Open Access Open Access  Restricted Access Subscription or Fee Access


Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria



Brachycephaloidea is a monophyletic group of frogs with more than 1000 species distributed throughout the New World tropics, subtropics, and Andean regions. Recently, the group has been the target of multiple molecular phylogenetic analyses, resulting in extensive changes in its taxonomy. Here, we test previous hypotheses of phylogenetic relationships for the group by combining available molecular evidence (sequences of 22 genes representing 431 ingroup and 25 outgroup terminals) and performing a tree-alignment analysis under the parsimony optimality criterion using the program POY. To elucidate the effects of alignment and optimality criterion on phylogenetic inferences, we also used the program MAFFT to obtain a similarity-alignment for analysis under both parsimony and maximum likelihood using the programs TNT and GARLI, respectively.

      Although all three analytical approaches agreed on numerous points, there was also extensive disagreement. Tree-alignment under parsimony supported the monophyly of the ingroup and the sister group relationship of the monophyletic marsupial frogs (Hemiphractidae), while maximum likelihood and parsimony analyses of the MAFFT similarity-alignment did not. All three methods differed with respect to the position of Ceuthomantis smaragdinus (Ceuthomantidae), with tree-alignment using parsimony recovering this species as the sister of Pristimantis + Yunganastes. All analyses rejected the monophyly of Strabomantidae and Strabomantinae as originally defined, and the tree-alignment analysis under parsimony further rejected the recently redefined Craugastoridae and Pristimantinae.

      Despite the greater emphasis in the systematics literature placed on the choice of optimality criterion for evaluating trees than on the choice of method for aligning DNA sequences, we found that the topological differences attributable to the alignment method were as great as those caused by the optimality criterion. Further, the optimal tree-alignment indicates that insertions and deletions occurred in twice as many aligned positions as implied by the optimal similarity-alignment, confirming previous findings that sequence turnover through insertion and deletion events plays a greater role in molecular evolution than indicated by similarity-alignments. Our results also provide a clear empirical demonstration of the different effects of wildcard taxa produced by missing data in parsimony and maximum likelihood analyses. Specifically, maximum likelihood analyses consistently (81% bootstrap frequency) provided spurious resolution despite a lack of evidence, whereas parsimony correctly depicted the ambiguity due to missing data by collapsing unsupported nodes.

      We provide a new taxonomy for the group that retains previously recognized Linnaean taxa except for Ceuthomantidae, Strabomantidae, and Strabomantinae. A phenotypically diagnosable superfamily is recognized formally as Brachycephaloidea, with the informal, unranked name terrarana retained as the standard common name for these frogs. We recognize three families within Brachycephaloidea that are currently diagnosable solely on molecular grounds (Brachycephalidae, Craugastoridae, and Eleutherodactylidae), as well as five subfamilies (Craugastorinae, Eleutherodactylinae, Holoadeninae, Phyzelaphryninae, and Pristimantinae) corresponding in large part to previous families and subfamilies. Our analyses upheld the monophyly of all tested genera, but we found numerous subgeneric taxa to be non-monophyletic and modified the taxonomy accordingly.


Brachycephalidae, Craugastoridae, dynamic homology, direct optimization, Eleutherodactylidae, maximum likelihood, missing data, Neotropics, parsimony, phylogeny, rogue taxa, sparse supermatrix, taxonomy, terrarana, wildcard

Full Text:

PDF/A (1.16 MB)


Abascal, F., Posada, D. & Zardoya, R. (2012) The evolution of the mitochondrial genetic code in arthropods revisited. Mitochondrial DNA, 23, 84–91.

Akaike, H. (1974) A new look at the statistical model identification. IEEE Transactions on Automatic Control, 19, 716–723.

Alkatib, S., Scharff, L.B., Rogalski, M., Fleischmann, T.T., Matthes, A., Seeger, S., Schöttler, M.A., Ruf, S. & Bock, R. (2012) The contributions of wobbling and superwobbling to the reading of the genetic code. PLoS Genetics, 8, e1003076.

Amaro, R.C., Nunes, I., Canedo, C., Napoli, M.F. & Juncá, F.A (2013) A molecular phylogeny recovers Strabomantis aramunha Cassimiro, Verdade and Rodrigues, 2008 and Haddadus binotatus (Spix, 1824)(Anura: Terrarana) as sister taxa. Zootaxa, 3741, 569–582.

Anisimova, M. & Gascuel, O. (2006) Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Systematic Biology, 55, 539–552.

Ardila-Robayo, M.C. (1979) Status sistematico del genero Geobatrachus Ruthven, 1915 (Amphibia: Anura). Caldasia, 12, 383–495.

Ayarzagüena, J. (1985 "1983") Una nueva especie de Dischidodactylus Lynch (Amphibia, Leptodactylidae) en la cumbre del Tepui Marahuaca, Territorio Federal Amazonas—Venezuela. Memorias de Sociedad de Ciencias Naturales La Salle, Caracas, 43, 215–220.

Barrio-Amorós, C.L. (2010) A new Ceuthomantis (Anura: Terrarana: Ceuthomantidae) from Saraisariñama Tepui, southern Venezuela. Herpetologica, 66, 172–181.

Barrio-Amorós, C.L. & Molina, C.R. (2006) A new Eleutherodactylus (Anura: Brachycephalidae) from the Venezuelan Guayana, and redescription of Eleutherodactylus vilarsi (Melin). Zootaxa, 1302, 1–20.

Barrio-Amorós, C.L., Heinicke, M.P. & Hedges, S.B. (2013) A new tuberculated Pristimantis (Anura, Terrarana, Strabomantidae) from the Venezuelan Andes, redescription of Pristimantis pleurostriatus, and variation within Pristimantis vanadisae. Zootaxa, 3647, 43–62.

Barry, D. & Hartigan, J. (1987) Statistical analysis of hominid molecular evolution. Statistical Science, 2, 191–210.

Blackburn, D.C. & Wake, D.B. (2011) Class Amphibia Gray, 182. In: Zhang, Z.-Q. (Ed.), Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness. Zootaxa, 3148, 39–55.

Blackburne, B.P. & Whelan, S. (2012) Measuring the distance between multiple sequence alignments. Bioinformatics, 28, 495–502.

Blair, C. & Murphy, R.W. (2011) Recent trends in molecular phylogenetic analysis: Where to next? Journal of Heredity, 102, 130–138.

Blotto, B.L., Nuñez, J.J., Basso, N.G., Úbeda, C.A., Wheeler, W.C. & Faivovich, J. (2013) Phylogenetic relationships of a Patagonian frog radiation, the Alsodes + Eupsophus clade (Anura: Alsodidae), with comments on the supposed paraphyly of Eupsophus. Cladistics, 29, 113–131.

Bock, R. (2000) Sense from nonsense: How the genetic information of chloroplasts is is altered by RNA editing. Biochimie, 82, 549–557.

Box, G.E. (1976) Science and statistics. Journal of the American Statistical Association, 71, 791–799.

Bremer, K. (1988) The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution, 42, 795–803.

Britten, R.J., Rowen, L., Williams, J. & Cameron, R.A. (2003) Majority of divergence between closely related DNA samples is due to indels. Proceedings of the National Academy of Sciences, 100, 4661–4665.

Brusquetti, F., Thomé, M.T.C., Canedo, C., Condez, T.H. & Haddad, C.F.B. (2013) A new species of Ischnocnema parva species series (Anura, Brachycephalidae) from northern state of Rio de Janeiro, Brazil. Herpetologica, 69, 175–185.

Burnham, K.P. & Anderson, D.R. (2004) Multimodel inference: understanding AIC and BIC in model selection. Sociological Methods and Research, 33, 261–304.

Canedo, C. & Haddad, C.F.B. (2012) Phylogenetic relationships within anuran clade Terrarana, with emphasis on the placement of Brazilian Atlantic rainforest frogs genus Ischnocnema (Anura: Brachycephalidae). Molecular Phylogenetics and Evolution, 65, 610–620.

Caramaschi, U. & Canedo, C. (2006) Reassessment of the taxonomic status of the genera Ischnocnema Reinhardt and Lütken, 1862, and Oreobates Jiménez-de-la-Espada, 1872, with notes on the synonymy of Leiuperus verrucosus Reinhardt and Lütken, 1862 (Anura: Leptodactylidae). Zootaxa, 1116, 43–54.

Cassimiro, J., Verdade, V.K. & Rodrigues, M.T. (2008) A large and enigmatic new eleutherodactyline frog (Anura, Strabomantidae) from Serra do Sincorá, Espinhaço range, northeastern Brazil. Zootaxa, 1761, 59–68.

Chan, S.C., Wong, A.K.C. & Chiu, D.K.Y. (1992) A survey of multiple sequence comparison methods. Bulletin of Mathematical Biology, 54, 563–598.

Chaparro, J.C., Motta, A.P., Gutiérrez, R.C. & Padial, J.M. (2012) A new species of Pristimantis (Anura: Strabomantidae) from Andean cloud forests of northern Peru. Zootaxa, 3192, 39–48.

Cisneros-Heredia, D.F. (2006) La herpetofauna de la Estación de Biodiversidad Tiputini, Ecuador. B.Sc. Thesis. Universidad San Francisco de Quito, Quito, 129 pp.

Clemente-Carvalho, R.B.G., Klaczko, J., Perez, I.S., Alves, A.C.R., Haddad, C.F.B. & Reis, S.F. (2011) Molecular phylogenetic relationships and phenotypic diversity in miniaturized toadlets, genus Brachycephalus (Amphibia: Anura: Brachycephalidae). Molecular Phylogenetics and Evolution, 61, 79–89.

Cracraft, J. (1981) The use of functional and adaptive criteria in phylogenetic systematics. American Zoologist, 21, 21–36.

Crawford, A.J. & Smith, E.E. (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.

Crawford, A.J., Lips, K.R. & Bermingham, E. (2010a) Epidemic disease decimates amphibian abundance, species diversity, and evolutionary history in the highlands of central Panama. Proceedings of the National Academy of Sciences USA, 107, 13777–13782.

Crawford, A.J., Ryan, M.J. & Jaramillo, C.A. (2010b) A new species of Pristimantis (Anura: Strabomantidae) from the Pacific coast of the Darien Province, Panama, with a molecular analysis of its phylogenetic position. Herpetologica, 66, 192–206.

Crother, B.I. (2009) Are standard names lists taxonomic straightjackets? Herpetologica, 65, 129–135.

Darst, C.R. & Cannatella, D.C. (2004) Novel relationships among hyloid frogs inferred from 12S and 16S mitochondrial DNA sequences. Molecular Phylogenetics and Evolution, 31, 462–475.

De la Riva, I. (2007) Bolivian frogs of the genus Phrynopus, with the description of twelve new species (Anura: Brachycephalidae). Herpetological Monographs, 21, 241–277.

De la Riva, I. & Lynch, J.D. (1997) New species of Eleutherodactylus from Bolivia (Amphibia: Leptodactylidae). Copeia, 1997, 151–157.

De la Riva, I., Chaparro, J.C. & Padial, J.M. (2008) The taxonomic status of Phyllonastes Heyer and Phrynopus peruvianus (Noble) (Lissamphibia, Anura): resurrection of Noblella Barbour. Zootaxa, 1685, 67–68.

Denton, J.S. & Wheeler, W.C. (2012) Indel information eliminates trivial sequence alignment in maximum likelihood phylogenetic analysis. Cladistics, 28, 514–528.

Dubois, A. (2005a) Amphibia Mundi 1.1. An ergotaxonomy of recent amphibians. Alytes, 23, 1–24.

Dubois, A. (2005b) Proposed rules for the incorporation of nomina of higher-ranked zoological taxa in the International Code of Zoological Nomenclature. 1. Some general questions, concepts and terms of biological nomenclature. Zoosystema, 27, 365–426.

Dubois, A. (2006) Incorporation of nomina of higher-ranked taxa into the International Code of Zoological Nomenclature: some basic questions. Zootaxa, 1337, 1–37.

Duellman, W.E. (1978) The biology of an equatorial herpetofauna in Amazonian Ecuador. Miscellaneous Publications of the University of Kansas, Museum of Natural History, Lawrence, 65, 1–352.

Duellman, W.E. & Lynch, J.D. (1969) Descriptions of Atelopus tadpoles and their relevance to atelopodid classification. Herpetologica, 25, 231–240.

Duellman, W.E. & Hedges, S.B. (2005) Eleutherodactyline frogs (Anura, Leptodactylidae) from the Cordillera Yanachaga in central Peru. Copeia, 2005, 526–538.

Duellman, W.E. & Köhler, J. (2005) New species of marsupial frog (Hylidae, Hemiphractinae, Gastrotheca) from the yungas of Bolivia. Journal of Herpetology, 39, 91–100.[0091:nsomfh];2

Duellman, W.E. & Hedges, S.B. (2007) Three new species of Pristimantis (Lissamphibia, Anura) from montane forests of the Cordillera Yanachaga in central Peru. Phyllomedusa, 6, 119–135.

Duellman, W.E. & Lehr, E. (2009) Terrestrial–breeding frogs (Strabomantidae) in Peru. Nature und Tier Verlag, Münster, Germany, 384 pp.

Duellman, W.E., Jungfer, K.-H. & Blackburn, D.C. (2011) The phylogenetic relationship of geographically separated "Flectonotus" (Anura, Hemiphractidae), as revealed by molecular, behavioral, and morphological data. Phyllomedusa, 10, 15–29.

The ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57–74.

Edgar, R.C. (2004) MUSCLE, multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792–1797.

Edgar, R.C. & Sjölander, K. (2003) SATCHMO, sequence alignment and tree construction using hidden Markov models. Bioinformatics, 19, 1404–1411.

Eernisse, D.J. & Kluge, A.G. (1993) Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology. Molecular Biology and Evolution, 10, 1170–1195.

Efron, B. (1979) Bootstrap methods, another look at the jackknife. The Annals of Statistics, 7, 1–26.

Efron, B., Halloran, E. & Holmes, S. (1996) Bootstrap confidence levels for phylogenetic trees. Proceedings of the National Academy of Sciences, 93, 13429–13429.

Eizirik, E., Yuhki, N., Johnson, W.E., Menotti-Raymond, M., Hannah, S.S. & O'Brien, S.J. (2003) Molecular genetics and evolution of melanism in the cat family. Current Biology, 13, 448–453.

Elmer, K.R. & Cannatella, D.C. (2008) Three new species of leaflitter frogs from the upper Amazon forests, cryptic diversity within Pristimantis "ockendeni" (Anura, Strabomantidae) in Ecuador. Zootaxa, 1784, 11–38.

Estabrook, G.F. (1997) Ancestor–descendant relations and incompatible data, motivation for research in discrete mathematics. In: Mirkin, B. McMorris, F., Roberts, R. & Rzhetsky, A. (Eds.), Mathematical Hierarchies and Biology. Providence, pp. 1–28.

Faivovich, J., Haddad, C.F.B., García, P.C.A., Frost, D.R., Campbell, J.A. & Wheeler, W.C. (2005) Systematic revision of the frog family Hylidae, with special reference to Hylinae, phylogenetic analysis and taxonomic revision. Bulletin of the American Museum of Natural History, 294, 1–240.[0001:srotff];2

Farris, J.S. (1966) Estimation of conservatism of characters by constancy within biological populations. Evolution, 20, 587–591.

Farris, J.S. (1969) A successive approximations approach to character weighting. Systematic Biology, 18, 374–385.

Farris, J.S. (1970) On the relationship between variation and conservatism. Evolution, 24, 825–827.

Farris, J.S. (1973) A probability model for inferring evolutionary trees. Systematic Biology, 22, 250–256.

Farris, J.S. (1983) The logical basis of phylogenetic analysis. In: Platnick, N.I. & Funk, V.A. (Eds.), Advances in Cladistics. Proceedings of the Second Meeting of the Willi Hennig Society, Volume 2. Columbia University Press, New York, pp. 7–36.

Farris, J.S. (1999) Likelihood and inconsistency. Cladistics, 15, 199–204.

Farris, J.S. (2001) Support weighting. Cladistics, 17, 389–394.

Farris, J.S., Albert, V.A., Källersjö, M., Lipscomb, D. & Kluge, A.G. (1996) Parsimony jackknifing outperforms neighbor–joining. Cladistics, 12, 99–124.

Farris, J.S., Kluge, A.G. & Carpenter, J.M. (2001) Popper and likelihood versus "Popper*". Systematic Biology, 50, 438–444.

Felsenstein, J. (1973) Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Systematic Biology, 22, 240–249.

Felsenstein, J. (1985) Confidence limits on phylogenies, an approach using the bootstrap. Evolution, 39, 783–791.

Felsenstein, J. (1988) Phylogenies from molecular sequences: Inference and reliability. Annual Review of Genetics, 22, 521–565.

Felsenstein, J. (2004) Inferring phylogenies. Sinauer Associates, Sunderland (MA), 664 pp.

Fleissner, R., Metzler, D. & von Haeseler, A. (2005) Simultaneous statistical multiple alignment and phylogeny reconstruction. Systematic Biology, 54, 548–561.

Fontanillas, E., Welch, J.J., Thomas, J.A. & Bromham, L. (2007) The influence of body size and net diversification rate on molecular evolution during the radiation of animal phyla. BMC Evolutionary Biology, 7, 95.

Fouquet, A., Loebmann, D., Castroviejo-Fisher, S., Padial, J.M., Orrico, V.G.D., Lyra, M.L., Roberto, I.J., 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.

Fouquet, P., Martinez, Q., Courtois, E. A., Dewynter, M., Pineau, K., Gaucher, P., Blanc, M., Marty, C. & Kok, P.J.R. (2013a) A new species of the genus Pristimantis (Amphibia, Craugastoridae) associated with the moderately elevated massifs of French Guiana. Zootaxa, 3750, 569–586.

Fouquet, A., Blotto, B.L., Maronna, M.M., Verdade, V.K., Juncá, F.A., Sá, R.D. & Rodrigues, M.T. (2013b) Unexpected phylogenetic positions of the genera Rupirana and Crossodactylodes reveal insights into the biogeography and reproductive evolution of leptodactylid frogs. Molecular Phylogenetics and Evolution, 67, 445–457.

Frost, D.R. (2014) Amphibian Species of the World, an Online Reference. Version 6.0 American Museum of Natural History, New York, USA. Available at (accessed February 04 2014)

Frost, D.R., Grant, T., Faivovich, J., Bain, R.H., Haas, A., Haddad, C.F.B., De Sa, R.O., Channing, A., Wilkinson, M., Donnellan, S.C., Raxworthy, C.J., Campbell, J.A., Blotto, B.L., Moler, P., 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.[0001:tatol];2

Frost, D.R., Grant, T., Faivovich, J., Bain, R.H., Haas, A., Haddad, C.F.B., de Sa, 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. (2008) Is the Amphibian Tree of Life really fatally flawed? Cladistics, 24, 384–395.

Fusinatto, L.A., Alexandrino, J., Haddad, C.F.B., Brunes, T.O., Rocha, C.F.D. & Sequeira, F. (2013) Cryptic genetic diversity is paramount in small-bodied amphibians of the genus Euparkerella (Anura: Craugastoridae) endemic to the Brazilian Atlantic forest. PLoS ONE, 8, e79504.

Gallardo, J.M. (1965) A propósito de los Leptodactylidae (Amphibia Anura). Papéis Avulsos do Departamento de Zoologia, 17, 77–87.

García-R, J.C., Crawford, A.J., Mendoza, A.M, Ospina, O., Cardenas, H. & Castro, F. (2012) comparative phylogeography of direct–developing frogs (Anura, Craugastoridae, Pristimantis) in the southern Andes of Colombia. PLoS One, 7, e46077.

García-R, J.C., Mendoza A.M., Ospina, O., Cardenas, H. & Castro, F. (2014) A morphometric and molecular approach to define three closely related species of frogs of the genus Pristimantis (Anura: Craugastoridae) from the Cordillera Occidental in Colombia. Journal of Herpetology. [in press]

Gehara, M., Canedo, C., Haddad, C.F.B. & Vences, M. (2013) From widespread to microendemic, molecular and acoustic analyses show that Ischnocnema guentheri (Amphibia, Brachycephalidae) is endemic to Rio de Janeiro, Brazil. Conservation Genetics, 14, 973–982.

Giribet, G. (2005) Generating implied alignments under direct optimization using POY. Cladistics, 21, 396–402.

Goldberg, C.S., Sullivan, B.K., Malone, J.H. & Schwalbe, C.R. (2004) Divergence among barking frogs (Eleutherodactylus augusti) in the southwestern United Stated. Herpetologica, 60, 312–320.

Goldman, N. (1990) Maximum–likelihood inference of phylogenetic trees, with special reference to Poisson process model of DNA substitution and to parsimony analysis. Systematic Zoology, 39, 345–361.

Goloboff, P.A. (1993) Estimating character weights during tree search. Cladistics, 9, 83–91.

Goloboff, P.A. (1996) Methods for faster parsimony analysis. Cladistics, 12, 199–220.

Goloboff, P.A. (1999) Analyzing large data sets in reasonable times, solutions for composite optima. Cladistics, 15, 415–428.

Goloboff, P.A. (2003) Parsimony, likelihood, and simplicity. Cladistics, 19, 91–103.

Goloboff, P.A. (2008) Calculating SPR distances between trees. Cladistics, 24, 591–597.

Goloboff, P.J., Farris, S. & Nixon, K. (2008) TNT, a free program for phylogenetic analysis. Cladistics, 24, 774–786.

Goodman, M., Weiss, M.L. & Czelusniak, J. (1982) Molecular evolution above the species level, branching patterns, rates, and mechanisms. Systematic Zoology, 31, 376–399.

Grant, T. (2002) Testing methods, the evaluation of discovery operations in evolutionary biology. Cladistics, 18, 94–111.

Grant, T. & Kluge, A.G. (2003) Data exploration in phylogenetic inference, scientific, heuristic, or neither. Cladistics, 19, 379–418.

Grant, T. & Kluge, A.G. (2004) Transformation series as an ideographic character concept. Cladistics, 20, 23–31.

Grant, T. & Kluge, A.G. (2008a) Clade support measures and their adequacy. Cladistics, 24, 1051–1064.

Grant, T. & Kluge, A.G. (2008b) Credit where credit is due: The Goodman-Bremer support metric. Molecular Phylogenetics and Evolution, 49, 405–406.

Grant T. & Kluge, A.G. (2009) Parsimony, explanatory power, and dynamic homology testing. Systematics and Biodiversity, 7, 357–363.

Grant, T., Frost, D.R., Caldwell, J.P., Gagliardo, R., Haddad, C.F.B., Kok, P.J.R., Means, B.D., Noonan, B.P., Schargel, W. & Wheeler, W.C. (2006) Phylogenetic systematics of dart–poison frogs and their relatives (Anura, Athesphatanura, Dendrobatidae) Bulletin of the American Museum of Natural History, 299, 1–262.[1:psodfa];2

Haas, A. (2001) Mandibular arch musculature of anuran tadpoles, with comments on homologies of amphibian jaw muscles. Journal of Morphology, 247, 1–33.<1::aid-jmor1000>;2-3

Hacking, I. (1965) The Logic of Statistical Inference. Cambridge University Press, Cambridge, 244 pp.

Haszprunar, G. (1998) Parsimony analysis as a specific kind of homology estimation and the implications for character weighting. Molecular Phylogenetics and Evolution, 9, 333–339.

Hecht, M.K. & Edwards, J.L. (1976) The determination of parallel or monophyletic relationships, the proteid salamanders—a test case. American Naturalist, 653–677.

Hedges, S.B., Duellman, W.E. & Heinicke, M.P. (2008a) New World direct-developing frogs (Anura, Terrarana), molecular phylogeny, classification, biogeography, and conservation. Zootaxa, 1737, 1–182.

Hedges, S.B., Duellman, W.E. & Heinicke, M.P. (2008b) A replacement name for Isodactylus Hedges, Duellman, and Heinicke, 2008. Zootaxa, 1795, 67–68.

Heinicke, M.P., Duellman, W.E. & Hedges, S.B. (2007) Major Caribbean and Central American frog faunas originated by oceanic dispersal. Proceedings of the National Academy of Sciences, USA, 104, 10092–10097.

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.

Hennig, W. (1966) Phylogenetic Systematics. University of Illinois Press, Chicago, 280 pp.

Hertz, A., Hauenschild, F., Lotzkat, S. & Köhler, G. (2012) A new golden frog species of the genus Diasporus (Amphibia, Eleutherodactylidae) from the Cordillera Central, western Panama. ZooKeys, 196, 23–46.

Heyer, W.R. (1975) A preliminary analysis of the intergeneric relationships of the frog family Leptodactylidae. Smithsonian Contributions to Zoology, 199, 1–55.

Heyer, W.R. (1977) Taxonomic notes on frogs from the Madeira and Purus rivers, Brasil. Papeis Avulsos de Zoologia. São Paulo, 31, 141–162.

Hickson, R.E., Simon, C. & Perrey, S.W. (2000) The performance of several multiple–sequence alignment programs in relation to secondary-structure features for an rRNA sequence. Molecular Biology and Evolution, 17, 530–539.

Hillis, D.M. (1995) Approaches for assessing phylogenetic accuracy. Systematic Biology, 44, 3–16.

Ho, S.Y. (2009) An examination of phylogenetic models of substitution rate variation among lineages. Biology Letters, 5, 421–424.

Ho, S.Y., Lanfear, R., Bromham, L., Phillips, M.J., Soubrier, J., Rodrigo, A.G. & Cooper, A. (2011) Time-dependent rates of molecular evolution. Molecular Ecology, 20, 3087–3101.

Hogeweg, P. & Hesper, B. (1984) The alignment of sets of sequences and the construction of phyletic trees, an integrated method. Journal of Molecular Evolution, 20, 175–186.

Holmes, S. (2003) Bootstrapping phylogenetic trees, theory and methods. Statistical Science, 18, 241–255.

Holder, M.T., Lewis, P.O. & Swofford, D.L. (2010) The Akaike information criterion will not choose the no common mechanism model. Systematic Biology, 59, 477–485.

Hoogmoed, M.S. & Lescure, J. (1984) A new genus and two new species of minute leptodactylid frogs from northern South America, with comments upon Phyzelaphryne (Amphibia, Anura, Leptodactylidae). Zoologische Mededelingen, 58, 85–113.

Huelsenbeck, J.P. (1995) Performance of phylogenetic methods in simulation. Systematic Biology, 44, 17–48.

Huelsenbeck, J.P. & Crandall, K.A. (1997) Phylogeny estimation and hypothesis testing using maximum likelihood. Annual Review of Ecology and Systematics, 28, 437–466.

Huelsenbeck, J.P. & Rannala, B. (1997) Phylogenetic methods come of age: Testing hypotheses in an evolutionary context. Science, 276, 227–232.

Huelsenbeck, J.P., Hillis, D.M. & Nielsen, R. (1996) A likelihood-ratio test of monophyly. Systematic Biology, 45, 546–558.

Huelsenbeck, J.P., Alfaro, M.E. & Suchard, M.A. (2011) Biologically inspired phylogenetic models strongly outperform the No Common Mechanism model. Systematic Biology, 60, 225–232.

ICZN (1999) International Code of Zoological Nomenclature. Fourth edition. International Trust for Zoological Nomenclature, London, U.K. Available from: (accessed 6 May 2014)

Izecksohn, E. (1971) Nôvo gênero e nova espécie de Brachycephalidae do Estado do Rio do Janeiro, Brazil. (Amphibia, Anura). Boletim do Museu Nacional, Nova Série, Zoologia, 280, 1–12.

Izecksohn, E. (1988) Algumas consideraçoes sôbre or genero Euparkerella, com a descrição de tres novas especies (Amphibia, Anura, Leptodactylidae). Revista Brasileira de Biologia, 48, 59–74.

Johnson, J.B. & Omland, K.S. (2004) Model selection in ecology and evolution. Trends in Ecology & Evolution, 19, 101–108.

Kaplan, M. (2002) Histology of the anteroventral part of the breast-shoulder apparatus of Brachycephalus ephippium (Brachycephalidae) with comments on the validity of the genus Psyllophryne (Brachycephalidae). Amphibia-Reptilia, 23, 225–227.

Katoh, K., Kuma, K., Toh, H. & Miyata, T. (2005) MAFFT, a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30, 3059–3066.

Kearney, M. (2002) Fragmentary taxa, missing data, and ambiguity: mistaken assumptions and conclusions. Systematic Biology, 51, 369–381.

Kelchner, S.A. & Thomas, M.A. (2007) Model use in phylogenetics, nine key questions. Trends in Ecology and Evolution, 22, 87–94.

Kieswetter, C.M. & Schneider, C.J. (2013) Phylogeography in the northern Andes, complex history and cryptic diversity in a cloud forest frog, Pristimantis w–nigrum (Craugastoridae). Molecular Phylogenetics and Evolution, 69, 417–429.

Kim, J., Kim, I., Yang, J.S., Shin, Y.E., Hwang, J., Park, S., Choi, Y.S. & Kim, S. (2012) Rewiring of PDZ domain–ligand interaction network contributed to eukaryotic evolution. PLoS Genetics, 8, e1002510.

Kluge, A.G. (1999) The science of phylogenetic systematics, explanation, prediction, and test. Cladistics, 15, 429–436.

Kluge, A.G. (2001) Philosophical conjectures and their refutation. Systematic Biology, 50, 322–330.

Kluge, A.G. (2009) Explanation and falsification in phylogenetic inference, exercises in Popperian philosophy. Acta Biotheoretica, 57, 171–186.

Kluge, A.G. & Farris, J.S. (1969) Quantitative phyletics and the evolution of anurans. Systematic Zoology, 18, 1–32.

Kluge, A.G. & Kerfoot, W.C. (1973) The predictability and regularity of character divergence. American Naturalist, 107, 426–442.

Kluge, A.G. & Grant, T. (2006) From conviction to anti–superfluity, old and new justifications for parsimony in phylogenetic inference. Cladistics, 22, 276–288.

Köhler, J. (2000) New species of Eleutherodactylus (Anura, Leptodactylidae) from cloud forest of Bolivia. Copeia, 2000, 516–520.[0516:nsoeal];2

Kok, P.J.R. & Barrio-Amorós, C.L. (2013) On the taxonomic validity of Pristimantis tepuiensis (Schlüter & Rödder, 2007) and P. stegolepis (Schlüter & Rödder, 2007), with remarks on the type series of P. guaiquinimensis (Schlüter & Rödder, 2007). Zootaxa, 3694, 75–80.

Kolaczkowski, B. & Thornton, J.W. (2004) Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogenous. Nature, 431, 980–984.

Kück, P., Mayer, C., Wägele, J.W. & Misof, B. (2012) Long branch effects distort maximum likelihood phylogenies in simulations despite selection of the correct model. PLoS One, 7 (5), e36593.

Kuhn, T.S. (1962) The Structure of Scientific Revolutions. University of Chicago Press. Chicago, USA, 226 pp.

La Marca, E. (2007) Sinopsis taxonómica de dos géneros nuevos de anfibios (Anura, Leptodactylidae) de los Andes de Venezuela. Herpetotropicos, 3, 67–87.

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

Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J. & Higgins, D.G. (2007) Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947–2948.

Laurent, R.F. (1980 "1979") Esquisse d’une phylogenese des Anoures. Bulletin de la Société Zoologique de France, 104, 397–422.

Laurent, R.F. (1986) Sous classe des lissamphibiens (Lissamphibia). In: Grassé, P.-P. & Delsol, M. (Eds.), Traité de Zoologie. Anatomie, Systematique, Biologie. Vol. 14. (Batraciens). Fascicule 1B. Masson Paris, France, pp. 594–797.

Le Quesne, W.J. (1974) The uniquely evolved character concept and its cladistic application. Systematic Biology, 23, 513–517.

Leavitt, J.R., Hiatt, K.D., Whiting, M.F. & Song, H. (2013) Searching for the optimal data partitioning strategy in mitochondrial phylogenomics, a phylogeny of Acridoidea (Insecta, Orthoptera, Caelifera) as a case study. Molecular Phylogenetics and Evolution, 67, 494–508.

Lehr, E. (2007) New eleutherodactyline frogs (Leptodactylidae, Pristimantis, Phrynopus) from Peru. Bulletin of the Museum of Comparative Zoology, 159, 145–178.[145:neflpp];2

Lehr, E., Fritzsch, G. & Müller, A. (2005) Analysis of Andes frogs (Phrynopus, Leptodactylidae, Anura) phylogeny based on 12S and 16S mitochondrial rDNA sequences. Zoologica Scripta, 34, 593–603.

Lehr, E., Lundberg, M., Aguilar, C. & von May, R. (2006) New species of Eleutherodactylus (Anura, Leptodactylidae) from the eastern Andes of central Peru with comments on central Peruvian Eleutherodactylus. Herpetological Monographs, 20, 105–128.[105:nsoeal];2

Lehr, E., Torres-Gastello, C.P. & Suárez-Segovia, J. (2007) A new species of arboreal Eleutherodactylus (Anura, Leptodactylidae) from the Amazonian lowlands of central Peru. Herpetologica, 63, 94–99.[94:ansoae];2

Lehr, E., Gregory, C. & Catenazzi, A. (2013) A new species of Pristimantis (Amphibia: Anura: Strabomantidae) from the Río Abiseo National Park, Peru. Zootaxa, 3731, 201–211.

Lemmon, A.R. & Moriarty, E.C. (2004) The importance of proper model assumption in Bayesian phylogenetics. Systematic Biology, 53, 265–277.

Lemmon, A.R., Brown, J.M., Stanger–Hall, K. & Lemmon, E.M. (2009) The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Systematic Biology, 58, 130–145.

Liu, K., Warnow, T.J., Holder, M.T., Nelesen, S.M., Yu, J., Stamatakis, A.P. & Linder, C.R. (2012) SATé–II, very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Systematic Biology, 61, 90–106.

Liu K., Raghavan, S., Nelesen, S., Linder, C.R. & Warnow, T. (2009) Rapid and accurate large–scale coestimation of sequence alignments and phylogenetic trees. Science, 324, 1561–1564.

Li, C., Lu, G. & Orti, G. (2008) Optimal data partitioning and a test case for ray-finned fishes (Actinopterygii) based on ten nuclear loci. Systematic Biology, 57, 519–539.

Löytynoja, A. & Goldman, N. (2008) Phylogeny–aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science, 320, 1632–1635.

Lutz, B. (1954) Anfíbios anuros do Distrito Federal. Memórias do Instituto Oswaldo Cruz, 52, 155–238.

Lynch, J.D. (1971) Evolutionary relationships, osteology, and zoogeography of leptodactyloid frogs. University of Kansas Museum of Natural History, Miscellaneous Publications, 53, 1–238.

Lynch, J.D. (1973) A new narrow-toed frog from Andean Ecuador (Leptodactylidae, Eleutherodactylus). Copeia, 1973, 222–225.

Lynch, J.D. (1974) New species of frogs (Leptodactylidae, Eleutherodactylus) from the Amazonian lowlands of Ecuador. Occasional Papers of the Museum of Natural History, University of Kansas, 31, 1–22.

Lynch, J.D. (1975a) A review of the broad-headed eleutherodactyline frogs of South America. Occasional Papers of the Museum of Natural History, University of Kansas, 38, 1–46.

Lynch, J.D. (1975b) A review of the Andean leptodactylid frog genus Phrynopus. Occasional Papers of the Museum of Natural History, University of Kansas, 35, 1–51.

Lynch, J.D. (1976a) The species groups of the South American frogs of the genus Eleutherodactylus (Leptodactylidae). Occasional Papers of the Museum of Natural History, University of Kansas, 61, 1–24.

Lynch, J.D. (1976b) Two new species of frogs of the genus Euparkerella (Amphibia, Leptodactylidae) from Ecuador and Perú. Herpetologica, 32, 48–53.

Lynch, J.D. (1979) A new genus for Elosia duidensis Rivero (Amphibia, Leptodactylidae) from southern Venezuela. American Museum Novitates, 2680, 1–8.

Lynch, J.D. (1986a) The definition of the Middle American clade of Eleutherodactylus based on jaw musculature (Amphibia, Leptodactylidae). Herpetologica, 42, 248–58.

Lynch, J.D. (1986b) New species of minute leptodactylid frogs from the Andes of Ecuador and Peru. Journal of Herpetology, 20, 423–431.

Lynch, J.D. (1993) The value of m. depresor mandibulae in phylogenetic hypothesis for Eleutherodactylus and its allies (Amphibia, Leptodactylidae). Herpetologica, 49, 32–41.

Lynch, J.D. (1997) Intrageneric relationships of mainland Eleutherodactylus II. A review of the Eleutherodactylus sulcatus group. Revista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturales, 21, 353–372.

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.

Lynch, J.D. (2001) Three new rainfrogs of the Eleutherodactylus diastema group from Colombia and Panama. Revista de la Academia Colombiana de Ciencias Exactas, Fisicas y Naturales, 25, 287–297.

Lynch, J.D. (2005) Discovery of the richest frog fauna in the world—an exploration of the forests to the north of Leticia. Revista de la Academia Colombiana Ciencias, 29, 581–588.

Lynch, J.D. & Ruiz-Carranza, P.M. (1982) A new genus and species of poison–dart frog (Amphibia, Dendrobatidae) from the Andes of Northern Colombia. Proceedings of the Biological Society of Washington, 95, 557–562.

Lynch, J.D. & Myers, C.W. (1983) Frogs of the fitzingeri group of Eleutherodactylus in eastern Panama and Chocoan South America (Leptodactylidae). Bulletin of the American Museum of Natural History, 175, 481–572.

Lynch, J.D. & McDiarmid, R.W. (1987) Two new species of Eleutherodactylus (Amphibia, Anura, Leptodactylidae) from Bolivia. Proceedings of the Biological Society of Washington, 100, 337–346.

Lynch, J.D. & Duellman, W.E. (1997) Frogs of the genus Eleutherodactylus (Leptodactylidae) in western Ecuador, systematics, ecology, and biogeography. University of Kansas Natural History Museum Special Publications, 23, 1–236.

Maciel, N., Vaz-Silva, W., de Oliveira, R.M. & Padial, J.M. (2012) A new species of Pristimantis (Anura, Strabomantidae) from the Brazilian Cerrado. Zootaxa, 3265, 43–56.

Masuda, I., Matsuzaki, M. & Kita, K. (2010) Extensive frameshift at all AGG and CCC codons in the mitochondrial cytochrome c oxidase subunit 1 gene of Perkinsus marinus (Alveolata; Dinoflagellata). Nucleic Acids Research, 38, 6186–6194.

McGuire, J.A., Witt, C.C., Altshuler, D.L. & Remsen, J.V. (2007) Phylogenetic systematics and biogeography of hummingbirds, Bayesian and maximum likelihood analyses of partitioned data and selection of an appropriate partitioning strategy. Systematic Biology, 56, 837–856.

Means, D.B. & Savage, J.M. (2007) Three new malodorous rainfrogs of the genus Pristimantis (Anura, Brachycephalidae) from the Wohomung Massif in west-central Guyana, South America. Zootaxa, 1638, 39–56.

Meireles, C.M., Czelusniak, J., Schneider, M.P., Muniz, J.A., Brigido, M.C., Ferreira, H.S. & Goodman, M. (1999) Molecular phylogeny of ateline new world monkeys (Platyrrhini, Atelinae) based on gamma-globin gene sequences, evidence that Brachyteles is the sister group of Lagothrix. Molecular Phylogenetics and Evolution, 12, 10–30.

Moravec, J., Lehr, E., Perez-Peña, P.E., Lopez, J.J., Gagliardi-Urrutia, L.A.G. & Arista-Tuanama, I. (2010) A new green, arboreal species of Pristimantis (Anura, Strabomantidae) from Amazonian Peru. Vertebrate Zoology, 60, 225–232.

Morrison, D.A. (2007) Increasing the efficiency of searches for the maximum likelihood tree in a phylogenetic analysis of up to 150 nucleotide sequences. Systematic Biology, 56, 988–1010.

Morrison, D.A. & Ellis, J.T. (1997) Effects of nucleotide sequence alignment on phylogeny estimation, a case study of 18S rDNAs of Apicomplexa. Molecular Biology and Evolution, 14, 428–441.

Myers, C.W. & Ford, L.S. (1986) On Atopophrynus, a recently described frog wrongly assigned to the Dendrobatidae. American Museum Novitates, 2843, 1–15.

Myers, C.W. & Donnelly, M.A. (1997) A tepui herpetofauna on a granitic mountain (Tamacuari) in the borderland between Venezuela and Brazil, Report from the Phipps Tapirapecó Expedition. American Museum Novitates, 3213, 1–71.

Nadeau, N.J. & Jiggins, C.D. (2010) A golden age for evolutionary genetics? Genomic studies of adaptation in natural populations. Trends in Genetics, 26, 484–92.

Neff, N.A. (1986) A rational basis for a priori character weighting. Systematic Biology, 35, 110–123.

Noble, G.K. (1926) The hatching process in Alytes, Eleutherodactylus and other amphibians. American Museum Novitates, 229, 1–7.

Novák, Á., Miklós, I., Lyngsø, R. & Hein, J. (2008) StatAlign, an extendable software package for joint Bayesian estimation of alignments and evolutionary trees. Bioinformatics, 24, 2403–2404.

Nixon, K.C. (1999) The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics, 15, 407–414.

Ohler, A. & Dubois A. (2012) Validation of two familial nomina nuda of Amphibia Anura. Alytes, 28, 162–167.

Oreskes N., Shrader-Frechette K. & Belitz K. (1994) Verification, validation, and confirmation of numerical models in the earth sciences. Science, 263, 641–646.

Owen, R. (1843) Lectures on the Comparative Anatomy and Physiology of the Invertebrate Animals. Longman, Brown, Green and Longmans, London, 392 pp.

Padial, J.M. & de la Riva, I. (2009) Integrative taxonomy reveals cryptic Amazonian species of Pristimantis (Anura). Zoological Journal of the Linnean Society, 155, 97–122.

Padial, J.M., McDiarmid, R.W. & de la Riva, I. (2006) Distribution and morphological variation of Eleutherodactylus mercedesae Lynch and McDiarmid, 1987 (Amphibia, Anura, Leptodactylidae) with first record for Peru. Zootaxa, 1278, 49–56.

Padial, J.M., Castroviejo-Fisher, S., Köhler, J., Domic, E. & de la Riva, I. (2007) Systematics of the Eleutherodactylus fraudator species group (Anura, Brachycephalidae). Herpetological Monographs, 21, 214–241.

Padial, J.M., Castroviejo-Fisher, S. & de la Riva, I. (2009) The phylogenetic relationships of Yunganastes revisited (Anura, Terrarana). Molecular Phylogenetics and Evolution, 52, 911–915.

Padial, J.M., Chaparro, J.C., Castroviejo-Fisher, S., Guayasamín, J.M., Lehr, E., Delgado, A.J., Vaira, M., Teixeira, M. Jr., Aguayo, R. & de la Riva, I. (2012) A revision of species diversity in the Neotropical genus Oreobates (Anura, Strabomantidae), with the description of three new species from the Amazonian slopes of the Andes. American Museum Novitates, 3752, 1–55.

Pereyra, M.O., Cardozo, D.E., Baldo, J., & Baldo, D. (2014) Description and phylogenetic position of a new species of Oreobates (Anura: Craugastoridae) from northwestern Argentina. Herpetologica, 70, 211–227.

Philippe, H., Zhou, Y., Brinkmann, H., Rodrigues, N. & Delsuc, F.


  • There are currently no refbacks.

ISSN 1175-5326 (Print Edition) & ISSN 1175-5334 (Online Edition)
Published by Magnolia Press, Auckland, New Zealand
A founding journal of Biotaxa