The amphibian tree of life.

is a journal article

Bulletin of the American Museum of Natural History 297: 1 (2006)
 Darrel R Frost   Taran Grant   JuliΓ‘n Faivovich   Raoul H Bain   Alexander Haas   Celio F B Haddad   Rafael O De Sa   A Channing   Mark Wilkinson   Stephen C Donnellan   Christopher J Raxworthy   Jonathan A Campbell   Boris L Blotto   Paul Moler   Robert C Drewes   Ronald A Nussbaum   John D Lynch   David M Green   Ward C Wheeler 

The evidentiary basis of the currently accepted classification of living amphibians is discussed and shown not to warrant the degree of authority conferred on it by use and tradition. A new taxonomy of living amphibians is proposed to correct the deficiencies of the old one. This new taxonomy is based on the largest phylogenetic analysis of living Amphibia so far accomplished. We combined the comparative anatomical character evidence of Haas (2003) with DNA sequences from the mitochondrial transcription unit H1 (12S and 16S ribosomal RNA and tRNA[superscript Valine] genes, [approximately equal to] 2,400 bp of mitochondrial sequences) and the nuclear genes histone H3, rhodopsin, tyrosinase, and seven in absentia, and the large ribosomal subunit 28S ([approximately equal to] 2,300 bp of nuclear sequences; ca. 1.8 million base pairs; x [arithmetic mean] = 3.7 kb/terminal). The dataset includes 532 terminals sampled from 522 species representative of the global diversity of amphibians as well as seven of the closest living relatives of amphibians for outgroup comparisons. The primary purpose of our taxon sampling strategy was to provide strong tests of the monophyly of all 'family-group' taxa. All currently recognized nominal families and subfamilies were sampled, with the exception of Protohynobiinae (Hynobiidae). Many of the currently recognized genera were also sampled. Although we discuss the monophyly of genera, and provide remedies for nonmonophyly where possible, we also make recommendations for future research. A parsimony analysis was performed under Direct Optimization, which simultaneously optimizes nucleotide homology (alignment) and tree costs, using the same set of assumptions throughout the analysis. Multiple search algorithms were run in the program POY over a period of seven months of computing time on the AMNH Parallel Computing Cluster. Results demonstrate that the following major taxonomic groups, as currently recognized, are nonmonophyletic: Ichthyophiidae (paraphyletic with respect to Uraeotyphlidae), Caeciliidae (paraphyletic with respect to Typhlonectidae and Scolecomorphidae), Salamandroidea (paraphyletic with respect to Sirenidae), Leiopelmatanura (paraphyletic with respect to Ascaphidae), Discoglossanura (paraphyletic with respect to Bombinatoridae), Mesobatrachia (paraphyletic with respect to Neobatrachia), Pipanura (paraphyletic with respect to Bombinatoridae and Discoglossidae/Alytidae), Hyloidea (in the sense of containing Heleophrynidae; paraphyletic with respect to Ranoidea), Leptodactylidae (polyphyletic, with Batrachophrynidae forming the sister taxon of Myobatrachidae + Limnodynastidae, and broadly paraphyletic with respect to Hemiphractinae, Rhinodermatidae, Hylidae, Allophrynidae, Centrolenidae, Brachycephalidae, Dendrobatidae, and Bufonidae), Microhylidae (polyphyletic, with Brevicipitinae being the sister taxon of Hemisotidae), Microhylinae (poly/paraphyletic with respect to the remaining non-brevicipitine microhylids), Hyperoliidae (para/polyphyletic, with Leptopelinae forming the sister taxon of Arthroleptidae + Astylosternidae), Astylosternidae (paraphyletic with respect to Arthroleptinae), Ranidae (paraphyletic with respect to Rhacophoridae and Mantellidae). In addition, many subsidiary taxa are demonstrated to be nonmonophyletic, such as (1) Eleutherodactylus with respect to Brachycephalus; (2) Rana (sensu Dubois, 1992), which is polyphyletic, with various elements falling far from each other on the tree; and (3) Bufo, with respect to several nominal bufonid genera. A new taxonomy of living amphibians is proposed, and the evidence for this is presented to promote further investigation and data acquisition bearing on the evolutionary history of amphibians. The taxonomy provided is consistent with the International Code of Zoological Nomenclature (ICZN, 1999). Salient features of the new taxonomy are (1) the three major groups of living amphibians, caecilians/Gymnophiona, salamanders/Caudata, and frogs/Anura, form a monophyletic group, to which we restrict the name Amphibia; (2) Gymnophiona forms the sister taxon of Batrachia (salamanders + frogs) and is composed of two groups, Rhinatrematidae and Stegokrotaphia; (3) Stegokrotaphia is composed of two families, Ichthyophiidae (including Uraeotyphlidae) and Caeciliidae (including Scolecomorphidae and Typhlonectidae, which are regarded as subfamilies); (4) Batrachia is a highly corroborated monophyletic group, composed of two taxa, Caudata (salamanders) and Anura (frogs); (5) Caudata is composed of two taxa, Cryptobranchoidei (Cryptobranchidae and Hynobiidae) and Diadectosalamandroidei new taxon (all other salamanders); (6) Diadectosalamandroidei is composed of two taxa, Hydatinosalamandroidei new taxon (composed of Perennibranchia and Treptobranchia new taxon) and Plethosalamandroidei new taxon; (7) Perennibranchia is composed of Proteidae and Sirenidae; (8) Treptobranchia new taxon is composed of two taxa, Ambystomatidae (including Dicamptodontidae) and Salamandridae; (9) Plethosalamandroidei new taxon is composed of Rhyacotritonidae and Xenosalamandroidei new taxon; (10) Xenosalamandroidei is composed of Plethodontidae and Amphiumidae; (11) Anura is monophyletic and composed of two clades, Leiopelmatidae (including Ascaphidae) and Lalagobatrachia new taxon (all other frogs); (12) Lalagobatrachia is composed of two clades, Xenoanura (Pipidae and Rhinophrynidae) and Sokolanura new taxon (all other lalagobatrachians); (13) Bombinatoridae and Alytidae (former Discoglossidae) are each others' closest relatives and in a clade called Costata, which, excluding Leiopelmatidae and Xenoanura, forms the sister taxon of all other frogs, Acosmanura; (14) Acosmanura is composed of two clades, Anomocoela (5 Pelobatoidea of other authors) and Neobatrachia; (15) Anomocoela contains Pelobatoidea (Pelobatidae and Megophryidae) and Pelodytoidea (Pelodytidae and Scaphiopodidae), and forms the sister taxon of Neobatrachia, together forming Acosmanura; (16) Neobatrachia is composed of two clades, Heleophrynidae, and all other neobatrachians, Phthanobatrachia new taxon; (17) Phthanobatrachia is composed of two major units, Hyloides and Ranoides; (18) Hyloides comprises Sooglossidae (including Nasikabatrachidae) and Notogaeanura new taxon (the remaining hyloids); (19) Notogaeanura contains two taxa, Australobatrachia new taxon and Nobleobatrachia new taxon; (20) Australobatrachia is a clade composed of Batrachophrynidae and its sister taxon, Myobatrachoidea (Myobatrachidae and Limnodynastidae), which forms the sister taxon of all other hyloids, excluding sooglossids; (21) Nobleobatrachia new taxon, is dominated at its base by frogs of a treefrog morphotype, several with intercalary phalangeal cartilages--Hemiphractus (Hemiphractidae) forms the sister taxon of the remaining members of this group, here termed Meridianura new taxon; (22) Meridianura comprises Brachycephalidae (former Eleutherodactylinae + Brachycephalus) and Cladophrynia new taxon; (23) Cladophrynia is composed of two groups, Cryptobatrachidae (composed of Cryptobatrachus and Stefania, previously a fragment of the polyphyletic Hemiphractinae) and Tinctanura new taxon; (24) Tinctanura is composed of Amphignathodontidae (Gastrotheca and Flectonotus, another fragment of the polyphyletic Hemiphractinae) and Athesphatanura new taxon; (25) Athesphatanura is composed of Hylidae (Hylinae, Pelodryadinae, and Phyllomedusinae, and excluding former Hemiphractinae, whose inclusion would have rendered this taxon polyphyletic) and Leptodactyliformes new taxon;

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Taxon/gene matrix

Table lens view of sequences, grouped by taxon and gene feature. Click on accession number to see details for sequence. Note that if more than one sequence exists for the same gene for the same taxon, only one will be displayed here.


Sequence features (such as genes) in this study

 28S ribosomal RNA   seventh in absentia   rhodopsin   histone H3a   tyrosine precursor   16S ribosomal RNA   1   12S ribosomal RNA 


Taxa sequenced in thius study

 Scolecomorphus vittatus   Bufo regularis   Calluella guttulata   Chirixalus vittatus   Hoplobatrachus rugulosus   Chirixalus doriae   Ichthyophis sp. FMNH 256425   Geotrypetes seraphini   Rana erythraea   Kassina senegalensis   Bufo gutturalis   Callulina kisiwamsitu   Schismaderma carens   Phrynobatrachus mababiensis   Probreviceps macrodactylus   Hoplophryne rogersi   Bufo brauni   Arthroleptides sp. RdS 862   Phrynobatrachus natalensis   Nectophrynoides tornieri   Stumpffia cf. psologlossa AMNH A167359   Platypelis grandis   Plethodontohyla sp. AMNH A167315   Ambystoma tigrinum   Caecilia tentaculata   Leptodactylus fuscus   Afrixalus fornasini   Hyperolius tuberilinguis   Kaloula pulchra   Rana taipehensis   Rana guentheri   Odorrana chloronota   Philautus rhododiscus   Ophryophryne microstoma   Bufo maculatus   Bufo amboroensis   Rana palmipes   Ctenophryne geayi   Microhyla heymonsi   Leptolalax bourreti   Rhacophorus calcaneus   Paa cf. verrucospinosa AMNH A163740   Limnonectes poilani   Ophryophryne hansi   Bufo galeatus   Odorrana chapaensis   Occidozyga martensii   Odorrana nasica   Bufo melanostictus   Rana maculata   Pelomedusa subrufa   Odorrana grahami   Phrynobatrachus calcaratus   Leptobrachium hasseltii   Micrixalus borealis   Afrixalus pygmaeus   Nesionixalus thomensis   Bufo andrewsi   Occidozyga lima   Phrynobatrachus dispar   Rana johnsi   Phrynobatrachus africanus   Aubria subsigillata   Alexteroon obstetricans   Bufo quercicus   Eleutherodactylus planirostris   Platymantis pelewensis   Pipa pipa   Allobates femoralis   Allobates undulatus   Schoutedenella xenodactyloides   Arthroleptis tanneri   Leptopelis bocagei   Phrynopus sp. AMNH A165108   Schoutedenella taeniata   Sphaerotheca pluvialis   Megaelosia goeldii   Hoplobatrachus occipitalis   Mantidactylus cf. femoralis AMNH A167581   Ptychadena mascareniensis   Xenopus gilli   Arthroleptides yakusini   Elachistocleis ovalis   Rhinatrema bivittatum   Bufo guttatus   Bufo granulosus   Atelopus zeteki   Schoutedenella schubotzi   Ambystoma cingulatum   Hemidactylium scutatum   Rana galamensis   Leptobrachium chapaense   Aquixalus gracilipes   Rhacophorus orlovi   Polypedates leucomystax   Telmatobius sp. AMNH A165130   Telmatobius jahuira   Mantella nigricans   Boophis albilabris   Boophis tephraeomystax   Pristimantis pluvicanorus   Fejervarya limnocharis   Lithodytes lineatus   Pleurodema brachyops   Hyloscirtus armatus   Gastrotheca cf. marsupiata NK A5286   Telmatobius marmoratus   Nymphargus bejaranoi 

Sequences 451

Sequences cited by this article.

Distribution of object

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Overlapping (3)

Studies in the same area, based on intersecting polygons enclosing all point localities associated with the study. Due to limitations of the underlying database the overlap is calculated using the minimum bounding rectangle, not the actual polygon.
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  2. A molecular phylogeny of the genus Gammarus (Crustacea: Amphipoda) based on mitochondrial and nuclear gene sequences
  3. Multigenic and morphometric differentiation of ground squirrels (Spermophilus, Scuiridae, Rodentia) in Turkey, with a description of a new species