Amphibian Species of the World - Over-arching philosopy

Higher taxonomy and progress, with comments on taxonomic philosophy

With the appearance of six publications (Chippindale et al., 2004; Faivovich et al., 2005; Macey, 2005; Frost et al., 2006; and Grant et al., 2006; Roelants et al., 2007), amphibian systematics moved substantially towards a taxonomy consistent with evolutionary relationships. Concomitantly, we entered a period of nomenclatural instability in which workers will rush to tie up all of the loose ends that are no longer concealed by nonmonophyletic groupings (e.g., the older senses of Pseudoeurycea, Plethodontinae, Bufo, Hyla, Hyperoliidae, Leptodactylidae, Eleutherodactylinae, Rana, Hylarana, Ranidae, Microhylidae, and Caeciliinae). Because taxonomic stability must be an artifact of understanding, not authoritarian decree, I think this instability reflects the health of amphibian systematics as a scientific endeavor driven by evidence and not something that makes systematics a "laughingstock" of science (Wake, 2006 [cf. Sokal and Sneath, 1963]; for more scientific views of this issue see Dominguez and Wheeler, 1997, and Grant and Kluge, 2005). Adherence to nonevolutionary/nonmonophyletic groups by social compact would be quaintly anachronistic were it not such a threat to progress in systematics research.

Over the next several years there will be considerable discussion of the higher taxonomy of amphibians. This will include nomenclatural discussions of how best to name evolutionary groups as well as more important discussions of epistemology, evidence, and analytical methods as they impact inferential biology. Throughout the ensuing debate, it will be important to distinguish legitimate scientific disagreements grounded in evidence and analysis from authoritarian posturing based only on opinion and deference to tradition and social conservativeness. This kind of resistance will rest largely on nonscientific propaganda and innuendo. Nevertheless, what should come out of the scientific exercises associated with the controversies will be a huge increase in the amount of evidence and the number of explicitly tested phylogenetic hypotheses, as well as more philosophically rigorous discussions of analytical methods and their underlying justifications.

Even though I have been part of this recent push towards monophyly in amphibian taxonomy, my ongoing objective is to continue to update ASW as evidence accumulates and the current phylogenetic hypotheses (e.g., Chippindale et al., 2004; Faivovich et al., 2005; Macey, 2005; Frost et al., 2006; and Grant et al., 2006) are refined or refuted by additional evidence (e.g., Che et al., 2007). My intention is to continue to give new ideas and nomenclatural novelties an airing, to let this online catalog support change and the younger workers who make systematics the dynamic field that it is.

A comparison of the family-group names applied in ASW versions 3.0 and 5.3 provides a general road-map for the number of changes in amphibian taxonomy made in the recent past.

Version 3.0 (2004) families and subfamilies	Version 5.3 (2009) families and subfamilies	Notes and explanations
Anura
Allophrynidae	Centrolenidae: Allophrynidae	Placed as a subfamily of Centrolenidae by Frost et al., 2006, to reflect the sister taxon relationship of Allophryne ruthveni with the traditional Centrolenidae.
Arthroleptidae	Arthroleptini (roughly) of Arthroleptidae: Arthroleptinae	Frost et al., 2006, placed former Arthroleptidae, Astylosternidae, and Leptopelinae (formerly in Hyperoliidae) into a reformulated Arthroleptidae, containing two subfamilies Arthroleptinae (for former Arthroleptidae [sensu stricto] and Astylosternidaee) and Leptopelinae (for a taxon formerly attached to Hyperoliidae).
Ascaphidae	Leiopelmatidae	Frost et al., 2006, returned Ascaphus to Leiopelmatidae to reflect the sister-taxon relationship of Ascaphus and Leiopelma.
Astylosternidae	Arthroleptidae: Arthroleptinae	See comment under Arthroleptidae.
Bombinatoridae	Bombinatoridae
Brachycephalidae	Brachycephalidae, Craugastoridae, Eleutherodactylidae, Strabomantidae	Frost et al., 2006, following Dubois, 2005, severely modified the content of Brachycephalidae by the inclusion of the former Eleutherodactylinae. Heinicki et al., 2007, severely revised the generic concepts on the basis of molecular data. Hedges, Duellman, and Heinicke, 2008, Zootaxa, 1737: 1-182, subsequently partitioned the monophyletic group into four families
Bufonidae	Bufonidae	Frost et al., 2006, rendered a number of generic rearrangements to render a monophyletic Bufo and to formulate a taxonomy that invites additional work.
Centrolenidae	Centrolenidae: Centroleninae	Frost et al., 2006, by inclusion of Allophryidae as a subfamily of Centrolenidae, rendered the former content of Centrolenidae equal to the new subfamily Centroleninae.
Dendrobatidae	Aromobatidae and Dendrobatidae	Grant et al., 2006, rendered extensive changes to the generic taxonomy of former Dendrobatidae (now Dendrobatoidea) and considered it to be composed of sister families, Aromobatidae and Dendrobatidae.
Discoglossidae	Alytidae	Following Dubois, 2005, Frost et al., 2006, used the name of priority for this taxon.
Heleophrynidae	Heleophrynidae
Hemisotidae	Hemisotidae
Hylidae: Hemiphractinae	Hemiphractidae	Darst and Cannatella, 2004; Faivovich et al., 2005, and Wiens et al., 2005, showed that Hemiphractinae was not in Hylidae. Frost et al., 2006, recognized former Hemiphractidae as three families phylogenetically distant from each other. Guayasamin et al., 2008, suggested that these three groups (Amphignathodontidae, Hemiphractidae, and Cryptobatrachidae) form a monophyletic group and recognized one family, Hemiphractidae.
Hylidae: Hylinae	Hylinae: Hylinae	Faivovich et al., 2005, rendered extensive generic changes to render a monophyletic taxonomy.
Hylidae: Pelodryadinae	Hylinae: Pelodryadinae	Frost et al., 2006, placed Cyclorana and Nyctimystes in the synonymy of Litoria to render a monophyletic taxonomy.
Hylidae: Phyllomedusinae	Hylinae: Phyllomedusinae	Faivovich et al., 2005, rendered generic changes to render a monophyletic taxonomy.
Hyperoliidae: Hyperoliinae	Hyperoliidae	Frost et al., 2006, rendered former Hyperoliinae as coextensive with Hyperoliidae by transfer of Leptopelinae to Arthroleptidae.
Hyperoliidae: Leptopelinae	Arthroleptidae: Leptopelinae	See comment under Arthroleptidae.
Leiopelmatidae	Leiopelmatidae	Frost et al., 2006, reincluded Ascaphidae in Leiopelmatidae.
Leptodactylidae: Ceratophryinae	Ceratophryidae (part) and Cycloramphidae (part)	Ceratophryini was transferred by Frost et al., 2006, to a reformulated Ceratophryidae; they also transferred Odontophrynini into a reformulated Cycloramphidae.
Leptodactylidae: Cycloramphinae	Leptodactylidae (part), Hylodidae, and Cyclramphidae	Frost et al., 2006, transferred Scythrophrys and Paratelmatobius into Leptodactylidae from former Cycloramphinae; their reformulated Cycloramphidae contained the remainder of the former Cycloramphinae + Rhinodermatidae + part of Telmatobiinae, except for Thoropa, which they placed in a new family, Thoropidae. Grant et al., 2006, recognized that Thoropidae is in Cycloramphidae, but excluded Hylodidae (Cycloramphidae: Hylodinae of Frost et al., 2006) from Cycloramphidae sensu Frost et al., 2006, to render a monophyletic taxonomy.
Leptodactylidae: Eleutherodactylinae	Brachycephalidae (part)	See comment under Brachycephalidae.
Leptodactylidae: Leptodactylinae	Leptodactylidae (redelimited), Leiuperidae	Frost et al., 2006, included the former cycloramphines Paratelmatobius and Scythrophrys in Leptodactylidae but otherwise treated former Leptodactylinae as a family. Grant et al., 2006, showed that Leptodactylidae sensu Frost et al., 2006, is polyphyletic, composed to two families: Leptodactylidae (for Hydrolaetare, Leptodactylus, Paratelmatobius, and Scythrophrys) and Leiuperidae (for Edalorhina, Engystomops, Eupemphix, Physalameus, Pleurodema, Pseudopaludicola,and Somuncuria).
Leptodactylidae: Telmatobiinae	Calyptocephalellidae, Ceratophryidae (part), Cycloramphidae (part)	Frost et al., 2006, showed that former Telmatobiinae is polyphyletic, with one group (Calyptocephalellidae [Batrachophrynidae in their work]) most close to the myobatrachoids, another group (Telmatobius, Batrachyla, and Atelognathus) most closely related to former Ceratophryini in a reformulated Ceratophryidae, and another group (including Hylorina, Alsodes, and Eupsophus) in a reformulated Cycloramphinae. Aguilar and Pacheco, 2005, and Cordova and Descailleaux, 2005, demonstrated that Batrachophrynus is in Ceratophryidae, leaving the remainder of "Batrachophrynidae" as Calyptocephalellidae
Limnodynastidae	Limnodynastidae (part)	Frost et al., 2006, transferred Mixophyes from Limnodynastidae into Myobatrachidae.
Mantellidae: Boophinae	Mantellidae: Boophinae
Mantellidae: Laliostominae	Mantellidae: Laliostominae	Frost et al., 2006, considered Mantellinae and Laliostominae as tribes within a reformulated Mantellinae. Glaw and Vences, 2006, provided an extensively reformulated Mantellidae and retained the three-subfamily arrangement without rejecting the evidence or tree of Frost et al., 2006
Mantellidae: Mantellinae	Mantellidae: Mantellinae	See comment under Laliostominae.
Megophryidae	Megophryidae
Microhylidae: Asterophryinae	Microhylidae: Asterophryinae	Frost et al., 2006, placed Genyophryninae as a synonym of Asterophryinae to prevent the paraphyly of Genyophryninae.
Microhylidae: Brevicipitinae	Brevicipitidae	Frost et al., 2006, recognized Brevicipitidae as a family, phylogenetically distant from Microhylidae.
Microhylidae: Cophylinae	Microhylidae: Cophylinae
Microhylidae: Dyscophinae	Microhylidae: Dyscophinae
Microhylidae: Genyophryninae	Microhylidae: Asterophryinae (part)	See comment under Microhylidae: Asterophryinae.
Microhylidae: Melanobatrachinae	Microhylidae: Melanobatrachinae	Frost et al., 2006, retained Melanobatrachinae, but noted that its content will likely change substantially with additional work.
Microhylidae: Microhylinae	Microhylidae (several incertae sedis genera), Microhylidae: Microhylinae, and Microhylidae: Gastrophryninae	Frost et al., 2006, demonstrated that former Microhylinae is polyphyletic. They recognized a monophyletic Microhylinae and Gastrophryninae, but excluded severa genera from either subfamily and placed them incertae sedis at the level of Microhylidae.
Microhylidae: Phrynomerinae	Microhylidae (see comment)	Frost et al., 2006, did not recognize Phrynomerinae for Phrynomantis. Retained in this catalog.
Microhylidae: Scaphiophryninae	Microhylidae: Scaphiophryninae (see comment)	Frost et al., 2006, followed Haas, 2004, in excluding Paradoxophyla from this taxon, placing it incertae sedis within Microhylidae. Van der Meijden et al. (2007) subsequently showed Paradoxophyla to be a scaphiophrynine
Myobatrachidae	Myobatrachidae (part)	Frost et al., 2006, reformulated Myobatrachidae by placing Rheobatrachus and Mixophyes in this group. Roelants et al. (2006) suggested that Mixophyes is a limnodynastine; the jury is out on this.
Nasikabatrachidae	Nasikabatrachidae	Frost et al., 2006, placed Nasikabatrachidae in Sooglossidae, although Roelants et al. (2006) continued its recognition.
Pelobatidae	Pelobatidae
Pelodytidae	Pelodytidae
Petropedetidae	Petropedetidae (reformulated) and Ranixalidae	Frost et al., 2006, reformulated Petropedetidae to exclude Phrynobatrachidae, and to include Conraua and Indirana. Roelants et al. (2006) on the basis of additional evidence removed Indirana to its own family, Ranixalidae
Pipidae: Dactylethrinae	Pipidae (part)	Frost et al., 2006, rejected subfamilies within Pipidae.
Pipidae: Pipinae	Pipidae (part)	See comment under Pipidae: Dactylethrinae.
Rhacophoridae: Buergeriinae	Rhacophoridae: Buergeriinae
Rhacophoridae: Rhacophorinae	Rhacophoridae: Rhacophorinae
Rheobatrachidae	Myobatrachidae (part)	Frost et al., 2006, placed Rheobatrachus in Myobatrachidae
Rhinodermatidae	Cycloramphidae (part)	Frost et al., 2006, placed Rhinodermatidae in a newly demarcated Cycloramphidae.
Rhinophrynidae	Rhinophrynidae
Scaphiopodidae	Scaphiopodidae
Sooglossidae	Sooglossidae (part)	See comment under Nasikabatrachidae.
Urodela	Caudata	Frost et al., 2006, explained the nomenclatural change.
Ambystomatidae	Ambystomatidae (part)	See comment under Dicamptodontidae.
Amphiumidae	Amphiumidae
Cryptobranchidae	Cryptobranchidae
Dicamptodontidae	Ambystomatidae (part)	Frost et al., 2006, replaced Dicamptodon as the sister taxon of Ambystoma, within Ambystomatidae.
Hynobiidae	Hynobiidae
Plethodontidae: Desmognathinae	Plethodontidae: Plethodontinae (part)	Chippindale et al. (2004) and Macey (2005) provided a monophyletic taxonomy of Plethodontidae that does not resemble the older, nonevolutionary taxonomy.
Plethodontidae: Plethodontinae	Plethodontidae: Bolitoglossinae, Plethodontidae: Hemidactyliinae, and Plethodontidae: Spelerpinae	See comment under Plethodontidae; Desmognathinae.
Proteidae	Proteidae
Rhyacotritonidae	Rhyacotritonidae
Salamandridae	Salamandridae	Frost et al., 2006, recognized two subfamilies within Salamandridae, but this was superseded by Zhang et al., 2008, who showed this to be incorrect
Sirenidae	Sirenidae
Gymnophiona	Gymnophiona
Caeciliidae: Caeciliinae	Caeciliidae (part)	Frost et al,. 2006, rejected the use of Caeciliinae as paraphyletic.
Caeciliidae: Typhlonectinae	Caeciliidae: Typhlonectinae
Ichthyophiidae	Ichthyophiidae	See comment under Uraeotyphlidae.
Rhinatrematidae	Rhinatrematidae
Scolecomorphidae	Caeciliidae: Scolecomorphinae	Frost et al., 2006, placed Scolecomorphidae as a subfamily of Caeciliidae.
Uraeotyphlidae	Ichthyophiidae (part)	Frost et al., 2006, placed Uraeotyphlidae into the synonymy of Ichthyophiidae.

LITERATURE CITED

Aguilar, C. and V. Pacheco. 2005. Contribución de la morfología bucofaríngea larval a la filogenia de Batrachophrynus y Telmatobius. In E.O. Lavilla and I. De la Riva (eds.), Estudio sobre las rana andinas de los géneros Telmatobius y Batrachophrynus (Anura: Leptodactylidae). Monografías de Herpetología, 7: 219-238.

Che, J., J. Pang, H. Zhao, G. Wu, E. Zhao, and Y.-p. Zhang. 2007. Phylogeny of Raninae (Anura: Ranidae) inferred from mitochondrial and nuclear sequences. Molecular Phylogenetics and Evolution 43: 113.

Chippindale, P.T., R.M. Bonett, A.S. Baldwin, and J.J. Wiens. 2004. Phylogenetic evidence for a major reversal of life-history evolution in plethodontid salamanders. Evolution 58: 2809-2822.

Córdova, J.H. and J. Descailleaux. 2005. El análisis cladistico preliminar de los cariotipos de cinco especies de Telmatobius y dos de Batrachophrynus no apoya su separación genérica. In E.O. Lavilla and I. De la Riva (eds.), Estudio sobre las rana andinas de los géneros Telmatobius y Batrachophrynus (Anura: Leptodactylidae). Monografías de Herpetología, 7: 187-217.

Dominguez, E. and Q.D. Wheeler.1997.Taxonomic stability is ignorance. Cladistics 13: 367-372

Faivovich, J., C.F.B., Haddad, P.C.A. Garcia, D.R. Frost, J.A. Campbell., and W.C. Wheeler. 2005. Systematic review of the frog family Hylidae, with special reference to Hylinae: a phylogenetic analysis and taxonomic revision. Bulletin of the American Museum of Natural History 294: 1-240.

Frost, D.R., T. Grant, J. Faivovich, R.H. Bain, A. Haas, C.F.B. Haddad, R.O de Sa, A. Channing, M. Wilkinson, S.C. Donnellan, C. Raxworthy, J.A. Campbell., B.L. Blotto, P. Moler, R.C. Drewes, R.A. Nussbaum, J.D. Lynch, D.M. Green, and W.C. Wheeler. 2006. The amphibian tree of life. Bulletin of the American Museum of Natural History 297: 1-370.

Glaw, F. and M. Vences. 2006. Phylogeny and genus-level classification of mantellid frogs (Amphibia, Anura). Organisms, Diversity & Evolution 6: 236-253.

Grant, T., D.R. Frost, J.P. Caldwell, R. Gagliardo, C.F.B. Haddad, P.J.R. Kok, B.D. Means, B.D. Means, B.P. Noonan, W. Schargel, and W.C. Wheeler. 2006. Phylogenetic systematics of dart-poison frogs and their relatives (Amphibia: Athesphatanura: Dendrobatoidea). Bulletin of the American Museum of Natural History 299: 1-262.

Grant, T., and A.G. Kluge. 2005. Stability, sensitivity, science and heurism. Cladistics 21: 597-605.

Guayasamin, J.M., S. Castroviejo-Fisher, J. Ayarzagüena, L. Trueb, and C. Vilà. 2008. Phylogenetic relationships of glassfrogs (Centrolenidae) based on mitochondrial and nuclear genes. Molecular Phylogenetics and Evolution 48: 574-595.

Hedges, S. Blair, William E. Duellman, and Matthew P. Heinicke. 2008. New World direct-developing frogs (Anura: Terrarana): molecular phylogeny, classification, biogeography, and conservation. Zootaxa 1737: 1182

Heinicke, M.P., W.E. Duellman, and S.B. Hedges. 2007. Major Caribbean and Central American frog faunas originated by ancient oceanic dispersal. Proceedings of the National Academy of Sciences of the USA 104: 10092-97.

Macey, J.R. 2005. Plethodontid salamander mitochondrial genomics: a parsimony evaluation of character conflict and implications for historical biogeography. Cladistics 21: 194-202.

Roelants, K., D.J. Gower, M. Wilkinson, S.P. Loader, S.D. Biju, K. Guillaume, L. Moriau, and F. Bossuyt. 2007. Global patterns of diversification in the history of modern amphibians. Proceedings of the National Academy of Sciences of the United States of America 104: 887-892.

Sokal, R.R., and P.H.A. Sneath. 1963. Principles of Numerical Taxonomy. Freeman & Sons, San Francisco.

Van der Meijden, A., M. Vencens, S. Hoegg, R. Boistel, A. Channing, and A. Meyer. 2007. Nuclear gene phylogeny of narrow-mouthed toads (family Microhylidae) and a discussion of competing hypotheses concerning their biogeographical origins. Molecular Phylogenetics and Evolution. In press.

Wake, D.B. 2006. Quotation in Anonymous, "Hoppers and creepers treed". Science 312: 31.

Wiens, J.J., J.W. Fetzner, C.L. Parkinson, and T.W. Reeder. 2005. Hylid frog phylogeny and sampling strategies for speciose clades. Systematic Biology 54: 719-748.

Zhang, P., T.J. Papenfuss, M.H. Wake, L. Qu, and D.B. Wake. 2008. Phylogeny and biogeography of the family Salamandridae (Amphibia: Caudata) inferred from complete mitochondrial genomes. Molecular Phylogenetics and Evolution 49: 586-597.

Amphibian Species of the World 5.3, an Online Reference

Higher taxonomy and progress, with comments on taxonomic philosophy