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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

a r t i c l e i n f o a b s t r a c t

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
Anura
nuclear), with an average of 2563 bp per species. This data set provides strong support for many groups
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-

With over 6800 known species (AmphibiaWeb; http://www.
amphibiaweb.org/, accessed April, 2011; hereafter ‘‘AW’’) the extant
amphibians (frogs, salamanders, and caecilians) are one of the most
diverse radiations of terrestrial vertebrates. The number of known
extant amphibians has increased rapidly in recent years, with over
2700 species (40%) described in the last 26 years (Duellman,
1999; Lannoo, 2005). This newly discovered diversity includes doz-
ens of new species from known genera in poorly studied tropical re-
gions such as Madagascar (Vieites et al., 2009), but also new genera
in relatively well-explored regions such as the southeastern United
States (Camp et al., 2009), and even new families such as Nasikabatr-
achidae (Biju and Bossuyt, 2003). Unfortunately, much extant
amphibian diversity is currently under extreme threat from pres-
sures such as habitat loss, global climate change, and infectious dis-
ease, and many species have gone extinct in the last few decades
(Blaustein and Wake, 1990; Stuart et al., 2004).
⇑ Corresponding author.
E-mail addresses: rpyron@colubroid.org (R. Alexander Pyron), wiensj@life.bio.
sunysb.edu (John J. Wiens).
standing, and preserving extant amphibian diversity, but a large-
scale phylogeny for extant amphibians is presently lacking. How-
ever, recent molecular and combined-data studies have made
important contributions to higher-level phylogeny (Frost et al.,
2006; Roelants et al., 2007; Wiens, 2007a, 2011) and to the phylog-
eny of many major groups, such as caecilians (San Mauro et al.,
2009; Zhang and Wake, 2009b), hyloid frogs (Darst and Cannatella,
2004), ranoid frogs (e.g., Bossuyt et al., 2006; Wiens et al., 2009),
microhylid frogs (van der Meijden et al., 2007), bufonid frogs
(Pauly et al., 2004; Pramuk et al., 2008; Van Bocxlaer et al.,
2009), centrolenid frogs (Guayasamin et al., 2009), dendrobatid
frogs (Grant et al., 2006; Santos et al., 2009), hemiphractid frogs
(Wiens et al., 2007a), hylid frogs (Faivovich et al., 2005, 2010;
Wiens et al., 2005b, 2010), terraranan frogs (Hedges et al., 2008;
Heinicke et al., 2009), and salamanders (Kozak et al., 2009; Vieites
et al., 2011; Wiens et al., 2005a, 2007b; Zhang and Wake, 2009a).
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)
and characters (up to 4.9 kb of sequence data from 2 mitochondrial
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-
onomy, especially for taxa delimited at the family and genus level.
However, that study has also been criticized on numerous grounds,
including concerns about taxon sampling and methodological
strategies (Marjanović and Laurin, 2007; Pauly et al., 2009; Wiens,
2007b, 2008). For example, those authors collected up to 4900
characters per species, but their analysis is apparently based on
15,320 characters, suggesting that their controversial approach to
sequence alignment (POY) dominates their results (Wiens, 2008).
Although some of the changes made by Frost et al. (2006) have
been widely adopted, others are more controversial, such as the
partitioning of Bufo and Rana (Marjanović and Laurin, 2007; Pauly
et al., 2009; AW). Indeed, many of these changes are no longer sup-
ported, even in Frost’s (2011) taxonomic database of extant
amphibians (e.g., the families Amphignathodontidae, Batrachoph-
rynidae, Cryptobatrachidae, and Thoropidae recognized by Frost
et al. (2006)). Much of the most unstable taxonomy involves the
family-level assignment of many of the genera of hyloid frogs, par-
ticularly those traditionally assigned to the family Leptodactylidae.
Clearly, extant amphibian phylogeny and classification is still in
need of additional study. Fortunately, the numerous studies refer-
enced above (and many others) have produced a massive amount
of data that are potentially suitable for a combined, supermatrix
approach (e.g., de Queiroz and Gatesy, 2007; Driskell et al., 2004;
Pyron et al., 2011; Thomson and Shaffer, 2010; Wiens et al.,
2005b). This includes thousands of species represented in GenBank
for numerous nuclear and mitochondrial genes, often with sub-
stantial overlap of genes among species.
Here, we present a large-scale estimate of amphibian phylog-
eny, including 2871 species (42% of the 6807 known, extant
amphibian species) from 432 of the 504 currently recognized gen-
era (86%), and representatives from every currently delimited, ex-
tant family and subfamily. This is 5.5 times more species and
nearly twice as many genes as the largest previous study (Frost
et al., 2006). The data matrix includes up to 12,712 bp for each spe-
cies from 12 genes (three mitochondrial, nine nuclear). Impor-
tantly, rather than simply reanalyzing published data for
relatively well-studied families (e.g., dendrobatids, hylids), we ad-
dress the monophyly and relationships of many smaller groups
that have not been the subject of focused studies (e.g., Ceratophryi-
dae, Cylcoramphidae), as well as relationships among families. We
produce a revised classification of extant amphibians, focusing on
taxa traditionally ranked as families and subfamilies. This study
also provides additional support for the value of the supermatrix
approach to large-scale phylogenetic inference (e.g., de Queiroz
and Gatesy, 2007; Driskell et al., 2004; Pyron et al., 2011; Thomson
and Shaffer, 2010; Wiens et al., 2005b).
2. Materials and methods
2.1. Taxonomic reference
This analysis has been several years in the making. Our initial
taxonomy was based on the September 2009 update of the
AmphibiaWeb (AW) database. However, when we refer to current
numbers, these are taken from the April, 2011 update. The AW list
is fairly current in terms of recently described species, but more
conservative than the Amphibian Species of the World (Frost,
2011; hereafter ‘‘ASW’’) regarding some of the more controversial
of the recent taxonomic changes (e.g., Bufo and Rana maintain sim-
ilar composition as they did prior to Frost et al., 2006). We note
some instances where recent updates have modified our original
classification. Note that even when not made explicit, we refer in
all instances to the known extant diversity of Lissamphibia, given
that the clade Amphibia includes numerous extinct stem-group
members that are not lissamphibians. The gymnophionans, cau-
dates, and anurans also contain numerous extinct taxa, many of
which are grouped in separate genera, subfamilies, and families
that are not addressed in our analyses or included in our discussion
of phylogeny. See Marjanović and Laurin (2007), Carroll (2009),
and Pyron (2011) for an overview of these taxa, their phylogenetic
affinities, and the origins of Amphibia and Lissamphibia.
2.2. Molecular data
We identified 12 candidate loci that have been broadly sampled
and successfully used in amphibian phylogenetics at both lower
and higher taxonomic levels. These 12 genes included nine nuclear
genes: C-X-C chemokine receptor type 4 (CXCR4), histone 3a
(H3A), sodium–calcium exchanger (NCX1), pro-opiomelanocortin
(POMC), recombination-activating gene 1 (RAG1), rhodopsin
(RHOD), seventh-in-absentia (SIA), solute-carrier family 8
(SLC8A3), and tyrosinase (TYR). Three mitochondrial genes were
also included: cytochrome b (cyt-b), and the large and small sub-
units of the mitochondrial ribosome genes (12S/16S; omitting
the adjacent tRNAs as they were difficult to align and represented
only a small amount of data). This selection of genes includes al-
most all of those genes used in the higher-level analyses by Frost
et al. (2006) and Roelants et al. (2007), and most of those used in
other large-scale studies (Faivovich et al., 2005; Grant et al.,
2006; Wiens et al., 2009, 2010). However, we did not include the
nuclear gene 28S (used by Frost et al. (2006)), as previous analyses
of this gene region alone suggest that it contains relatively few
informative characters and supports some relationships that are
grossly inconsistent with other studies (see Wiens et al., 2006).
We conducted GenBank searches by family and subfamily to gath-
er all available sequences, using a minimum-length threshold of
200 bp (a somewhat arbitrary threshold of 1.5% of the total matrix
length, to avoid including very short [e.g., <50 bp] fragments), and
stopping in August of 2010. Only species in the taxonomic data-
base were included in the sequence matrix, which excluded
numerous named taxa of ambiguous status, and many sequences
labeled ‘sp.’ We removed a few (<10) taxa with identical sequence
data for all genes (arbitrarily retaining the first in alphabetical or-
der), to avoid potentially misidentified or otherwise confounded
specimens or sequences.
For the protein-coding genes, alignment was relatively straight-
forward. Conceptual translations were used to ensure an open
reading frame, and sequences were aligned using the translation-
alignment algorithm in the program Geneious v4.8.4 (GeneMatters
Corp.), with the default cost matrix (Blosum62) and gap penalties
(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
(Larkin et al., 2007) algorithms under a variety of gap-cost param-
eters yielded low-quality results (i.e., alignments with large num-
bers of gaps and little overlap of potentially homologous
characters).
We subsequently employed a two-step strategy for these data.
First, we identified sequence clusters of similar length and cover-
age from the global alignment. These were subsequently aligned
separately using the MUSCLE algorithm with the default high-
accuracy parameters, which have been shown to outperform CLUS-
TAL in a variety of settings (Edgar, 2004). These alignments were
subsequently refined using the MUSCLE refinement algorithm,
and then adjusted manually and trimmed for quality and maxi-
mum coverage (i.e., end sequences with low overlap and poor
apparent alignment were deleted using the alignment editor in
Geneious). These length and position-based sequence groups were
then aligned to each other using the profile-profile alignment
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
manually adjusted and trimmed again for maximum quality and
coverage, and refined a second time. Final adjustments were made
by eye for a small number of sequences. This process was repeated
for 12S and 16S separately. For 12S, four clusters were produced
and combined using profile alignment, with five clusters for 16S.
The final concatenated alignment consists of 12,712 bp for 2871
species. These species included 42% of the currently recognized
amphibian species (6807; this and subsequent numbers from AW
2011), representing 41 caecilian species in 23 genera (22% of 189
known extant species and 70% of 33 genera), 436 salamander spe-
cies in 68 genera (72% of 608 species and 99% of 69 genera), and
2394 frog species from 341 genera (40% of 6010 species and 85%
of 402 genera). We selected Homo as an outgroup because data
were available for Homo from all 12 genes, and the sister group
to Amphibia is Amniota (e.g., Alfaro et al., 2009; Hugall et al.,
2007; Pyron, 2010). The matrix contains data from 2572 species
for 16S (90%, 1986 bp), 2312 species for 12S (81%, 1357 bp), 1241
for cyt-b (43%, 1140 bp), 1049 for RAG-1 (37%, 2700 bp), 606 for
TYR (21%, 1132 bp), 589 for RHOD1 (21%, 315 bp), 478 for SIA
(17%, 397 bp), 445 for POMC (16%, 666 bp), 352 for H3A (12%,
328 bp), 284 for CXCR4 (10%, 753 bp), 220 for NCX1 (8%,
1338 bp), and 175 for SLC8A3 (6%, 1132 bp). The mean length per
species is 2563 bp (20% of the total length of the matrix,
12,712 bp), with a range from 249 to 11,462 bp (2–90%), and is
available in Dryad repository doi:10.5061/dryad.vd0m7. GenBank
numbers are listed in Appendix S1.
Clearly, many taxa had large amounts of missing data (some
>97%), and on average each species had 80% missing cells. How-
ever, several lines of evidence suggest that these missing data
are not problematic. First, two genes (12S/16S) were shared by
the vast majority of taxa (90% and 81%, respectively), providing
a ‘‘backbone’’ for the placement of most taxa based on overlap-
ping sequence data. Simulations suggest that this sampling design
can be critically important for allowing the accurate placement of
taxa with extensive missing data, as opposed to having all genes
be randomly sampled across species with limited overlap (Wiens,
2003). Second, a large body of empirical and theoretical studies
suggests that highly incomplete taxa can be accurately placed
in model-based phylogenetic analyses (and with high levels of
branch support), especially if a large number of characters have
been sampled (recent review in Wiens and Morrill, 2011). Finally,
several recent empirical studies have shown that the supermatrix
approach (with extensive missing data in some taxa) yields
generally well-supported large-scale trees that are in general
highly congruent with both existing taxonomies and previous
phylogenetic estimates (e.g., Driskell et al., 2004; McMahon and
Sanderson, 2006; Pyron et al., 2011; Thomson and Shaffer,
2010; Wiens et al., 2005b).
2.3. Phylogenetic analyses
We performed phylogenetic inference using maximum likeli-
hood (ML) and assessed support using non-parametric bootstrap-
ping (BS). We assume that Bayesian analysis would yield very
similar results (but would be very difficult to implement for so many
taxa), and we strongly prefer model-based methods to parsimony
(for reasons described in Felsenstein (2004)). We performed ML tree
inference and non-parametric bootstrapping using the program
RAxMLv7.0.4 (Stamatakis, 2006) with the 12-gene concatenated
matrix (species-tree methods were not practical given the large
number of taxa). We used the GTRGAMMA model for all genes and
partitions because GTR is the only substitution model implemented
in RAxML, and all other substitution models are encompassed with-
in the GTR model (Felsenstein, 2004). The GTRGAMMA model in
RAxML is recommended over the GTR + C + I because the large
number of rate categories for C (25, as opposed to the usual 4)
545
should adequately account for potentially invariant sites without
the need for an extra parameter (Stamatakis, 2006). Even though
the GTR + C + I model is implemented in some versions of RAxML,
its use is explicitly not recommended (Stamatakis, 2006).
Previous phylogenetic analyses of these data show that
GTR + C + I is generally the best-fitting model for these genes
(e.g., Roelants et al., 2007; Wiens et al., 2005a,b, 2009, 2010). These
previous analyses also suggest that the protein-coding genes
should be partitioned by codon position, whereas the ribosomal
genes (12S, 16S) should be partitioned by stems and loops, with
separate partitions within and between genes. These secondary
structures were identified and coded following the protocol used
by Wiens et al. (2005b), based on predicted features from Pseuda-
cris regilla (12S; AY819376) and Rana temporaria (16S; AY326063)
from the European Ribosomal RNA database (http://bioinformat-
ics.psb.ugent.be/webtools/rRNA/). The placement of stems and
loops appears to be conserved across most sites, at least within
frogs (Wiens et al., 2005b). Our final analysis was partitioned by
gene, codon position (for protein-coding genes), and stems and
loops (for ribosomal genes).
To find the optimal ML tree, we used a searching strategy that
combined the rapid bootstrapping algorithm (100 non-parametric
bootstrap replicates) with the thorough ML search option (20 inde-
pendent searches, starting from every fifth bootstrap replicate).
Similar analyses were performed numerous (>10) times as new
taxa and sequences were added to the near-final matrix. These
analyses collectively represent hundreds of independent searches
from random starting points. All of these preliminary analyses
showed high congruence with the final ML topology. This concor-
dance strongly suggests that our final ML estimate represents the
optimal topology for these data (or close to it). Given that BS values
generally appear to be conservative (Felsenstein, 2004), we consid-
ered clades with values of 70% or greater to be well-supported.
These analyses were performed on a 240-core Dell PowerEdge
supercomputing system at the High Performance Computing Cen-
ter at the City University of New York, and were completed in
16 days using 24 nodes of the CUNY cluster.
2.4. Taxonomic revision
A major goal of this study was to revise the higher-level taxon-
omy of extant amphibians to correspond with the new phylogeny,
given several major problems that were discovered. In the Results
section below, we compare our results with existing phylogenies
and classifications, and describe our proposed solutions to taxo-
nomic problems as we describe them (rather than having a separate
section discussing taxonomy). In general, we attempt to alter exist-
ing classifications (e.g., AW, ASW) as little as possible, and only when
existing groups are not monophyletic. Furthermore, we recognize
new groups only if they are strongly supported. Given the size of
these phylogenies, we do not detail every congruence and discor-
dance between our phylogeny and all previous studies (especially
within families). Instead, we emphasize necessary taxonomic
changes revealed by our study. We also focus our phylogenetic com-
parisons on the largest of the previous analyses (in terms of taxo-
nomic scope and number of species sampled), those of Frost et al.
(2006), Roelants et al. (2007), and Wiens (2007a, 2011). The generic
composition of all families and subfamilies in our revised classifica-
tion is provided in Appendix B. Genus names follow our original tax-
onomic database from the 2009 AW update.
In some cases, our analyses show that higher taxa (i.e., families
and subfamilies) are not monophyletic, but not all genera have
been included in our tree. Some of these genera are effectively
‘‘orphaned’’ because it is no longer clear to which higher taxon they
belong. We generally denote these as incertae sedis within the
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
and classification will require additional data and analyses. We
consider this a more conservative strategy than simply placing
them in the nominate group without data. While in theory this
strategy creates more ‘‘instability’’ by removing taxa from named
groups, it highlights the need for their study in future analyses,
and does not promote the taxonomic burden of heritage (Pyron
and Burbrink, 2009) in further propagating classifications with
high probability of error based solely on the status quo.
3. Results
A summary of the ML tree based on the rapid-bootstrapping anal-
ysis from RAxMLv7.0.4 (lnL = 1704992.20) is shown in Fig. 1. This
phylogeny is generally well-supported, with 64% of nodes having BS
proportions >70. Our analyses support the monophyly of frogs, cae-
cilians, and salamanders, respectively, and weakly support a sister-
group relationship between frogs and salamanders, as found in most
other studies of extant lissamphibian phylogeny (Frost et al., 2006;
Pyron, 2011; Roelants et al., 2007; San Mauro, 2010; Wiens, 2011;
Zhang et al., 2005). An alternative grouping of Gymnophiona and
Caudata (i.e., Procera) has been supported by some studies (e.g.,
Feller and Hedges, 1998), and in re-analyses of others (e.g., Zhang
et al., 2005; San Mauro et al., 2005; see Marjanović and Laurin,
2007; Pyron, 2011). Many of the family-level relationships within
these three groups remain unchanged from recent estimates (Frost
et al., 2006; Pyron, 2011; Roelants et al., 2007; San Mauro, 2010;
Wiens, 2007a, 2011). However, we find some significant deviations
from previous phylogenies and taxonomies, which we describe be-
low along with proposed solutions.
Within caecilians (Fig. 2A), our results agree with other recent
studies in supporting clades corresponding to Rhinatrematidae,
Ichthyophiidae, and Caeciliidae (Frost et al., 2006; Roelants et al.,
2007; San Mauro et al., 2009; Zhang and Wake, 2009b). The tradi-
tional family-level classification of caecilians (still used by AW,
2011) is not supported, given that Uraeotyphlidae renders Ichthy-
ophiidae paraphyletic and that Scolecomorphidae and Typhlonect-
idae render Caeciliidae paraphyletic. Furthermore, we find (Fig. 2A)
the caeciliid subfamily Typhlonectinae (recognized by ASW) to be
paraphyletic with respect to Caeciliinae (Cthonerpeton and Typhlo-
nectes are not sister taxa, although this is weakly supported), and
also makes Caeciliinae non-monophyletic (i.e., the caeciliines Cae-
cilia and Oscaecilia are in a strongly supported clade with Cthonerp-
eton and Typhlonectes, which excludes all other caeciliine genera
such as Dermophis, Gegeneophis, and Siphonops). Typhlonectinae
is synonymized with Caeciliinae in our classification. Within Cae-
ciliidae, we concur with ASW in recognizing the strongly supported
subfamily Scolecomorphinae for Crotaphatrema and Scolecomor-
phus, which is the sister group to all other caeciliids. Although
we could recognize Caeciliinae as the sister group to Scolecomor-
phinae, this clade is only weakly supported, despite strong support
for each subfamily-level clade. Thus, we recognize these two clades
as separate subfamilies. We restore the subfamily Herpelinae (Lau-
rent, 1984) for the clade comprising Herpele and Boulengerula. We
recognize the other strongly supported clade as Caeciliinae (Figs. 1,
2A; Appendix B). This arrangement accommodates all taxa in-
cluded in our tree, though many other genera have not yet been
sampled. The following genera are thus considered Caeciliidae
incertae sedis: Atretochoana, Brasilotyphlus, Idiocranium, Indotyphlus,
Microcaecilia, Mimosiphonops, Nectocaecilia, Parvicaecilia, Potomo-
typhlus, and Sylvacaecilia.
Within salamanders, the family and subfamily-level relation-
ships are mostly consistent with most recent model-based molec-
ular analyses (Roelants et al., 2007; Wiens, 2011; Wiens et al.,
2005a; Zhang and Wake, 2009a) and current classifications (AW,
ASW). However, our results differ strongly from Frost et al.
(2006) with respect to relationships among the salamander fami-
lies. Frost et al. (2006) recover a clade comprising Sirenidae, Dica-
mptodontidae, Ambystomatidae, and Salamandridae. In contrast,
we find strong support for a sister-group relationship between
Sirenidae and all salamanders exclusive of Cryptobranchidae and
Hynobiidae (Figs. 1 and 2B and C), as do Wiens et al. (2005a), Roe-
lants et al. (2007), and Wiens (2007a, 2011). While some classifica-
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.,
2011; Wiens, 2007a) and ASW in recognizing four subfamilies in
Plethodontidae (Bolitoglossinae, Hemidactylinae, Plethodontinae,
and Spelerpinae; Figs. 1 and 2D–F). We do not recognize a separate
subfamily for Protohynobius (contra AW), given that it is likely
nested in Hynobiinae (Peng et al., 2010).
Within frogs, strongly-supported higher-level groups and rela-
tionships (e.g., among the non-neobatrachian frogs, Neobatrachia,
Hyloidea, and Ranoidea) are consistent with most recent studies
(Frost et al., 2006; Roelants et al., 2007; Wiens, 2007a, 2011), with
some notable exceptions. We find (Fig. 2G) strong support for plac-
ing Discoglossoidea (Alytidae + Bombinatoridae + Discoglossidae)
as the sister group to all other frogs exclusive of Ascaphidae + Leio-
pelmatidae (see also Roelants et al., 2007), whereas Frost et al.
(2006) and Wiens (2007a, 2011) placed Pipoidea (Pipidae + Rhin-
ophrynidae) in this position. Within Neobatrachia (Fig. 1), we cor-
roborate the placement of Heleophrynidae as the sister taxon to all
other neobatrachian frogs (Frost et al., 2006; Roelants et al., 2007;
Wiens, 2007a, 2011). We find a weakly supported sister-group rela-
tionship between the clade Sooglossidae + Nasikabatrachidae and
all neobatrachian frogs to the exclusion of Heleophrynidae (Fig. 1).
In contrast, both Roelants et al. (2007) and Wiens (2007a, 2011; Soo-
glossidae only) placed this clade as the sister-taxon to Ranoidea,
whereas Frost et al. (2006) found it to be the sister-group of Hyloidea
(including Myobatrachidae + Calyptocephalellidae).
Within Hyloidea, our results suggest that several families cur-
rently recognized by both AW and ASW are not monophyletic.
All of these problematic taxa were previously placed in the family
Leptodactylidae (subdivided extensively by Frost et al., 2006), and
include Ceratophryidae, Cycloramphidae, Leptodactylidae, and
Strabomantidae. Below we describe the specific problems and
our proposed taxonomic solutions. These solutions include recog-
nizing several additional families relative to current classifications
(Alsodidae, Batrachylidae, Odontophrynidae, Rhinodermatidae,
Telmatobiidae) and synonymizing one (Strabomantidae with
Craugastoridae). These newly recognized families are either re-def-
initions of previously recognized families (Rhinodermatidae,
Telmatobiidae), or elevation of existing taxa presently below fam-
ily rank (Alsodinae, Batrachylinae, Odontophrynini) to the rank of
families.
Most of these problematic taxa are contained in a weakly sup-
ported clade (Fig. 2Z) that includes the currently recognized families
Ceratophryidae, Cycloramphidae, and Hylodidae (note that the
content of these families and their subfamilies are the same in both
AW and ASW). Under these classifications, Ceratophryidae is
presently divided into the subfamilies Batrachylinae (Atelognathus,
Batrachyla), Ceratophryinae (Ceratophrys, Chacophrys, Lepidobatra-
chus), and Telmatobiinae (Telmatobius, including Batrachophrynus
in AW). Cycloramphidae comprises Alsodinae (Alsodes, Eupsophus,
Hylorina, Insuetophrynus, Limnomedusa, Macrogenioglottus, Odon-
tophrynus, Proceratophrys, Thoropa) and Cycloramphinae (Crossodac-
tylodes, Cycloramphus, Rhinoderma, Zachaenus), and one genus of
uncertain placement (Rupirana). Hylodidae contains Crossodactylus,
Hylodes, and Megaelosia. With respect to this classification, we find
strong support for monophyly of Hylodidae (Fig. 2Z), but the families
Ceratophryidae and Cycloramphidae are non-monophyletic, with
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R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 547

100 Rhinatrematidae
Ichthyophiidae
98 Scolecomorphinae Gymnophiona
100 Caeciliinae Caeciliidae
59 Herpelinae
100 Hynobiidae
Cryptobranchidae
Sirenidae
99 100 Ambystomatidae
Dicamptodontidae
71 98 Salamandrininae
100 Pleurodelinae Salamandridae
97 85 Salamandrinae Caudata
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
98
Rhinophrynidae
100 Scaphiopodidae
Pelodytidae
96 Megophryidae
92 99 Pelobatidae
Heleophrynidae
100 Sooglossidae
98 Nasikabatrachidae
100 Calyptocephalellidae
Myobatrachinae Myobatrachidae
98 Limnodynastinae
98 97
Ceuthomantidae
Brachycephalidae
57 Eleutherodactylinae Eleutherodactylidae
Phyzelaphryninae
93 Pristimantinae
98 Holoadeninae Craugastoridae
86 Craugastorinae
Neobatrachia Strabomantinae
Hemiphractidae
56 Hylinae
96
100 Pelodryadinae Hylidae
63 Phyllomedusinae
Bufonidae
Hyloidea Dendrobatidae
54 100 Allophrynidae
Centroleninae Centrolenidae
100 Hyalinobatrachinae
79 Leptodactylinae
Leuiperinae Leptodactylidae
Paratelmatobiinae
Ceratophryidae
Odontophrynidae
Cycloramphidae Anura
53 Alsodidae
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
76 Microhylinae
Dyscophinae
Kalophryninae
Asterophryninae
Ranoidea Melanobatrachinae
Ptychadenidae
Micrixalidae
99 Phrynobatrachidae
50 Conrauidae
Petropedetidae
91 Cacosterninae Pyxicephalidae
Pyxicephalinae
54 Ceratobatrachidae
Nyctibatrachidae
Ranixalidae
88 Dicroglossinae Dicroglossidae
Occidozyginae
Ranidae
100 Rhacophorinae Rhacophoridae
0.2 subst./site 74 Buergeriinae
96 Laliostominae
100 60 Mantellinae Mantellidae
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.
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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.
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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

100 Ranodon sibiricus

Hynobiidae Paradactylodon mustersi
79
Paradactylodon gorganensis
100 Paradactylodon persicus
100 75
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 Hynobius glacialis
93
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 Hynobius takedai
B
Fig. 2 (continued)
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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
100 75 Dicamptodon copei
Ambystoma cingulatum
Ambystoma gracile
Ambystoma opacum
Ambystomatidae 100 Ambystoma californiense
93 Ambystoma tigrinum
68 Ambystoma
Ambystoma
dumerilii
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
100 Salamandra salamandra
97 Salamandra algira
Salamandridae 100 Lyciasalamandra luschani
Lyciasalamandra fazilae
100 Lyciasalamandra helverseni
64 Lyciasalamandra flavimembris
Lyciasalamandra atifi
74 Lyciasalamandra antalyana
85 100 Lyciasalamandra billae
Pleurodeles waltl
100 Pleurodeles poireti
99 Pleurodeles nebulosus
100 91 Echinotriton andersoni
Echinotriton chinhaiensis
99 Tylototriton asperrimus
D-F 81
Tylototriton wenxianensis
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
82 Paramesotriton hongkongensis
65 Paramesotriton deloustali
Paramesotriton fuzhongensis
82 Paramesotriton guangxiensis
98
C
Fig. 2 (continued)
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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
52 Rhyacotriton kezeri
Rhyacotritonidae 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 Hydromantes italicus
100
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 Desmognathus planiceps
55
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 Plethodon virginia
97
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
95 Plethodon shermani
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)
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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 Eurycea longicauda
99 61
Eurycea cirrigera
Spelerpinae Eurycea wilderae
93 Eurycea bislineata
Eurycea junaluska
69 100 Eurycea aquatica
Eurycea quadridigitata
100 Eurycea naufragia
86 Eurycea tonkawae
Eurycea chisholmensis
100 100 Eurycea
Eurycea waterlooensis
rathbuni
83 99 Eurycea troglodytes
85 Eurycea sosorum
Eurycea nana
100 Eurycea neotenes
53 Eurycea pterophila
88
65 Eurycea tridentifera
100 76 Eurycea latitans
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
91 77 Chiropterotriton lavae
Chiropterotriton arboreus
64 Chiropterotriton multid entatus
93 98 Chiropterotriton cracens
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
77 96 Nototriton picadoi
77 Nototriton gamezi
65 Nototriton abscondens
Bradytriton silus
Oedipina quadra
52 98 Oedipina kasios
Oedipina gephyra
50 86 Oedipina carablanca
72 Oedipina elongata
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)
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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
59 Pseudoeurycea werleri
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)
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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
Barbourula kalimantanensis
Bombinatoridae 100 Barbourula busuangensis
99 Bombina maxima
100 Bombina lichuanensis
62 Bombina microdeladigitora
Bombina fortinuptialis
100 86 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 84 Discoglossus pictus
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
Xenopusgilli
95 Xenopus laevis
97 Xenopus petersii
100 Xenopus victorianus
61 Xenopus boumbaensis
Xenopus andrei
58 Xenopus pygmaeus
Xenopus fraseri
100 Xenopus wittei
Xenopus largeni
50 Xenopus ruwenzoriensis
Xenopus longipes
Xenopus amieti
100 Scaphiopus couchii
Scaphiopodidae Scaphiopus hurterii
92 99 Scaphiopus holbrookii
100 100 Spea multiplicata
Spea hammondii
86 Spea bombifrons
Spea intermontana
Pelodytidae 77
Pelodytes caucasicus
100 100 Pelodytes ibericus
100 Pelodytes punctatus
Pelobatidae Pelobates syriacus
Pelobates fuscus
100 Pelobates cultripes
59
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
98
Megophryidae 81 100 Leptolalax arayai
Leptolalax oshanensis
100 Leptolalax liui
97 Leptolalaxpelodytoides
99 Leptolalaxbourreti
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
90 93 Scutiger tuberculatus
Oreolalax rhodostigmatus
100 Oreolalax lichuanensis
Oreolalax pingii
100 95 Oreolalax schmidti
Oreolalax rugosus
80 Oreolalax jingdongensis
99 Oreolalax xiangchengensis
85 Oreolalax major
66 97Oreolalax liangbeiensis
Oreolalax multipunctatus
57 Oreolalax chuanbeiensis
G 100 Oreolalax omeimontis
100 Oreolalax popei
100 Oreolalax nanjiangensis

Fig. 2 (continued)
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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
68 Leptodactylodon bicolor
Scotobleps gabonicus
Nyctibates corrugatus
59 Trichobatrachus robustus Astylosterninae
71 98 Astylosternus diadematus
Astylosternus schioetzi
100 Astylosternus batesi
98 80 Leptopelis brevirostris
Leptopelis argenteus
99 Leptopelis modestus
97 Leptopelis vermiculatus
94 Leptopelis natalensis Leptopelinae
99 Leptopelis kivuensis
98 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
69 Arthroleptis reichei
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
97 100 Acanthixalus spinosus
Opisthothylax immaculatus
Morerella cyanophthalma
100 Afrixalus knysnae
Afrixalus delicatus
82 100 Afrixalus stuhlmanni
Afrixalus fornasini
99 99 100 Afrixalus laevis
Afrixalus dorsalis
77 96 Afrixalus paradorsalis
100 Tachycnemis seychellensis
100 Heterixalus madagascariensis
100 Heterixalus boettgeri
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
56 Hyperolius pardalis
Hyperolius guttulatus
99 Hyperolius fusciventris
98 Hyperolius argus
Hyperolius glandicolor
77 Hyperolius phantasticus
100 94 Hyperolius tuberculatus
84 84 Hyperolius angolensis
88 Hyperolius viridiflavus
97 Hyperolius marmoratus
Hyperolius tuberilinguis
Alexteroon obstetricans
100 100 Hyperolius Hyperolius kivuensis
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
I
Hyperolius zonatus
71 Hyperolius montanus
H 61 Hyperolius puncticulatus

P-AE J-O
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Phrynomerinae Phrynomantis annectens

99 Phrynomantis bifasciatus
Otophryninae 100 Phrynomantis microps
Otophryne pyburni
71 Synapturanus mirandaribeiroi
100 Chiasmocleis hudsoni
96 Chiasmocleis shudikarensis
99 Nelsonophryne aequatorialis
Ctenophryne geayi
100 Dasypops schirchi
100 Hamptophryne boliviana
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
95 90 Anodonthyla boulengerii
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
98 Stumpffia gimmeli
100 Stumpffia psologlossa
76 Stumpffia tetradactyla
Stumpffia grandis
99 Stumpffia roseifemoralis
64 100 Cophyla phyllodactyla
Cophyla berara
Plethodontohyla mihanika
Plethodontohyla fonetana
78 Plethodontohyla guentheri
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
99 63 Scaphiophryne calcarata
Scaphiophryne gottlebei
Scaphiophryninae 85 98 Scaphiophryne marmorata
Scaphiophryne boribory
65 Scaphiophryne madagascariensis
Scaphiophryne menabensis
Dyscophinae 100 Dyscophus insularis
Dyscophus guineti
100 100 Dyscophus antongilii
76 Metaphrynella sundana
81 Kaloula pulchra
100 Kaloula conjuncta
Kaloula taprobanica
78 Uperodon systoma
92 Ramanella variegata
95 Ramanella obscura
100
Micryletta inornata
Chaperina fusca
Glyphoglossus molossus
100 Calluella guttulata
Microhylinae Microhyla butleri
100 Microhyla pulchra
100 Microhyla rubra
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
Asterophryninae 58 Albericus laurini
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
78 Xenorhina oxycephala
66 Asterophrys turpicola
I 93
Callulops slateri
Callulops eurydactylus
Callulops pullifer

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H Hildebrandtia ornata
93 Ptychadena mascareniensis
99 100 Ptychadena newtoni
Ptychadena pumilio
Ptychadena taenioscelis
82 Ptychadena subpunctata
88 Ptychadena longirostris Ptychadenidae
75
Ptychadena anchietae
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
66
Pyxicephalidae
74 83 Tomopterna
Tomopterna
luganga
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
100 Arthroleptella drewesii
Arthroleptella landdrosia
Arthroleptella bicolor
59 Arthroleptella subvoce
Lankanectes corrugatus
74 Nyctib atrachus 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
Platymantis punctatus
97 69 Discodeles guppyi
76 Platymantis vitiensis
Platymantis bimaculatus
69 Platymantis wuenscheorum
Platymantis weberi
99 Platymantis papuensis
100 Platymantis pelewensis
94 Platymantis cryptotis
J
K-O
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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
100 Fejervarya triora
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
80 Paa taihangnicus
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
100 Limnonectes fragilis
80 Limnonectes fujianensis
100 63 Limnonectes bannaensis
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
67 Limnonectes paramacrodon
Limnonectes macrodon
91 100 Limnonectes shompenorum
71 Limnonectes malesianus
K 100 Limnonectes ingeri
100 Limnonectes finchi

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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
100 Boophis marojezensis
Mantellidae 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
88 Mantidactylus grandidieri
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)
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Buergeriinae 100 Buergeria oxycephlus

Buergeria japonica
83 Buergeria buergeri
98 Buergeria robusta
Philautus hainanus
100 Philautus ocellatus
100 58 Liuixalus romeri
96 Nyctixalus spinosus
Rhacophoridae 99 Nyctixalus pictus
Theloderma corticale
99 Theloderma rhododiscus
Theloderma bicolor
Theloderma asperum
100 Ghatixalus variabilis
76 Chiromantis vittatus
Rhacophorinae 98 Chiromantis doriae
69 Chiromantis rufescens
85 Chiromantis xerampelina
66 Feihyla palpebralis
Polypedates eques
99 Polypedates fastigo
94 58 Polypedates colletti
62 Polypedates maculatus
100 Polypedates cruciger
78 Polypedates leucomystax
88 Polypedates mutus
99 99 Polypedates megacephalus
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
68 acutirostris
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
89 98 Philautus travancoricus
70 Philautus griet
Philautus charius
100 100 Philautus signatus
Philautus tinniens
Philautus ponmudi
59 Philautus longchuanensis
92 Philautus gryllus
100 73 Philautus menglaensis
52 Philautus bombayensis
100 Philautus tuberohumerus
Philautus zorro
100 Philautus wynaadensis
Philautus leucorhinus
Philautus simba
98 Philautus decoris
53 100 Philautus mittermeieri
Philautus tanu
Philautus ocularis
54 Philautus pleurotaenia
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

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100 Staurois latopalmatus

Staurois natator
100 100 Staurois parvus
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
90 97 Amolops wuyiensis
100 Amolops ricketti
96 Amolops cremnobatus
96 Amolops larutensis
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
100 Rana perezi
Rana esculenta
100 Rana lessonae
Rana cretensis
80 Rana epeirotica
76 71 Rana kurtmuelleri
Rana ridibunda
53 Rana bedriagae
Rana cerigensis
Rana shqiperica
70 85 Rana bergeri
Rana sanguinea
100 Rana igorota
94 100
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
71 Rana milleti
97 Rana arfaki
Rana jimiensis
Rana daemeli
98 Rana faber
Rana nigrovittata
95 Rana cubitalis
Rana latouchii
99 Rana maosonensis
Rana spinulosa
Rana mocquardii
95 56 Rana chalconota
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
Rana laterimaculata
N Ranidae cont.
67

Fig. 2 (continued)
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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
94 Rana margaretae
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 92 Rana pretiosa
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 Rana omeimontis
77 Rana zhenhaiensis
93
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
100 63 Rana palustris
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
O 77
Rana brownorum
Rana taylori
72 Rana macroglossa

Fig. 2 (continued)
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R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 563

100Calyptocephallela 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 Ischnocnema juipoca
97
Ischnocnema holti
Brachycephalidae
100 Ischnocnema parva
93 Ischnocnema guentheri
98 66
Ischnocnema hoehnei
Q-S
P
T-AE
Fig. 2 (continued)
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564 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583

Adelophryne gutturosa
100 Phyzelaphryne miriamae
Diasporus diastema
Phyzelaphryninae Eleutherodactylus counouspeus
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
55 99 Eleutherodactylus bartonsmithi
81 Eleutherodactylus auriculatus
100 Eleutherodactylus principalis
Eleutherodactylus pinchoni
Eleutherodactylus barlagnei
85 100 100 Eleutherodactylus johnstonei
Eleutherodactylus amplinympha
97 Eleutherodactylus martinicensis
81 Eleutherodactylus flavescens
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
100 Eleutherodactylus nitidus
100 Eleutherodactylus pipilans
Eleutherodactylus klinikowskii
90 100 Eleutherodactylus zugi
86 98 Eleutherodactylus ventrilineatus
Eleutherodactylus brevirostris
100 Eleutherodactylus sciagraphus
Eleutherodactylus glandulifer
100 Eleutherodactylus paulsoni
100 Eleutherodactylus furcyensis
100 Eleutherodactylus rufifemoralis
64 97 Eleutherodactylus apostates
55 Eleutherodactylus oxyrhyncus
71 Eleutherodactylus jugans
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
71 Eleutherodactylus etheridgei
100 80100 98 Eleutherodactylus iberia
Eleutherodactylus jaumei
Eleutherodactylus limbatus
97 Eleutherodactylus alcoae
98 Eleutherodactylus armstrongi
Eleutherodactylus leoncei
100 Eleutherodactylus darlingtoni
Eleutherodactylus bresslerae
100 Eleutherodactylus ricordii
Eleutherodactylus acmonis
Eleutherodactylus probolaeus
Eleutherodactylus monensis
100 100 Eleutherodactylus pictissimus
Eleutherodactylus grahami
77 Eleutherodactylus lentus
74 Eleutherodactylus rhodesi
90 83 Eleutherodactylus weinlandi
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
Q
Eleutherodactylus glaucoreius
92 Eleutherodactylus cundalli
Eleutherodactylus pentasyringos
86 Eleutherodactylus pantoni

Fig. 2 (continued)
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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 mon tanus
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 80 Craugastor fitzingeri
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
76Phrynopuspesantesi
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 Oreobates saxatilis
100
100 Oreobates choristolemma
81
100 Oreobates sanctaecrucis
Oreobates granulosus
76 98 Oreobates sanderi
Pristimantinae 100 Oreobates discoidalis
Oreobates ibischi
87 Oreobates cruralis
Oreobates heterodactylus
65 Oreobates madidi
R Pristimantinae cont.

Fig. 2 (continued)
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566 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583

Pristimantinae cont. Pristimantis ashkapara

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
99 Pristimantis chiastonotus
99 Pristimantis koehleri
50
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 Pristimantis thymelensis
85
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
76 Pristimantis bromeliaceus
94 Pristimantis schultei
58
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
Pristimantis cryophilius
99 100 Pristimantis spinosus
81 Pristimantis phoxocephalus
100 Pristimantis versicolor
86 Pristimantis riveti
Pristimantis orestes
78 100 Pristimantis simonbolivari
93 Pristimantis chalceus
Pristimantis parvillus
100 100 Pristimantis luteolateralis
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
S 77
100 Pristimantis imitatrix
Pristimantis croceoinguinis
Pristimantis llojsintuta

Fig. 2 (continued)
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R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583 567

100 Flectonotus fitzgeraldi

Flectonotus pygmaeus
61 Hemiphractus scutatus
100 Hemiphractus helioi
100
Hemiphractidae 100 Hemiphractusproboscideus
Hemiphractus bubalus
Stefania ginesi
100
Stefania schuberti
65
100 Stefania coxi
81 Stefania scalae
100 Stefania evansi
64
Gastrotheca fissipes
Gastrotheca walkeri
100 Gastrotheca guentheri
100 Gastrotheca weinlandii
100 98
Gastrotheca dendronastes
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-
cause relationships amongst these groups are weakly supported,
we split these clades into multiple, strongly supported families,
rather than recognizing larger, weakly supported families that
would possibly be found non-monophyletic in future studies.
The subfamily Ceratophryinae is the sister group to all other
members of this clade (Fig. 2Z). Although this placement of the
group is weakly supported, monophyly of Ceratophryinae is well
supported. We restrict the family Ceratophryidae to include only
this subfamily. Within the sister group to ceratophryids is a
strongly supported clade (BS = 100%) that includes the cyclor-
hamphid alsodine genera Macrogenioglottus, Odontophrynus, and
Proceratophrys. This clade is here named Odontophrynidae,
corresponding to the former telmatobiine leptodactylid tribe
Odontophrynini (Lynch, 1971). Within the larger sister-group of
Odontophrynidae is a weakly supported clade comprising the gen-
era Insuetophrynus, Rhinoderma, Batrachyla (B. leptopus), Atelogna-
thus, and Telmatobius. Within this clade, the cycloramphid genera
Insuetophrynus and Rhinoderma are strongly supported as sister
taxa, for which we resurrect the family Rhinodermatidae (Günther,
1858). This family was widely recognized prior to revision by Frost
et al. (2006), but containing only Rhinoderma (e.g., Duellman and
Trueb, 1994).
The sister group to Rhinodermatidae (Fig. 2Z) is a strongly sup-
ported clade consisting of Atelognathus and Batrachyla leptopus
(type species of the genus; ASW), a clade corresponding primarily
to the ceratophryid subfamily Batrachylinae. We recognize this
clade as a distinct family (Batrachylidae). The other two Batrachyla
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Phrynomedusa marginata
Cruziohyla calcarifer
Hylidae: 100 Hylomantis aspera
Phyllomedusinae Hylomantis granulosa
100 100 Hylomantis lemur
Hylomantis hulli
78 Pachymedusa dacnicolor

Hylidae cont.
100 100 Agalychnis litodryas
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)
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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 Litoria darlingtoni
100 92
Hylidae: 99 Litoria amboinensis
58 100 Litoria congenita
Pelodryadinae Litoria dentata
Litoria rubella
72 Litoria electrica
Litoria jervisiensis
Litoria ewingii
100 Litoria littlejohni
81
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
55 Litoria citropa
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 Litoria cyclorhyncha
80
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
V 74 Litoria longipes
79 Litoria maculosa
53 Litoria maini

Fig. 2 (continued)
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570 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583

Myersiohyla inparquesi
Myersiohyla kanaima
Hylidae: Hyloscirtus simmonsi
71
Hylinae Hyloscirtus colymba
100
98 Hyloscirtus phyllognathus
Hyloscirtus palmeri
100 65 Hyloscirtus lascinius
Hyloscirtus armatus
63 100 Hyloscirtus charazani
Hylinae cont. Hyloscirtus tapichalaca
94 Hyloscirtus lindae
100
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 Hypsiboas dentei
100
Hypsiboas calcaratus
Hypsiboas lanciformis
57 83
55 Hypsiboas multifasciatus
100 Hypsiboas albopunctatus
Hypsiboas pellucens
100
Hypsiboas rufitelus
Hypsiboas albomarginatus
94 Hypsiboas rosenbergi
66 99
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
100 79
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,
Eupsophus, and Hylorina (see below). The sister group to the clade
of Rhinodermatidae + Batrachylidae is the ceratophryid genus Tel-
matobius (Fig. 2Z). We resurrect the family Telmatobiidae (Miran-
da-Ribeiro, 1920) for this strongly supported clade (containing
only Telmatobius, which likely contains Batrachophrynus; ASW),
which was previously recognized as a ceratophryid subfamily
(Telmatobiinae) by ASW and AW. Next up the tree is a moderately
well supported clade (BS = 79%) consisting of two cycloramphid
genera, the cycloramphine genus Cycloramphus and the alsodine
genus Thoropa. We recognize this clade as the family Cycloramphi-
dae (a greatly restricted version relative to current classifications).
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Hylinae cont.
100 Sphaenorhynchus orophilus
97 Sphaenorhynchus lacteus
Sphaenorhynchus dorisae
100 Scinax berthae
Scinax catharinae
97 Scinax uruguayus
Scinax acuminatus
100 Scinax boulengeri
100
95 Scinax sugillatus
52 Scinax rostratus
96 Scinax nebulosus
60 Scinax proboscideus
97 Scinax jolyi
65
Scinax garbei
Scinax crospedospilus
Scinax squalirostris
51 Scinax elaeochroa
95 Scinax staufferi
88
Scinax boesemani
96 Scinax cruentommus
80
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 Dendropsophus robertmertensi
81
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 Osteocephalus buckleyi
99
Osteocephalus verruciger
100 Osteocephalus alboguttatus
97 Osteocephalus planiceps
85 Osteocephalus leprieurii
X 87
100
Osteocephalus taurinus
Osteocephalus oophagus
Hylinae cont.

Fig. 2 (continued)
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572 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583

100 Acris gryllus

Hylidae cont. 90 Acris blanchardi
98 Acris crepitans
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
68 Plectrohyla guatemalensis
Plectrohyla matudai
96 Plectrohyla siopela
80 Plectrohyla arborescandens
Plectrohyla cyclada
56 Plectrohyla ameibothalame
Plectrohyla bistincta
74 Plectrohyla pentheter
83 Plectrohyla calthula
84
Ecnomiohyla minera
92 100 Ecnomiohyla miliaria
100 Ecnomiohyla miotympanum
Ptychohyla spinipollex
Bromeliohyla bromeliacia
88 Duellmanohyla soralia
Duellmanohyla rufioculis
100 89 Ptychohyla dendrophasma
Ptychohyla hypomykter
99 Ptychohyla euthysanota
100 Ptychohyla leonhardschultzei
89
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
100 Hyla femoralis
61 Hyla versicolor
100 Hyla chrysoscelis
98 100 Hyla avivoca
Hyla japonica
Hyla immaculata
80 Hyla arenicolor
Hyla wrightorum
95 Hyla walkeri
95 Hyla eximia
96 Hyla euphorbiacea
Y 83
73 Hyla plicata

Fig. 2 (continued)

The sister group to Cycloramphidae consists of Hylodidae
(strongly supported as monophyletic), and a clade consisting of
some of the former alsodine cycloramphid genera (Alsodes, Eupso-
phus, Hylorina, Limnomedusa) and two species of the ceratophryid
genus Batrachyla. Support for the monophyly of this group is
relatively weak (54%) including Limnomedusa but is strong (91%)
without it. We tentatively recognize this clade as a distinct family
(Alsodidae), comprising Alsodes, Eupsophus, Hylorina, and Limnome-
dusa. This is the only family that we recognize (that was not in-
cluded in previous classifications) that is not strongly supported,
but we prefer this taxonomy as opposed to recognizing a mono-
typic family containing only Limnomedusa. While we generally
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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 100 Odontophrynus occidentalis
99 Odontophrynus achalensis
85 Proceratophrys cristiceps
Proceratophrys schirchi
57 Proceratophrys melanopogon
50 Proceratophrys appendiculata
100 Proceratophrys bigibbosa
Proceratophrys avelinoi
Proceratophrys goyana
67 59 Proceratophrys concavitympanum
99 Odontophrynus moratoi
Proceratophrys cururu
Proceratophrys laticeps
77 Proceratophrys boiei
99
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
Telmatobius verrucosus
73 85 71 Telmatobius sanborni
57 Telmatobiusvilamensis
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
92 Crossodactylus schmidti
97
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 represents a special case, being split between two fam-
ilies. As Batrachyla taeniata, Batrachyla antartandica, and Hylorina
sylvatica are strongly placed within Eupsophus, we synonymize
those three species with Eupsophus. We keep the other two
Batrachyla species (Batrachyla fitzroya and Batrachyla nibaldoi) in
Batrachyla with the type species B. leptopus in Batrachylidae.
In summary, our new taxonomy replaces the non-monophyletic
interdigitating families Ceratophryidae and Cycloramphidae with a
somewhat larger set of families that are each generally strongly
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Paratelmatobiinae 93 Scythrophrys sawayae

93 Paratelmatobius cardosoi
Leiuperinae Paratelmatobius poecilogaster
100
Paratelmatobius gaigeae
Pseudopaludicola falcipes
Pleurodema brachyops
91 Pleurodema marmoratum
65 Pleurodema bufoninum
99
94 Pleurodem a 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
79 98
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)
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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
61 88
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
66 Vitreorana oyampiensis
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 Sachatamia punctulata
100
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 griffiths i
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-
ment of the cycloramphid genera Rupirana (no subfamily assigned
by AW or ASW), Zachaenus, and Crossodactylodes (both previously
Cycloramphinae; AW; ASW) are uncertain in our classification
(Hyloidea incertae sedis), given the lack of molecular data for these
genera and the apparent problems in the previous taxonomy
(Figs. 1 and 2Z). Assuming that they are cycloramphids as the fam-
ily is defined here (Figs. 1 and 2; Appendix B) may be incorrect.
We also find that the currently recognized families Leiuperidae
and Leptodactylidae are also problematic (Fig. 2AA). Our results
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Rheobates palmatus
98 Anomaloglossus stepheni
100 Anomaloglossus baeobatrachus
Anomaloglossus tepuyensis
100 Anomaloglossus degranvillei
87 Anomaloglossus praderioi
100 Anomaloglossus roraima
64
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
88 Allobatesgasconi
85 Allobates caeruleodactylus
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
80 Hyloxalus leucophaeus
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
Dendrobatescaptivus
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
AC Dendrobates amazonicus
Dendrobates variabilis
59 Dendrobates ventrimaculatus

Fig. 2 (continued)
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100 Melanophryniscusrubriventris
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
100 100 Atelopus bomolochos
Atelopus longirostris
Atelopus spurrelli
70 Atelopus chiriquiensis
100 98
90 Atelopus zeteki
81 Atelopus varius
100 Atelopus senex
100 Osornophryne sumacoensis
Osornophryne guacamayo
Osornophryne puruanta
61 Osornophryne antisana
99
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
54 64 Bufo arenarum
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 Bufo occidentalis
58
95 Bufo tacanensis
100 Bufo canaliferus
Bufo marmoreus
95 Bufo fastidiosus
90
Bufo coniferus
100 100 Bufo coccifer
Bufo cycladen
65 84 Bufo ibarrai
Bufo melanochlorus
90 100 Bufo luetkenii
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 Bufo debilis
97
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 Bufonidae cont.
100 Bufo americanus
97 Bufo houstonensis

Fig. 2 (continued)
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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
57 Bufo brauni
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 Bufo hololius
100
97 Bufo stomaticus
73 Bufo crocus
Bufo stuarti
98 Bufo himalayanus
62 100 Bufo scaber
100 Bufo atukoralei
Bufo melanostictus
AE 99
100 Bufo brevirostris
55 Bufo parietalis

Fig. 2 (continued)
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R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583
(Fig. 2AA) show that Leptodactylidae is paraphyletic with respect
to Leiuperidae, given that the leptodactylid genera Paratelmatobius
and Scythrophrys are more closely related to leiuperids than they
are to other leptodactylids (although this is not strongly sup-
ported). We solve this taxonomic problem by expanding Leptodac-
tylidae to again include all leiuperid genera, and recognizing
Leiuperinae and Leptodactylinae as subfamilies. This arrangement
treats Leptodactylidae as the strongly supported clade (BS = 79%)
of mostly foam-nesting frogs that has long been recognized as
behaviorally and morphologically distinctive (as the leptodactyline
leptodactylids; Lynch, 1971; Duellman and Trueb, 1994). We con-
sider this preferable to recognizing a new family for Paratelmatobi-
us and Scythrophrys, genera for which we recognize a new
subfamily (Paratelmatobiinae subfam. nov.; Appendix A), to avoid
a paraphyletic Leptodactylinae.
According to our results, the family Strabomantidae (sensu AW,
ASW) is also paraphyletic (Fig. 2R). Strabomantidae is a recently
described family (Hedges et al., 2008) that includes many species
that were traditionally classified as Eleutherodactylus (in the family
Leptodactylidae; see ASW). Specifically, we find that the strabo-
mantid genera Hypodactylus and Strabomantis are more closely re-
lated to craugastorids (Haddadus, Craugastor) than they are to the
other sampled strabomantid genera (e.g., Barycholos, Bryophryne,
Holoaden, Lynchius, Noblella, Oreobates, Phrynopus, Pristimantis,
Psychrophrynella). To resolve this problem (and to reduce the pro-
liferation of terraranan families), we subsume Strabomantidae into
Craugastoridae, given that Craugastoridae occurs first in Hedges
et al. (2008), though we recognize that this is an arbitrary criterion.
Within Craugastoridae, we recognize a subfamily Craugastorinae
(Fig. 2R) that corresponds to the previously recognized family
(e.g., Hedges et al., 2008; AW, ASW).
The former members of Strabomantidae are apportioned among
three strongly supported clades (which we recognize as subfamilies
within Craugastoridae) and one weakly supported clade (which we
consider incertae sedis). One of the strongly supported clades con-
sists solely of the genus Strabomantis, for which we recognize
a restricted subfamily Strabomantinae (Appendix B). Another com-
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
comprises the genera Lynchius, Oreobates, Phrynopus, and Pristiman-
tis. We recognize this clade as a new subfamily, Pristimantinae sub-
fam. nov. (see Appendix A for formal definition). The weakly
supported clade is the genus Hypodactylus. Rather than recognizing
a new subfamily for this genus (or allowing it to render other sub-
families non-monophyletic), we consider this genus incertae sedis,
along with several other genera of the former Strabomantidae that
were not included in this (or other molecular phylogenies), includ-
ing Atopophrynus, Dischiodactylus, Geobatrachus, Mucubatrachus,
Niceforonia, and Paramophrynella. In theory, some of these closely re-
lated subfamilies could be combined (e.g., Craugastorinae and Strab-
omantinae or Holoadeninae and Pristimantinae), but the resulting
subfamilies would then not be strongly supported.
As in most previous studies (Darst and Cannatella, 2004; Roe-
lants et al., 2007; Wiens, 2007a, 2011), we find strong support
for monophyly of Hyloidea, but relationships among the families
are weakly supported (Figs. 1 and 2P-AE). Therefore, we do not
present extensive comparison of among-family relationships be-
tween our study and previous studies. Nevertheless, there are
some intriguing patterns that occur in multiple studies, such as
placement of bufonids with dendrobatids (e.g., this study, Frost
et al., 2006; Roelants et al., 2007; Wiens, 2011). We also corrobo-
rate the monophyly and current composition of Brachycephalidae
(Hedges et al., 2008), Hemiphractidae (Wiens et al., 2007a,b;
Wiens, 2011), Hylidae (with subfamilies Hylinae, Phyllomedusinae,
and Pelodryadinae; Wiens et al., 2010), Bufonidae (Pramuk et al.,
579
2008; Van Bocxlaer et al., 2009), Allophrynidae and Centrolenidae.
Within Centrolenidae (Fig. 2AB), we support the subfamilies Cen-
troleninae and Hyalinobatrachinae, and we place the previously
incertae sedis genus Ikakogi in Centroleninae with strong (70%)
bootstrap support. We do not recognize a family Aromobatidae
separate from Dendrobatidae, as there is no phylogenetic justifica-
tion for splitting Dendrobatidae (Fig. 2AC). We follow Santos et al.
(2009) in recognizing a single family Dendrobatidae, including the
former aromobatids and containing no subfamilies (see also AW).
Our higher-level phylogeny within Ranoidea is generally similar
to other recent estimates (e.g., Frost et al., 2006; Roelants et al., 2007;
Wiens, 2011), and many of these relationships are well supported in
our study and previous studies (e.g., among brevicipitids, hemisot-
ids, microhylids, hyperoliids, arthroleptids). Our results also support
current delimitation of subfamilies (Figs. 1 and 2H–I; see Appendix
B) in Microhylidae (van der Meijden et al., 2007) and Arthroleptidae
(including Astylosterninae; see ASW). Some previous taxonomies
(e.g., Bossuyt et al., 2006; Wiens et al., 2009) and current taxonomies
(including AW) recognize a large (>1400 species) family Ranidae
(with 13 subfamilies) as the sister group to all other ranoids. Other
recent authors have considered these subfamilies distinct families
(Bossuyt and Roelants, 2009; Frost et al., 2006; Roelants et al.,
2007). We follow this latter arrangement here, recognizing the fam-
ilies Ptychadenidae, Micrixalidae, Phrynobatrachidae, Conrauidae,
Petropedetidae, Pyxicephalidae, Nyctibatrachidae, Ceratobatrachi-
dae, Ranixalidae, Dicroglossidae, Ranidae, and Rhacophoridae, and
Mantellidae, all of which are strongly supported (Figs. 1 and 2J–O).
Within these families, subfamilies follow Frost (2011): within Pyxi-
cephalidae, we recognize Cacosterninae and Pyxicephalinae;
Dicroglossidae comprises Occidozyginae and Dicroglossinae; Rhac-
ophoridae consists of Buergeriinae and Rhacophorinae; and Mantel-
lidae is composed of Laliostominae, Boophinae, and Mantellinae
(Figs. 1 and 2J–O). Relationships among many of these families re-
main poorly supported, as in previous studies (Roelants et al.,
2007; Wiens et al., 2009). Given the extensive sampling of taxa in
this clade, resolving their relationships may instead require adding
many more characters (i.e., more genes).
4. Discussion
4.1. Systematics of extant lissamphibians
Here, we provide a large-scale estimate of amphibian phylogeny,
containing over 2800 species (42% of the known extant diversity).
This phylogeny is largely congruent with those of several recent
molecular analyses (Frost et al., 2006; Roelants et al., 2007; Wiens,
2007a, 2011). Nevertheless, our increased sampling of taxa and
characters (especially among former leptodactylid frogs) reveals
that several currently recognized families are not monophyletic as
currently delimited (i.e., Ceratophryidae, Cycloramphidae, Lepto-
dactylidae, Strabomantidae). To correct these problems, we present
a new classification of extant amphibians. We have been as conser-
vative as possible in our taxonomic changes, such that deviations
from current taxonomy are made only when necessitated by non-
monophyly of higher taxa, and in such a way that newly recognized
taxa are strongly supported (with the exception of Alsodidae as de-
scribed above). It is possible that future phylogenies might reveal
some of our changes to be unnecessary (e.g., in cases where there
was weak support for non-monophyly of families, future analyses
might strongly resolve them as monophyletic). However, by focus-
ing on only strongly supported clades, the higher taxa that we recog-
nize should not be misleading, even as new data are added. We are
also conservative in that we only address taxonomy at the subfamily
level and above, given that our sampling of genera is mostly com-
plete whereas our sampling of species is not. Nevertheless, our study
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580 R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583
corroborates previous studies showing the paraphyly of numerous
genera (e.g., Bufo, Rana) and shows many additional genera to be
non-monophyletic (e.g., Batrachyla). Importantly, our study also
provides a framework to which additional sequences can be readily
added. Our data matrix is available at Dryad repository doi:10.5061/
dryad.vd0m7. It should thus be relatively straightforward to add
more taxa to this tree.
4.2. Supermatrices and large-scale phylogenetic inference
This analysis corroborates several recent studies suggesting that
the supermatrix approach is a powerful strategy for large-scale
phylogenetic inference (e.g., Driskell et al., 2004; McMahon and
Sanderson, 2006; Thomson and Shaffer, 2010; Pyron et al., 2011;
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-
onomy, often with very strong support. In cases where we found
that currently recognized families were not monophyletic, this
was not due to species being randomly placed on the tree, but
rather due to differences in the placement of strongly supported
clades of species and genera. Moreover, all of our 67 families and
all but two of the 50 subfamilies are strongly supported.
Despite the overall strong support for most of the tree (i.e., 64%
of all nodes have BS >70), certain clades remain poorly supported.
Therefore, a potential criticism of the supermatrix approach is that
this poor support may have arisen due to missing data in many
taxa. However, several lines of evidence suggest that this is not
the case. First, many previous studies have shown that there is typ-
ically little relationship between the support for clades and the
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
see Wiens and Morrill, 2011). Second, we find that most of the
clades that are weakly supported in our study are also weakly sup-
ported in other studies that have more limited missing data (and
the same is true for strongly supported clades). For example, in
their study of extant amphibian phylogeny based on multiple nu-
clear and mitochondrial genes (with little missing data), Roelants
et al. (2007) showed weak support for relationships among hyloid
families, microhylid subfamilies, and the families of former ranids,
but strong support for relationships among the major clades of
frogs, salamanders, and caecilians. These same patterns of weak
and strong support appear in our study (Fig. 1). Previous studies
suggest that these patterns of support are more likely to reflect
underlying branch lengths, such as weak support for short
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-
scale phylogenies with the supermatrix approach. Nevertheless,
one aspect of our sampling design may have greatly facilitated
the integration of the different genes used in this study. Specifi-
cally, 90% of the species had sequence data for the 16S gene and
81% had data for 12S. Thus, most species had comparable data
for at least one gene, which may have greatly facilitated placing
them on the tree with only a limited amount of character data
(Wiens et al., 2005b). Although it is possible to reconstruct a phy-
logeny when missing and non-missing data are randomly distrib-
uted among characters, the number of genes and characters
required to obtain accurate phylogenies may be much higher than
when the non-missing data are all in the same characters (e.g.,
Wiens, 2003). A clear lesson for future studies is that adding taxa
to this large-scale phylogeny will be greatly facilitated if research-
ers include these same 12S and 16S genes, along with widely sam-
pled nuclear genes such as RAG-1. Increasing sampling of the other
nuclear genes may be advantageous as well.
Acknowledgments
We thank the many researchers who made this study possible
through their detailed studies of amphibian phylogeny with a (mostly)
shared set of molecular markers, and uploading their sequence data to
GenBank. We would like to thank F.T. Burbrink (CUNY-CSI), J. Lom-
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
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
A. Larson, and two anonymous reviewers for helpful comments that
substantially improved this manuscript.
Appendix A. Description of new subfamilies
Pristimantinae subfam. nov. (family Craugastoridae)
Type: genus and species Pristimantis galdi Jiménez de la
Espada, 1870.
Content: four genera, >465 species; Lynchius, Oreobates,
Phrynopus, Pristimantis.
Phylogenetic Definition: this subfamily consists of the most
recent common ancestor of Lynchius, Oreobates, Phrynopus,
and Pristimantis, and all descendants thereof.
Distribution: these frogs are primarily restricted to the Andes
and Amazon Basin of South America (Hedges et al., 2008).
Remarks: The four genera of this subfamily are grouped with
strong support (81% BS proportion; Fig. 2R), and we find
weak support for their placement as the sister group to
Holoadeninae (Fig. 2R).
Paratelmatobiinae subfam. nov. (family Leptodactylidae)
Type: genus and species Paratelmatobius lutzii Lutz and
Carvalho 1958.
Content: two genera, eight species; Paratelmatobius and
Scythrophrys.
Phylogenetic Definition: this subfamily consists of the most
recent common ancestor of Paratelmatobius and
Scythrophrys, and all descendants thereof.
Distribution: these frogs are primarily restricted to southern
and eastern Brazil (AW; ASW).
Remarks: The two genera of this subfamily are grouped with
strong support (93% BS proportion), and we find weak
support for placing them as the sister group of Leiuperinae
(Fig. 2AA).
Appendix B. Generic content of families and subfamilies
The list below accounts for all extant amphibian genera currently
recognized by AW and ASW, with family and subfamily classification
updated to reflect our phylogenetic estimate and taxonomic changes.
The 72 genera not sampled in our phylogeny are either included in
their previously delimited groups (when these were found to be
strongly supported), or considered incertae sedis (along with any
sampled taxa explicitly delimited as such) when their placement
was ambiguous due to non-monophyly of previously recognized
higher taxa. As noted above, Lissamphibia also contains numerous
extinct taxa, including gymnophionans, caudates, and anurans,
which are not considered here (Marjanović and Laurin, 2007).
B.1. Gymnophiona
Caeciliidae: incertae sedis: (Atretochoana, Brasilotyphlus, Idiocra-
nium, Indotyphlus, Microcaecilia, Mimosiphonops, Nectocaecilia, Par-
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R. Alexander Pyron, J.J. Wiens / Molecular Phylogenetics and Evolution 61 (2011) 543–583
vicaecilia, Potomotyphlus, Sylvacaecilia); Caeciliinae (Caecilia,
Chthonerpeton, Dermophis, Gegeneophis, Geotrypetes, Grandisonia,
Gymnopis, Hypogeophis, Luetkenotyphlus, Oscaecilia, Praslinia,
Typhlonectes, Schistometopum, Siphonops), Herpelinae (Herpele,
Boulengerula), Scolecomorphinae (Crotaphotrema, Scolecomorphus);
Ichthyophiidae: Caudacaecilia, Ichthyophis, Uraeotyphlus; Rhinatr-
ematidae: Epicrionops, Rhinatrema.
B.2. Caudata
Ambystomatidae: Ambystoma; Amphiumidae: Amphiuma;
Cryptobranchidae: Andrias, Cryptobranchus; Dicamptodontidae:
Dicamptodon; Hynobiidae: Batrachuperus, Hynobius, Liua, Onycho-
dactylus, Pachyhynobius, Paradactylodon, Protohynobius, Pseudohyno-
bius, Ranodon, Salamandrella; Plethodontidae: Bolitoglossinae
(Batrachoseps, Bolitoglossa, Bradytriton, Chiropterotriton, Cryptotriton,
Dendrotriton, Ixalotriton, Lineatriton, Nototriton, Nyctanolis, Oedipina,
Parvimolge, Pseudoeurycea, Thorius), Hemidactylinae (Hemidactyli-
um), Plethodontinae (Aneides, Desmognathus, Ensatina, Hydromantes,
Karsenia, Phaeognathus, Plethodon), Spelerpinae (Eurycea, Gyrinophi-
lus, Haideotriton, Pseudotriton, Stereochilus, Urspelerpes); Proteidae:
Necturus, Proteus; Rhyacotritonidae: Rhyacotriton; Salamandri-
dae: Pleurodelinae (Calotriton, Cynops, Echinotriton, Euproctus,
Ichthyosaura, Laotriton, Lissotriton, Neurergus, Notophthalmus,
Ommatotriton, Pachytriton, Paramesotriton, Pleurodeles, Taricha, Trit-
urus, Tylototriton), Salamandrinae (Chioglossa, Lyciasalamandra, Mer-
tensiella, Salamandra), Salamandrininae (Salamandrina); Sirenidae:
Siren, Pseudobranchus.
B.3. Anura
Incertae sedis in Hyloidea (Crossodactylodes, Rupirana,
Zachaenus).
Allophrynidae: Allophryne; Alsodidae: Alsodes, Eupsophus, Lim-
nomedusa; Alytidae: Alytes; Arthroleptidae: Arthroleptinae (Athro-
leptis, Cardioglossa), Astylosterninae (Astylosternus, Leptodactylodon,
Nyctibates, Scotobleps, Trichobatrachus), Leptopelinae (Leptopelis);
Ascaphidae: Ascaphus; Batrachylidae: Atelognathus, Batrachyla;
Bombinatoridae: Barbaroula, Bombina; Brachycephalidae: Brachy-
cephalus, Ischnocnema; Brevicipitidae: Balebreviceps, Breviceps,
Callulina, Probreviceps, Spelaeophryne; Bufonidae: Adenomus, Altiph-
rynoides, Andinophryne, Ansonia, Atelopus, Bufo, Bufoides, Capensi-
bufo, Churamiti, Crepidophryne, Dendrophryniscus, Didynamipus,
Frostius, Laurentophryne, Leptophryne, Melanophryniscus, Merten-
sophryne, Metaphryniscus, Nectophryne, Nectophrynoides, Nimbaph-
rynoides, Oreophrynella, Osornophryne, Parapelophryne, Pedostibes,
Pelophryne, Pseudobufo, Rhamphophryne, Sabahphrynus, Schismader-
ma, Spinophrynoides, Stephopaedes, Truebella, Werneria, Wolterstorffi-
na; Calyptocephalellidae: Calyptocephalella, Telmatobufo;
Centrolenidae: Centroleninae (Centrolene, Chimerella, Cochranella,
Espadarana, Ikakogi, Nymphargus, Rulyrana, Sachatamia, Teratohyla,
Vitreorana), Hyalinobatrachinae (Celsiella, Hyalinobatrachium); Cer-
atobatrachidae: Batrachylodes, Ceratobatrachus, Discodeles, Inger-
ana, Palmatorappia, Platymantis; Ceratophryidae: Ceratophrys,
Chacophrys, Lepidobatrachus; Ceuthomantidae: Ceuthomantis; Con-
rauidae: Conraua; Craugastoridae: incertae sedis (Atopophrynus,
Dischiodactylus, Geobatrachus, Hypodactylus, Mucubatrachus, Nicef-
oronia, Paramophrynella), Craugastorinae (Craugastor, Haddadus),
Holoadeninae (Barycholos, Bryophryne, Euparkerella, Holoaden,
Noblella, Psychrophrynella), Pristimantinae (Lynchius, Oreobates,
Phrynopus, Pristimantis), Strabomantinae (Strabomantis); Cycloram-
phidae: Cycloramphus, Thoropa; Dendrobatidae: Allobates, Ameere-
ga, Anomaloglossus, Aromobates, Colostethus, Dendrobates,
Epipedobates, Hyloxalus, Mannophryne, Phyllobates, Rheobates,
Silverstoneia; Dicroglossidae: Dicroglossinae (Chaparana, Chirixalus,
Euphlyctis, Fejervarya, Hoplobatrachus, Limnonectes, Nannophrys,
581
Nanorana, Paa, Sphaerotheca), Occidozyginae (Ingerana, Occidozyga);
Discoglossidae: Discoglossus; Eleutherodactylidae: Eleutherodac-
tylinae (Diasporus, Eleutherodactylus), Phyzelaphryninae (Adeloph-
ryne, Phyzelaphryne); Heleophrynidae: Hadromophryne,
Heleophryne; Hemiphractidae: Cryptobatrachus, Flectonotus, Gas-
trotheca, Hemiphractus, Stefania; Hemisotidae: Hemisus; Hylidae:
Hylinae (Acris, Anotheca, Aparasphenodon, Aplastodiscus,
Argenteohyla, Bokermannohyla, Bromeliohyla, Charadrahyla, Corytho-
mantis, Dendropsophus, Diaglena, Duellmanohyla, Ecnomiohyla, Exer-
odonta, Hyla, Hyloscirtus, Hypsiboas, Isthmohyla, Itapotihyla,
Megastomatohyla, Myersiohyla, Nyctimantis, Osteocephalus, Osteopi-
lus, Phyllodytes, Plectrohyla, Pseudacris, Pseudis, Ptychohyla, Scarthyla,
Scinax, Smilisca, Sphaenorhynchus, Tepuihyla, Tlalocohyla, Trachy-
cephalus, Triprion, Xenohyla), Pelodryadinae (Litoria), Phyllomedusi-
nae (Agalychnis, Cruziohyla, Hylomantis, Pachymedusa, Phasmahyla,
Phrynomedusa, Phyllomedusa); Hylodidae: Crossodactylus, Hylodes,
Megaelosia; Hyperoliidae: Acanthixalus, Afrixalus, Alexteroon, Arl-
equinus, Callixalus, Chlorolius, Chrysobatrachus, Cryptothylax, Heterix-
alus, Hyperolius, Kassina, Kassinula, Morerella, Opisthothylax,
Paracassina, Phlyctimantis, Semnodactylus, Tachycnemis; Leiopel-
matidae: Leiopelma; Leptodactylidae: Leptodactylinae (Adenomera,
Hydrolaetere, Leptodactylus, Lithodytes), Leiuperinae (Edalorhina,
Engystomops, Eupemphix, Physalaemus, Pleurodema, Pseudopaludico-
la, Somuncuria), Paratelmatobiinae (Paratelmatobius, Scythrophrys);
Mantellidae: Boophinae (Boophis), Laliostominae (Aglyptodactylus,
Laliostoma), Mantellinae (Blommersia, Boehmantis, Gephyromantis,
Guibemantis, Mantella, Mantidactylus, Spinomantis, Tsingymantis,
Wakea); Megophryidae: Borneophrys, Brachytarsophrys, Leptobrach-
ella, Leptobrachium, Leptolalax, Megophrys, Ophryophryne, Oreolalax,
Scutiger, Vibrissaphora, Xenophrys; Micrixalidae: Micrixalus; Micro-
hylidae: incertae sedis (Gastrophrynoides, Paramophrynella),
Asterophryninae (Albericus, Aphantophryne, Asterophrys, Austrocha-
perina, Barygenys, Callulops, Choerophryne, Cophixalus, Copiula, Geny-
ophryne, Hylophorbus, Liophryne, Mantophryne, Oreophryne,
Oxydactyla, Pherohapsis, Sphenophryne, Xenorhina), Cophylinae
(Anodonthyla, Cophyla, Madecassophryne, Platypelis, Plethodontohyla,
Rhombophryne, Stumpffia), Dyscophinae (Dyscophus), Gastrophryni-
nae (Adelastes, Altigius, Arcovomer, Chiasmocleis, Ctenophryne, Dasy-
pops, Dermatonotus, Elachistocleis, Gastrophryne, Hamptophryne,
Hyophryne, Hypopachus, Melanophryne, Myersiella, Nelsonophryne,
Relictivomer, Stereocyclops, Syncope), Hoplophryninae (Hoplophryne,
Parhoplophryne), Kalophryninae (Kalophrynus), Melanobatrachinae
(Melanobatrachus), Microhylinae (Calluella, Chaperina, Glyphoglos-
sus, Kaloula, Metaphrynella, Microhyla, Micryletta, Ramanella, Uper-
odon), Otophryninae (Otophryne, Synapturanus), Phrynomerinae
(Phrynomantis), Scaphiophryne (Paradoxophyla, Scaphiophryne);
Myobatrachidae: Limnodynastinae (Adelotus, Heleioporus, Lechrio-
dus, Limnodynastes, Mixophyes, Neobatrachus, Notaden, Philoria,
Platyplectrum, Pseudophryne), Myobatrachinae (Arenophryne, Assa,
Crinia, Geocrinia, Metacrinia, Myobatrachus, Paracrinia, Rheobatra-
chus, Spicospina, Taudactylus, Uperoleia); Nasikabatrachidae: Nasik-
abatrachus; Nyctibatrachidae: Lankanectes, Nyctibatrachus;
Odontophrynidae: Macrogenioglottus, Odontophrynus, Proceratoph-
rys; Pelobatidae: Pelobates; Pelodytidae: Pelodytes; Petropedeti-
dae: Petropedetes; Phrynobatrachidae: Phrynobatrachus; Pipidae:
Hymenochirus, Pipa, Pseudhymenochirus, Silurana, Xenopus; Ptycha-
denidae: Hildebrandtia, Lanzarana, Ptychadena; Pyxicephalidae:
Cacosterninae (Amietia, Anhydrophryne, Arthroleptella, Cacosternum,
Ericabatrachus, Microbatrachella, Natalobatrachus, Nothophryne,
Poyntonia, Strongylopus, Tomopterna), Pyxicephalinae (Aubria,
Pyxicephalus); Ranidae: Amnirana, Amolops, Huia, Hylarana, Meris-
togenys, Odorrana, Pseudoamolops, Pterorana, Rana, Staurois; Ranix-
alidae: Indirana; Rhacophoridae: Buergeriinae (Buergeria),
Rhacophorinae (Chiromantis, Dendrobatorana, Feihyla, Ghatixalus,
Gracixalus, Kurixalus, Liuixalus, Nyctixalus, Philautus, Polypedates,
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:
Scaphiopus, Spea; Sooglossidae: Sechellophryne, Sooglossus; Telma-
tobiidae: Batrachophrynus, Telmatobius.
Appendix C. Supplementary material
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.ympev.2011.06.012.
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