Biology and Evolution 5, 393–414.
   PubMed Web of Science ®Google Scholar
• Heinicke, M.P., Duellman, W.E. & Hedges, S.B. 2007. Major Caribbean and Central American frog faunas originated by ancient oceanic dispersal. Proceedings of the National Academy of Sciences USA 104, 10092–10097.
   Google Scholar
• Heinicke, M.P., Duellman, W.E., Trueb, L., Means, D.B., Macculloch, R.D. & Hedges, S.B. 2009. A new frog family (Anura: Terrarana) from South America and an expanded direct-developing clade revealed by molecular phylogeny. Zootaxa 2211, 1–35.
   Google Scholar
• Hedges, S.B. 1992. The number of replications needed for accurate estimation of the bootstrap P value in phylogenetic studies. Molecular Biology and Evolution 9, 366–369.
   PubMed Web of Science ®Google Scholar
• Hedges, S.B., Duellman, W.E. & Heinicke, M.P. 2008. New World direct-developing frogs (Anura: Terrarana): molecular phylogeny, classification, biogeography, and conservation. Zootaxa 1737, 1–182.
   Google Scholar
• Hickson, R.E., Simon, C., Cooper, A., Spicer, G.S., Sullivan, J.J. & Penny, D. 1996. Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA. Molecular Biology and Evolution 13, 150–169.
   PubMed Web of Science ®Google Scholar
• Hoffman, E.A. & Blouin, M.S. 2000. A review of colour and pattern polymorphisms in anurans. Biological Journal of the Linnean Society 70, 633–665.
   Web of Science ®Google Scholar
• Kellogg, R. 1932. Mexican tailless amphibians in the United States National Museum. Bulletin of the United States National Museum 160, 1–224.
   Google Scholar
• Kjer, K.M. 1997. An alignment template for amphibian 12S rRNA, domain III: conserved primary and secondary structural motifs. Journal of Herpetology 31, 599–604.
   Web of Science ®Google Scholar
• Köhler, G., Vesely, M. & Greenbaum, E. 2005 “2006”. The amphibians and reptiles of El Salvador. Krieger Publishing Company, Malabar, Florida USA.
   Google Scholar
• Leaché, A.D. & Fujita, M.K. 2010. Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus). Proceedings of the Royal Society B 277, 3071–3077.
   Google Scholar
• Lee, J.C. 1996. The amphibians and reptiles of the Yucatan peninsula. Comstock Publishing Associates, Cornell University Press, Cornell, NY, USA.
   Google Scholar
• Lee, J.C. 2000. A field guide to the amphibians and reptiles of the Maya world: The lowlands of Mexico, northern Guatemala, and Belize. Cornell University Press, Cornell, NY, USA, pp. 402.
   Google Scholar
• Liner, E.A. 1994. Scientific and common names for the amphibians and reptiles of Mexico in English and Spanish. Herpetological Circular 23, 113 pp.
   Google Scholar
• Linter, E.A. & Casas-Andreu, G. 2008. Standard Spanish, English and scientific names of the amphibians and reptiles of Mexico. Herpetological Circular 38, 1–162.
   Google Scholar
• Lynch, J.D. 1965. A review of frogs of the mexicanus and rhodopis groups (genus Eleutherodactylus) and the evolution of the genus in northern Central America. Masters Thesis (Zool.). University of Illinois, Champaign-Urbana, USA, pp. 150.
   Google Scholar
• Lynch, J.D. 1966a. A new species of Eleutherodactylus from Chiapas, Mexico (Amphibia: Leptodactylidae). Transactions of the Kansas Academy of Science 69, 76–78.
   Google Scholar
• Lynch, J.D. 1966b. Multiple morphotypy and parallel polymorphisms in some neotropical frogs. Systematic Zoology 15, 18–23.
   Google Scholar
• Lynch, J.D. 1976. A third species of Hylactophryne (Amphibia: Leptodactylidae). Herpetologica 32, 346–347.
   Google Scholar
• Lynch, J.D. 1993. The value of the m. depressor mandibulae in phylogenetic hypothesis for Eleutherodactylus and its allies (Amphibia: Leptodactylidae). Herpetologica 49, 32–41.
   Web of Science ®Google Scholar
• Lynch, J.D. 2000. The relationships of an ensemble of Guatemalan and Mexican frogs (Eleutherodactylus: Leptodactylidae: Amphibia). Revista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturales 24, 129–156.
   Google Scholar
• Lynch, J.D. & Fugler, C.M. 1965. A survey of frogs of Honduras. Journal of the Ohio Herpetological Society 5, 5–18.
   Google Scholar
• Mccranie, J.R. 2007. Distribution of the amphibians of Honduras by departments. Herpetological Review 38, 35–39.
   Google Scholar
• Mccranie, J.R. & Wilson, L.D. 2002. The amphibians of Honduras. Society for the Study of Amphibians and Reptiles. Ithaca, NY, USA. p. 625.
   Google Scholar
• Miyamoto, M.M. 1983. Biochemical variation in the frog Eleutherodactylus bransfordii: geographic patterns and cryptic species. Systematic Zoology 32, 43–51.
   Google Scholar
• Mulcahy, D.G. & Mendelson III, J.R. 2000. Phylogeography of the morphologically variable, widespread species Bufo valliceps, based on molecular evidence from mtDNA. Molecular Phylogenetics and Evolution 17, 173–189.
   PubMed Web of Science ®Google Scholar
• Nasrallah, C.A. & Huelsenbeck, J.P. 2013. A phylogenetic model for the detection of epistatic interactions. Molecular Biology and Evolution 30, 2197–2208.
   Google Scholar
• Ornelas, J.F., Sosa, V., Soltis, D.E., Daza, J.M., González, C., Soltis, P.S., Gutiérrez-Rodríguez, C., Espinoza De Los Monteros, A., Castoe, T.A., Bell, C. & Ruiz-Sanchez, E. 2013. Comparative phylogeographic analyses illustrate the complex evolutionary history of threatened cloud forests of Northern Mesoamerica. Public Library of Science ONE 8, e56283.
   Google Scholar
• Pérez-Higareda, G. & Navarro L.D. 1980. The faunistic districts of the low plains of Veracruz, Mexico, base don reptilians and mammalian data. Bulletion of the Maryland Herpetological Society 16, 54–69.
   Google Scholar
• Poulin, B., Lefebvre, G., Ibáñez, R., Jaramillo, C., Hernández, C. & Rand, A.S. 2001. Avian predation upon lizards and frogs in a neotropical forest understory. Journal of Tropical Ecology 17, 21–40.
   Web of Science ®Google Scholar
• Pyron, R.A. & Wiens, J.J. 2011. A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of advanced frogs, salamanders, and caecilians. Molecular Phylogenetics and Evolution 61, 543–583.
   PubMed Web of Science ®Google Scholar
• Ronquist, F. & Huelsenbeck, J.P. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572–1574.
   PubMed Web of Science ®Google Scholar
• Rovito, S.M., Parra-Olea, G., Vásquez-Almazán, C., Luna-Reyes, R. & Wake, D.B. 2012. Deep divergence and extensive phylogeographic structure in a clade of lowland tropical salamanders. BioMed Central Evolutionary Biology 12, 255.
   PubMedGoogle Scholar
• Savage, J.M. 1987. Systematics and distribution of the Mexican and Central American rainfrogs of the Eleutherodactylus gollmeri group (Amphibia: Leptodactylidae). Fieldiana Zoology 33, 1–57.
   Google Scholar
• Savage, J.M. 2002. The amphibians and reptiles of Costa Rica: A herpetofauna between two continents, between two seas. University of Chicago Press, Chicago, Il, USA, pp. 934.
   Google Scholar
• Savage, J.M. & Emerson, S.B. 1970. Central American frogs allied to Eleutherodactylus bransfordii (Cope): a problem of polymorphism. Copeia 1970, 623–644.
   Google Scholar
• Schmid, M., Bogart, J.P. & Hedges, S.B., Eds. 2010. The chromosomes of terraranan frogs: Insights into vertebrate cytogenetics. Karger Publishing, Basel, Switzerland, pp. 568.
   Google Scholar
• Schneider, C.A., Rasband, W.S. & Eliceiri, K.W. 2012. NIH Image to Image J: 25 years of image analysis. Nature Methods 9, 671–675.
   PubMed Web of Science ®Google Scholar
• Shannon, F.A. & Werler, J.E. 1955. Notes on amphibians of the Los Tuxtlas range of Veracruz. Transactions of the Kansas Academy of Sciences 58, 360–386.
   Google Scholar
• Smith, H.M. & Taylor, E.H. 1948. An annotated checklist and key to the Amphibia of Mexico. United States National Museum, Bulletin 194, 1–118.
   Google Scholar
• Smith, H.M. & Taylor, E.H. 1950. Type localities of Mexican reptiles and amphibians. University of Kansas Science Bulletin 33, 313–380.
   Google Scholar
• Spriner, M., Hollar, L. & Burk, A. 1995. Compensatory substitutions and the evolution of the mitochondrial 12S rRNA gene in mammals. Molecular Biology and Evolution 12, 1138–1150.
   PubMed Web of Science ®Google Scholar
• Stejneger, L. 1904. The herpetology of Porto Rico. Annual Report of the United States National Museum for 1902, 549–734.
   Google Scholar
• Streicher, J.W. 2012. Evolutionary relationships among some northern groups of the direct-developing frog genus Craugastor (Anura: Craugastoridae). Dissertation. The University of Texas at Arlington. Arlington, Texas, USA. p. 92.
   Google Scholar
• Streicher, J.W., Crawford, A.J. & Edwards, C.W. 2009. Multilocus molecular phylogenetic analysis of the montane Craugastor podiciferus species complex (Anura: Craugastoridae) in Isthmian Central America. Molecular Phylogenetics and Evolution 53, 620–630.
   PubMed Web of Science ®Google Scholar
• Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar S. 2011. MEGA 5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28, 2731–2739.
   PubMed Web of Science ®Google Scholar
• Taylor, E.H. 1941a. Some Mexican frogs. Proceedings of the Biological Society of Washington 54, 87–94.
   Google Scholar
• Taylor, E.H. 1941b. New amphibians from the Hobart M. Smith Mexican collections. University of Kansas Science Bulletin 27, 141–167.
   Google Scholar
• Woolbright, L.L. & Stewart, M.M. 2008. Spatial and temporal variation in color pattern morphology in the tropical frog, Eleutherodactylus coqui. Copeia 2008, 431–437.
   Google Scholar