This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier’s archiving and manuscript policies are encouraged to visit: http://www.elsevier.com/copyright Author's personal copy

Molecular Phylogenetics and Evolution 61 (2011) 543–583

Contents lists available at ScienceDirect

Molecular Phylogenetics and Evolution

journal homepage: www.elsevier.com/locate/ympev

A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians ⇑ R. Alexander Pyron a, , John J. Wiens b a Dept. of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, United States b Dept. of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, United States article info abstract

Article history: The extant amphibians are one of the most diverse radiations of terrestrial vertebrates (>6800 species). Received 7 May 2011 Despite much recent focus on their conservation, diversification, and systematics, no previous phylogeny Revised 10 June 2011 for the group has contained more than 522 species. However, numerous studies with limited taxon sam- Accepted 12 June 2011 pling have generated large amounts of partially overlapping sequence data for many species. Here, we Available online 23 June 2011 combine these data and produce a novel estimate of extant amphibian phylogeny, containing 2871 spe- cies (40% of the known extant species) from 432 genera (85% of the 500 currently recognized extant Keywords: genera). Each sampled species contains up to 12,712 bp from 12 genes (three mitochondrial, nine Amphibia nuclear), with an average of 2563 bp per species. This data set provides strong support for many groups Anura Apoda recognized in previous studies, but it also suggests non-monophyly for several currently recognized fam- Caudata ilies, particularly in hyloid frogs (e.g., Ceratophryidae, Cycloramphidae, Leptodactylidae, Strabomanti- Lissamphibia dae). To correct these and other problems, we provide a revised classification of extant amphibians for Gymnophiona taxa traditionally delimited at the family and subfamily levels. This new taxonomy includes several fam- Phylogeny ilies not recognized in current classifications (e.g., Alsodidae, Batrachylidae, Rhinodermatidae, Odontoph- Supermatrix rynidae, Telmatobiidae), but which are strongly supported and important for avoiding non-monophyly of Systematics current families. Finally, this study provides further evidence that the supermatrix approach provides an effective strategy for inferring large-scale phylogenies using the combined results of previous studies, despite many taxa having extensive missing data. Ó 2011 Elsevier Inc. All rights reserved.

1. Introduction A phylogenetic framework is critical for discovering, under- standing, and preserving extant amphibian diversity, but a large- With over 6800 known species (AmphibiaWeb; http://www. scale phylogeny for extant amphibians is presently lacking. How- amphibiaweb.org/, accessed April, 2011; hereafter ‘‘AW’’) the extant ever, recent molecular and combined-data studies have made amphibians (frogs, salamanders, and caecilians) are one of the most important contributions to higher-level phylogeny (Frost et al., diverse radiations of terrestrial vertebrates. The number of known 2006; Roelants et al., 2007; Wiens, 2007a, 2011) and to the phylog- extant amphibians has increased rapidly in recent years, with over eny of many major groups, such as caecilians (San Mauro et al., 2700 species (40%) described in the last 26 years (Duellman, 2009; Zhang and Wake, 2009b), hyloid frogs (Darst and Cannatella, 1999; Lannoo, 2005). This newly discovered diversity includes doz- 2004), ranoid frogs (e.g., Bossuyt et al., 2006; Wiens et al., 2009), ens of new species from known genera in poorly studied tropical re- microhylid frogs (van der Meijden et al., 2007), bufonid frogs gions such as Madagascar (Vieites et al., 2009), but also new genera (Pauly et al., 2004; Pramuk et al., 2008; Van Bocxlaer et al., in relatively well-explored regions such as the southeastern United 2009), centrolenid frogs (Guayasamin et al., 2009), dendrobatid States (Camp et al., 2009), and even new families such as Nasikabatr- frogs (Grant et al., 2006; Santos et al., 2009), hemiphractid frogs achidae (Biju and Bossuyt, 2003). Unfortunately, much extant (Wiens et al., 2007a), hylid frogs (Faivovich et al., 2005, 2010; amphibian diversity is currently under extreme threat from pres- Wiens et al., 2005b, 2010), terraranan frogs (Hedges et al., 2008; sures such as habitat loss, global climate change, and infectious dis- Heinicke et al., 2009), and salamanders (Kozak et al., 2009; Vieites ease, and many species have gone extinct in the last few decades et al., 2011; Wiens et al., 2005a, 2007b; Zhang and Wake, 2009a). (Blaustein and Wake, 1990; Stuart et al., 2004). The largest estimate of extant amphibian phylogeny to date is that of Frost et al. (2006). Those authors reconstructed amphibian phylogeny based on relatively intensive sampling of species (522) ⇑ Corresponding author. and characters (up to 4.9 kb of sequence data from 2 mitochondrial E-mail addresses: [email protected] (R. Alexander Pyron), [email protected]. sunysb.edu (John J. Wiens). and 5 nuclear genes [mean = 3.5 kb], and 152 morphological

1055-7903/$ - see front matter Ó 2011 Elsevier Inc. All rights reserved. doi:10.1016/j.ympev.2011.06.012 Author's personal copy

544 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 characters). Those authors also proposed extensive changes in tax- members that are not lissamphibians. The gymnophionans, cau- onomy, especially for taxa delimited at the family and genus level. dates, and anurans also contain numerous extinct taxa, many of However, that study has also been criticized on numerous grounds, which are grouped in separate genera, subfamilies, and families including concerns about taxon sampling and methodological that are not addressed in our analyses or included in our discussion strategies (Marjanovic´ and Laurin, 2007; Pauly et al., 2009; Wiens, of phylogeny. See Marjanovic´ and Laurin (2007), Carroll (2009), 2007b, 2008). For example, those authors collected up to 4900 and Pyron (2011) for an overview of these taxa, their phylogenetic characters per species, but their analysis is apparently based on affinities, and the origins of Amphibia and Lissamphibia. 15,320 characters, suggesting that their controversial approach to sequence alignment (POY) dominates their results (Wiens, 2008). 2.2. Molecular data Although some of the changes made by Frost et al. (2006) have been widely adopted, others are more controversial, such as the We identified 12 candidate loci that have been broadly sampled partitioning of Bufo and Rana (Marjanovic´ and Laurin, 2007; Pauly and successfully used in amphibian phylogenetics at both lower et al., 2009; AW). Indeed, many of these changes are no longer sup- and higher taxonomic levels. These 12 genes included nine nuclear ported, even in Frost’s (2011) taxonomic database of extant genes: C-X-C chemokine receptor type 4 (CXCR4), histone 3a amphibians (e.g., the families Amphignathodontidae, Batrachoph- (H3A), sodium–calcium exchanger (NCX1), pro-opiomelanocortin rynidae, Cryptobatrachidae, and Thoropidae recognized by Frost (POMC), recombination-activating gene 1 (RAG1), rhodopsin et al. (2006)). Much of the most unstable taxonomy involves the (RHOD), seventh-in-absentia (SIA), solute-carrier family 8 family-level assignment of many of the genera of hyloid frogs, par- (SLC8A3), and tyrosinase (TYR). Three mitochondrial genes were ticularly those traditionally assigned to the family Leptodactylidae. also included: cytochrome b (cyt-b), and the large and small sub- Clearly, extant amphibian phylogeny and classification is still in units of the mitochondrial ribosome genes (12S/16S; omitting need of additional study. Fortunately, the numerous studies refer- the adjacent tRNAs as they were difficult to align and represented enced above (and many others) have produced a massive amount only a small amount of data). This selection of genes includes al- of data that are potentially suitable for a combined, supermatrix most all of those genes used in the higher-level analyses by Frost approach (e.g., de Queiroz and Gatesy, 2007; Driskell et al., 2004; et al. (2006) and Roelants et al. (2007), and most of those used in Pyron et al., 2011; Thomson and Shaffer, 2010; Wiens et al., other large-scale studies (Faivovich et al., 2005; Grant et al., 2005b). This includes thousands of species represented in GenBank 2006; Wiens et al., 2009, 2010). However, we did not include the for numerous nuclear and mitochondrial genes, often with sub- nuclear gene 28S (used by Frost et al. (2006)), as previous analyses stantial overlap of genes among species. of this gene region alone suggest that it contains relatively few Here, we present a large-scale estimate of amphibian phylog- informative characters and supports some relationships that are eny, including 2871 species (42% of the 6807 known, extant grossly inconsistent with other studies (see Wiens et al., 2006). amphibian species) from 432 of the 504 currently recognized gen- We conducted GenBank searches by family and subfamily to gath- era (86%), and representatives from every currently delimited, ex- er all available sequences, using a minimum-length threshold of tant family and subfamily. This is 5.5 times more species and 200 bp (a somewhat arbitrary threshold of 1.5% of the total matrix nearly twice as many genes as the largest previous study (Frost length, to avoid including very short [e.g., <50 bp] fragments), and et al., 2006). The data matrix includes up to 12,712 bp for each spe- stopping in August of 2010. Only species in the taxonomic data- cies from 12 genes (three mitochondrial, nine nuclear). Impor- base were included in the sequence matrix, which excluded tantly, rather than simply reanalyzing published data for numerous named taxa of ambiguous status, and many sequences relatively well-studied families (e.g., dendrobatids, hylids), we ad- labeled ‘sp.’ We removed a few (<10) taxa with identical sequence dress the monophyly and relationships of many smaller groups data for all genes (arbitrarily retaining the first in alphabetical or- that have not been the subject of focused studies (e.g., Ceratophryi- der), to avoid potentially misidentified or otherwise confounded dae, Cylcoramphidae), as well as relationships among families. We specimens or sequences. produce a revised classification of extant amphibians, focusing on For the protein-coding genes, alignment was relatively straight- taxa traditionally ranked as families and subfamilies. This study forward. Conceptual translations were used to ensure an open also provides additional support for the value of the supermatrix reading frame, and sequences were aligned using the translation- approach to large-scale phylogenetic inference (e.g., de Queiroz alignment algorithm in the program Geneious v4.8.4 (GeneMatters and Gatesy, 2007; Driskell et al., 2004; Pyron et al., 2011; Thomson Corp.), with the default cost matrix (Blosum62) and gap penalties and Shaffer, 2010; Wiens et al., 2005b). (open = 12, extension = 3). For the ribosomal RNA sequences (12S and 16S sequences), alignment was more challenging. Preliminary global alignments using the MUSCLE (Edgar, 2004) and CLUSTAL 2. Materials and methods (Larkin et al., 2007) algorithms under a variety of gap-cost param- eters yielded low-quality results (i.e., alignments with large num- 2.1. Taxonomic reference bers of gaps and little overlap of potentially homologous characters). This analysis has been several years in the making. Our initial We subsequently employed a two-step strategy for these data. taxonomy was based on the September 2009 update of the First, we identified sequence clusters of similar length and cover- AmphibiaWeb (AW) database. However, when we refer to current age from the global alignment. These were subsequently aligned numbers, these are taken from the April, 2011 update. The AW list separately using the MUSCLE algorithm with the default high- is fairly current in terms of recently described species, but more accuracy parameters, which have been shown to outperform CLUS- conservative than the Amphibian Species of the World (Frost, TAL in a variety of settings (Edgar, 2004). These alignments were 2011; hereafter ‘‘ASW’’) regarding some of the more controversial subsequently refined using the MUSCLE refinement algorithm, of the recent taxonomic changes (e.g., Bufo and Rana maintain sim- and then adjusted manually and trimmed for quality and maxi- ilar composition as they did prior to Frost et al., 2006). We note mum coverage (i.e., end sequences with low overlap and poor some instances where recent updates have modified our original apparent alignment were deleted using the alignment editor in classification. Note that even when not made explicit, we refer in Geneious). These length and position-based sequence groups were all instances to the known extant diversity of Lissamphibia, given then aligned to each other using the profile-profile alignment that the clade Amphibia includes numerous extinct stem-group algorithm in MUSCLE. The resulting final global alignment was Author's personal copy

R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 545 manually adjusted and trimmed again for maximum quality and should adequately account for potentially invariant sites without coverage, and refined a second time. Final adjustments were made the need for an extra parameter (Stamatakis, 2006). Even though by eye for a small number of sequences. This process was repeated the GTR + C + I model is implemented in some versions of RAxML, for 12S and 16S separately. For 12S, four clusters were produced its use is explicitly not recommended (Stamatakis, 2006). and combined using profile alignment, with five clusters for 16S. Previous phylogenetic analyses of these data show that The final concatenated alignment consists of 12,712 bp for 2871 GTR + C + I is generally the best-fitting model for these genes species. These species included 42% of the currently recognized (e.g., Roelants et al., 2007; Wiens et al., 2005a,b, 2009, 2010). These amphibian species (6807; this and subsequent numbers from AW previous analyses also suggest that the protein-coding genes 2011), representing 41 caecilian species in 23 genera (22% of 189 should be partitioned by codon position, whereas the ribosomal known extant species and 70% of 33 genera), 436 salamander spe- genes (12S, 16S) should be partitioned by stems and loops, with cies in 68 genera (72% of 608 species and 99% of 69 genera), and separate partitions within and between genes. These secondary 2394 frog species from 341 genera (40% of 6010 species and 85% structures were identified and coded following the protocol used of 402 genera). We selected Homo as an outgroup because data by Wiens et al. (2005b), based on predicted features from Pseuda- were available for Homo from all 12 genes, and the sister group cris regilla (12S; AY819376) and Rana temporaria (16S; AY326063) to Amphibia is Amniota (e.g., Alfaro et al., 2009; Hugall et al., from the European Ribosomal RNA database (http://bioinformat- 2007; Pyron, 2010). The matrix contains data from 2572 species ics.psb.ugent.be/webtools/rRNA/). The placement of stems and for 16S (90%, 1986 bp), 2312 species for 12S (81%, 1357 bp), 1241 loops appears to be conserved across most sites, at least within for cyt-b (43%, 1140 bp), 1049 for RAG-1 (37%, 2700 bp), 606 for frogs (Wiens et al., 2005b). Our final analysis was partitioned by TYR (21%, 1132 bp), 589 for RHOD1 (21%, 315 bp), 478 for SIA gene, codon position (for protein-coding genes), and stems and (17%, 397 bp), 445 for POMC (16%, 666 bp), 352 for H3A (12%, loops (for ribosomal genes). 328 bp), 284 for CXCR4 (10%, 753 bp), 220 for NCX1 (8%, To find the optimal ML tree, we used a searching strategy that 1338 bp), and 175 for SLC8A3 (6%, 1132 bp). The mean length per combined the rapid bootstrapping algorithm (100 non-parametric species is 2563 bp (20% of the total length of the matrix, bootstrap replicates) with the thorough ML search option (20 inde- 12,712 bp), with a range from 249 to 11,462 bp (2–90%), and is pendent searches, starting from every fifth bootstrap replicate). available in Dryad repository doi:10.5061/dryad.vd0m7. GenBank Similar analyses were performed numerous (>10) times as new numbers are listed in Appendix S1. taxa and sequences were added to the near-final matrix. These Clearly, many taxa had large amounts of missing data (some analyses collectively represent hundreds of independent searches >97%), and on average each species had 80% missing cells. How- from random starting points. All of these preliminary analyses ever, several lines of evidence suggest that these missing data showed high congruence with the final ML topology. This concor- are not problematic. First, two genes (12S/16S) were shared by dance strongly suggests that our final ML estimate represents the the vast majority of taxa (90% and 81%, respectively), providing optimal topology for these data (or close to it). Given that BS values a ‘‘backbone’’ for the placement of most taxa based on overlap- generally appear to be conservative (Felsenstein, 2004), we consid- ping sequence data. Simulations suggest that this sampling design ered clades with values of 70% or greater to be well-supported. can be critically important for allowing the accurate placement of These analyses were performed on a 240-core Dell PowerEdge taxa with extensive missing data, as opposed to having all genes supercomputing system at the High Performance Computing Cen- be randomly sampled across species with limited overlap (Wiens, ter at the City University of New York, and were completed in 2003). Second, a large body of empirical and theoretical studies 16 days using 24 nodes of the CUNY cluster. suggests that highly incomplete taxa can be accurately placed in model-based phylogenetic analyses (and with high levels of 2.4. Taxonomic revision branch support), especially if a large number of characters have been sampled (recent review in Wiens and Morrill, 2011). Finally, A major goal of this study was to revise the higher-level taxon- several recent empirical studies have shown that the supermatrix omy of extant amphibians to correspond with the new phylogeny, approach (with extensive missing data in some taxa) yields given several major problems that were discovered. In the Results generally well-supported large-scale trees that are in general section below, we compare our results with existing phylogenies highly congruent with both existing taxonomies and previous and classifications, and describe our proposed solutions to taxo- phylogenetic estimates (e.g., Driskell et al., 2004; McMahon and nomic problems as we describe them (rather than having a separate Sanderson, 2006; Pyron et al., 2011; Thomson and Shaffer, section discussing taxonomy). In general, we attempt to alter exist- 2010; Wiens et al., 2005b). ing classifications (e.g., AW, ASW) as little as possible, and only when existing groups are not monophyletic. Furthermore, we recognize 2.3. Phylogenetic analyses new groups only if they are strongly supported. Given the size of these phylogenies, we do not detail every congruence and discor- We performed phylogenetic inference using maximum likeli- dance between our phylogeny and all previous studies (especially hood (ML) and assessed support using non-parametric bootstrap- within families). Instead, we emphasize necessary taxonomic ping (BS). We assume that Bayesian analysis would yield very changes revealed by our study. We also focus our phylogenetic com- similar results (but would be very difficult to implement for so many parisons on the largest of the previous analyses (in terms of taxo- taxa), and we strongly prefer model-based methods to parsimony nomic scope and number of species sampled), those of Frost et al. (for reasons described in Felsenstein (2004)). We performed ML tree (2006), Roelants et al. (2007), and Wiens (2007a, 2011). The generic inference and non-parametric bootstrapping using the program composition of all families and subfamilies in our revised classifica- RAxMLv7.0.4 (Stamatakis, 2006) with the 12-gene concatenated tion is provided in Appendix B. Genus names follow our original tax- matrix (species-tree methods were not practical given the large onomic database from the 2009 AW update. number of taxa). We used the GTRGAMMA model for all genes and In some cases, our analyses show that higher taxa (i.e., families partitions because GTR is the only substitution model implemented and subfamilies) are not monophyletic, but not all genera have in RAxML, and all other substitution models are encompassed with- been included in our tree. Some of these genera are effectively in the GTR model (Felsenstein, 2004). The GTRGAMMA model in ‘‘orphaned’’ because it is no longer clear to which higher taxon they RAxML is recommended over the GTR + C + I because the large belong. We generally denote these as incertae sedis within the number of rate categories for C (25, as opposed to the usual 4) higher taxon in which they were embedded in previous Author's personal copy

546 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 classifications. Resolving the placement of these taxa in the tree ASW). However, our results differ strongly from Frost et al. and classification will require additional data and analyses. We (2006) with respect to relationships among the salamander fami- consider this a more conservative strategy than simply placing lies. Frost et al. (2006) recover a clade comprising Sirenidae, Dica- them in the nominate group without data. While in theory this mptodontidae, Ambystomatidae, and Salamandridae. In contrast, strategy creates more ‘‘instability’’ by removing taxa from named we find strong support for a sister-group relationship between groups, it highlights the need for their study in future analyses, Sirenidae and all salamanders exclusive of Cryptobranchidae and and does not promote the taxonomic burden of heritage (Pyron Hynobiidae (Figs. 1 and 2B and C), as do Wiens et al. (2005a), Roe- and Burbrink, 2009) in further propagating classifications with lants et al. (2007), and Wiens (2007a, 2011). While some classifica- high probability of error based solely on the status quo. tions recognize only two subfamilies in Plethodontidae (Hemidactylinae and Plethodontinae; AW), we follow most recent authors (Chippindale et al., 2004; Kozak et al., 2009; Vieites et al., 3. Results 2011; Wiens, 2007a) and ASW in recognizing four subfamilies in Plethodontidae (Bolitoglossinae, Hemidactylinae, Plethodontinae, A summary of the ML tree based on the rapid-bootstrapping anal- and Spelerpinae; Figs. 1 and 2D–F). We do not recognize a separate ysis from RAxMLv7.0.4 (lnL = À1704992.20) is shown in Fig. 1. This subfamily for Protohynobius (contra AW), given that it is likely phylogeny is generally well-supported, with 64% of nodes having BS nested in Hynobiinae (Peng et al., 2010). proportions >70. Our analyses support the monophyly of frogs, cae- Within frogs, strongly-supported higher-level groups and rela- cilians, and salamanders, respectively, and weakly support a sister- tionships (e.g., among the non-neobatrachian frogs, Neobatrachia, group relationship between frogs and salamanders, as found in most Hyloidea, and Ranoidea) are consistent with most recent studies other studies of extant lissamphibian phylogeny (Frost et al., 2006; (Frost et al., 2006; Roelants et al., 2007; Wiens, 2007a, 2011), with Pyron, 2011; Roelants et al., 2007; San Mauro, 2010; Wiens, 2011; some notable exceptions. We find (Fig. 2G) strong support for plac- Zhang et al., 2005). An alternative grouping of Gymnophiona and ing Discoglossoidea (Alytidae + Bombinatoridae + Discoglossidae) Caudata (i.e., Procera) has been supported by some studies (e.g., as the sister group to all other frogs exclusive of Ascaphidae + Leio- Feller and Hedges, 1998), and in re-analyses of others (e.g., Zhang pelmatidae (see also Roelants et al., 2007), whereas Frost et al. et al., 2005; San Mauro et al., 2005; see Marjanovic´ and Laurin, (2006) and Wiens (2007a, 2011) placed Pipoidea (Pipidae + Rhin- 2007; Pyron, 2011). Many of the family-level relationships within ophrynidae) in this position. Within Neobatrachia (Fig. 1), we cor- these three groups remain unchanged from recent estimates (Frost roborate the placement of Heleophrynidae as the sister taxon to all et al., 2006; Pyron, 2011; Roelants et al., 2007; San Mauro, 2010; other neobatrachian frogs (Frost et al., 2006; Roelants et al., 2007; Wiens, 2007a, 2011). However, we find some significant deviations Wiens, 2007a, 2011). We find a weakly supported sister-group rela- from previous phylogenies and taxonomies, which we describe be- tionship between the clade Sooglossidae + Nasikabatrachidae and low along with proposed solutions. all neobatrachian frogs to the exclusion of Heleophrynidae (Fig. 1). Within caecilians (Fig. 2A), our results agree with other recent In contrast, both Roelants et al. (2007) and Wiens (2007a, 2011; Soo- studies in supporting clades corresponding to Rhinatrematidae, glossidae only) placed this clade as the sister-taxon to Ranoidea, Ichthyophiidae, and Caeciliidae (Frost et al., 2006; Roelants et al., whereas Frost et al. (2006) found it to be the sister-group of Hyloidea 2007; San Mauro et al., 2009; Zhang and Wake, 2009b). The tradi- (including Myobatrachidae + Calyptocephalellidae). tional family-level classification of caecilians (still used by AW, Within Hyloidea, our results suggest that several families cur- 2011) is not supported, given that Uraeotyphlidae renders Ichthy- rently recognized by both AW and ASW are not monophyletic. ophiidae paraphyletic and that Scolecomorphidae and Typhlonect- All of these problematic taxa were previously placed in the family idae render Caeciliidae paraphyletic. Furthermore, we find (Fig. 2A) Leptodactylidae (subdivided extensively by Frost et al., 2006), and the caeciliid subfamily Typhlonectinae (recognized by ASW) to be include Ceratophryidae, Cycloramphidae, Leptodactylidae, and paraphyletic with respect to Caeciliinae (Cthonerpeton and Typhlo- Strabomantidae. Below we describe the specific problems and nectes are not sister taxa, although this is weakly supported), and our proposed taxonomic solutions. These solutions include recog- also makes Caeciliinae non-monophyletic (i.e., the caeciliines Cae- nizing several additional families relative to current classifications cilia and Oscaecilia are in a strongly supported clade with Cthonerp- (Alsodidae, Batrachylidae, Odontophrynidae, Rhinodermatidae, eton and Typhlonectes, which excludes all other caeciliine genera Telmatobiidae) and synonymizing one (Strabomantidae with such as Dermophis, Gegeneophis, and Siphonops). Typhlonectinae Craugastoridae). These newly recognized families are either re-def- is synonymized with Caeciliinae in our classification. Within Cae- initions of previously recognized families (Rhinodermatidae, ciliidae, we concur with ASW in recognizing the strongly supported Telmatobiidae), or elevation of existing taxa presently below fam- subfamily Scolecomorphinae for Crotaphatrema and Scolecomor- ily rank (Alsodinae, Batrachylinae, Odontophrynini) to the rank of phus, which is the sister group to all other caeciliids. Although families. we could recognize Caeciliinae as the sister group to Scolecomor- Most of these problematic taxa are contained in a weakly sup- phinae, this clade is only weakly supported, despite strong support ported clade (Fig. 2Z) that includes the currently recognized families for each subfamily-level clade. Thus, we recognize these two clades Ceratophryidae, Cycloramphidae, and Hylodidae (note that the as separate subfamilies. We restore the subfamily Herpelinae (Lau- content of these families and their subfamilies are the same in both rent, 1984) for the clade comprising Herpele and Boulengerula.We AW and ASW). Under these classifications, Ceratophryidae is recognize the other strongly supported clade as Caeciliinae (Figs. 1, presently divided into the subfamilies Batrachylinae (Atelognathus, 2A; Appendix B). This arrangement accommodates all taxa in- Batrachyla), Ceratophryinae (Ceratophrys, Chacophrys, Lepidobatra- cluded in our tree, though many other genera have not yet been chus), and Telmatobiinae (Telmatobius, including Batrachophrynus sampled. The following genera are thus considered Caeciliidae in AW). Cycloramphidae comprises Alsodinae (Alsodes, Eupsophus, incertae sedis: Atretochoana, Brasilotyphlus, Idiocranium, Indotyphlus, Hylorina, Insuetophrynus, Limnomedusa, Macrogenioglottus, Odon- Microcaecilia, Mimosiphonops, Nectocaecilia, Parvicaecilia, Potomo- tophrynus, Proceratophrys, Thoropa) and Cycloramphinae (Crossodac- typhlus, and Sylvacaecilia. tylodes, Cycloramphus, Rhinoderma, Zachaenus), and one genus of Within salamanders, the family and subfamily-level relation- uncertain placement (Rupirana). Hylodidae contains Crossodactylus, ships are mostly consistent with most recent model-based molec- Hylodes, and Megaelosia. With respect to this classification, we find ular analyses (Roelants et al., 2007; Wiens, 2011; Wiens et al., strong support for monophyly of Hylodidae (Fig. 2Z), but the families 2005a; Zhang and Wake, 2009a) and current classifications (AW, Ceratophryidae and Cycloramphidae are non-monophyletic, with Author's personal copy

R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 547

Rhinatrematidae 100 Ichthyophiidae 98 Scolecomorphinae Gymnophiona 100 Caeciliinae Caeciliidae 59 Herpelinae 100 Hynobiidae Cryptobranchidae Sirenidae 99 100 Ambystomatidae Dicamptodontidae 71 98 Salamandrininae 100 Pleurodelinae Salamandridae 85 Salamandrinae Caudata 97 Proteidae 92 Rhyacotritonidae 54 97 Amphiumidae 88 Plethodontinae 98 Hemidactylinae Plethodontidae 87 Bolitoglossinae 83 Spelerpinae 98 Leiopelmatidae Ascaphidae 100 Bombinatoridae Discoglossidae 99 100 Alytidae 100 Pipidae Rhinophrynidae 98 100 Scaphiopodidae Pelodytidae 96 Megophryidae 92 99 Pelobatidae Heleophrynidae 100 Sooglossidae 98 Nasikabatrachidae 100 Calyptocephalellidae Myobatrachinae Myobatrachidae 98 Limnodynastinae 98 Ceuthomantidae 97 Brachycephalidae 57 Eleutherodactylinae Phyzelaphryninae Eleutherodactylidae 93 Pristimantinae 98 Holoadeninae Craugastoridae 86 Craugastorinae Neobatrachia Strabomantinae Hemiphractidae 56 Hylinae 96 Pelodryadinae Hylidae 100 Phyllomedusinae 63 Bufonidae Hyloidea Dendrobatidae Allophrynidae 54 100 Centroleninae 100 Hyalinobatrachinae Centrolenidae Leptodactylinae 79 Leuiperinae Leptodactylidae Paratelmatobiinae Ceratophryidae Odontophrynidae Cycloramphidae Alsodidae Anura 53 Hylodidae Telmatobiidae Batrachylidae Rhinodermatidae 100 Brevicipitidae 97 Hemisotidae Hyperoliidae 98 Arthroleptinae 77 99 Leptopelinae Arthroleptidae 71 Astylosterninae Phrynomerinae Otophryninae 97 Gastrophryninae Cophylinae Hoplophryninae 100 Scaphiophryninae Microhylidae Microhylinae 76 Dyscophinae Kalophryninae Asterophryninae Ranoidea Melanobatrachinae Ptychadenidae Micrixalidae 99 Phrynobatrachidae 50 Conrauidae Petropedetidae Cacosterninae 91 Pyxicephalinae Pyxicephalidae Ceratobatrachidae 54 Nyctibatrachidae Ranixalidae Dicroglossinae 88 Occidozyginae Dicroglossidae Ranidae 100 Rhacophorinae Rhacophoridae 0.2 subst./site 74 Buergeriinae 96 Laliostominae 100 Mantellinae Mantellidae 60 Boophinae

Fig. 1. Skeletal representation of the 2871-species tree from maximum likelihood analysis, with tips representing families and subfamilies based on our taxonomic revision. Numbers at nodes are BS proportions greater than 50%. The full version of this tree is presented in Fig. 2, with multiple panels indicated by bold italic letters. Author's personal copy

548 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583

54 Epicrionops marmoratus Epicrionops niger Rhinatrematidae 73 Rhinatrema bivittatum Uraeotyphlus narayani Ichthyophis bombayensis Gymnophiona 100 100 Ichthyophis tricolor 100 100 Ichthyophis orthoplicatus Ichthyophiidae Ichthyophis glutinosus Caudacaecilia asplenia 100 Ichthyophis bannanicus Scolecomorphinae 98 Crotaphatrema tchabalmbaboensis 95 100 Scolecomorphus uluguruensis Scolecomorphus vittatus Herpelinae Herpele squalostoma

100 98 Boulengerula boulengeri Caeciliidae 88 Boulengerula uluguruensis 100 Boulengerula taitana Chthonerpeton indistinctum 100 Typhlonectes natans 59 Caecilia tentaculata 100 Caecilia volcani 70 Oscaecilia ochrocephala

99 Gegeneophis ramaswamii 98 Gegeneophis seshachari 56 Caeciliinae Hypogeophis rostratus

62 Praslinia cooperi 94 Grandisonia alternans 92 Grandisonia brevis 55 Grandisonia larvata 97 Grandisonia sechellensis Luetkenotyphlus brasiliensis 51 Siphonops hardyi Siphonops paulensis 99 Siphonops annulatus 52 Geotrypetes seraphini

100 Schistometopum gregorii 62 Schistometopum thomense 99 Gymnopis multiplicata

100 Dermophis parviceps 69 Dermophis oaxacae Dermophis mexicanus A

Fig. 2. Large-scale maximum likelihood estimate of amphibian phylogeny, containing 2871 species represented by up to 12,871 bp of sequence data from 12 genes (three mitochondrial, nine nuclear). Numbers at nodes are maximum likelihood BS proportions greater than 50%. A skeletal version of this tree at the subfamily level is presented in Fig. 1. Bold italic letters indicate figure panels. Author's personal copy

R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 549

Cryptobranchidae 100 Cryptobranchus alleganiensis 100 Andrias japonicus Andrias davidianus 100 Onychodactylus fischeri 100 Onychodactylus japonicus 74 Pachyhynobius shangchengensis Salamandrella keyserlingii Rano 100 don sibiricus Hynobiidae Paradactylodon mustersi 79 Paradactylodon gorganensis 100 Paradactylodon persicus 75 100 100 Pseudohynobius flavomaculatus Pseudohynobius shuichengensis 54 Liua tsinpaensis 100 Liua shihi Batrachuperus yenyuanensis 98 Batrachuperus pinchonii 97 Batrachuperus londongensis 58 93 Batrachuperus tibetanus 100 Batrachuperus karlschmidti Hynobius retardatus 100 Hynobius boulengeri Hynobius kimurae Hynobius fuca 99 93 Hynobius glacialis 99 Hynobius formosanus 99 Caudata 74 Hynobius arisanensis 95 Hynobius sonani 50 Hynobius naevius Hynobius amjiensis Hynobius katoi 86 Hynobius hidamontanus Hynobius yiwuensis Hynobius guabangshanensis 100 Hynobius chinensis 61 Hynobius maoershanensis 59 Hynobius leechii Hynobius yangi Hynobius quelpaertensis Hynobius dunni Hynobius okiensis Hynobius tsuensis Hynobius nebulosus Hynobius stejnegeri Hynobius lichenatus 54 Hynobius abei 95 Hynobius tokyoensis 61 Hynobius nigrescens C-F 98 B Hynobius takedai

Fig. 2 (continued) Author's personal copy

550 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583

B

Sirenidae Pseudobranchus striatus 100 100 Pseudobranchus axanthus Siren intermedia 100 Siren lacertina Dicamptodontidae 100 Dicamptodon tenebrosus Dicamptodon ensatus 87 Dicamptodon aterrimus 75 Dicamptodon copei 100 Ambystoma cingulatum Ambystoma gracile Ambystoma opacum Ambystomatidae 100 Ambystoma californiense Ambystoma tigrinum 93 Ambystoma dumerilii 68 Ambystoma mexicanum 63 Ambystoma andersoni 70 Ambystoma ordinarium Ambystoma mabeei 71 62 Ambystoma texanum 100 Ambystoma barbouri 98 Ambystoma macrodactylum Ambystoma talpoideum Salamandrininae Ambystoma maculatum Salamandrinae Ambystoma laterale 58 Ambystoma jeffersonianum Salamandrina terdigitata 100 Salamandrina perspicillata Chioglossa lusitanica 90 Mertensiella caucasica Salamandra atra 67 Salamandra corsica Salamandra lanzai 92 Salamandra infraimmaculata Salamandra salamandra 97 100 Salamandra algira Salamandridae 100 Lyciasalamandra luschani Lyciasalamandra fazilae 100 Lyciasalamandra helverseni 64 Lyciasalamandra flavimembris Lyciasalamandra atifi 74 Lyciasalamandra antalyana 100 Lyciasalamandra billae 85 Pleurodeles waltl 100 Pleurodeles poireti 99 91 Pleurodeles nebulosus 100 Echinotriton andersoni Echinotriton chinhaiensis Tylototriton asperrimus D-F 99 Tylototriton wenxianensis 81 Tylototriton taliangensis 64 Tylototriton shanjing 64 Tylototriton verrucosus 91 Tylototriton kweichowensis 100 Taricha rivularis Pleurodelinae 98 Taricha torosa 99 100 Taricha granulosa 100 Notophthalmus meridionalis Notophthalmus perstriatus 82 Notophthalmus viridescens Lissotriton boscai Lissotriton italicus 100 Lissotriton helveticus 97 Lissotriton vulgaris 100 Lissotriton montandoni Ommatotriton vittatus 97 100 Ommatotriton ophryticus Neurergus strauchii 99 Neurergus kaiseri 95 74 88 Neurergus crocatus 100 Neurergus microspilotus Calotriton arnoldi 100 Calotriton asper Triturus marmoratus 85 100 Triturus pygmaeus 100 Triturus dobrogicus 100 Triturus carn ifex 91 Triturus karelinii 66 Triturus cristatus 100 Euproctus platycephalus Euproctus montanus Ichthyosaura alpestris Laotriton laoensis 86 93 Pachytriton labiatus Pachytriton brevipes 88 91 Cynops pyrrhogaster Cynops ensicauda 65 Cynops cyanurus 57 Cynops orphicus 97 Cynops orientalis 65 Paramesotriton caudopunctatus 59 Paramesotriton zhijinensis 68 Paramesotriton chinensis Paramesotriton hongkongensis 82 Paramesotriton deloustali 65 Paramesotriton fuzhongensis 82 Paramesotriton guangxiensis C 98

Fig. 2 (continued) Author's personal copy

R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 551

C Proteidae Proteus anguinus 99 Necturus lewis i 99 Necturus punctatus 64 Necturus beyeri 68 Necturus alabamensis 80 Necturus maculosus Rhyacotritonidae 52 Rhyacotriton kezeri Rhyacotriton cascadae 100 Rhyacotriton olympicus 100 Rhyacotriton variegatus Amphiumidae Amphiuma tridactylum 92 100 Amphiuma pholeter 99 Amphiuma means Hydromantes shastae 100 Hydromantes brunus 98 Hydromantes platycephalus 100 Hydromantes genei 100 Hydromantes imperialis 100 Hydromantes flavus 72 Hydromantes supramontis Hydromantes strinatii 94 100 Hydromantes italicus 97 76 Hydromantes ambrosii Ensatina eschscholtzii 100 Aneides aeneus Aneides hardii 99 Aneides lugubris 99 Aneides flavipunctatus 52 99 Aneides vagrans 100 Aneides ferreus Karsenia koreana Phaeognathus hubrichti Desmognathus wrighti 84 Desmognathus folkertsi 88 99 Desmognathus quadramaculatus 94 Desmognathus marmoratus Desmognathus aeneus 50 Desmognathus imitator Desmognathus monticola Desmognathus carolinensis Plethodontinae Desmognathus brimleyorum 99 55 Desmognathus planiceps Desmognathus welteri 51 Desmognathus fuscus 61 Desmognathus auriculatus Desmognathus ocoee Desmognathus ochrophaeus 100 Desmognathus orestes 88 Desmognathus apalachicolae Desmognathus conanti Desmognathus santeetlah 99 Plethodon larselli Plethodon vandykei 96 100 Plethodon idahoensis Plethodon neomexicanus Plethodon vehiculum 98 Plethodon dunni 87 70 Plethodon asupak Plethodontidae 100 Plethodon stormi 50 Plethodon elongatus Plethodon serratus 100 97 Plethodon virginia Plethodon shenandoah 77 Plethodon cinereus 96 Plethodon hoffmani 52 Plethodon nettingi 55 Plethodon hubrichti 95 Plethodon electromorphus 99 96 Plethodon richmondi Plethodon websteri Plethodon punctatus 77 100 Plethodon wehrlei 62 Plethodon welleri 98 Plethodon angusticlavius 73 Plethodon dorsalis 58 Plethodon ventralis E-F 66 100 Plethodon petraeus Plethodon metcalfi 98 98 Plethodon montanus 63 Plethodon amplus 99 Plethodon meridianus Plethodon chattahoochee 54 Plethodon chlorobryonis 98 Plethodon variolatus 77 Plethodon glutinosus Plethodon cylindraceus 57 Plethodon teyahalee Plethodon aureolus 72 Plethodon cheoah 57 Plethodon caddoensis Plethodon ouachitae Plethodon fourchensis Plethodon kentucki Plethodon jordani 94 Plethodon yonahlossee Plethodon shermani 95 Plethodon mississippi 68 Plethodon kiamichi 74 Plethodon sequoyah 74 Plethodon albagula 92 Plethodon kisatchie Plethodon grobmani D 70 Plethodon ocmulgee 93 Plethodon savannah

Fig. 2 (continued) Author's personal copy

552 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583

Plethodontidae cont. Hemidactylinae Hemidactylium scutatum 100 Gyrinophilus porphyriticus 100 Gyrinophilus gulolineatus 100 Gyrinophilus palleucus Stereochilus marginatus 71 Pseudotriton ruber 98 100 Pseudotriton montanus Urspelerpes brucei Eurycea multiplicata Eurycea spelaea Eurycea tynerensis 97 68 Haideotriton wallacei 100 Eurycea lucifuga 87 61 Eurycea longicauda 99 Eurycea cirrigera Spelerpinae Eurycea wilderae 93 Eurycea bislineata Eurycea junaluska 69 100 Eurycea aquatica Eurycea quadridigitata 100 Eurycea naufragia Eurycea tonkawae 86 Eurycea chisholmensis 100 Eurycea waterlooensis 100 Eurycea rathbuni 83 99 Eurycea troglodytes 85 Eurycea sosorum 100 Eurycea nana 53 Eurycea neotenes 88 Eurycea pterophila 65 Eurycea tridentifera 76 Eurycea latitans 100 Batrachoseps wrighti Batrachoseps campi Batrachoseps diabolicus 92 96 Batrachoseps regius Batrachoseps kawia 53 100 Batrachoseps relictus Batrachoseps gabrieli 100 Batrachoseps gavilanensis 62 Batrachoseps major 99 Batrachoseps pacificus Batrachoseps attenuatus 53 Batrachoseps gregarius 98 100 Batrachoseps simatus 84 Batrachoseps nigriventris Bolitoglossinae Thorius minutissimus 100 Thorius troglodytes 94 Thorius dubitus Chiropterotriton dimidiatus 67 Chiropterotriton orculus 77 Chiropterotriton lavae 91 Chiropterotriton arboreus 64 Chiropterotriton multid entatus 98 Chiropterotriton cracens 93 Chiropterotriton magnipes Chiropterotriton priscus Chiropterotriton terrestris Chiropterotriton chondrostega 61 Dendrotriton rabbi Nyctanolis pernix 94 Cryptotriton alvarezdeltoroi Cryptotriton nasalis 58 Cryptotriton veraepacis Nototriton brodiei 61 95 Nototriton barbouri 62 53 Nototriton limnospectator Nototriton lignicola 100 Nototriton richardi Nototriton guanacaste 96 Nototriton picadoi 77 77 Nototriton gamezi 65 Nototriton abscondens Bradytriton silus Oedipina quadra 52 98 Oedipina kasios Oedipina gephyra 50 86 Oedipina carablanca Oedipina elongata 72 Oedipina maritima Oedipina parvipes 99 Oedipina complex Oedipina savagei 66 Oedipina alleni Oedipina stenopodia Oedipina grandis Oedipina collaris Oedipina pseudouniformis Bolitoglossinae cont. 100 Oedipina cyclocauda Oedipina poelzi Oedipina leptopoda Oedipina gracilis E 74 Oedipina pacificensis 67 Oedipina uniformis

Fig. 2 (continued) Author's personal copy

R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 553

Parvimolge townsendi Bolitoglossinae cont. 91 Pseudoeurycea cephalica Pseudoeurycea galeanae 74 68 Pseudoeurycea scandens Pseudoeurycea boneti 70 96 Pseudoeurycea maxima 90 Pseudoeurycea bellii 65 Pseudoeurycea naucampatepetl 87 Pseudoeurycea gigantea 70 Lineatriton orchileucos Lineatriton lineolus 89 Pseudoeurycea lynchi 74 Pseudoeurycea firscheini 86 Pseudoeurycea leprosa 87 Pseudoeurycea unguidentis Pseudoeurycea ruficauda 71 Pseudoeurycea juarezi 100 Pseudoeurycea saltator Pseudoeurycea nigromaculata Pseudoeurycea mystax Pseudoeurycea werleri 59 Pseudoeurycea obesa Pseudoeurycea conanti Pseudoeurycea rex Ixalotriton niger 100 Ixalotriton parvus 94 Pseudoeurycea papenfussi Pseudoeurycea smithi 88 Pseudoeurycea tenchalli 60 Pseudoeurycea longicauda 88 97 Pseudoeurycea altamontana Pseudoeurycea robertsi 69 Pseudoeurycea gadovii Pseudoeurycea melanomolga 88 Pseudoeurycea cochranae Pseudoeurycea anitae Pseudoeurycea exspectata 57 Pseudoeurycea goebeli Pseudoeurycea brunnata Bolitoglossa hartwegi 59 Bolitoglossa rufescens 96 Bolitoglossa occidentalis Bolitoglossa platydactyla Bolitoglossa flaviventris 92 100 Bolitoglossa odonnelli Bolitoglossa mexicana 86 Bolitoglossa lignicolor 69 Bolitoglossa yucatana 88 Bolitoglossa striatula 94 Bolitoglossa mombachoensis Bolitoglossa subpalmata 100 Bolitoglossa gracilis 80 Bolitoglossa pesrubra 99 Bolitoglossa cerroensis Bolitoglossa epimela 95 Bolitoglossa mar morea 58 Bolitoglossa sooyorum 99 Bolitoglossa minutula Bolitoglossa robusta Bolitoglossa schizodactyla Bolitoglossa colonnea 94 Bolitoglossa paraensis 100 Bolitoglossa biseriata 93 Bolitoglossa sima 68 Bolitoglossa adspersa Bolitoglossa medemi 80 Bolitoglossa altamazonica Bolitoglossa peruviana Bolitoglossa equatoriana Bolitoglossa palmata 90 Bolitoglossa alvaradoi Bolitoglossa dofleini 100 Bolitoglossa engelhardti Bolitoglossa rostrata 92 Bolitoglossa helmrichi Bolitoglossa oaxacensis 99 100 Bolitoglossa macrinii Bolitoglossa zapoteca 52 52 Bolitoglossa hermosa 100 Bolitoglossa riletti 100 Bolitoglossa franklini Bolitoglossa lincolni 58 Bolitoglossa decora 96 Bolitoglossa porrasorum Bolitoglossa longissima Bolitoglossa celaque 90 100 Bolitoglossa synoria Bolitoglossa morio 84 100 Bolitoglossa flavimembris Bolitoglossa dunni 52 Bolitoglossa diaphora F Bolitoglossa conanti Bolitoglossa carri

Fig. 2 (continued) Author's personal copy

554 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583

Ascaphidae 100 Ascaphus montanus 98 Ascaphus truei 99 Leiopelma hochstetteri 99 Leiopelma archeyi Leiopelma hamiltoni Leiopelmatidae 99 Leiopelma pakeka Bombinatoridae Barbourula kalimantanensis 100 Barbourula busuangensis 99 Bombina maxima 100 Bombina lichuanensis 62 Bombina microdeladigitora 86 Bombina fortinuptialis 100 Bombina orientalis 99 Bombina bombina 100 60 Bombina pachypus Anura 100 Bombina variegata Alytidae 100 Alytes cisternasii 100 Alytes obstetricans Alytes maurus 72 Alytes dickhilleni 100 64 Alytes muletensis Discoglossus montalentii 95 Discoglossus sardus Discoglossidae 100 Discoglossus pictus 84 Discoglossus galganoi Rhinophrynidae 86 Discoglossus jeanneae Rhinophrynus dorsalis 100 100 Pipa carvalhoi Pipa pipa 98 100 100 Pipa parva Hymenochirus boettgeri Pipidae 100 Silurana epitropicalis Silurana tropicalis 100 77 Xenopus borealis 100 Xenopus muelleri Xenopus clivii 100 69 Xenopus vestitus Xenopus gilli 95 Xenopus laevis 97 Xenopus petersii 100 Xenopus victorianus 61 Xenopus boumbaensis Xenopus andrei 58 Xenopus pygmaeus Xenopus fraseri 100 Xenopus wittei Xenopus largeni Xenopus ruwenzoriensis 50 Xenopus longipes Xenopus amieti 100 Scaphiopus couchii Scaphiopodidae Scaphiopus hurterii 92 99 Scaphiopus holbrookii 100 100 Spea multiplicata Spea hammondii 86 Spea bombifrons 77 Spea intermontana Pelodytidae Pelodytes caucasicus 100 100 Pelodytes ibericus 100 Pelodytes punctatus Pelobatidae Pelobates syriacus Pelobates fuscus 100 59 Pelobates cultripes 100 Pelobates varaldii 96 Ophryophryne microstoma 100 Ophryophryne hansi Xenophrys baluensis 100 100 Megophrys nasuta Megophrys lekaguli 95 Xenophrys major 99 Xenophrys minor Xenophrys spinata 100 Xenophrys omeimontis Xenophrys nankiangensis 99 Xenophrys shapingensis 94 Brachytarsophrys feae 100 100 Brachytarsophrys platyparietus Leptolalax pictus Megophryidae 100 Leptolalax arayai 98 81 Leptolalax oshanensis 100 Leptolalax liui 97 Leptolalax pelodytoides 99 Leptolalax bourreti Leptobrachium hasseltii 100 100 Leptobrachium smithi 100 Leptobrachium gunungense Leptobrachium montanum 100 Leptobrachium banae 100 Leptobrachium xanthospilum 67 Leptobrachium hainanense 58 Leptobrachium ngoclinhense 99 99 Leptobrachium mouhoti 100 Leptobrachium promustache Leptobrachium boringii 90 Leptobrachium liui 79 Leptobrachium leishanense 100 Vibrissaphora echinata 100 Leptobrachium ailaonicum Leptobrachium huashen 100 Leptobrachium chapaense 100 Scutiger chintingensis H-AE Scutiger glandulatus 78 Scutiger boulengeri 59 Scutiger mammatus 100 Scutiger muliensis 93 Scutiger tuberculatus 90 Oreolalax rhodostigmatus 100 Oreolalax lichuanensis Oreolalax pingii 100 95 Oreolalax schmidti Oreolalax rugosus 80 Oreolalax jingdongensis 99 Oreolalax xiangchengensis 85 Oreolalax major Oreolalax liangbeiensis 66 97 Oreolalax multipunctatus 57 Oreolalax chuanbeiensis 100 Oreolalax omeimontis G 100 Oreolalax popei 100 Oreolalax nanjiangensis

Fig. 2 (continued) Author's personal copy

R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 555

G 100 Hadromophryne natalensis Heleophryne regis Heleophrynidae 99 Heleophryne purcelli Nasikabatrachidae Nasikabatrachus sahyadrensis 100 100 Sechellophryne gardineri Sechellophryne pipilodryas Sooglossidae 100 Sooglossus sechellensis 99 Sooglossus thomasseti Hemisus marmoratus Hemisotidae 100 100 Breviceps fuscus Breviceps mossambicus 98 Breviceps fichus 100 Callulina kisiwamsitu 100 Callulina kreffti Brevicipitidae 100 Spelaeophryne methneri 60 Probreviceps durirostris 98 Probreviceps uluguruensis 97 Probreviceps macrodactylus Leptodactylodon bicolor 68 Scotobleps gabonicus Nyctibates corrugatus 59 Trichobatrachus robustus Astylosterninae 71 Astylosternus diadematus 98 Astylosternus schioetzi 100 Astylosternus batesi 98 80 Leptopelis brevirostris Leptopelis argenteus 99 Leptopelis modestus 97 Leptopelis vermiculatus 94 Leptopelis natalensis Leptopelinae Leptopelis kivuensis 98 99 56 Leptopelis palmatus 73 Leptopelis bocagii 87 Leptopelis concolor 100 Cardioglossa elegans Cardioglossa gratiosa 100 Cardioglossa leucomystax Arthroleptidae Cardioglossa occidentalis 51 Cardioglossa pulchra 100 100 Cardioglossa oreas 100 Cardioglossa manengouba Cardioglossa schioetzi Cardioglossa gracilis 100 Arthroleptis xenodactylus Arthroleptis xenodactyloides 55 Arthroleptis schubotzi Arthroleptis taeniatus Arthroleptinae 100 Arthroleptis sylvaticus 98 Arthroleptis aureoli 86 Arthroleptis wahlbergii 85 Arthroleptis francei Arthroleptis tanneri Arthroleptis reichei 69 Arthroleptis nikeae 100 Arthroleptis affinis 99 Arthroleptis stenodactylus Arthroleptis variabilis 68 Arthroleptis krokosua 75 Arthroleptis adelphus 100 Arthroleptis poecilonotus 56 Cryptothylax greshoffii 63 Kassina senegalensis 100 Semnodactylus wealii Phlyctimantis leonardi 99 82 Phlyctimantis verrucosus 63 Kassina maculata Acanthixalus sonjae 100 Acanthixalus spinosus 97 Opisthothylax immaculatus Morerella cyanophthalma 100 Afrixalus knysnae Afrixalus delicatus 82 100 Afrixalus stuhlmanni Afrixalus fornasini 99 99 Afrixalus laevis 100 Afrixalus dorsalis 77 96 Afrixalus paradorsalis 100 Tachycnemis seychellensis 100 Heterixalus madagascariensis Heterixalus boettgeri 100 Heterixalus alboguttatus 98 Heterixalus punctatus Heterixalus luteostriatus Heterixalus rutenbergi Heterixalus betsileo 67 Heterixalus carbonei 55 Heterixalus andrakata 100 Heterixalus tricolor 93 Heterixalus variabilis Hyperolius semidiscus Hyperolius horstockii 97 Hyperolius pusillus Hyperolius acuticeps Hyperoliidae 56 Hyperolius nasutus Hyperolius pardalis 56 Hyperolius guttulatus 99 Hyperolius fusciventris Hyperolius argus 98 Hyperolius glandicolor 77 Hyperolius phantasticus 100 94 Hyperolius tuberculatus 84 Hyperolius angolensis 84 88 Hyperolius viridiflavus Hyperolius marmoratus 97 Hyperolius tuberilinguis Alexteroon obstetricans Hyperolius kivuensis 100 100 Hyperolius mosaicus 72 Hyperolius ocellatus Hyperolius alticola Hyperolius lateralis 86 Hyperolius castaneus 80 Hyperolius frontalis Hyperolius cystocandicans 54 Hyperolius picturatus 92 Hyperolius baumanni 50 Hyperolius chlorosteus 64 Hyperolius torrentis Hyperolius cinnamomeoventris Hyperolius thomensis 100 100 Hyperolius molleri Hyperolius concolor Hyperolius zonatus I 71 Hyperolius montanus H 61 Hyperolius puncticulatus P-AE J-O

Fig. 2 (continued) Author's personal copy

556 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583

Phrynomerinae Phrynomantis annectens 99 Phrynomantis bifasciatus 100 Phrynomantis microps Otophryninae Otophryne pyburni Synapturanus mirandaribeiroi 71 100 Chiasmocleis hudsoni Chiasmocleis shudikarensis 96 99 Nelsonophryne aequatorialis Ctenophryne geayi 100 Dasypops schirchi Hamptophryne boliviana 100 Dermatonotus muelleri Gastrophryninae Elachistocleis ovalis Microhylidae 97 72 Hypopachus variolosus Gastrophryne elegans 94 Gastrophryne carolinensis 85 100 Gastrophryne olivacea Hoplophryninae Hoplophryne rogersi 100 Hoplophryne uluguruensis Anodonthyla rouxae 88 Anodonthyla montana Anodonthyla moramora 95 100 Anodonthyla nigrigularis 90 Anodonthyla boulengerii 95 Anodonthyla hutchisoni Plethodontohyla inguinalis 100 61 100 Plethodontohyla tuberata Cophylinae Plethodontohyla bipunctata 85 Plethodontohyla brevipes 100 Plethodontohyla ocellata Platypelis grandis Platypelis milloti 84 Platypelis mavomavo 71 Platypelis tuberifera 54 Platypelis pollicaris 82 Platypelis barbouri Stumpffia tridactyla 100 Stumpffia pygmaea Stumpffia gimmeli 98 Stumpffia psologlossa 76 100 Stumpffia tetradactyla Stumpffia grandis 99 Stumpffia roseifemoralis 64 100 Cophyla phyllodactyla Cophyla berara Plethodontohyla mihanika Plethodontohyla fonetana Plethodontohyla guentheri 78 Plethodontohyla notosticta Stumpffia helenae 60 Rhombophryne coudreaui Rhombophryne coronata 90 80 Rhombophryne serratopalpebrosa Rhombophryne minuta Rhombophryne testudo 51 95 Rhombophryne alluaudi Rhombophryne laevipes 95 Paradoxophyla palmata 80 Paradoxophyla tiarano Scaphiophryne brevis 72 Scaphiophryne spinosa Scaphiophryne calcarata 99 63 Scaphiophryne gottlebei Scaphiophryninae 85 98 Scaphiophryne marmorata Scaphiophryne boribory 65 Scaphiophryne madagascariensis 100 Scaphiophryne menabensis Dyscophinae Dyscophus insularis Dyscophus guineti 100 100 Dyscophus antongilii Metaphrynella sundana 76 81 Kaloula pulchra 100 Kaloula conjuncta Kaloula taprobanica Uperodon systoma 78 92 95 Ramanella variegata 100 Ramanella obscura Micryletta inornata Chaperina fusca Glyphoglossus molossus 100 Calluella guttulata Microhylinae Microhyla butleri 100 Microhyla pulchra Microhyla rubra 100 87 Microhyla heymonsi Microhyla borneensis 73 Microhyla okinavensis 99 Microhyla fissipes 88 Microhyla ornata Kalophryninae 100 Kalophrynus baluensis Kalophrynus intermedius Melanobatrachinae Kalophrynus pleurostigma Melanobatrachus indicus Genyophryne thomsoni Liophryne schlaginhaufeni Copiula major 67 Austrochaperina derongo 94 Copiula pipiens 100 Copiula obsti Cophixalus sphagnicola Barygenys exsul Choerophryne rostellifer 58 Albericus laurini Asterophryninae Aphantophryne pansa 99 Cophixalus humicola 100 Cophixalus tridactylus Oreophryne clamata 100 Oreophryne waira Oreophryne sibilans Cophixalus balbus Oreophryne asplenicola 100 Oreophryne pseudasplenicola Oreophryne unicolor 100 Oreophryne brachypus 100 Oreophryne wapoga Oreophryne atrigularis Liophryne rhododactyla Oxydactyla crassa Xenorhina obesa Liophryne dentata Sphenophryne cornuta Hylophorbus rufescens 68 Callulops robustus Hylophorbus nigrinus 97 Hylophorbus wondiwoi 74 Hylophorbus tetraphonus 67 Hylophorbus picoides Barygenys flavigularis 90 Xenorhina lanthanites Xenorhina bouwensi 98 100 Xenorhina varia Xenorhina oxycephala 66 78 Asterophrys turpicola I Callulops slateri 93 Callulops eurydactylus Callulops pullifer

Fig. 2 (continued) Author's personal copy

R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 557

H Hildebrandtia ornata 93 Ptychadena mascareniensis 99 100 Ptychadena newtoni Ptychadena pumilio Ptychadena taenioscelis 82 Ptychadena subpunctata 88 Ptychadena longirostris Ptychadena anchietae Ptychadenidae 75 93 Ptychadena tellinii 98 Ptychadena oxyrhynchus Ptychadena cooperi Ptychadena aequiplicata Ptychadena bibroni 80 Ptychadena porosissima 99 98 Ptychadena mahnerti 100 Micrixalus kottigeharensis Micrixalidae Micrixalus fuscus 99 Phrynobatrachus sandersoni Phrynobatrachidae 99 Phrynobatrachus krefftii Phrynobatrachus dendrobates 99 100 Phrynobatrachus mababiensis Phrynobatrachus calcaratus Phrynobatrachus leveleve 100 Phrynobatrachus dispar 99 94 Phrynobatrachus natalensis 50 Phrynobatrachus auritus 98 Phrynobatrachus acridoides Phrynobatrachus cricogaster 62 Phrynobatrachus africanus 100 Conraua robusta Conraua goliath Conrauidae 100 Conraua crassipes Petropedetes yakusini 100 100 Petropedetes martiensseni Petropedetes palmipes Petropedetidae 94 Petropedetes cameronensis 100 Petropedetes parkeri 100 Petropedetes newtoni 100 Aubria subsigillata Pyxicephalus adspersus Pyxicephalinae 76 Pyxicephalus edulis 91 Anhydrophryne rattrayi Tomopterna natalensis 96 Tomopterna krugerensis Tomopterna delalandii 92 Tomopterna tuberculosa 74 66 Tomopterna luganga Pyxicephalidae 83 Tomopterna marmorata 95 Tomopterna damarensis 56 Tomopterna cryptotis 96 Tomopterna tandyi 61 100 Strongylopus bonaespei Strongylopus fasciatus Poyntonia paludicola 80 100 Microbatrachella capensis 88 Cacosternum platys Cacosterninae 99 Cacosternum nanum 78 Cacosternum capense Cacosternum boettgeri 91 Amietia fuscigula 83 Strongylopus grayii Amietia angolensis Amietia vertebralis 55 Natalobatrachus bonebergi 100 Arthroleptella lightfooti 94 Arthroleptella villiersi Arthroleptella drewesii 100 Arthroleptella landdrosia Arthroleptella bicolor 59 Arthroleptella subvoce Lankanectes corrugatus 74 Nyctibatrachus aliciae Nyctibatrachidae 98 Nyctibatrachus major Ceratobatrachidae 54 Ingerana baluensis 100 Platymantis montanus 95 Platymantis hazelae 100 Platymantis corrugatus 97 Platymantis dorsalis 91 Platymantis mimulus 100 89 Platymantis naomii Batrachylodes vertebralis 57 Ceratobatrachus guentheri 69 Platymantis punctatus 97 Discodeles guppyi 76 Platymantis vitiensis Platymantis bimaculatus 69 Platymantis wuenscheorum Platymantis weberi 99 Platymantis papuensis 100 Platymantis pelewensis J 94 Platymantis cryptotis K-O

Fig. 2 (continued) Author's personal copy

558 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583

Ranixalidae 99 Indirana beddomii Indirana semipalmata Ingerana tenasserimensis 100 100 Occidozyga borealis Occidozyga lima Occidozyga baluensis 78 Occidozyga laevis Occidozyga martensii Occidozyginae 100 Occidozyga magnapustulosa 100 Nannophrys ceylonensis Nannophrys marmorata 100 87 Euphlyctis hexadactylus 100 Euphlyctis cyanophlyctis Euphlyctis ehrenbergii 97 Hoplobatrachus occipitali s 97 Hoplobatrachus crassus 100 Hoplobatrachus tigerinus 100 93 Hoplobatrachus rugulosus Sphaerotheca dobsonii 100 Sphaerotheca breviceps Fejervarya cancrivora 88 88 100 Fejervarya vittigera Fejervarya triora 100 Fejervarya iskandari 54 98 Fejervarya orissaensis 100 Fejervarya sakishimensis 95 85 Fejervarya limnocharis Fejervarya mudduraja 56 Fejervarya pierrei 100 100 Fejervarya greenii Dicroglossidae Fejervarya kirtisinghei 97 Fejervarya kudremukhensis Dicroglossinae Fejervarya rufescens 51 Fejervarya caperata 58 59 Fejervarya syhadrensis Fejervarya granosa 82 Chaparana delacouri Paa fasciculispina 99 93 Paa robertingeri Paa shini Paa verrucospinosa 100 Paa boulengeri 99 Paa yei Paa jiulongensis 99 Paa exilispinosa 100 100 Paa spinosa Paa liebigii Paa taihangnicus 80 Chaparana quadranus 51 Chaparana unculuanus 100 72 Chaparana aenea 100 Chaparana fansipani 57 88 Paa bourreti Paa yunnanensis 100 Paa liui 100 Nanorana ventripunctata Nanorana pleskei 91 Nanorana parkeri 99 Paa conaensis 89 Paa medogensis 90 Paa maculosa 80 Paa chayuensis 99 Paa arnoldi Limnonectes microdiscus 86 100 Limnonectes kadarsani Limnonectes laticeps Limnonectes limborgi 66 100 Limnonectes hascheanus 74 100 Limnonectes dabanus Limnonectes gyldenstolpei Limnonectes asperatus Limnonectes fragilis 100 80 Limnonectes fujianensis 100 Limnonectes bannaensis 63 Limnonectes kuhlii Limnonectes leytensis Limnonectes acanthi 100 65 Limnonectes microtympanum 78 Limnonectes arathooni 57 Limnonectes magnus Limnonectes heinrichi Limnonectes modestus 100 Limnonectes woodworthi 100 69 Limnonectes macrocephalus Limnonectes visayanus Limnonectes leporinus Limnonectes parvus 100 Limnonectes palavanensis 56 Limnonectes ibanorum 63 Limnonectes grunniens Limnonectes blythii 100 Limnonectes poilani Limnonectes paramacrodon 67 Limnonectes macrodon 91 100 Limnonectes shompenorum 71 Limnonectes malesianus K 100 Limnonectes ingeri 100 Limnonectes finchi

Fig. 2 (continued) Author's personal copy

R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 559

Laliostominae 99 Laliostoma labrosum 99 Aglyptodactylus madagascariensis Aglyptodactylus laticeps 87 Boophis pauliani Boophis idae 78 Boophis xerophilus 94 Boophis tephraeomystax Boophinae 100 Boophis doulioti 100 Boophis luteus 82 Boophis madagascariensis 93 Boophis goudotii 100 87 Boophis boehmei Boophis marojezensis Mantellidae 100 100 Boophis vittatus Boophis albilabris 100 Boophis occidentalis Boophis microtympanum Boophis sibilans 55 100 Boophis rappiodes Boophis viridis 100 Guibemantis tornieri 99 Guibemantis depressiceps 100 Guibemantis albolineatus 99 Guibemantis bicalcaratus Guibemantis liber 60 Blommersia wittei 96 Blommersia blommersae 95 Blommersia domerguei 99 Blommersia grandisonae 99 Blommersia sarotra 100 Blommersia kely Wakea madinika Mantella bernhardi 100 100 Mantella cowanii Mantella baroni 96 93 Mantella haraldmeieri 92 Mantella nigricans 93 Mantella madagascariensis Mantella pulchra 100 100 Mantella aurantiaca 99 Mantella crocea Mantellinae 97 Mantella milotympanum 91 Mantella laevigata 100 Mantella manery 74 Mantella ebenaui 100 Mantella expectata 94 Mantella viridis 73 Mantella betsileo 100 Spinomantis aglavei Spinomantis elegans 94 Spinomantis peraccae Boehmantis microtympanum Mantidactylus grandidieri 88 Mantidactylus argenteus Mantidactylus lugubris 76 90 Mantidactylus biporus 52 64 90 Mantidactylus charlotteae Mantidactylus op iparis 51 Mantidactylus ulcerosus 94 Mantidactylus ambreensis 86 61 Mantidactylus mocquardi 96 Mantidactylus femoralis 62 Gephyromantis corvus Gephyromantis azzurrae Gephyromantis sculpturatus 99 Gephyromantis plicifer 73 Gephyromantis luteus Gephyromantis pseudoasper Gephyromantis granulatus 99 Gephyromantis tschenki Gephyromantis cornutus 57 Gephyromantis redimitus Gephyromantis moseri Gephyromantis tandroka Gephyromantis salegy Gephyromantis zavona Gephyromantis leucomaculatus Gephyromantis boulengeri Gephyromantis asper 55 Gephyromantis blanci 97 Gephyromantis enki 95 Gephyromantis eiselti 52 Gephyromantis leucocephalus 64 Gephyromantis decaryi Gephyromantis webbi Gephyromantis silvanus 64 Gephyromantis rivicola Gephyromantis ambohitra Gephyromantis klemmeri Gephyromantis horridus 58 Gephyromantis ventrimaculatus L 85 100 Gephyromantis malagasius Gephyromantis striatus

Fig. 2 (continued) Author's personal copy

560 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583

Buergeriinae 100 Buergeria oxycephlus Buergeria japonica 83 Buergeria buergeri 98 Buergeria robusta Philautus hainanus 100 Philautus ocellatus 58 Liuixalus romeri 100 96 Nyctixalus spinosus Rhacophoridae 99 Nyctixalus pictus Theloderma corticale Theloderma rhododiscus 99 Theloderma bicolor Theloderma asperum 100 Ghatixalus variabilis 76 Chiromantis vittatus Rhacophorinae 98 Chiromantis doriae 69 Chiromantis rufescens 85 Chiromantis xerampelina Feihyla palpebralis 66 Polypedates eques 99 Polypedates fastigo Polypedates colletti 62 94 58 Polypedates maculatus 100 Polypedates cruciger 78 Polypedates leucomystax 88 Polypedates mutus 99 Polypedates megacephalus 99 Rhacophorus annamensis Rhacophorus orlovi Rhacophorus malabaricus Rhacophorus calcaneus 99 Rhacophorus rhodopus 98 Rhacophorus bipunctatus 52 Rhacophorus kio 92 87 Rhacophorus reinwardtii 99 Rhacophorus lateralis Rhacophorus feae Rhacophorus dennysi 100 Rhacophorus maximus 73 93 Rhacophorus chenfui 74 Rhacophorus nigropunctatus Rhacophorus schlegelii 55 Rhacophorus arboreus Rhacophorus moltrechti 61 92 Rhacophorus taronensis Rhacophorus omeimontis 77 Rhacophorus hui 60 Rhacophorus minimus 53 Rhacophorus hungfuensis Rhacophorus dugritei 89 Rhacophorus puerensis 98 Kurixalus jinxiuensis Gracixalus gracilipes 96 Philautus quyeti Philautus ingeri Philautus abditus 88 Philautus aurifasciatus 100 Philautus acutirostris 68 Philautus surdus 86 68 Philautus mjobergi Philautus petersi Theloderma moloch Philautus banaensis Kurixalus eiffingeri 52 Kurixalus idiootocus 96 Philautus carinensis 100 Kurixalus odontotarsu s 80 Kurixalus hainanus 62 Philautus beddomii Philautus glandulosus Philautus anili Philautus bobingeri Philautus graminirupes Philautus nerostagona 67 Philautus neelanethrus 98 Philautus travancoricus 89 Philautus griet 70 100 Philautus charius 100 Philautus signatus Philautus tinniens Philautus ponmudi Philautus longchuanensis 59 Philautus gryllus 100 92 Philautus menglaensis 73 Philautus bombayensis 52 100 Philautus tuberohumerus Philautus zorro 100 Philautus wynaadensis Philautus leucorhinus Philautus simba 98 Philautus decoris 53 100 Philautus mittermeieri Philautus tanu Philautus ocularis Philautus pleurotaenia 54 100 Philautus asankai 91 Philautus hoffmanni Philautus papillosus Philautus microtympanum Philautus steineri 89 Philautus mooreorum Philautus poppiae 99 Philautus femoralis Philautus popularis Philautus stuarti 55 Philautus lunatus Philautus cavirostris M Philautus schmarda

Fig. 2 (continued) Author's personal copy

R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 561

100 Staurois latopalmatus Staurois natator 100 Staurois parvus 100 Staurois tuberilinguis Huia melasma 100 Rana curtipes 67 Rana alticola 58 100 Huia masonii Huia sumatrana Huia cavitympanum 82 96 Meristogenys kinabaluensis 100 58 Meristogenys whiteheadi 96 Meristogenys orphnocnemis Ranidae Meristogenys poecilus 61 Meristogenys jerboa 53 Meristogenys phaeomerus Amolops spinapectoralis 93 100 Amolops hainanensis 99 Amolops torrentis 100 Amolops hongkongensis Amolops daiyunensis 97 Amolops wuyiensis 90 100 Amolops ricketti 96 Amolops cremnobatus Amolops larutensis 96 100 Amolops panhai 94 Amolops marmoratus 97 Amolops bellulus 90 Amolops chunganensis Amolops viridimaculatus 98 100 Amolops lifanensis 92 Amolops granulosus 71 Amolops kangtingensis 93 98 Amolops mantzorum Amolops jinjiangensis 91 Amolops loloensis 100 Amolops liangshanensis 100 Rana fukienensis Rana porosa 95 Rana hubeiensis 97 Rana plancyi 65 Rana nigromaculata 56 100 Rana saharica Rana perezi 100 Rana esculenta 100 Rana lessonae Rana cretensis 80 Rana epeirotica Rana kurtmuelleri 76 71 Rana ridibunda 53 Rana bedriagae Rana cerigensis Rana shqiperica 70 85 Rana bergeri Rana sanguinea 100 94 100 Rana igorota Rana luzonensis Rana minima 100 Rana tientaiensis 98 Rana emeljanovi Rana rugosa Rana luctuosa 100 Rana erythraea 95 Rana taipehensis 96 Rana macrodactyla Rana guentheri 100 Rana lateralis 82 Rana miopus 100 Rana aurantiaca Rana temporalis Rana malabarica Rana gracilis Rana milleti 71 97 Rana arfaki Rana jimiensis Rana daemeli 98 Rana faber Rana nigrovittata 95 Rana cubitalis Rana latouchii 99 Rana maosonensis Rana spinulosa Rana mocquardii Rana chalconota 95 56 Rana megalonesa Rana raniceps 100 Rana labialis 99 Rana parvaccola 98 Rana eschatia Hylarana nicobariensis Amnirana galamensis 60 99 Amnirana albolabris Amnirana lepus 60 Rana siberu 59 Rana picturata 76 Rana signata Rana banjarana 100 Rana glandulosa Rana baramica N 67 Rana laterimaculata Ranidae cont.

Fig. 2 (continued) Author's personal copy

562 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583

100 Rana pleuraden 100 Rana chapaensis Rana adenopleura 94 Odorrana absita Rana khalam Odorrana chapaensis 90 Rana hmongorum Rana andersonii 100 68 Odorrana junlianensis Rana grahami Rana margaretae 94 Odorrana jingdongensis 100 88 Rana iriodes 66 Rana daorum Rana archotaphus 98 98 Rana vitrea Ranidae cont. Rana compotrix 94 Rana cucae Rana ishikawae 97 Rana bacboensis Rana hejiangensis 93 Odorrana schmackeri Odorrana tormota Odorrana nasica 97 51 Rana versabilis 73 100 Rana swinhoana Rana utsunomiyaorum 99 100 Rana supranarina 86 Rana amamiensis Rana narina Rana megatympanum Rana tiannanensis 88 100 Rana banaorum 63 Rana morafkai 52 Rana hosii 51 Rana chloronota 93 99 Rana livida Odorrana aureola Rana weiningensis Rana shuchinae 100 Rana luteiventris 92 Rana pretiosa 92 Rana boylii 81 Rana aurora 88 Rana muscosa 92 Rana cascadae 78 Rana tagoi 99 Rana johnsi Rana zhengi Pseudoamolops sauteri 85 Rana asiatica Rana latastei 76 Rana dalmatina 73 Rana graeca Rana macrocnemis 81 Rana holsti Rana okinavana 70 Rana tsushimensis 91 Rana pyrenaica Rana temporaria Rana italica 63 Rana iberica Rana kunyuensis 99 Rana amurensis Rana ornativentris 67 55 Rana dybowskii 97 Rana pirica 86 Rana huanrensis Rana kukunoris 57 Rana chensinensis Rana arvalis Rana japonica Rana chaochiaoensis 81 77 Rana omeimontis 93 Rana zhenhaiensis 84 Rana longicrus Rana sylvatica Rana catesbeiana 52 Rana septentrionalis 100 Rana grylio 84 Rana virgatipes Rana heckscheri 100 Rana okaloosae 100 Rana clamitans Rana sierramadrensis 67 Rana pustulosa 100 Rana tarahumarae 98 98 Rana zweifeli 72 73 Rana psilonota Rana maculata 95 Rana vibicaria 100 Rana warszewitschii 97 99 Rana palmipes Rana bwana 100 Rana juliani 100 Rana vaillanti 63 Rana palustris 100 Rana areolata 79 100 Rana sevosa 100 Rana capito Rana pipiens 100 Rana chiricahuensis 100 Rana dunni 100 Rana montezumae 100 98 Rana magnaocularis 99 Rana yavapaiensis Rana onca 90 Rana sphenocephala 99 99 Rana blairi Rana berlandieri 95 Rana neovolcanica 66 88 Rana tlaloci Rana omiltemana Rana forreri 54 Rana spectabilis Rana brownorum O 77 Rana taylori 72 Rana macroglossa

Fig. 2 (continued) Author's personal copy

R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 563

100 Calyptocephallela gayi Telmatobufo venustus Calyptocephallelidae 94 Telmatobufo bullocki 100 Notaden melanoscaphus Notaden bennettii Neobatrachus pelobatoides 100 Neobatrachus pictus 100 99 Neobatrachus sudelli Platyplectrum spenceri 100 100 Platyplectrum ornatum 98 A-O Lechriodus fletcheri Heleioporus australiacus Adelotus brevis Philoria sphagnicolus Limnodynastinae Limnodynastes salmini 100 Limnodynastes lignarius 65 Limnodynastes convexiusculus 54 Limnodynastes peronii 98 93 Limnodynastes tasmaniensis 78 Limnodynastes depressus Limnodynastes fletcheri Limnodynastes terraereginae 100 Limnodynastes dorsalis 65 Limnodynastes interioris 97 Limnodynastes dumerilii Myobatrachidae Rheobatrachus silus Mixophyes balbus 100 Mixophyes carbinensis Mixophyes coggeri 74 64 68 Mixophyes schevilli Mixophyes fasciolatus 71 Taudactylus acutirostris 57 Spicospina flammocaerulea 76 Uperoleia littlejohni 100 100 Uperoleia laevigata 99 100 Pseudophryne coriacea Pseudophryne bibronii Myobatrachinae 100 Myobatrachus gouldii 100 Metacrinia nichollsi 100 Paracrinia haswelli 100 Geocrinia victoriana 100 Assa darlingtoni 81 Crinia nimbus 89 Crinia riparia 100 Crinia signifera 100 Crinia deserticola Crinia parinsignifera 67 Crinia tinnula Ceuthomantidae Ceuthomantis smaragdinus Brachycephalus ephippium 97 97 Ischnocnema juipoca Ischnocnema holti Brachycephalidae 100 Ischnocnema parva 93 Ischnocnema guentheri 98 66 Ischnocnema hoehnei Q-S P T-AE

Fig. 2 (continued) Author's personal copy

564 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583

Adelophryne gutturosa 100 Phyzelaphryne miriamae Diasporus diastema Eleutherodactylus counouspeus Phyzelaphryninae 52 100 Eleutherodactylus inoptatus 100 Eleutherodactylus nortoni Eleutherodactylus chlorophenax 93 100 Eleutherodactylus bothroboans 100 Eleutherodactylus ruthae Eleutherodactylidae 82 Eleutherodactylus parapelates Eleutherodactylus hypostenor 89 79 Eleutherodactylus richmondi 100 Eleutherodactylus unicolor Eleutherodactylus patriciae 92 Eleutherodactylus auriculatoides Eleutherodactylus sommeri 60 100 Eleutherodactylus wetmorei 90 Eleutherodactylus fowleri 100 Eleutherodactylus lamprotes 59 82 Eleutherodactylus melacara 90 100 Eleutherodactylus leberi 99 Eleutherodactylus varians 100 Eleutherodactylus ionthus 100 Eleutherodactylus guantanamera Eleutherodactylinae 51 Eleutherodactylus poolei Eleutherodactylus minutus 90 64 Eleutherodactylus pituinus Eleutherodactylus parabates 98 Eleutherodactylus abbotti 54 Eleutherodactylus haitianus Eleutherodactylus audanti Eleutherodactylus eileenae Eleutherodactylus glamyrus 83 100 Eleutherodactylus ronaldi 93 Eleutherodactylus mariposa Eleutherodactylus bartonsmithi 55 99 Eleutherodactylus auriculatus 81 Eleutherodactylus principalis 100 Eleutherodactylus pinchoni Eleutherodactylus barlagnei 85 Eleutherodactylus johnstonei 100 100 Eleutherodactylus amplinympha 97 Eleutherodactylus martinicensis Eleutherodactylus flavescens 81 100 Eleutherodactylus cooki Eleutherodactylus eneidae 100 93 Eleutherodactylus locustus 93 Eleutherodactylus antillensis 92 Eleutherodactylus brittoni 97 Eleutherodactylus hedricki 89 Eleutherodactylus cochranae 66 Eleutherodactylus gryllus 64 Eleutherodactylus wightmanae 84 Eleutherodactylus portoricensis 92 89 Eleutherodactylus coqui Eleutherodactylus schwartzi Eleutherodactylus zeus 99 100 Eleutherodactylus symingtoni Eleutherodactylus marnockii Eleutherodactylus nitidus 100 100 Eleutherodactylus pipilans Eleutherodactylus klinikowskii 100 Eleutherodactylus zugi 86 90 Eleutherodactylus ventrilineatus 98 Eleutherodactylus brevirostris 100 Eleutherodactylus sciagraphus Eleutherodactylus glandulifer 100 Eleutherodactylus paulsoni 100 Eleutherodactylus furcyensis 100 Eleutherodactylus rufifemoralis 64 97 Eleutherodactylus apostates 55 Eleutherodactylus oxyrhyncus Eleutherodactylus jugans 71 Eleutherodactylus glanduliferoides 59 Eleutherodactylus thorectes 70 Eleutherodactylus bakeri Eleutherodactylus dolomedes Eleutherodactylus glaphycompus 97 Eleutherodactylus heminota Eleutherodactylus corona 62 Eleutherodactylus amadeus 51 Eleutherodactylus eunaster 100 Eleutherodactylus caribe 100 Eleutherodactylus schmidti Eleutherodactylus albipes Eleutherodactylus maestrensis 100 Eleutherodactylus dimidiatus 99 Eleutherodactylus emiliae Eleutherodactylus greyi Eleutherodactylus guanahacabibes Eleutherodactylus planirostris 65 70 100 100 Eleutherodactylus casparii Eleutherodactylus goini Eleutherodactylus tonyi Eleutherodactylus rogersi 50 Eleutherodactylus pezopetrus Eleutherodactylus pinarensis 61 100 Eleutherodactylus blairhedgesi 95 98 Eleutherodactylus thomasi Eleutherodactylus atkinsi Eleutherodactylus gundlachi 60 Eleutherodactylus intermedius 100 Eleutherodactylus varleyi Eleutherodactylus cubanus Eleutherodactylus orientalis Eleutherodactylus etheridgei 71 Eleutherodactylus iberia 100 8010098 Eleutherodactylus jaumei Eleutherodactylus limbatus 97 Eleutherodactylus alcoae 98 Eleutherodactylus armstrongi Eleutherodactylus leoncei 100 Eleutherodactylus darlingtoni Eleutherodactylus bresslerae Eleutherodactylus ricordii 100 Eleutherodactylus acmonis Eleutherodactylus probolaeus Eleutherodactylus monensis 100 100 Eleutherodactylus pictissimus Eleutherodactylus grahami 77 Eleutherodactylus lentus 74 Eleutherodactylus rhodesi 83 Eleutherodactylus weinlandi 90 Eleutherodactylus turquinensis Eleutherodactylus cuneatus Eleutherodactylus riparius Eleutherodactylus rivularis Eleutherodactylus toa Eleutherodactylus luteolus 60 Eleutherodactylus sisyphodemus Eleutherodactylus grabhami 72 Eleutherodactylus cavernicola 64 Eleutherodactylus jamaicensis Eleutherodactylus nubicola Eleutherodactylus andrewsi Eleutherodactylus orcutti Eleutherodactylus alticola Eleutherodactylus fuscus Eleutherodactylus junori Eleutherodactylus gossei Eleutherodactylus griphus Eleutherodactylus glaucoreius Q 92 Eleutherodactylus cundalli Eleutherodactylus pentasyringos 86 Eleutherodactylus pantoni

Fig. 2 (continued) Author's personal copy

R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 565

incertae sedis Hypodactylus dolops 61 100 Hypodactylus peraccai Hypodactylus elassodiscus Hypodactylus brunneus 100 Strabomantis sulcatus 100 Strabomantis biporcatus 100 Strabomantis necerus Strabomantinae 98 Strabomantis bufoniformis Strabomantis anomalus Haddadus binotatus Craugastorinae Craugastor daryi Craugastor augusti 77 100 Craugastor tarahumaraensis 100 Craugastor alfredi 89 100 Craugastor uno Craugastor stuarti 67 Craugastor bocourti Craugastor spatulatus Craugastor montanus 81 84 Craugastor pygmaeus 97 Craugastor sartori Craugastor laticeps 100 Craugastor lineatus 69 99 Craugastor podiciferus 85 Craugastor bransfordii 99 Craugastor mexicanus 100 Craugastor loki 69 Craugastor rhodopis Craugastor sandersoni 98 100 Craugastor obesus 52 Craugastor punctariolus Craugastor angelicus 85 Craugastor megacephalus 86 Craugastor rupinius Craugastor fleischmanni Craugastoridae 98 Craugastor rugulosus 100 Craugastor ranoides 89 Craugastor emcelae Craugastor melanostictus 77 Craugastor andi 100 100 Craugastor cuaquero 77 Craugastor longirostris Craugastor tabasarae 76 Craugastor raniformis 98 Craugastor fitzingeri 80 Craugastor crassidigitus 90 Craugastor talamancae Noblella peruviana 100 Psychrophrynella wettsteini 100 Psychrophrynella iatamasi 93 Bryophryne cophites 100 Holoaden bradei 77 Holoaden luederwaldti Holoadeninae Noblella lochites 100 100 Barycholos ternetzi Barycholos pulcher Phrynopus bracki 100 Phrynopus bufoides 76Phrynopuspes antesi 100 88 Phrynopus horstpauli Phrynopus barthlenae 58 Phrynopus tautzorum 59 85 95 Phrynopus kauneorum Phrynopus juninensis 100 Lynchius flavomaculatus Lynchius parkeri Lynchius nebulanastes 72 Oreobates lehri Oreobates quixensis 100 100 Oreobates saxatilis Oreobates choristolemma 81 100 100 Oreobates sanctaecrucis Oreobates granulosus 76 98 Oreobates sanderi Pristimantinae 100 Oreobates discoidalis Oreobates ibischi 87 Oreobates cruralis Oreobates heterodactylus R 65 Oreobates madidi Pristimantinae cont.

Fig. 2 (continued) Author's personal copy

566 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583

Pristimantis ashkapara Pristimantinae cont. 100 Pristimantis mercedesae 92 Pristimantis fraudator Pristimantis bisignatus 100 Pristimantis crenunguis 93 Pristimantis labiosus Pristimantis lanthanites 100 100 Pristimantis w-nigrum 100 Pristimantis actites Pristimantis ridens Pristimantis caryophyllaceus 75 93 Pristimantis cremnobates 67 Pristimantis cruentus 62 100 Pristimantis colomai Pristimantis latidiscus Pristimantis caprifer 100 Pristimantis shrevei Pristimantis euphronides 100 Pristimantis peruvianus Pristimantis reichlei 99 100 Pristimantis aniptopalmatus Pristimantis stictogaster 83 Pristimantis sagittulus 98 88 Pristimantis danae 83 Pristimantis pluvicanorus 64 89 Pristimantis rhabdolaemus 94 Pristimantis toftae Pristimantis terraebolivaris Pristimantis samaipatae Pristimantis chiastonotus 99 99 50 Pristimantis koehleri 80 Pristimantis fenestratus 66 Pristimantis skydmainos 99 Pristimantis bipunctatus 99 Pristimantis lymani Pristimantis achatinus 70 Pristimantis conspicillatus 99 Pristimantis condor 100 Pristimantis malkini 99 Pristimantis citriogaster 90 Pristimantis buccinator Pristimantis prolatus Pristimantis urichi Pristimantis rozei 100 Pristimantis eriphus 100 Pristimantis chloronotus Pristimantis supernatis 100 Pristimantis verecundus 60 100 Pristimantis celator Pristimantis leoni Pristimantis pyrrhomerus 100 85 Pristimantis thymelensis 100 Pristimantis ocreatus 100 94 Pristimantis thymalopsoides Pristimantis duellmani 90 Pristimantis quinquagesimus 100 Pristimantis surdus Pristimantis devillei 99 88 Pristimantis vertebralis Pristimantis buckleyi 65 Pristimantis curtipes 100 Pristimantis gentryi 100 Pristimantis truebae 84 Pristimantis crucifer 75 100 Pristimantis nyctophylax 56 Pristimantis subsigillatus Pristimantis galdi 85 Pristimantis zeuctotylus Pristimantis bromeliaceus 94 76 58 Pristimantis schultei Pristimantis acuminatus 100 Pristimantis acerus Pristimantis inusitatus 82 Pristimantis glandulosus 86 Pristimantis orcesi 95 Pristimantis pycnodermis 84 Pristimantis appendiculatus 55 Pristimantis calcarulatus 90 88 Pristimantis dissimulatus 86 Pristimantis rhodoplichus 63 Pristimantis simonsii Pristimantis melanogaster 88 Pristimantis rhabdocnemus 99 Pristimantis quaquaversus 81 Pristimantis petrobardus 71 Pristimantis wiensi 100 Pristimantis cryophilius 99 Pristimantis spinosus 81 Pristimantis phoxocephalus 100 Pristimantis versicolor 86 Pristimantis riveti Pristimantis orestes 78 100 Pristimantis simonbolivari 93 Pristimantis chalceus Pristimantis parvillus 100 Pristimantis luteolateralis 100 100 Pristimantis walkeri 98 79 Pristimantis ceuthospilus Pristimantis cajamarcensis 57 Pristimantis ardalonychus Pristimantis unistrigatus 100 68 Pristimantis ockendeni Pristimantis diadematus 95 Pristimantis platydactylus 98 Pristimantis altamazonicus 96 Pristimantis pulvinatus 100 Pristimantis inguinalis 87 Pristimantis marmoratus 98 Pristimantis lirellus 100 Pristimantis imitatrix S 77 Pristimantis croceoinguinis Pristimantis llojsintuta

Fig. 2 (continued) Author's personal copy

R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 567

100 Flectonotus fitzgeraldi Flectonotus pygmaeus

61 Hemiphractus scutatus Hemiphractus helioi 100 100 Hemiphractidae 100 Hemiphractusproboscideus Hemiphractus bubalus Stefania ginesi 100 Stefania schuberti 65 100 Stefania coxi 81 Stefania scalae 100 Stefania evansi Gastrotheca fissipes 64 Gastrotheca walkeri 100 Gastrotheca guentheri 100 Gastrotheca weinlandii Gastrotheca dendronastes 100 98 100 Gastrotheca cornuta 66 Gastrotheca longipes 100 Gastrotheca helenae

99 Gastrotheca zeugocystis Gastrotheca galeata Gastrotheca monticola

93 Gastrotheca litonedis 89 Gastrotheca orophylax 100 Gastrotheca plumbea 100 Gastrotheca riobambae Gastrotheca nicefori 93 Gastrotheca dunni 65 97 Gastrotheca ruizi 52 Gastrotheca aureomaculata 90 Gastrotheca trachyceps 100 Gastrotheca argenteovirens Gastrotheca psychrophila

99 Gastrotheca excubitor Gastrotheca ochoai 64 98 Gastrotheca atympana Gastrotheca stictopleura

100 Gastrotheca peruana Gastrotheca pseustes Gastrotheca marsupiata Gastrotheca griswoldi Gastrotheca gracilis

90 Gastrotheca christiani T 85 Gastrotheca chrysosticta

Fig. 2 (continued)

genera interdigitating amongst each other and with Hylodidae. Be- Odontophrynini (Lynch, 1971). Within the larger sister-group of cause relationships amongst these groups are weakly supported, Odontophrynidae is a weakly supported clade comprising the gen- we split these clades into multiple, strongly supported families, era Insuetophrynus, Rhinoderma, Batrachyla (B. leptopus), Atelogna- rather than recognizing larger, weakly supported families that thus, and Telmatobius. Within this clade, the cycloramphid genera would possibly be found non-monophyletic in future studies. Insuetophrynus and Rhinoderma are strongly supported as sister The subfamily Ceratophryinae is the sister group to all other taxa, for which we resurrect the family Rhinodermatidae (Günther, members of this clade (Fig. 2Z). Although this placement of the 1858). This family was widely recognized prior to revision by Frost group is weakly supported, monophyly of Ceratophryinae is well et al. (2006), but containing only Rhinoderma (e.g., Duellman and supported. We restrict the family Ceratophryidae to include only Trueb, 1994). this subfamily. Within the sister group to ceratophryids is a The sister group to Rhinodermatidae (Fig. 2Z) is a strongly sup- strongly supported clade (BS = 100%) that includes the cyclor- ported clade consisting of Atelognathus and Batrachyla leptopus hamphid alsodine genera Macrogenioglottus, Odontophrynus, and (type species of the genus; ASW), a clade corresponding primarily Proceratophrys. This clade is here named Odontophrynidae, to the ceratophryid subfamily Batrachylinae. We recognize this corresponding to the former telmatobiine leptodactylid tribe clade as a distinct family (Batrachylidae). The other two Batrachyla Author's personal copy

568 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583

Phrynomedusa marginata Cruziohyla calcarifer Hylomantis aspera Hylidae: 100 Phyllomedusinae Hylomantis granulosa 100 100 Hylomantis lemur Hylomantis hulli

78 Pachymedusa dacnicolor 100 Agalychnis litodryas Hylidae cont. 100 Agalychnis spurrelli 99 Agalychnis callidryas

74 Agalychnis saltator 73 Agalychnis annae 82 Agalychnis moreletii 62 Phasmahyla jandaia 100 Phasmahyla exilis Phasmahyla guttata Phasmahyla cochranae 71 Phasmahyla cruzi

100 Phyllomedusa bicolor Phyllomedusa vaillantii Phyllomedusa camba 100 100 Phyllomedusa tarsius 73 100 Phyllomedusa trinitatis 100 Phyllomedusa neildi 92 Phyllomedusa boliviana Phyllomedusa sauvagii 99 100 Phyllomedusa bahiana Phyllomedusa burmeisteri 100 89 Phyllomedusa iheringii 99 Phyllomedusa tetraploidea 71 Phyllomedusa distincta Phyllomedusa tomopterna 86 Phyllomedusa atelopoides

90 Phyllomedusa perinesos 59 100 Phyllomedusa baltea 100 Phyllomedusa duellmani Phyllomedusa palliata 70 Phyllomedusa nordestina 100 100 Phyllomedusa hypochondrialis 100 Phyllomedusa azurea Phyllomedusa megacephala 100 Phyllomedusa rohdei

100 Phyllomedusa itacolomi 63 Phyllomedusa ayeaye 100 Phyllomedusa centralis 99 Phyllomedusa araguari U 89 Phyllomedusa oreades

Fig. 2 (continued) Author's personal copy

R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 569

100 Litoria olongburensis Litoria fallax 94 Litoria bicolor 65 Litoria pronimia Litoria multiplica 76 Litoria havina 83 100 Litoria iris 78 Litoria majikthise 91 Litoria nigropunctata Litoria prora Litoria leucova Litoria modica 87 Litoria micromembrana 79 Litoria angiana 93 Litoria spartacus 67 98 Litoria wollastoni Litoria arfakiana 100 Litoria meiriana Litoria longirostris 69 Litoria dorsalis 72 86 Litoria microbelos Litoria personata Litoria nigrofrenata Hylidae cont. Litoria nasuta 100 Litoria watjulumensis 93 Litoria coplandi 100 Litoria latopalmata Litoria freycineti Litoria tornieri 93 Litoria pallida Litoria inermis Litoria burrowsi Litoria adelaidensis 58 Litoria rothii Litoria tyleri 53 Litoria peronii 100 92 Litoria darlingtoni Hylidae: 100 99 Litoria amboinensis 58 100 Litoria congenita Pelodryadinae Litoria dentata Litoria rubella 72 Litoria electrica Litoria jervisiensis Litoria ewingii 100 81 Litoria littlejohni 91 Litoria revelata 55 Litoria verreauxii 56 Litoria paraewingi 98 Litoria dux 100 Litoria infrafrenata Litoria brevipalmata Litoria kubori 89 100 Litoria narinosus Litoria zweifeli 100 100 Litoria humeralis Litoria semipalmatus 95 100 Litoria foricula 56 Litoria cheesmani 99 Litoria papua 94 Litoria pulcher 100 Litoria thesaurensis 76 54 Litoria impura Litoria dayi 91 Litoria nannotis 100 Litoria nyakalensis 93 Litoria rheocola Litoria spenceri 97 Litoria subglandulosa Litoria daviesae Litoria citropa 55 Litoria phyllochroa 100 Litoria nudidigita 95 100 Litoria barringtonensis 100 Litoria pearsoniana Litoria exophthalmia 54 Litoria eucnemis 82 Litoria genimaculata Litoria andiirrmalin Litoria lesueurii 100 Litoria booroolongensis 75 Litoria jungguy 87 Litoria wilcoxii 98 Litoria cavernicola Litoria splendida Litoria caerulea Litoria gilleni 96 Litoria kumae 100 Litoria gracilenta Litoria chloris 100 Litoria xanthomera 86 Litoria raniformis Litoria aurea 100 80 Litoria cyclorhyncha Litoria moorei 79 Litoria dahlii Litoria australis 92 100 Litoria novaehollandiae 74 Litoria platycephala Litoria verrucosa Litoria brevipes Litoria alboguttata Litoria cryptotis Litoria manya 100 Litoria cultripes 94 Litoria vagitus 74 Litoria longipes V 79 Litoria maculosa 53 Litoria maini

Fig. 2 (continued) Author's personal copy

570 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583

Myersiohyla inparquesi Myersiohyla kanaima Hylidae: 71 Hyloscirtus simmonsi Hylinae 100 Hyloscirtus colymba 98 Hyloscirtus phyllognathus Hyloscirtus palmeri 100 65 Hyloscirtus lascinius Hyloscirtus armatus 63 100 Hyloscirtus charazani Hylinae cont. Hyloscirtus tapichalaca 94 100 Hyloscirtus lindae 79 Hyloscirtus pantostictus 100 Hyloscirtus pacha Bokermannohyla martinsi 80 97 Bokermannohyla astartea 81 Bokermannohyla hylax 92 Bokermannohyla circumdata 100 Aplastodiscus albofrenatus Aplastodiscus eugenioi Aplastodiscus arildae 82 100 Aplastodiscus weygoldti 97 99 Aplastodiscus perviridis Aplastodiscus cochranae 90 Aplastodiscus albosignatus 90 Aplastodiscus callipygius 50 Aplastodiscus cavicola 100 Aplastodiscus leucopygius 76 Hypsiboas cinerascens Hypsiboas boans 100 Hypsiboas semilineatus 100 Hypsiboas geographicus Hypsiboas sibleszi Hypsiboas roraima 91 Hypsiboas microderma 100 93 Hypsiboas nympha Hypsiboas ornatissimus 99 Hypsiboas benitezi 100 Hypsiboas lemai 51 Hypsiboas picturatus Hypsiboas heilprini Hypsiboas raniceps 84 Hypsiboas fasciatus 72 100 Hypsiboas dentei Hypsiboas calcaratus Hypsiboas lanciformis 57 55 83 Hypsiboas multifasciatus 100 Hypsiboas albopunctatus Hypsiboas pellucens 100 Hypsiboas rufitelus Hypsiboas albomarginatus 94 Hypsiboas rosenbergi 99 66 Hypsiboas crepitans 65 Hypsiboas faber 90 Hypsiboas pardalis 100 Hypsiboas lundii 94 Hypsiboas ericae 100 Hypsiboas semiguttatus Hypsiboas joaquini Hypsiboas leptolineatus 100 91 100 Hypsiboas polytaenius Hypsiboas latistriatus 100 Hypsiboas balzani 100 100 Hypsiboas marianitae Hypsiboas riojanus 100 Hypsiboas andinus Hypsiboas guentheri 79 100 Hypsiboas marginatus 99 Hypsiboas bischoffi 87 Hypsiboas caingua Hypsiboas prasinus 70 100 Hypsiboas cordobae W 100 Hypsiboas pulchellus

Fig. 2 (continued) species included in our analysis are placed in a clade with Alsodes, which was previously recognized as a ceratophryid subfamily Eupsophus, and Hylorina (see below). The sister group to the clade (Telmatobiinae) by ASW and AW. Next up the tree is a moderately of Rhinodermatidae + Batrachylidae is the ceratophryid genus Tel- well supported clade (BS = 79%) consisting of two cycloramphid matobius (Fig. 2Z). We resurrect the family Telmatobiidae (Miran- genera, the cycloramphine genus Cycloramphus and the alsodine da-Ribeiro, 1920) for this strongly supported clade (containing genus Thoropa. We recognize this clade as the family Cycloramphi- only Telmatobius, which likely contains Batrachophrynus; ASW), dae (a greatly restricted version relative to current classifications). Author's personal copy

R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 571

Hylinae cont. 100 Sphaenorhynchus orophilus 97 Sphaenorhynchus lacteus Sphaenorhynchus dorisae 100 Scinax berthae Scinax catharinae 97 Scinax uruguayus Scinax acuminatus 100 100 Scinax boulengeri 95 Scinax sugillatus 52 Scinax rostratus 96 Scinax nebulosus Scinax proboscideus 97 60 65 Scinax jolyi Scinax garbei Scinax crospedospilus Scinax squalirostris 51 Scinax elaeochroa 95 88 Scinax staufferi Scinax boesemani 96 80 Scinax cruentommus 87 Scinax fuscovarius Scinax nasicus 96 100 Scinax x-signatus 100 Scinax ruber Scarthyla goinorum 76 Pseudis laevis 99 Pseudis limellum 100 Pseudis caraya Pseudis cardosoi 99 100 Pseudis minuta Pseudis fusca 54 87 94 99 Pseudis tocantins Pseudis bolbodactyla 56 80 Pseudis paradoxa Xenohyla truncata Dendropsophus allenorum Dendropsophus marmoratus 97 100 Dendropsophus seniculus 100 Dendropsophus koechlini 89 Dendropsophus parviceps 59 75 Dendropsophus brevifrons Dendropsophus giesleri 100 Dendropsophus carnifex Dendropsophus labialis 100 Dendropsophus pelidna Dendropsophus anceps Dendropsophus aperomeus Dendropsophus schubarti Dendropsophus miyatai Dendropsophus elegans Dendropsophus ebraccatus 88 Dendropsophus triangulum 97 100 Dendropsophus leucophyllatus 82 Dendropsophus sarayacuensis 83 Dendropsophus bifurcus Dendropsophus minutus 85 Dendropsophus leali Dendropsophus rhodopeplus Dendropsophus microcephalus 90 81 Dendropsophus robertmertensi 55 100 Dendropsophus sartori 94 Dendropsophus riveroi Dendropsophus walfordi 100 Dendropsophus nanus 66 Dendropsophus bipunctatus Dendropsophus berthalutzae Dendropsophus branneri Dendropsophus minusculus 73 Dendropsophus sanborni 93 Dendropsophus rubicundulus 53 Itapotihyla langsdorffii Phyllodytes auratus Corythomantis greeningi 81 Aparasphenodon brunoi 100 Nyctimantis rugiceps 100 66 91 Argenteohyla siemersi Trachycephalus jordani Trachycephalus coriaceus 100 Trachycephalus mesophaeus 84 Trachycephalus imitatrix 51 Trachycephalus nigromaculatus Trachycephalus resinifictrix 100 Trachycephalus venulosus 76 Trachycephalus hadroceps Phyllodytes luteolus Osteopilus vastus 100 Osteopilus septentrionalis Osteopilus dominicensis 65 57 Osteopilus pulchrilineatus 94 Osteopilus brunneus 53 Osteopilus crucialis 69 86 90 Osteopilus marianae Osteopilus wilderi Tepuihyla edelcae 95 Osteocephalus mutabor Osteocephalus cabrerai 90 99 Osteocephalus buckleyi Osteocephalus verruciger 100 Osteocephalus alboguttatus 97 Osteocephalus planiceps 85 Osteocephalus leprieurii X 87 Osteocephalus taurinus Hylinae cont. 100 Osteocephalus oophagus

Fig. 2 (continued) Author's personal copy

572 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583

100 Acris gryllus Hylidae cont. 90 Acris blanchardi Acris crepitans 98 100 Pseudacris cadaverina Pseudacris regilla 100 Pseudacris ocularis 97 Pseudacris crucifer 100 Pseudacris ornata 100 100 Pseudacris illinoensis Pseudacris streckeri 100 Pseudacris brachyphona 71 Pseudacris brimleyi Pseudacris fouquettei 100 100 Pseudacris clarkii 67 Pseudacris maculata Pseudacris feriarum 100 Pseudacris triseriata 52 100 Pseudacris kalmi Pseudacris nigrita 100 100 Exerodonta perkinsi 100 Exerodonta abdivita 100 Exerodonta sumichrasti Exerodonta melanomma 76 100 Exerodonta chimalapa Exerodonta smaragdina 100 64 Exerodonta xera 92 Plectrohyla glandulosa Plectrohyla chrysopleura Plectrohyla guatemalensis 68 Plectrohyla matudai 96 Plectrohyla siopela 80 Plectrohyla arborescandens Plectrohyla cyclada 56 Plectrohyla ameibothalame Plectrohyla bistincta 74 83 Plectrohyla pentheter 84 Plectrohyla calthula Ecnomiohyla minera 92 100 Ecnomiohyla miliaria 100 Ecnomiohyla miotympanum Ptychohyla spinipollex Bromeliohyla bromeliacia 88 Duellmanohyla soralia 89 Duellmanohyla rufioculis 100 Ptychohyla dendrophasma Ptychohyla hypomykter 99 100 Ptychohyla euthysanota 89 Ptychohyla leonhardschultzei 100 Ptychohyla zophodes 95 Megastomatohyla mixe 94 100 Charadrahyla taeniopus Charadrahyla nephila Tlalocohyla smithii 100 99 Tlalocohyla picta Tlalocohyla godmani 100 Tlalocohyla loquax 99 100 Isthmohyla pseudopuma 83 Isthmohyla zeteki 100 Isthmohyla tica 86 Isthmohyla rivularis 87 Triprion spatulatus 94 Triprion petasatus 84 Anotheca spinosa 100 Smilisca baudinii 98 Smilisca sila 100 Smilisca sordida 99 Smilisca fodiens 95 Smilisca cyanosticta 100 97 96 Smilisca puma Smilisca phaeota 100 Hyla chinensis 100 Hyla tsinlingensis 100 Hyla annectans Hyla meridionalis 92 Hyla sarda Hyla savignyi 100 52 Hyla arborea Hyla orientalis 92 Hyla intermedia 77 Hyla molleri 100 Hyla squirella 99 Hyla gratiosa Hyla cinerea 81 Hyla andersonii Hyla femoralis 100 61 Hyla versicolor 100 Hyla chrysoscelis 100 Hyla avivoca 98 Hyla japonica Hyla immaculata 80 Hyla arenicolor Hyla wrightorum 95 95 Hyla walkeri 96 Hyla eximia Y 83 Hyla euphorbiacea 73 Hyla plicata

Fig. 2 (continued)

The sister group to Cycloramphidae consists of Hylodidae without it. We tentatively recognize this clade as a distinct family (strongly supported as monophyletic), and a clade consisting of (Alsodidae), comprising Alsodes, Eupsophus, Hylorina, and Limnome- some of the former alsodine cycloramphid genera (Alsodes, Eupso- dusa. This is the only family that we recognize (that was not in- phus, Hylorina, Limnomedusa) and two species of the ceratophryid cluded in previous classifications) that is not strongly supported, genus Batrachyla. Support for the monophyly of this group is but we prefer this taxonomy as opposed to recognizing a mono- relatively weak (54%) including Limnomedusa but is strong (91%) typic family containing only Limnomedusa. While we generally Author's personal copy

R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 573

Ceratophrys cornuta Ceratophryidae 100 82 Chacophrys pierottii Lepidobatrachus laevis 65 Ceratophrys cranwelli 100 Ceratophrys ornata Macrogenioglottus alipioi 100 Odontophrynus carvalhoi 61 Odontophrynus cultripes 66 Odontophrynus americanus Odontophrynidae Odontophrynus occidentalis 100 99 Odontophrynus achalensis 85 Proceratophrys cristiceps Proceratophrys schirchi 57 Proceratophrys melanopogon 50 Proceratophrys appendiculata 100 Proceratophrys bigibbosa Proceratophrys avelinoi 59 Proceratophrys goyana 67 Proceratophrys concavitympanum 99 Odontophrynus moratoi Proceratophrys cururu Proceratophrys laticeps 77 99 Proceratophrys boiei Rhinodermatidae Proceratophrys renalis 96 Insuetophrynus acarpicus Rhinoderma darwinii Batrachyla leptopus 96 100 Atelognathus jeinimenensis Batrachylidae Atelognathus patagonicus 76 Telmatobius zapahuirensis Telmatobius niger Telmatobius vellardi Telmatobius truebae 100 Telmatobius espadai 85 Telmatobius verrucosus 73 71 Telmatobius sanborni 57 Telmatobius vilamensis Telmatobius marmoratus Telmatobiidae 50 Telmatobius simonsi Telmatobius sibiricus Telmatobius yuracare Telmatobius bolivianus 88 Telmatobius culeus 68 Telmatobius gigas 93 Telmatobius hintoni 96 Telmatobius huayra 100 Cycloramphus boraceiensis 79 Cycloramphus acangatan Thoropa miliaris Cycloramphidae 100 Thoropa taophora Crossodactylus caramaschii Crossodactylus schmidti 97 92 Hylodes dactylocinus Megaelosia goeldii 92 Hylodes meridionalis Hylodes perplicatus Hylodidae 54 Hylodes phyllodes Hylodes sazimai 53 Hylodes ornatus Limnomedusa macroglossa 56 Alsodes vanzolinii Alsodes nodosus 54 Alsodes australis 61 Alsodes tumultuosus 75 Alsodes gargola 68 Alsodes kaweshkari 91 Alsodes monticola Alsodidae 89 Alsodes barrioi 61 Eupsophus emiliopugini Eupsophus calcaratus Eupsophus vertebralis 97 Hylorina sylvatica 95 Batrachyla taeniata 90 Batrachyla antartandica 95 Eupsophus migueli 99 Eupsophus nahuelbutensis Eupsophus insularis 50 Eupsophus roseus Z Eupsophus contulmoensis

Fig. 2 (continued)

refrain from addressing generic-level taxonomy here, the genus Batrachyla species (Batrachyla fitzroya and Batrachyla nibaldoi)in Batrachyla represents a special case, being split between two fam- Batrachyla with the type species B. leptopus in Batrachylidae. ilies. As Batrachyla taeniata, Batrachyla antartandica, and Hylorina In summary, our new taxonomy replaces the non-monophyletic sylvatica are strongly placed within Eupsophus, we synonymize interdigitating families Ceratophryidae and Cycloramphidae with a those three species with Eupsophus. We keep the other two somewhat larger set of families that are each generally strongly Author's personal copy

574 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583

Scythrophrys sawayae Paratelmatobiinae 93 93 Paratelmatobius cardosoi Paratelmatobius poecilogaster Leiuperinae 100 Paratelmatobius gaigeae Pseudopaludicola falcipes Pleurodema brachyops 91 Pleurodema marmoratum 65 Pleurodema bufoninum 99 94 Pleurodema thaul 94 Pleurodema bibroni Edalorhina perezi 99 Engystomops pustulosus 98 Engystomops petersi 99 Engystomops freibergi 99 99 Engystomops pustulatus 94 Engystomops guayaco 100 Engystomops coloradorum 100 Engystomops montubio 98 79 100 Engystomops randi 100 Eupemphix nattereri Leptodactylidae Physalaemus signifer 100 Physalaemus albonotatus 100 Physalaemus cuvieri 100 Physalaemus ephippifer 98 80 Physalaemus biligonigerus Physalaemus riograndensis 99 Physalaemus gracilis 96 Physalaemus barrioi 93 Lithodytes lineatus Adenomera andreae 93 Adenomera hylaedactyla 54 Adenomera heyeri 93 Leptodactylus rhodomystax Leptodactylus silvanimbus 80 92 Leptodactylus chaquensis Leptodactylus ocellatus Leptodactylus leptodactyloides 100 Leptodactylus riveroi Leptodactylinae 54 Leptodactylus melanonotus Leptodactylus wagneri 69 Leptodactylus pallidirostris 100 Leptodactylus validus Leptodactylus podicipinus Leptodactylus diedrus 58 Leptodactylus discodactylus Leptodactylus griseigularis Leptodactylus rhodonotus Leptodactylus vastus Leptodactylus fallax 100 Leptodactylus labyrinthicus 95 Leptodactylus knudseni 52 Leptodactylus pentadactylus 56 Leptodactylus mystacinus Leptodactylus spixi 70 Leptodactylus elenae 84 56 Leptodactylus notoaktites 66 Leptodactylus didymus 88 Leptodactylus mystaceus Leptodactylus fuscus Leptodactylus bufonius Leptodactylus longirostris Leptodactylus albilabris 62 Leptodactylus gracilis AA 94 Leptodactylus plaumanni

Fig. 2 (continued) Author's personal copy

R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 575

Allophrynidae Allophryne ruthveni Celsiella vozmedianoi 100 Celsiella revocata Hyalinobatrachium valerioi 100 Hyalinobatrachium aureoguttatum Hyalinobatrachinae 85 62 Hyalinobatrachium bergeri 100 Hyalinobatrachium pellucidum 100 Hyalinobatrachium talamancae 70 Hyalinobatrachium chirripoi 100 98 100 Hyalinobatrachium colymbiphyllum Hyalinobatrachium iaspidiense 100 Hyalinobatrachium taylori 88 Hyalinobatrachium ignioculus 72 Hyalinobatrachium eccentricum Hyalinobatrachium crurifasciatum Hyalinobatrachium mondolfii 88 61 Hyalinobatrachium carlesvilai 82 Hyalinobatrachium tatayoi 92 Hyalinobatrachium fleischmanni 83 58 Hyalinobatrachium orientale 100 Hyalinobatrachium fragile Centrolenidae 95 Hyalinobatrachium orocostale 93 Hyalinobatrachium duranti 100 Hyalinobatrachium pallidum 99 Hyalinobatrachium ibama Ikakogi tayrona Vitreorana eurygnatha 50 Vitreorana antisthenesi 95 96 Vitreorana castroviejoi Vitreorana gorzulae Vitreorana oyampiensis 66 100 Vitreorana helenae 100 Teratohyla pulverata 50 Teratohyla midas 99 Teratohyla spinosa Cochranella litoralis 70 100 Cochranella nola Centroleninae Cochranella granulosa 96 Cochranella mache 100 Cochranella euknemos Chimerella mariaelenae 76 61 Espadarana andina 100 Espadarana callistomma 96 Espadarana prosoblepon Sachatamia ilex 100 100 Sachatamia punctulata Sachatamia albomaculata 60 85 88 Rulyrana flavopunctata Rulyrana spiculata 100 Rulyrana susatamai 97 Rulyrana adiazeta Centrolene grandisonae 57 Nymphargus mixomaculatus 90 Nymphargus pluvialis 100 84 80 Nymphargus bejaranoi Nymphargus posadae Nymphargus griffithsi Nymphargus wileyi 98 Nymphargus cochranae 76 Nymphargus puyoensis 81 Nymphargus rosadus 80 89 85 Nymphargus megacheirus Nymphargus siren 100 Centrolene daidaleum Centrolene savagei 100 Centrolene peristictum 100 Centrolene antioquiense Centrolene geckoideum 61 Centrolene bacatum 95 Centrolene hybrida 100 Centrolene pipilatum 86 Centrolene venezuelense 83 Centrolene hesperium 89 Centrolene buckleyi AB 67 Centrolene notostictum 99 Centrolene altitudinale

Fig. 2 (continued) supported. However, we acknowledge that the family-level place- genera and the apparent problems in the previous taxonomy ment of the cycloramphid genera Rupirana (no subfamily assigned (Figs. 1 and 2Z). Assuming that they are cycloramphids as the fam- by AW or ASW), Zachaenus, and Crossodactylodes (both previously ily is defined here (Figs. 1 and 2; Appendix B) may be incorrect. Cycloramphinae; AW; ASW) are uncertain in our classification We also find that the currently recognized families Leiuperidae (Hyloidea incertae sedis), given the lack of molecular data for these and Leptodactylidae are also problematic (Fig. 2AA). Our results Author's personal copy

576 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583

Rheobates palmatus 98 Anomaloglossus stepheni 100 Anomaloglossus baeobatrachus Anomaloglossus tepuyensis Anomaloglossus degranvillei 100 87 Anomaloglossus praderioi 100 64 Anomaloglossus roraima 100 Anomaloglossus beebei 50 100 Aromobates saltuensis Aromobates nocturnus 99 100 Mannophryne herminae 100 Mannophryne trinitatis Mannophryne venezuelensis Allobates undulatus 100 Allobates talamancae Allobates brunneus 100 Allobates nidicola Allobates zaparo 99 100 Allobates femoralis 91 Allobates juanii Allobates gasconi 88 Allobates caeruleodactylus 85 Allobates trilineatus 83 Allobates conspicuus 77 Silverstoneia nubicola Silverstoneia flotator 100 Epipedobates boulengeri Dendrobatidae 100 Epipedobates espinosai 100 59 Epipedobates machalilla 87 Epipedobates anthonyi 95 Epipedobates tricolor 100 Colostethus latinasus 100 100 Colostethus pratti Colostethus imbricolus 100 Colostethus inguinalis 97 Colostethus panamansis 98 85 Colostethus fraterdanieli 100 Colostethus fugax Colostethus argyrogaster 83 Ameerega altamazonica Ameerega simulans 100 Ameerega silverstonei 97 Ameerega flavopicta Ameerega braccata Ameerega bassleri 85 Ameerega bilinguis Ameerega parvula 82 Ameerega pongoensis Ameerega trivittata Ameerega pulchripecta Ameerega hahneli 88 Ameerega picta Ameerega macero 97 Ameerega rubriventris 89 Ameerega smaragdina Ameerega cainarachi 86 Ameerega petersi 57 Hyloxalus subpunctatus Hyloxalus leucophaeus 80 100 Hyloxalus sordidatus Hyloxalus maculosus 100 Hyloxalus bocagei 99 Hyloxalus sauli 99 Hyloxalus vertebralis 100 Hyloxalus pulchellus 100 Hyloxalus delatorreae Hyloxalus anthracinus Hyloxalus pulcherrimus 100 100 Hyloxalus sylvaticus Hyloxalus nexipus 100 Hyloxalus azureiventris Hyloxalus chlorocraspedus 91 Hyloxalus idiomelus 100 Hyloxalus insulatus 65 Hyloxalus elachyhistus 80 Hyloxalus infraguttatus 71 100 Hyloxalus toachi 100 Hyloxalus awa 100 Phyllobates vittatus 100 Phyllobates lugubris Phyllobates bicolor 100 Phyllobates aurotaenia 75 Phyllobates terribilis 62 Dendrobates steyermarki 72 Dendrobates quinquevittatus Dendrobates castaneoticus 70 Dendrobates galactonotus Dendrobates truncatus 100 71 100 Dendrobates auratus 100 Dendrobates tinctorius 96 Dendrobates leucomelas Dendrobates granuliferus 98 Dendrobates histrionicus 100 Dendrobates sylvaticus 94 Dendrobates lehmanni 61 Dendrobates arboreus 57 Dendrobates speciosus 99 95 Dendrobates vicentei 95 Dendrobates pumilio Dendrobatescaptiv us 84 Dendrobates mysteriosus 100 Dendrobates virolinensis Dendrobates bombetes 100 Dendrobates fulguritus 72 81 Dendrobates minutus 100 Dendrobates claudiae Dendrobates lamasi 58 89 100 Dendrobates biolat Dendrobates flavovittatus 84 Dendrobates imitator 93 Dendrobates vanzolinii 64 Dendrobates fantasticus Dendrobates duellmani 85 Dendrobates reticulatus 69 Dendrobates uakarii Dendrobates amazonicus AC Dendrobates variabilis 59 Dendrobates ventrimaculatus

Fig. 2 (continued) Author's personal copy

R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 577

100 Melanophryniscusrubriv entris Melanophryniscus stelzneri 100 Melanophryniscus klappenbachi Atelopus seminiferus Atelopus pulcher Bufonidae 100 100 Atelopus spumarius Atelopus franciscus 100 100 Atelopus flavescens Atelopus peruensis 96 100 Atelopus halihelos Atelopus ignescens 100Atelopus bomolochos 100 Atelopus longirostris Atelopus spurrelli 70 98 Atelopus chiriquiensis 100 90 Atelopus zeteki 81 Atelopus varius 100 Atelopus senex 100 Osornophryne sumacoensis Osornophryne guacamayo Osornophryne puruanta 61 99 Osornophryne antisana 73 Osornophryne bufoniformis Dendrophryniscus minutus 75 94 Bufo variegatus Bufo cophotis 100 Bufo lemur Bufo guentheri Bufo longinasus 90 95 Bufo gundlachi Bufo taladai Bufo empusus 66 Bufo fustiger 61 Bufo peltocephalus 100 99 Bufo nasicus Bufo haematiticus 100 Bufo glaberrimus 72 Bufo guttatus Bufo limensis 87 100 Bufo vellardi Bufo spinulosus 100 Bufo arequipensis 74 Bufo atacamensis 100 100 Bufo arunco Bufo granulosus 67 Bufo beebei 63 73 Bufo poeppigii Bufo marinus 100 Bufo schneideri 99 Bufo achavali Bufo crucifer 64 Bufo arenarum 54 78 Bufo ictericus Bufo veraguensis 100 Bufo amboroensis Bufo ocellatus 100 Bufo castaneoticus 100 64 Bufo dapsilis 75 Bufo margaritifer 61 100 Rhamphophryne festae 70 76 Rhamphophryne macrorhina 83 Rhamphophryne rostrata 100 Bufo chavin 53 Bufo nesiotes 99 Bufo manu Bufo bocourti Bufo alvarius 64 58 Bufo occidentalis 95 Bufo tacanensis 100 Bufo canaliferus Bufo marmoreus 95 90 Bufo fastidiosus Bufo coniferus 100 100 Bufo coccifer Bufo cycladen 65 84 Bufo ibarrai Bufo melanochlorus 100 Bufo luetkenii 90 Bufo mazatlanensis 100 Bufo nebulifer Bufo valliceps 100 Bufo campbelli 100 Bufo macrocristatus 84 Bufo nelsoni Bufo boreas 100 Bufo exsul 99 77 Bufo canorus Bufo punctatus Bufo quercicus 100 Bufo cognatus 100 97 Bufo debilis 100 Bufo retiformis 72 Bufo speciosus Bufo californicus 70 Bufo microscaphus 100 67 Bufo terrestris 89 Bufo fowleri 99 Bufo woodhousii 100 Bufo baxteri 100 Bufo hemiophrys AD 100 Bufo americanus Bufonidae cont. 97 Bufo houstonensis

Fig. 2 (continued) Author's personal copy

578 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583

Bufo angusticeps 100 Bufo inyangae Bufo amatolicus Bufonidae cont. Bufo robinsoni 56 Bufo gariepensis 89 Bufo fenoulheti Bufo dombensis 100 Bufo damaranus 100 Bufo uzunguensis Bufo taitanus 99 Mertensophryne micranotis Bufo lindneri 84 100 Stephopaedes anotis 100 Stephopaedes loveridgei Capensibufo tradouwi 99 Capensibufo rosei Bufo mauritanicus Bufo steindachneri 80 100 Bufo pardalis Bufo pantherinus 96 81 Bufo poweri Bufo brauni 57 Bufo lemairii 82 Bufo regularis Bufo maculatus 55 Bufo vertebralis Bufo latifrons 91 Bufo tuberosus 91 Bufo camerunensis Bufo kisoloensis 82 Bufo gracilipes 100 Bufo gutturalis 100 Bufo garmani Bufo xeros Werneria mertensiana 89 Wolterstorffina parvipalmata Nectophryne afra 100 Nectophryne batesii Leptophryne borbonica Bufo calamita Bufo raddei Bufo verrucosissimus 100 Bufo bufo Bufo tuberospinius 100 98 Bufo cryptotympanicus 73 Bufo aspinius 100 Bufo gargarizans 97 Bufo bankorensis 100 Bufo torrenticola 81 Bufo japonicus Bufo stejnegeri Bufo tuberculatus 97 Bufo tibetanus Bufo asper 98 100 Bufo juxtasper Pedostibes rugosus 90 Pedostibes hosii Sabahphrynus maculatus 90 Bufo biporcatus 100 Bufo divergens Bufo celebensis 52 Bufo macrotis 68 Bufo philippinicus Bufo galeatus Ansonia ornata Didynamipus sjostedti 100 Pelophryne misera 92 Pelophryne brevipes Pelophryne signata 70 Ansonia fuliginea 60 94 Ansonia muelleri 100 Ansonia leptopus Ansonia longidigita 98 Ansonia malayana Ansonia spinulifer 94 Ansonia hanitschi 97 74 Ansonia platysoma Ansonia minuta Pedostibes tuberculosus Schismaderma carens 91 Bufo boulengeri Bufo siculus 55 Bufo oblongus 100 Bufo pewzowi 81 Bufo balearicus Bufo viridis 59 Bufo variabilis Churamiti maridadi 98 Nectophrynoides viviparus 100 Nectophrynoides tornieri 95 Nectophrynoides minutus Bufo brongersmai Adenomus kelaartii Bufo koynayensis 59 Bufo dhufarensis 99 100 Bufo hololius 97 Bufo stomaticus 73 Bufo crocus Bufo stuarti 98 Bufo himalayanus 62 100 Bufo scaber 100 Bufo atukoralei AE 99 Bufo melanostictus 100 Bufo brevirostris 55 Bufo parietalis

Fig. 2 (continued) Author's personal copy

R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 579

(Fig. 2AA) show that Leptodactylidae is paraphyletic with respect 2008; Van Bocxlaer et al., 2009), Allophrynidae and Centrolenidae. to Leiuperidae, given that the leptodactylid genera Paratelmatobius Within Centrolenidae (Fig. 2AB), we support the subfamilies Cen- and Scythrophrys are more closely related to leiuperids than they troleninae and Hyalinobatrachinae, and we place the previously are to other leptodactylids (although this is not strongly sup- incertae sedis genus Ikakogi in Centroleninae with strong (70%) ported). We solve this taxonomic problem by expanding Leptodac- bootstrap support. We do not recognize a family Aromobatidae tylidae to again include all leiuperid genera, and recognizing separate from Dendrobatidae, as there is no phylogenetic justifica- Leiuperinae and Leptodactylinae as subfamilies. This arrangement tion for splitting Dendrobatidae (Fig. 2AC). We follow Santos et al. treats Leptodactylidae as the strongly supported clade (BS = 79%) (2009) in recognizing a single family Dendrobatidae, including the of mostly foam-nesting frogs that has long been recognized as former aromobatids and containing no subfamilies (see also AW). behaviorally and morphologically distinctive (as the leptodactyline Our higher-level phylogeny within Ranoidea is generally similar leptodactylids; Lynch, 1971; Duellman and Trueb, 1994). We con- to other recent estimates (e.g., Frost et al., 2006; Roelants et al., 2007; sider this preferable to recognizing a new family for Paratelmatobi- Wiens, 2011), and many of these relationships are well supported in us and Scythrophrys, genera for which we recognize a new our study and previous studies (e.g., among brevicipitids, hemisot- subfamily (Paratelmatobiinae subfam. nov.; Appendix A), to avoid ids, microhylids, hyperoliids, arthroleptids). Our results also support a paraphyletic Leptodactylinae. current delimitation of subfamilies (Figs. 1 and 2H–I; see Appendix According to our results, the family Strabomantidae (sensu AW, B) in Microhylidae (van der Meijden et al., 2007) and Arthroleptidae ASW) is also paraphyletic (Fig. 2R). Strabomantidae is a recently (including Astylosterninae; see ASW). Some previous taxonomies described family (Hedges et al., 2008) that includes many species (e.g., Bossuyt et al., 2006; Wiens et al., 2009) and current taxonomies that were traditionally classified as Eleutherodactylus (in the family (including AW) recognize a large (>1400 species) family Ranidae Leptodactylidae; see ASW). Specifically, we find that the strabo- (with 13 subfamilies) as the sister group to all other ranoids. Other mantid genera Hypodactylus and Strabomantis are more closely re- recent authors have considered these subfamilies distinct families lated to craugastorids (Haddadus, Craugastor) than they are to the (Bossuyt and Roelants, 2009; Frost et al., 2006; Roelants et al., other sampled strabomantid genera (e.g., Barycholos, Bryophryne, 2007). We follow this latter arrangement here, recognizing the fam- Holoaden, Lynchius, Noblella, Oreobates, Phrynopus, Pristimantis, ilies Ptychadenidae, Micrixalidae, Phrynobatrachidae, Conrauidae, Psychrophrynella). To resolve this problem (and to reduce the pro- Petropedetidae, Pyxicephalidae, Nyctibatrachidae, Ceratobatrachi- liferation of terraranan families), we subsume Strabomantidae into dae, Ranixalidae, Dicroglossidae, Ranidae, and Rhacophoridae, and Craugastoridae, given that Craugastoridae occurs first in Hedges Mantellidae, all of which are strongly supported (Figs. 1 and 2J–O). et al. (2008), though we recognize that this is an arbitrary criterion. Within these families, subfamilies follow Frost (2011): within Pyxi- Within Craugastoridae, we recognize a subfamily Craugastorinae cephalidae, we recognize Cacosterninae and Pyxicephalinae; (Fig. 2R) that corresponds to the previously recognized family Dicroglossidae comprises Occidozyginae and Dicroglossinae; Rhac- (e.g., Hedges et al., 2008; AW, ASW). ophoridae consists of Buergeriinae and Rhacophorinae; and Mantel- The former members of Strabomantidae are apportioned among lidae is composed of Laliostominae, Boophinae, and Mantellinae three strongly supported clades (which we recognize as subfamilies (Figs. 1 and 2J–O). Relationships among many of these families re- within Craugastoridae) and one weakly supported clade (which we main poorly supported, as in previous studies (Roelants et al., consider incertae sedis). One of the strongly supported clades con- 2007; Wiens et al., 2009). Given the extensive sampling of taxa in sists solely of the genus Strabomantis, for which we recognize this clade, resolving their relationships may instead require adding a restricted subfamily Strabomantinae (Appendix B). Another com- many more characters (i.e., more genes). prises the genera Barycholos, Bryophryne, Holoaden, Noblella, and Psychrophrynella, for which we use the previously recognized sub- family Holoadeninae (e.g., ASW). The third strongly supported clade 4. Discussion comprises the genera Lynchius, Oreobates, Phrynopus, and Pristiman- tis. We recognize this clade as a new subfamily, Pristimantinae sub- 4.1. Systematics of extant lissamphibians fam. nov. (see Appendix A for formal definition). The weakly supported clade is the genus Hypodactylus. Rather than recognizing Here, we provide a large-scale estimate of amphibian phylogeny, a new subfamily for this genus (or allowing it to render other sub- containing over 2800 species (42% of the known extant diversity). families non-monophyletic), we consider this genus incertae sedis, This phylogeny is largely congruent with those of several recent along with several other genera of the former Strabomantidae that molecular analyses (Frost et al., 2006; Roelants et al., 2007; Wiens, were not included in this (or other molecular phylogenies), includ- 2007a, 2011). Nevertheless, our increased sampling of taxa and ing Atopophrynus, Dischiodactylus, Geobatrachus, Mucubatrachus, characters (especially among former leptodactylid frogs) reveals Niceforonia, and Paramophrynella. In theory, some of these closely re- that several currently recognized families are not monophyletic as lated subfamilies could be combined (e.g., Craugastorinae and Strab- currently delimited (i.e., Ceratophryidae, Cycloramphidae, Lepto- omantinae or Holoadeninae and Pristimantinae), but the resulting dactylidae, Strabomantidae). To correct these problems, we present subfamilies would then not be strongly supported. a new classification of extant amphibians. We have been as conser- As in most previous studies (Darst and Cannatella, 2004; Roe- vative as possible in our taxonomic changes, such that deviations lants et al., 2007; Wiens, 2007a, 2011), we find strong support from current taxonomy are made only when necessitated by non- for monophyly of Hyloidea, but relationships among the families monophyly of higher taxa, and in such a way that newly recognized are weakly supported (Figs. 1 and 2P-AE). Therefore, we do not taxa are strongly supported (with the exception of Alsodidae as de- present extensive comparison of among-family relationships be- scribed above). It is possible that future phylogenies might reveal tween our study and previous studies. Nevertheless, there are some of our changes to be unnecessary (e.g., in cases where there some intriguing patterns that occur in multiple studies, such as was weak support for non-monophyly of families, future analyses placement of bufonids with dendrobatids (e.g., this study, Frost might strongly resolve them as monophyletic). However, by focus- et al., 2006; Roelants et al., 2007; Wiens, 2011). We also corrobo- ing on only strongly supported clades, the higher taxa that we recog- rate the monophyly and current composition of Brachycephalidae nize should not be misleading, even as new data are added. We are (Hedges et al., 2008), Hemiphractidae (Wiens et al., 2007a,b; also conservative in that we only address taxonomy at the subfamily Wiens, 2011), Hylidae (with subfamilies Hylinae, Phyllomedusinae, level and above, given that our sampling of genera is mostly com- and Pelodryadinae; Wiens et al., 2010), Bufonidae (Pramuk et al., plete whereas our sampling of species is not. Nevertheless, our study Author's personal copy

580 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 corroborates previous studies showing the paraphyly of numerous Acknowledgments genera (e.g., Bufo, Rana) and shows many additional genera to be non-monophyletic (e.g., Batrachyla). Importantly, our study also We thank the many researchers who made this study possible provides a framework to which additional sequences can be readily through their detailed studies of amphibian phylogeny with a (mostly) added. Our data matrix is available at Dryad repository doi:10.5061/ shared set of molecular markers, and uploading their sequence data to dryad.vd0m7. It should thus be relatively straightforward to add GenBank. We would like to thank F.T. Burbrink (CUNY-CSI), J. Lom- more taxa to this tree. bardo (CUNY-CSI), and T.J. Guiher (CUNY-CSI) for computational assis- tance, and D.R. Frost (AMNH) and A.M. Bauer (Villanova) for advice on taxonomy. This research was supported in part by US National Science 4.2. Supermatrices and large-scale phylogenetic inference Foundation grants to R.A.P. (DBI-0905765), J.J.W. (EF 0334923), and the CUNY HPCC (CNS-0958379 and CNS-0855217). We would like to thank This analysis corroborates several recent studies suggesting that A. Larson, and two anonymous reviewers for helpful comments that the supermatrix approach is a powerful strategy for large-scale substantially improved this manuscript. phylogenetic inference (e.g., Driskell et al., 2004; McMahon and Sanderson, 2006; Thomson and Shaffer, 2010; Pyron et al., 2011; Appendix A. Description of new subfamilies Wiens et al., 2005b). For example, even though each taxon had (on average) 80% missing data, we found that most species were placed in the families and genera expected based on previous tax- Pristimantinae subfam. nov. (family Craugastoridae) onomy, often with very strong support. In cases where we found Type: genus and species Pristimantis galdi Jiménez de la that currently recognized families were not monophyletic, this Espada, 1870. was not due to species being randomly placed on the tree, but Content: four genera, >465 species; Lynchius, Oreobates, rather due to differences in the placement of strongly supported Phrynopus, Pristimantis. clades of species and genera. Moreover, all of our 67 families and Phylogenetic Definition: this subfamily consists of the most all but two of the 50 subfamilies are strongly supported. recent common ancestor of Lynchius, Oreobates, Phrynopus, Despite the overall strong support for most of the tree (i.e., 64% and Pristimantis, and all descendants thereof. of all nodes have BS >70), certain clades remain poorly supported. Distribution: these frogs are primarily restricted to the Andes Therefore, a potential criticism of the supermatrix approach is that and Amazon Basin of South America (Hedges et al., 2008). this poor support may have arisen due to missing data in many Remarks: The four genera of this subfamily are grouped with taxa. However, several lines of evidence suggest that this is not strong support (81% BS proportion; Fig. 2R), and we find the case. First, many previous studies have shown that there is typ- weak support for their placement as the sister group to ically little relationship between the support for clades and the Holoadeninae (Fig. 2R). amount of missing data in the included species (e.g., Pyron et al., 2011; Wiens et al., 2005b, and for an analysis of multiple datasets Paratelmatobiinae subfam. nov. (family Leptodactylidae) see Wiens and Morrill, 2011). Second, we find that most of the Type: genus and species Paratelmatobius lutzii Lutz and clades that are weakly supported in our study are also weakly sup- Carvalho 1958. ported in other studies that have more limited missing data (and Content: two genera, eight species; Paratelmatobius and the same is true for strongly supported clades). For example, in Scythrophrys. their study of extant amphibian phylogeny based on multiple nu- Phylogenetic Definition: this subfamily consists of the most clear and mitochondrial genes (with little missing data), Roelants recent common ancestor of Paratelmatobius and et al. (2007) showed weak support for relationships among hyloid Scythrophrys, and all descendants thereof. families, microhylid subfamilies, and the families of former ranids, Distribution: these frogs are primarily restricted to southern but strong support for relationships among the major clades of and eastern Brazil (AW; ASW). frogs, salamanders, and caecilians. These same patterns of weak Remarks: The two genera of this subfamily are grouped with and strong support appear in our study (Fig. 1). Previous studies strong support (93% BS proportion), and we find weak suggest that these patterns of support are more likely to reflect support for placing them as the sister group of Leiuperinae underlying branch lengths, such as weak support for short (Fig. 2AA). branches (Wiens et al., 2008), rather than impacts of missing data. Our results and those of other studies suggest that extensive missing data need not be an impediment to constructing large- Appendix B. Generic content of families and subfamilies scale phylogenies with the supermatrix approach. Nevertheless, one aspect of our sampling design may have greatly facilitated The list below accounts for all extant amphibian genera currently the integration of the different genes used in this study. Specifi- recognized by AW and ASW, with family and subfamily classification cally, 90% of the species had sequence data for the 16S gene and updated to reflect our phylogenetic estimate and taxonomic changes. 81% had data for 12S. Thus, most species had comparable data The 72 genera not sampled in our phylogeny are either included in for at least one gene, which may have greatly facilitated placing their previously delimited groups (when these were found to be them on the tree with only a limited amount of character data strongly supported), or considered incertae sedis (along with any (Wiens et al., 2005b). Although it is possible to reconstruct a phy- sampled taxa explicitly delimited as such) when their placement logeny when missing and non-missing data are randomly distrib- was ambiguous due to non-monophyly of previously recognized uted among characters, the number of genes and characters higher taxa. As noted above, Lissamphibia also contains numerous required to obtain accurate phylogenies may be much higher than extinct taxa, including gymnophionans, caudates, and anurans, when the non-missing data are all in the same characters (e.g., which are not considered here (Marjanovic´ and Laurin, 2007). Wiens, 2003). A clear lesson for future studies is that adding taxa to this large-scale phylogeny will be greatly facilitated if research- B.1. Gymnophiona ers include these same 12S and 16S genes, along with widely sam- pled nuclear genes such as RAG-1. Increasing sampling of the other Caeciliidae: incertae sedis: (Atretochoana, Brasilotyphlus, Idiocra- nuclear genes may be advantageous as well. nium, Indotyphlus, Microcaecilia, Mimosiphonops, Nectocaecilia, Par- Author's personal copy

R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 581 vicaecilia, Potomotyphlus, Sylvacaecilia); Caeciliinae (Caecilia, Nanorana, Paa, Sphaerotheca), Occidozyginae (Ingerana, Occidozyga); Chthonerpeton, Dermophis, Gegeneophis, Geotrypetes, Grandisonia, Discoglossidae: Discoglossus; Eleutherodactylidae: Eleutherodac- Gymnopis, Hypogeophis, Luetkenotyphlus, Oscaecilia, Praslinia, tylinae (Diasporus, Eleutherodactylus), Phyzelaphryninae (Adeloph- Typhlonectes, Schistometopum, Siphonops), Herpelinae (Herpele, ryne, Phyzelaphryne); Heleophrynidae: Hadromophryne, Boulengerula), Scolecomorphinae (Crotaphotrema, Scolecomorphus); Heleophryne; Hemiphractidae: Cryptobatrachus, Flectonotus, Gas- Ichthyophiidae: Caudacaecilia, Ichthyophis, Uraeotyphlus; Rhinatr- trotheca, Hemiphractus, Stefania; Hemisotidae: Hemisus; Hylidae: ematidae: Epicrionops, Rhinatrema. Hylinae (Acris, Anotheca, Aparasphenodon, Aplastodiscus, Argenteohyla, Bokermannohyla, Bromeliohyla, Charadrahyla, Corytho- B.2. Caudata mantis, Dendropsophus, Diaglena, Duellmanohyla, Ecnomiohyla, Exer- odonta, Hyla, Hyloscirtus, Hypsiboas, Isthmohyla, Itapotihyla, Ambystomatidae: Ambystoma; Amphiumidae: Amphiuma; Megastomatohyla, Myersiohyla, Nyctimantis, Osteocephalus, Osteopi- Cryptobranchidae: Andrias, Cryptobranchus; Dicamptodontidae: lus, Phyllodytes, Plectrohyla, Pseudacris, Pseudis, Ptychohyla, Scarthyla, Dicamptodon; Hynobiidae: Batrachuperus, Hynobius, Liua, Onycho- Scinax, Smilisca, Sphaenorhynchus, Tepuihyla, Tlalocohyla, Trachy- dactylus, Pachyhynobius, Paradactylodon, Protohynobius, Pseudohyno- cephalus, Triprion, Xenohyla), Pelodryadinae (Litoria), Phyllomedusi- bius, Ranodon, Salamandrella; Plethodontidae: Bolitoglossinae nae (Agalychnis, Cruziohyla, Hylomantis, Pachymedusa, Phasmahyla, (Batrachoseps, Bolitoglossa, Bradytriton, Chiropterotriton, Cryptotriton, Phrynomedusa, Phyllomedusa); Hylodidae: Crossodactylus, Hylodes, Dendrotriton, Ixalotriton, Lineatriton, Nototriton, Nyctanolis, Oedipina, Megaelosia; Hyperoliidae: Acanthixalus, Afrixalus, Alexteroon, Arl- Parvimolge, Pseudoeurycea, Thorius), Hemidactylinae (Hemidactyli- equinus, Callixalus, Chlorolius, Chrysobatrachus, Cryptothylax, Heterix- um), Plethodontinae (Aneides, Desmognathus, Ensatina, Hydromantes, alus, Hyperolius, Kassina, Kassinula, Morerella, Opisthothylax, Karsenia, Phaeognathus, Plethodon), Spelerpinae (Eurycea, Gyrinophi- Paracassina, Phlyctimantis, Semnodactylus, Tachycnemis; Leiopel- lus, Haideotriton, Pseudotriton, Stereochilus, Urspelerpes); Proteidae: matidae: Leiopelma; Leptodactylidae: Leptodactylinae (Adenomera, Necturus, Proteus; Rhyacotritonidae: Rhyacotriton; Salamandri- Hydrolaetere, Leptodactylus, Lithodytes), Leiuperinae (Edalorhina, dae: Pleurodelinae (Calotriton, Cynops, Echinotriton, Euproctus, Engystomops, Eupemphix, Physalaemus, Pleurodema, Pseudopaludico- Ichthyosaura, Laotriton, Lissotriton, Neurergus, Notophthalmus, la, Somuncuria), Paratelmatobiinae (Paratelmatobius, Scythrophrys); Ommatotriton, Pachytriton, Paramesotriton, Pleurodeles, Taricha, Trit- Mantellidae: Boophinae (Boophis), Laliostominae (Aglyptodactylus, urus, Tylototriton), Salamandrinae (Chioglossa, Lyciasalamandra, Mer- Laliostoma), Mantellinae (Blommersia, Boehmantis, Gephyromantis, tensiella, Salamandra), Salamandrininae (Salamandrina); Sirenidae: Guibemantis, Mantella, Mantidactylus, Spinomantis, Tsingymantis, Siren, Pseudobranchus. Wakea); Megophryidae: Borneophrys, Brachytarsophrys, Leptobrach- ella, Leptobrachium, Leptolalax, Megophrys, Ophryophryne, Oreolalax, B.3. Anura Scutiger, Vibrissaphora, Xenophrys; Micrixalidae: Micrixalus; Micro- hylidae: incertae sedis (Gastrophrynoides, Paramophrynella), Incertae sedis in Hyloidea (Crossodactylodes, Rupirana, Asterophryninae (Albericus, Aphantophryne, Asterophrys, Austrocha- Zachaenus). perina, Barygenys, Callulops, Choerophryne, Cophixalus, Copiula, Geny- Allophrynidae: Allophryne; Alsodidae: Alsodes, Eupsophus, Lim- ophryne, Hylophorbus, Liophryne, Mantophryne, Oreophryne, nomedusa; Alytidae: Alytes; Arthroleptidae: Arthroleptinae (Athro- Oxydactyla, Pherohapsis, Sphenophryne, Xenorhina), Cophylinae leptis, Cardioglossa), Astylosterninae (Astylosternus, Leptodactylodon, (Anodonthyla, Cophyla, Madecassophryne, Platypelis, Plethodontohyla, Nyctibates, Scotobleps, Trichobatrachus), Leptopelinae (Leptopelis); Rhombophryne, Stumpffia), Dyscophinae (Dyscophus), Gastrophryni- Ascaphidae: Ascaphus; Batrachylidae: Atelognathus, Batrachyla; nae (Adelastes, Altigius, Arcovomer, Chiasmocleis, Ctenophryne, Dasy- Bombinatoridae: Barbaroula, Bombina; Brachycephalidae: Brachy- pops, Dermatonotus, Elachistocleis, Gastrophryne, Hamptophryne, cephalus, Ischnocnema; Brevicipitidae: Balebreviceps, Breviceps, Hyophryne, Hypopachus, Melanophryne, Myersiella, Nelsonophryne, Callulina, Probreviceps, Spelaeophryne; Bufonidae: Adenomus, Altiph- Relictivomer, Stereocyclops, Syncope), Hoplophryninae (Hoplophryne, rynoides, Andinophryne, Ansonia, Atelopus, Bufo, Bufoides, Capensi- Parhoplophryne), Kalophryninae (Kalophrynus), Melanobatrachinae bufo, Churamiti, Crepidophryne, Dendrophryniscus, Didynamipus, (Melanobatrachus), Microhylinae (Calluella, Chaperina, Glyphoglos- Frostius, Laurentophryne, Leptophryne, Melanophryniscus, Merten- sus, Kaloula, Metaphrynella, Microhyla, Micryletta, Ramanella, Uper- sophryne, Metaphryniscus, Nectophryne, Nectophrynoides, Nimbaph- odon), Otophryninae (Otophryne, Synapturanus), Phrynomerinae rynoides, Oreophrynella, Osornophryne, Parapelophryne, Pedostibes, (Phrynomantis), Scaphiophryne (Paradoxophyla, Scaphiophryne); Pelophryne, Pseudobufo, Rhamphophryne, Sabahphrynus, Schismader- Myobatrachidae: Limnodynastinae (Adelotus, Heleioporus, Lechrio- ma, Spinophrynoides, Stephopaedes, Truebella, Werneria, Wolterstorffi- dus, Limnodynastes, Mixophyes, Neobatrachus, Notaden, Philoria, na; Calyptocephalellidae: Calyptocephalella, Telmatobufo; Platyplectrum, Pseudophryne), Myobatrachinae (Arenophryne, Assa, Centrolenidae: Centroleninae (Centrolene, Chimerella, Cochranella, Crinia, Geocrinia, Metacrinia, Myobatrachus, Paracrinia, Rheobatra- Espadarana, Ikakogi, Nymphargus, Rulyrana, Sachatamia, Teratohyla, chus, Spicospina, Taudactylus, Uperoleia); Nasikabatrachidae: Nasik- Vitreorana), Hyalinobatrachinae (Celsiella, Hyalinobatrachium); Cer- abatrachus; Nyctibatrachidae: Lankanectes, Nyctibatrachus; atobatrachidae: Batrachylodes, Ceratobatrachus, Discodeles, Inger- Odontophrynidae: Macrogenioglottus, Odontophrynus, Proceratoph- ana, Palmatorappia, Platymantis; Ceratophryidae: Ceratophrys, rys; Pelobatidae: Pelobates; Pelodytidae: Pelodytes; Petropedeti- Chacophrys, Lepidobatrachus; Ceuthomantidae: Ceuthomantis; Con- dae: Petropedetes; Phrynobatrachidae: Phrynobatrachus; Pipidae: rauidae: Conraua; Craugastoridae: incertae sedis (Atopophrynus, Hymenochirus, Pipa, Pseudhymenochirus, Silurana, Xenopus; Ptycha- Dischiodactylus, Geobatrachus, Hypodactylus, Mucubatrachus, Nicef- denidae: Hildebrandtia, Lanzarana, Ptychadena; Pyxicephalidae: oronia, Paramophrynella), Craugastorinae (Craugastor, Haddadus), Cacosterninae (Amietia, Anhydrophryne, Arthroleptella, Cacosternum, Holoadeninae (Barycholos, Bryophryne, Euparkerella, Holoaden, Ericabatrachus, Microbatrachella, Natalobatrachus, Nothophryne, Noblella, Psychrophrynella), Pristimantinae (Lynchius, Oreobates, Poyntonia, Strongylopus, Tomopterna), Pyxicephalinae (Aubria, Phrynopus, Pristimantis), Strabomantinae (Strabomantis); Cycloram- Pyxicephalus); Ranidae: Amnirana, Amolops, Huia, Hylarana, Meris- phidae: Cycloramphus, Thoropa; Dendrobatidae: Allobates, Ameere- togenys, Odorrana, Pseudoamolops, Pterorana, Rana, Staurois; Ranix- ga, Anomaloglossus, Aromobates, Colostethus, Dendrobates, alidae: Indirana; Rhacophoridae: Buergeriinae (Buergeria), Epipedobates, Hyloxalus, Mannophryne, Phyllobates, Rheobates, Rhacophorinae (Chiromantis, Dendrobatorana, Feihyla, Ghatixalus, Silverstoneia; Dicroglossidae: Dicroglossinae (Chaparana, Chirixalus, Gracixalus, Kurixalus, Liuixalus, Nyctixalus, Philautus, Polypedates, Euphlyctis, Fejervarya, Hoplobatrachus, Limnonectes, Nannophrys, Rhacophorus, Theloderma), Rhinodermatidae: Insuetophrynus, Author's personal copy

582 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583

Rhinoderma; Rhinophrynidae: Rhinophrynus; Scaphiopodidae: expanded direct-developing clade revealed by molecular phylogeny. Zootaxa Scaphiopus, Spea; Sooglossidae: Sechellophryne, Sooglossus; Telma- 2211, 1–35. Hugall, A.F., Foster, R., Lee, M.S.Y., 2007. Calibration choice, rate smoothing, and the tobiidae: Batrachophrynus, Telmatobius. pattern of tetrapod diversification according to the long nuclear gene RAG-1. Syst. Biol. 56, 543–563. Kozak, K.H., Mendyk, R.W., Wiens, J.J., 2009. Can parallel diversification occur in Appendix C. Supplementary material sympatry? Repeated patterns of body-size evolution in coexisting clades of North American salamanders. Evolution 63, 1769–1784. Lannoo, M.J., 2005. Amphibian Declines: The Conservation Status of United States Supplementary data associated with this article can be found, in Species. University of California Press, Berkeley. the online version, at doi:10.1016/j.ympev.2011.06.012. 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. ClustalW and ClustalX version 2.0. Bioinformatics 23, 2947– References 2948. Laurent, R.F., 1984. Heterogeneidad de la familia Caeciliidae (Amphibia–Apoda). Acta Zool. Lilloana 37, 199–200. Alfaro, M.E., Santini, F., Brock, C., Alamillo, H., Dornburg, A., Rabosky, D.L., Carnevale, Lynch, J.D., 1971. Evolutionary relationships, osteology, and zoogeography of G., Harmon, L.J., 2009. Nine exceptional radiations plus high turnover explain leptodactyloid frogs. Misc. Pub. Mus. Natl. Hist. Kansas 58, 1–238. species diversity in jawed vertebrates. Proc. Natl. Acad. Sci. USA 106, 13410– Marjanovic´, D., Laurin, M., 2007. Fossils, molecules, divergence times, and the origin 13414. of lissamphibians. Syst. Biol. 56, 369–388. Biju, S.D., Bossuyt, F., 2003. New frog family from India reveals an ancient McMahon, M.M., Sanderson, M.J., 2006. Phylogenetic supermatrix analysis of biogeographical link with the Seychelles. Nature 425, 711–714. GenBank sequences from 2228 papilionoid legumes. Syst. Biol. 55, 818–836. Blaustein, A.R., Wake, D.B., 1990. Declining amphibian populations – a global Miranda-Ribeiro, A.D., 1920. Algumas consideracões sobre Holoaden lüderwaldti e phenomenon. Trends Ecol. Evol. 5, 203–204. generos correlatos. Rev. Mus. Paulista, São Paulo 12, 319–320. Bossuyt, F., Roelants, K., 2009. Anura. In: Hedges, S.B., Kumar, S. (Eds.), The Timetree Pauly, G.B., Hillis, D.M., Cannatella, D.C., 2004. The history of a Nearctic of Life. Oxford University Press, New York, pp. 357–364. colonization: molecular phylogenetics and biogeography of the Nearctic Bossuyt, F., Brown, R.M., Hillis, D.M., Cannatella, D.C., Milinkovitch, M.C., 2006. Toads (Bufo). Evolution 58, 2517–2535. Phylogeny and biogeography of a cosmopolitan frog radiation: late Cretaceous Pauly, G.B., Hillis, D.M., Cannatella, D.C., 2009. Taxonomic freedom and the role of diversification resulted in continent-scale endemism in the family Ranidae. official lists of species names. Herpetologica 65, 115–128. Syst. Biol. 55, 579–594. Peng, R., Zhang, P., Xiong, J.-L., Gu, H.-J., Zeng, X.-M., Zou, F.-D., 2010. Rediscovery of Camp, C.D., Peterman, W.E., Milanovich, J.R., Lamb, T., Maerz, J.C., Wake, D.B., 2009. Protohynobius puxiongensis (Caudata: Hynobiidae) and its phylogenetic position A new genus and species of lungless salamander (family Plethodontidae) from based on complete mitochondrial genomes. Mol. Phylogenet. Evol. 56, 252–258. the Appalachian highlands of the south-eastern United States. J. Zool. 279, 86– Pramuk, J.B., Robertson, T., Sites, J.W., Noonan, B.P., 2008. Around the world in 10 94. million years: biogeography of the nearly cosmopolitan true toads (Anura: Carroll, R.L., 2009. The Rise of Amphibians: 365 Million Years of Evolution. Johns Bufonidae). Glob. Ecol. Biogeogr. 17, 72–83. Hopkins University Press, Baltimore. Pyron, R.A., 2010. A likelihood method for assessing molecular divergence time Chippindale, P.T., Bonett, R.M., Baldwin, A.S., Wiens, J.J., 2004. Phylogenetic evidence estimates and the placement of fossil calibrations. Syst. Biol. 59, 185–194. for a major reversal of life-history evolution in plethodontid salamanders. Pyron, R.A., 2011. Divergence time estimation using fossils as terminal taxa and the Evolution 58, 2809–2822. origins of Lissamphibia. Syst. Biol. 60, 466–481. Darst, C.R., Cannatella, D.C., 2004. Novel relationships among hyloid frogs inferred Pyron, R.A., Burbrink, F.T., 2009. Systematics of the Common Kingsnake from 12S and 16S mitochondrial DNA sequences. Mol. Phylogenet. Evol. 31, (Lampropeltis getula; Serpentes: Colubridae) and the burden of heritage in 462–475. taxonomy. Zootaxa 2241, 22–32. de Queiroz, A., Gatesy, J., 2007. The supermatrix approach to systematics. Trends Pyron, R.A., Burbrink, F.T., Colli, G.R., de Oca, A.N.M., Vitt, L.J., Kuczynski, C.A., Wiens, Ecol. Evol. 22, 34–41. J.J., 2011. The phylogeny of advanced snakes (Colubroidea), with discovery of a Driskell, A.C., Ane, C., Burleigh, J.G., McMahon, M.M., O’Meara, B.C., Sanderson, M.J., new subfamily and comparison of support methods for likelihood trees. Mol. 2004. Prospects for building the Tree of Life from large sequence databases. Phylogenet. Evol. 58, 329–342. Science 306, 1172–1174. Roelants, K., Gower, D.J., Wilkinson, M., Loader, S.P., Biju, S.D., Guillaume, K., Moriau, Duellman, W.E., 1999. Patterns of Distribution of Amphibians: A Global Perspective. L., Bossuyt, F., 2007. Global patterns of diversification in the history of modern Johns Hopkins University Press, Baltimore. amphibians. Proc. Natl. Acad. Sci. USA 104, 887–892. Duellman, W.E., Trueb, L., 1994. Biology of Amphibians. Johns Hopkins University San Mauro, D., 2010. A multilocus timescale for the origin of extant amphibians. Press, Baltimore. Mol. Phylogenet. Evol. 56, 554–561. Edgar, R.C., 2004. MUSCLE: multiple sequence alignment with high accuracy and San Mauro, D., Vences, M., Alcobendas, M., Zardoya, R., Meyer, A., 2005. Initial high throughput. Nucl. Acids Res. 32, 1792–1797. diversification of living amphibians predated the breakup of Pangaea. Am. Nat. Faivovich, J., Haddad, C.F.B., Garcia, P.C.A., Frost, D.R., Campbell, J.A., Wheeler, W.C., 165, 590–599. 2005. Systematic review of the frog family Hylidae, with special reference to Hylinae: phylogenetic analysis and taxonomic revision. Bull. Am. Mus. Natl. San Mauro, D., Gower, D.J., Massingham, T., Wilkinson, M., Zardoya, R., Cotton, J.A., Hist. 294, 6–228. 2009. Experimental design in caecilian systematics: phylogenetic information Faivovich, J., Haddad, C.F.B., Baeta, D., Jungfer, K.H., Alvares, G.F.R., Brandao, R.A., of mitochondrial genomes and nuclear RAG1. Syst. Biol. 58, 425–438. Sheil, C., Barrientos, L.S., Barrio-Amoros, C.L., Cruz, C.A.G., Wheeler, W.C., 2010. Santos, J.C., Coloma, L.A., Summers, K., Caldwell, J.P., Ree, R., Cannatella, D.C., 2009. The phylogenetic relationships of the charismatic poster frogs, Amazonian amphibian diversity is primarily derived from Late Miocene Andean Phyllomedusinae (Anura, Hylidae). Cladistics 26, 227–261. lineages. PLoS Biol. 7, 448–461. Feller, A.E., Hedges, S.B., 1998. Molecular evidence for the early history of living Stamatakis, A., 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic amphibians. Mol. Phylogenet. Evol. 9, 509–516. analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688– Felsenstein, J., 2004. Inferring Phylogenies. Sinauer Associates, Sunderland, Mass. 2690. Frost, Darrel, R., 2011. Amphibian Species of the World: an Online Reference. Stuart, S.N., Chanson, J.S., Cox, N.A., Young, B.E., Rodrigues, A.S.L., Fischman, D.L., Version 5.5 (31 January, 2011). American Museum of Natural History, New Waller, R.W., 2004. Status and trends of amphibian declines and extinctions York, USA. Electronic Database accessible at http://research.amnh.org/vz/ worldwide. Science 306, 1783–1786. herpetology/amphibia/. Thomson, R.C., Shaffer, H.B., 2010. Sparse supermatrices for phylogenetic inference. Frost, D.R., Grant, T., Faivovich, J., Bain, R.H., Haas, A., Haddad, C.F.B., De Sa, R.O., taxonomy, alignment, rogue taxa, and the phylogeny of living turtles. Syst. Biol. Channing, A., Wilkinson, M., Donnellan, S.C., Raxworthy, C.J., Campbell, J.A., 59, 42–58. Blotto, B.L., Moler, P., Drewes, R.C., Nussbaum, R.A., Lynch, J.D., Green, D.M., Van Bocxlaer, I., Biju, S.D., Loader, S.P., Bossuyt, F., 2009. Toad radiation reveals into- Wheeler, W.C., 2006. The amphibian tree of life. Bull. Am. Mus. Natl. Hist. 297, India dispersal as a source of endemism in the Western Ghats–Sri Lanka 8–370. biodiversity hotspot. BMC Evol. Biol. 9, 131. Grant, T., Frost, D.R., Caldwell, J.P., Gagliardo, R., Haddad, C.F.B., Kok, P.J.R., Means, van der Meijden, A., Vences, M., Hoegg, S., Boistel, R., Channing, A., Meyer, A., 2007. D.B., Noonan, B.P., Schargel, W.E., Wheeler, W.C., 2006. Phylogenetic Nuclear gene phylogeny of narrow-mouthed toads (Family: Microhylidae) and a systematics of dart-poison frogs and their relatives (Amphibia: discussion of competing hypotheses concerning their biogeographical origins. Athesphatanura: Dendrobatidae). Bull. Am. Mus. Natl. Hist. 299, 6–262. Mol. Phylogenet. Evol. 44, 1017–1030. Guayasamin, J.M., Castroviejo-Fisher, S., Trueb, L., Ayarzaguena, J., Rada, M., Vila, C., Vieites, D.R., Wollenberg, K.C., Andreone, F., Kohler, J., Glaw, F., Vences, M., 2009. 2009. Phylogenetic systematics of Glassfrogs (Amphibia: Centrolenidae) and Vast underestimation of Madagascar’s biodiversity evidenced by an integrative their sister taxon Allophryne ruthveni. Zootaxa 2100, 1–97. amphibian inventory. Proc. Natl. Acad. Sci. USA 106, 8267–8272. Günther, A.C.L.G., 1858. On the systematic arrangement of the tailless batrachians Vieites, D.R., Roman, S.R., Wake, M.H., Wake, D.B., 2011. A multigenic perspective on and the structure of Rhinophrynus dorsalis. Proc. Zool. Soc. Lond. 1858, 339–352. phylogenetic relationships in the largest family of salamanders, the Hedges, S.B., Duellman, W.E., Heinicke, M.P., 2008. New World direct-developing Plethodontidae. Mol. Phylogenet. Evol. 59, 623–635. frogs (Anura: Terrarana): molecular phylogeny, classification, biogeography, Wiens, J.J., 2003. Missing data, incomplete taxa, and phylogenetic accuracy. Syst. and conservation. Zootaxa 1737, 1–182. Biol. 52, 528–538. Heinicke, M.P., Duellman, W.E., Trueb, L., Means, D.B., MacCulloch, R.D., Hedges, S.B., Wiens, J.J., 2007a. Global patterns of diversification and species richness in 2009. A new frog family (Anura: Terrarana) from South America and an amphibians. Am. Nat. 170, S86–S106. Author's personal copy

R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 583

Wiens, J.J., 2007b. Review of ‘‘The amphibian tree of life’’ by Frost et al. Quart. Rev. Wiens, J.J., Parra-Olea, G., Garcia-Paris, M., Wake, D.B., 2007b. Phylogenetic history Biol. 82, 55–56. underlies elevational biodiversity patterns in tropical salamanders. Proc. Roy. Wiens, J.J., 2008. Systematics and herpetology in the age of genomics. Bioscience 58, Soc. Lond. B – Biol. Sci. 274, 919–928. 297–307. Wiens, J.J., Kuczynski, C.A., Smith, S.A., Mulcahy, D.G., Sites, J.W., Townsend, T.M., Wiens, J.J., 2011. Re-evolution of lost mandibular teeth in frogs after more than 200 Reeder, T.W., 2008. Branch lengths, support, and congruence: testing the million years, and re-evaluating Dollo’s law. Evolution 65, 1283–1296. phylogenomic approach with 20 nuclear loci in snakes. Syst. Biol. 57, 420–431. Wiens, J.J., Morrill, M.C., 2011. Missing data in phylogenetic analysis: reconciling Wiens, J.J., Sukumaran, J., Pyron, R.A., Brown, R.M., 2009. Evolutionary and results from simulations and empirical data. Syst. Biol. doi:10.1093/sysbio/ biogeographic origins of high tropical diversity in Old World frogs (Ranidae). syr025. Evolution 63, 1217–1231. Wiens, J.J., Bonett, R.M., Chippindale, P.T., 2005a. Ontogeny discombobulates Wiens, J.J., Kuczynski, C.A., Hua, X., Moen, D.S., 2010. An expanded phylogeny of phylogeny: paedomorphosis and higher-level salamander relationships. Syst. treefrogs (Hylidae) based on nuclear and mitochondrial sequence data. Mol. Biol. 54, 91–110. Phylogenet. Evol. 55, 871–882. Wiens, J.J., Fetzner, J.W., Parkinson, C.L., Reeder, T.W., 2005b. Hylid frog phylogeny Zhang, P., Wake, D.B., 2009a. Higher-level salamander relationships and divergence and sampling strategies for speciose clades. Syst. Biol. 54, 719–748. dates inferred from complete mitochondrial genomes. Mol. Phylogenet. Evol. Wiens, J.J., Graham, C.H., Moen, D.S., Smith, S.A., Reeder, T.W., 2006. Evolutionary 53, 492–508. and ecological causes of the latitudinal diversity gradient in hylid frogs: treefrog Zhang, P., Wake, M.H., 2009b. A mitogenomic perspective on the phylogeny and trees unearth the roots of high tropical diversity. Am. Nat. 168, 579–596. biogeography of living caecilians (Amphibia: Gymnophiona). Mol. Phylogenet. Wiens, J.J., Kuczynski, C.A., Duellman, W.E., Reeder, T.W., 2007a. Loss and re- Evol. 53, 479–491. evolution of complex life cycles in marsupial frogs: does ancestral trait Zhang, P., Zhou, H., Chen, Y.Q., Liu, Y.F., Qu, L.H., 2005. Mitogenomic perspectives on reconstruction mislead? Evolution 61, 1886–1899. the origin and phylogeny of living amphibians. Syst. Biol. 54, 391–400.