Browsing by Author "Bain, Raoul H."
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Item The amphibian tree of life. Bulletin of the AMNH ; no. 297(New York, NY : American Museum of Natural History, 2006) Frost, Darrel R.; Grant, Taran, 1972-; Faivovich, Julián.; Bain, Raoul H.; Haas, Alexander.; Haddad, Celio F. B.; De Sa, Rafael O.; Channing, A.; Wilkinson, Mark, 1963-; Donnellan, Stephen C.; Raxworthy, Christopher J.; Campbell, Jonathan A.; Blotto, Boris L.; Moler, Paul E.; Drewes, Robert C.; Nussbaum, Ronald A.; Lynch, John D.; Green, David Martin.; Wheeler, Ward.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; (26) Leptodactyliformes is composed of Diphyabatrachia new taxon (composed of Centrolenidae (including Allophryne) and Leptodactylidae, sensu stricto, including Leptodactylus and relatives) and Chthonobatrachia new taxon; (27) Chthonobatrachia is composed of a reformulated Ceratophryidae (which excludes such genera as Odontophrynus and Proceratophrys and includes other taxa, such as Telmatobius) and Hesticobatrachia new taxon; (28) Hesticobatrachia is composed of a reformulated Cycloramphidae (which includes Rhinoderma) and Agastorophrynia new taxon; (29) Agastorophrynia is composed of Bufonidae (which is partially revised) and Dendrobatoidea (Dendrobatidae and Thoropidae); (30) Ranoides new taxon forms the sister taxon of Hyloides and is composed of two major monophyletic components, Allodapanura new taxon (microhylids, hyperoliids, and allies) and Natatanura new taxon (ranids and allies); (31) Allodapanura is composed of Microhylidae (which is partially revised) and Afrobatrachia new taxon; (32) Afrobatrachia is composed of Xenosyneunitanura new taxon (the "strange-bedfellows" Brevicipitidae (formerly in Microhylidae) and Hemisotidae) and a more normal-looking group of frogs, Laurentobatrachia new taxon (Hyperoliidae and Arthroleptidae, which includes Leptopelinae and former Astylosternidae); (33) Natatanura new taxon is composed of two taxa, the African Ptychadenidae and the worldwide Victoranura new taxon; (34) Victoranura is composed of Ceratobatrachidae and Telmatobatrachia new taxon; (35) Telmatobatrachia is composed of Micrixalidae and a worldwide group of ranoids, Ametrobatrachia new taxon; (36) Ametrobatrachia is composed of Africanura new taxon and Saukrobatrachia new taxon; (37) Africanura is composed of two taxa: Phrynobatrachidae (Phrynobatrachus, including Dimorphognathus and Phrynodon as synonyms) and Pyxicephaloidea; (38) Pyxicephaloidea is composed of Petropedetidae (Conraua, Indirana, Arthroleptides, and Petropedetes), and Pyxicephalidae (including a number of African genera, e.g. Amietia (including Afrana), Arthroleptella, Pyxicephalus, Strongylopus, and Tomopterna); and (39) Saukrobatrachia new taxon is the sister taxon of Africanura and is composed of Dicroglossidae and Aglaioanura new taxon, which is, in turn, composed of Rhacophoroidea (Mantellidae and Rhacophoridae) and Ranoidea (Nyctibatrachidae and Ranidae, sensu stricto). Many generic revisions are made either to render a monophyletic taxonomy or to render a taxonomy that illuminates the problems in our understanding of phylogeny, so that future work will be made easier. These revisions are: (1) placement of Ixalotriton and Lineatriton (Caudata: Plethodontidae: Bolitoglossinae) into the synonymy of Pseudoeurycea, to render a monophyletic Pseudoeurycea; (2) placement of Haideotriton (Caudata: Plethodontidae: Spelerpinae) into the synonymy of Eurycea, to render a monophyletic Eurycea; (3) placement of Nesomantis (Anura: Sooglossidae) into the synonymy of Sooglossus, to assure a monophyletic Sooglossus; (4) placement of Cyclorana and Nyctimystes (Anura: Hylidae: Pelodryadinae) into Litoria, but retaining Cyclorana as a subgenus, to provide a monophyletic Litoria; (5) partition of "Limnodynastes" (Anura: Limnodynastidae) into Limnodynastes and Opisthodon to render monophyletic genera; (6) placement of Adenomera, Lithodytes, and Vanzolinius (Anura: Leptodactylidae) into Leptodactylus, to render a monophyletic Leptodactylus; (7) partition of "Eleutherodactylus" (Anura: Brachycephalidae) into Craugastor, "Eleutherodactylus", "Euhyas", "Pelorius", and Syrrhophus to outline the taxonomic issues relevant to the paraphyly of this nominal taxon to other nominal genera; (8) partition of "Bufo" (Anura: Bufonidae) into a number of new or revived genera (i.e., Amietophrynus new genus, Anaxyrus, Chaunus, Cranopsis, Duttaphrynus new genus, Epidalea, Ingerophrynus new genus, Nannophryne, Peltophryne, Phrynoidis, Poyntonophrynus new genus; Pseudepidalea new genus, Rhaebo, Rhinella, Vandijkophrynus new genus); (9) placement of the monotypic Spinophrynoides (Anura: Bufonidae) into the synonymy of (formerly monotypic) Altiphrynoides to make for a more informative taxonomy; (10) placement of the Bufo taitanus group and Stephopaedes (as a subgenus) into the synonymy of Mertensophryne (Anura: Bufonidae); (11) placement of Xenobatrachus (Anura: Microhylidae: Asterophryinae) into the synonymy of Xenorhina to render a monophyletic Xenorhina; (12) transfer of a number of species from Plethodontohyla to Rhombophryne (Microhylidae: Cophylinae) to render a monophyletic Plethodontohyla; (13) placement of Schoutedenella (Anura: Arthroleptidae) into the synonymy of Arthroleptis; (14) transfer of Dimorphognathus and Phrynodon (Anura: Phrynobatrachidae) into the synonymy of Phrynobatrachus to render a monophyletic Phrynobatrachus; (15) placement of Afrana into the synonymy of Amietia (Anura: Pyxicephalidae) to render a monophyletic taxon; (16) placement of Chaparana and Paa into the synonymy of Nanorana (Anura: Dicroglossidae) to render a monophyletic genus; (17) recognition as genera of Ombrana and Annandia (Anura: Dicroglossidae: Dicroglossinae) pending placement of them phylogenetically; (18) return of Phrynoglossus into the synonymy of Occidozyga to resolve the paraphyly of Phrynoglossus (Anura: Dicroglossidae: Occidozyginae); (19) recognition of Feihyla new genus for Philautus palpebralis to resolve the polyphyly of ''Chirixalus''; (20) synonymy of "Chirixalus" with Chiromantis to resolve the paraphyly of "Chirixalus"; (21) recognition of the genus Babina, composed of the former subgenera of Rana, Babina and Nidirana (Anura: Ranidae); (22) recognition of the genera Clinotarsus, Humerana, Nasirana, Pelophylax, Pterorana, Pulchrana, and Sanguirana, formerly considered subgenera of Rana (Anura: Ranidae), with no special relationship to Rana (sensu stricto); (23) consideration of Glandirana (Anura: Ranidae), formerly a subgenus of Rana, as a genus, with Rugosa as a synonym; (24) recognition of Hydrophylax (Anura: Ranidae) as a genus, with Amnirana and most species of former Chalcorana included in this taxon as synonyms; (25) recognition of Hylarana (Anura: Ranidae) as a genus and its content redefined; (26) redelimitation of Huia to include as synonyms Eburana and Odorrana (both former subgenera of Rana); (27) recognition of Lithobates (Anura: Ranidae) for all species of North American "Rana" not placed in Rana sensu stricto (Aquarana, Pantherana, Sierrana, Trypheropsis, and Zweifelia considered synonyms of Lithobates); (28) redelimitation of the genus Rana as monophyletic by inclusion as synonyms Amerana, Aurorana, Pseudoamolops, and Pseudorana, and exclusion of all other former subgenera; (29) redelimitation of the genus Sylvirana (Anura: Ranidae), formerly a subgenus of Rana, with Papurana and Tylerana included as synonyms.Item A biogeographic synthesis of the amphibians and reptiles of Indochina. (Bulletin of the American Museum of Natural History, no. 360)(American Museum of Natural History., 2011-11-23) Bain, Raoul H.; Hurley, Martha Maud, 1966-Indochina (Laos, Cambodia, and Vietnam) houses over 600 species of amphibians and reptiles, roughly a quarter of which has been described within the last 15 years. Herein, we undertake the first biogeographic synthesis of the regional herpetofauna since the first half of the 20th century. We review the literature to measure and map species richness and endemism, the contributions of regional faunas, and ecological characteristics of Indochina's amphibians (Anura, Caudata), and reptiles (Serpentes, Sauria, Testudines, Crocodylia). Dividing Indochina into 19 subregions defined by topography and geology, we estimate the similarity among the regional faunas and appraise the effects of area and survey effort on these comparative analyses. Variation in species composition is broadly correlated with topography, habitat complexity, and proximity to regions outside Indochina. Indochina's herpetofauna is dominated (in decreasing order) by endemic species, widely distributed species, a South China fauna, and a biota centered in Thailand and Myanmar. Species richness is highest in amphibians and snakes, and peaks in upland forests. Endemism, highest among amphibians and lizards, also peaks in forests of the region's northern uplands and Annamite Range. Endemic species occupy a narrower range of habitats than nonendemics. Patterns of richness and endemism are partially explained by ecological constraints: amphibians and lizards are more restricted to forests than snakes, turtles, and crocodiles; amphibians are more restricted to uplands, turtles to lowlands. We also assess biogeography in the context of Indochina's geology, climate, and land cover. In northern Indochina, the Red River either acts as or coincides with an apparent dispersal barrier. Herpetofauna in northeastern upland areas are closely allied with fauna of southeastern China. In southern Indochina there is little evidence that the Mekong River represents a biogeographic barrier to the regional herpetofauna. The Annamite Range is composed of at least three distinct units and its elevated species richness and endemism are also noted in adjacent lowlands. Contribution of subtropical biota to Indochina's fauna is significantly greater than that of tropical biota and there is little other evidence for intermixing at intermediate latitudes. Our results have implications for biogeography and conservation efforts, although they must be viewed in the context of rapidly evolving systematic knowledge of the region's amphibians and reptiles. Future survey efforts, and the phylogenetic analyses that come from them, are essential for supporting regional conservation efforts, as they will better resolve the known patterns of amphibian and reptile richness and endemism.Item Cryptic species of a cascade frog from Southeast Asia : taxonomic revisions and descriptions of six new species. American Museum novitates ; no. 3417(New York, NY : American Museum of Natural History, 2003) Bain, Raoul H.; Lathrop, Amy.; Murphy, Robert W. (Robert Ward), 1948-; Orlov, N. L. (Nikolaĭ Li︠u︡t︠s︡ianovich); Ĥò, Thu Cúc.The Southeast Asian cascade frog, Rana livida (Blyth, 1856), has long been suspected to be a complex of species. Several different forms are described from across its vast range. The loss of type material and disparate sampling efforts are challenges. Is variability in this species due to geographic variation or to the presence of multiple species? We use concordant evidence from morphology, morphometrics, cellular DNA content, and allozyme electrophoresis to investigate diversity in R. livida from Vietnam. Three distinct species are recognized on the basis of morphology, as are four other suspect groups (morphotypes). Discriminant function analyses of morphometric data detect patterns of morphological variation among all seven groups. Pairwise comparison of cellular DNA content using t-tests shows significant differences among sympatric morphotypes, suggesting they represent distinct species. This hypothesis is supported by an analysis of 14 allozymic loci, in which fixed allelic differences are found among specimens in sympatry and allopatry. Examination of available type material of four junior synonyms of R. livida results in their recognition as species. One of these species, R. chloronota, is a wide-ranging species erroneously referred to as R. livida. Seven species occur in Vietnam. We describe six new cryptic species belonging to the Rana chloronota complex, redescribe R. chloronota, R. livida, R. sinica, and R. graminea, and give comments on R. leporipes. Three of these new species (R. bacboensis, new species, R. hmongorum, new species, and R. daorum, new species) occur in montane forests in northern Vietnam, and two (R. banaorum, new species and R. morafkai, new species) are known only from the Tay Nguyen Plateau of Vietnam's Central Highlands. One species, R. megatympanum, new species, occurs in portions of both northern Vietnam and the Central Highlands. An identification key for the Rana chloronota complex from Vietnam is provided. The finding of six cryptic species within a small portion of the geographic region of R. chloronota suggests that many more cascade ranids await discovery. This documentation has serious implications for conservation; each of the new species occurs in sympatry with at least one other member of the complex. Consequently, far more species are being affected by habitat loss than was previously thought.Item Herpetofaunal diversity of Ha Giang Province in northeastern Vietnam, with descriptions of two new species. American Museum novitates ; no. 3453(New York, NY : American Museum of Natural History, 2004) Bain, Raoul H.; Nguŷẽn, Qủang Trừơng.In April and May of 2000, herpetological surveys of Ha Giang Province, Vietnam, near the Chinese border were undertaken. Surveys concentrated on isolated forests of Mount Tay Con Linh II (contiguous with the highest peak in eastern Vietnam, Mt. Tay Con Linh). The 26-day survey yielded 36 species of amphibians and 16 species of reptiles. The collection contains elements of Himalayan as well as Indo-Malayan assemblages and documents a new country record (Philautus rhododiscus), eight new records east of the Red River (Bombina microdeladigitora, Megophrys parva, Amolops chapaensis, Chaparana delacouri, Chirixalus gracilipes, Philautus odontotarsus, Polypedates dugritei, Rhacophorus hoanglienensis), seven species complexes (Fejervarya limnocharis, Hoplobatrachus rugulosus, Limnonectes kuhlii, Rana chloronota, R. maosonensis, Polypedates dugritei, and P. leucomystax), three unidentified amphibian species, and two previously undescribed species of cascade ranid (Rana iriodes, new species and Rana tabaca, new species). Rana iriodes differs from R. daorum and Amolops chunganensis in having an iridescent green-gold dorsum, orange-red dorsolateral folds, a goldwhite flank spot, vomerine teeth, and webbing to toe disks. Rana tabaca, new species, can be differentiated from other cascade ranids by a combination of characters: mottled brown upper lip, gold lip line below the eye to the arm insertion, shagreened dorsum, dorsolateral folds, and unpigmented eggs. Species accumulation curves indicate that the diversity of the region is still underestimated, which, along with the relatively extensive remnant forest, underscores the importance for a greater faunal understanding and conservation effort for the montane forests of the region.Item Supplemental Material for 'The amphibian tree of life. (Bulletin of the AMNH ; no. 297)'(New York, NY : American Museum of Natural History, 2006) Frost, Darrel R.; Grant, Taran, 1972-; Faivovich, Julián.; Bain, Raoul H.; Haas, Alexander; Haddad, Célio F. B.; De Sá, Rafael O.; Channing, A.; Wilkinson, Mark, 1963-; Donnellan, Stephen C.; Raxworthy, Christopher J.; Campbell, Jonathan A.; Blotto, Boris L.; Moler, Paul E.; Drewes, Robert C.; Nussbaum, Ronald A.; Lynch, John D.; Green, David Martin.; Wheeler, Ward.Supplemental Material for 'The amphibian tree of life. (Bulletin of the AMNH ; no. 297)' - http://hdl.handle.net/2246/5781