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A phylogeny and revised classification of Squamata, including 4161 species of
lizards and snakes
BMC Evolutionary Biology 2013, 13:93 doi:10.1186/1471-2148-13-93
Robert Alexander Pyron (rpyron@colubroid.org)
Frank T Burbrink (frank.burbrink@csi.cuny.edu)
John J Wiens (wiensj@email.arizona.edu)
ISSN 1471-2148
Article type Research article
Submission date 30 January 2013
Acceptance date 19 March 2013
Publication date 29 April 2013
Article URL http://www.biomedcentral.com/1471-2148/13/93
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A phylogeny and revised classification of Squamata,
including 4161 species of lizards and snakes
Robert Alexander Pyron
1*

*
Corresponding author
Email: rpyron@colubroid.org
Frank T Burbrink
2,3

Email: frank.burbrink@csi.cuny.edu
John J Wiens
4

Email: wiensj@email.arizona.edu
1
Department of Biological Sciences, The George Washington University, 2023 G
St. NW, Washington, DC 20052, USA
2
Department of Biology, The Graduate School and University Center, The City
University of New York, 365 5th Ave., New York, NY 10016, USA
3
Department of Biology, The College of Staten Island, The City University of
New York, 2800 Victory Blvd., Staten Island, NY 10314, USA
4
Department of Ecology and Evolutionary Biology, University of Arizona,
Tucson, AZ 85721-0088, USA
Abstract
Background
The extant squamates (>9400 known species of lizards and snakes) are one of the most
diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to
reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is
invaluable for comparative evolutionary studies, and to address their classification. Here, we
present the first large-scale phylogenetic estimate for Squamata.
Results
The estimated phylogeny contains 4161 species, representing all currently recognized
families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data
per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos,
NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome
b, ND2, and ND4). The tree provides important confirmation for recent estimates of higher-
level squamate phylogeny based on molecular data (but with more limited taxon sampling),
estimates that are very different from previous morphology-based hypotheses. The tree also
includes many relationships that differ from previous molecular estimates and many that
differ from traditional taxonomy.
Conclusions
We present a new large-scale phylogeny of squamate reptiles that should be a valuable
resource for future comparative studies. We also present a revised classification of squamates
at the family and subfamily level to bring the taxonomy more in line with the new
phylogenetic hypothesis. This classification includes new, resurrected, and modified
subfamilies within gymnophthalmid and scincid lizards and boid, colubrid, and lamprophiid
snakes.
Keywords
Amphisbaenia, Lacertilia, Likelihood support measures, Missing data, Serpentes, Squamata,
Phylogenetics, Reptiles, Supermatrices, Systematics
Background
Squamate reptiles (lizards, snakes, and amphisbaenians ["worm lizards"]) are among the most
diverse radiations of terrestrial vertebrates. Squamata includes more than 9400 species as of
December 2012 [1]. The rate of new species descriptions shows no signs of slowing, with a
record 168 new species described in 2012 [1], greater than the highest yearly rates of the 18th
and 19th centuries (e.g. 1758, 118 species; 1854, 144 species [1]). Squamates are presently
found on every continent except Antarctica, and in the Indian and Pacific Oceans, and span
many diverse ecologies and body forms, from limbless burrowers to arboreal gliders
(summarized in [2-4]).
Squamates are key study organisms in numerous fields, from evolution, ecology, and
behavior [3] to medicine [5,6] and applied physics [7]. They have also been the focus of
many pioneering studies using phylogenies to address questions about trait evolution (e.g.
[8,9]). Phylogenies are now recognized as being integral to all comparative studies of
squamate biology (e.g. [10,11]). However, hypotheses about squamate phylogeny have
changed radically in recent years [12], especially when comparing trees generated from
morphological [13-15] and molecular data [16-20]. Furthermore, despite extensive work on
squamate phylogeny at all taxonomic levels, a large-scale phylogeny (i.e. including thousands
of species and multiple genes) has never been attempted using morphological or molecular
data.
Squamate phylogenetics has changed radically in the last 10 years, revealing major conflicts
between the results of morphological and molecular analyses [12]. Early estimates of
squamate phylogeny [21] and recent studies based on morphological data [13-15,22]
consistently supported a basal division between Iguania (including chameleons, agamids, and
iguanids, sensu lato), and Scleroglossa, which comprises all other squamates (including
skinks, geckos, snakes, and amphisbaenians). Within Scleroglossa, many phylogenetic
analyses of morphological data have also supported a clade containing limb-reduced taxa,
including various combinations of snakes, dibamids, amphisbaenians, and (in some analyses)
limb-reduced skinks and anguids [13-15,19,22], though some of these authors also
acknowledged that this clade was likely erroneous.
In contrast, recent molecular analyses have estimated very different relationships. Novel
arrangements include placement of dibamids and gekkotans near the root of the squamate
tree, a sister-group relationship between amphisbaenians and lacertids, and a clade
(Toxicofera) uniting Iguania with snakes and anguimorphs within Scleroglossa [16-20,23,24].
These molecular results (and the results of combined morphological and molecular analyses)
suggest that some estimates of squamate phylogeny based on morphology may have been
misled, especially by convergence associated with adaptations to burrowing [19]. However,
there have also been disagreements among molecular studies, such as placement of dibamids
relative to gekkotans and other squamates and relationships among snakes, iguanians, and
anguimorphs (e.g. [17,20]).
Analyses of higher-level squamate relationships based on molecular data have so far included
relatively few (less than 200) species, and none have included representatives from all
described families and subfamilies [17-20,23,24]. This limited taxon sampling makes existing
molecular phylogenies difficult to use for broad-scale comparative studies, with some
exceptions based on supertrees [10,11]. In addition, limited taxon sampling is potentially a
serious issue for phylogenetic accuracy [25-28]. Thus, an analysis with extensive taxon
sampling is critically important to test hypotheses based on molecular datasets with more
limited sampling and to provide a framework for comparative analyses.
Despite the lack of a large-scale phylogeny across squamates, recent molecular studies have
produced phylogenetic estimates for many of the major groups of squamates, including
iguanian lizards [29-34], higher-level snake groups [35-37], typhlopoid snakes [38,39],
colubroid snakes [40-46], booid snakes [47,48], scincid lizards [49-52], gekkotan lizards [53-
60], teiioid lizards [61-64], lacertid lizards [65-69], and amphisbaenians [70,71]. These
studies have done an outstanding job of clarifying the phylogeny and taxonomy of these
groups, but many were limited in some ways by the number of characters and taxa that they
sampled (and which were available at the time for sequencing).
Here, we present a phylogenetic estimate for Squamata based on combining much of the
existing sequence data for squamate reptiles, using the increasingly well-established
supermatrix approach [41,72-77]. We present a new phylogenetic estimate including 4161
squamate species. The dataset includes up to 12896 bp per species from 12 loci (7 nuclear, 5
mitochondrial). We include species from all currently described families and subfamilies. In
terms of species sampled, this is 5 times larger than any previous phylogeny for any one
squamate group [30,41], 3 times larger than the largest supertree estimate [11], and 25 times
larger than the largest molecular study of higher-level squamate relationships [20]. While we
did not sequence any new taxa specifically for this project, much of the data in the combined
matrix were generated in our labs or from our previous collaborative projects
[16,19,20,34,36,37,41,44,78-82], including thousands of gene sequences from hundreds of
species (>550 species; ~13% of the total).
The supermatrix approach can provide a relatively comprehensive phylogeny, and uncover
novel relationships not seen in any of the separate analyses in which the data were generated.
Such novel relationships can be revealed via three primary mechanisms. First, different
studies may have each sampled different species from a given group for the same genes, and
combining these data may reveal novel relationships not apparent in the separate analyses.
Second, different studies may have used different genetic markers for the same taxa, and
combining these markers can dramatically increase character sampling, potentially revealing
new relationships and providing stronger support for previous hypotheses. Third, even for
clades that were previously studied using complete taxon sampling and multiple loci, novel
relationships may be revealed by including these lineages with other related groups in a large-
scale phylogeny.
The estimated tree and branch-lengths should be useful for comparative studies of squamate
biology. However, this phylogeny is based on a supermatrix with extensive missing data
(mean = 81% per species). Some authors have suggested that matrices with missing cells may
yield misleading estimates of topology, support, and branch lengths [83]. Nevertheless, most
empirical and simulation studies have not found this to be the case, at least for topology and
support [41,73,84,85]. Though fewer studies have examined the effects of missing data on
branch lengths [44,86,87], these also suggest that missing data do not strongly impact
estimates. Here, we test whether branch lengths for terminal taxa are related to their
completeness.
In general, our results corroborate those of many recent molecular studies with regard to
higher-level relationships, species-level relationships, and the monophyly, composition, and
relationships of most families, subfamilies, and genera. However, our results differ from
previous estimates for some groups, and reveal (or corroborate) numerous problems in the
existing classification of squamates. We therefore provide a conservative, updated
classification of extant squamates at the family and subfamily level based on the new
phylogeny, while highlighting problematic taxonomy at the genus level, without making
changes. The generic composition of all families and subfamilies under our revised taxonomy
are provided in Appendix I.
We note dozens of problems in the genus-level taxonomy suggested by our tree, but we
acknowledge in advance that we do not provide a comprehensive review of the previous
literature dealing with all these taxonomic issues (this would require a monographic
treatment). Similarly, we do not attempt to fix these genus-level problems here, as most will
require more extensive taxon (and potentially character) sampling to adequately resolve.
Throughout the paper, we address only extant squamates. Squamata also includes numerous
extinct species classified in both extant and extinct families, subfamilies, and genera.
Relationships and classification of extinct squamates based on morphological data from
fossils have been addressed by numerous authors (e.g. [14,15,19,22,88-93]). A classification
based only on living taxa may create some problems for classifying fossil taxa, but these can
be addressed in future studies that integrate molecular and fossil data [19,86].
Results
Supermatrix phylogeny
We generated the final tree (lnL = 2609551.07) using Maximum Likelihood (ML) in
RAxMLv7.2.8. Support was assessed using the non-parametric Shimodaira-Hasegawa-Like
(SHL) implementation of the approximate likelihood-ratio test (aLRT; see [94]). The tree and
data matrix are available in NEXUS format in DataDryad repository 10.5061/dryad.82h0m
and as Additional file 1: Data File S1. A skeletal representation of the tree (excluding several
species which are incertae sedis) is shown in Figure 1. The full species-level phylogeny
(minus the outgroup Sphenodon) is shown in Figures 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28. The analysis yields a generally well-
supported phylogenetic estimate for squamates (i.e. 70% of nodes have SHL values >85,
indicating they are strongly supported). There is no relationship between proportional
completeness (bp of non-missing data in species / 12896 bp of complete data) and branch
length (r = 0.29, P = 0.14) for terminal taxa, strongly suggesting that the estimated branch
lengths are not consistently biased by missing data.
Figure 1 Higher-level squamate phylogeny. Skeletal representation of the 4161-species tree
from maximum-likelihood analysis of 12 genes, with tips representing families and
subfamilies (following our taxonomic revision; species considered incertae sedis are not
shown). Numbers at nodes are SHL values greater than 50%. The full tree is presented in
Figures 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,
27, 28, with panels indicated by bold italic letters.
Figure 2 Species-level squamate phylogeny. Large-scale maximum likelihood estimate of
squamate phylogeny, containing 4161 species. Numbers at nodes are SHL values greater than
50%. A skeletal version of this tree is presented in Figure 1. Bold italic letters indicate figure
panels (A). Within panels, branch lengths are proportional to expected substitutions per site,
but the relative scale differs between panels.
Figure 3 Species-level squamate phylogeny continued (B).
Figure 4 Figure 5 Species-level squamate phylogeny continued (D)
Species-level squamate phylogeny continued (D).
Figure 6 Species-level squamate phylogeny continued (E).
Figure 7 Species-level squamate phylogeny continued (F).
Figure 8 Species-level squamate phylogeny continued (G).
Figure 9 Species-level squamate phylogeny continued (H).
Figure 10 Species-level squamate phylogeny continued (I).
Figure 11 Species-level squamate phylogeny continued (J).
Figure 12 Species-level squamate phylogeny continued (K)
Species-level squamate phylogeny continued (K).
Figure 13 Species-level squamate phylogeny continued (L).
Figure 14 Species-level squamate phylogeny continued (M).
Figure 15 Species-level squamate phylogeny continued (N).
Figure 16 Species-level squamate phylogeny continued (O).
Figure 17 Species-level squamate phylogeny continued (P).
Figure 18 Species-level squamate phylogeny continued (Q).
Figure 19 Species-level squamate phylogeny continued (R).
Figure 20 Species-level squamate phylogeny continued (S).
Figure 21 Species-level squamate phylogeny continued (T).
Figure 22 Species-level squamate phylogeny continued (U).
Figure 23 Species-level squamate phylogeny continued (V).
Figure 24 Species-level squamate phylogeny continued (W).
Figure 25 Species-level squamate phylogeny continued (X).
Figure 26 Species-level squamate phylogeny continued (Y).
Figure 27 Species-level squamate phylogeny continued (Z).
Figure 28 Species-level squamate phylogeny continued (AA).
Higher-level relationships
Our tree (Figure 1) is broadly congruent with most previous molecular studies of higher-level
squamate phylogeny using both nuclear data and combined nuclear and mitochondrial data
(e.g. [16-20]), providing important confirmation of previous molecular studies based on more
limited taxon sampling. Specifically we support (Figure 1): (i) the placement of dibamids and
gekkotans near the base of the tree (Figure 1A); (ii) a sister-group relationship between
Scincoidea (scincids, cordylids, gerrhosaurids, and xantusiids; Figure 1B) and a clade
(Episquamata; Figure 1C) containing the rest of the squamates excluding dibamids and
gekkotans; (iii) Lacertoidea (lacertids, amphisbaenians, teiids, and gymnophthalmids; Figure
1D), and (iv) a clade (Toxicofera; Figure 1E) containing anguimorphs (Figure 1F), iguanians
(Figure 1G), and snakes (Figure 1H) as the sister taxon to Lacertoidea.
These relationships are strongly supported in general (Figure 1), but differ sharply from most
trees based on morphological data [13-15,19,22,95]. Nevertheless, many clades found in
previous morphological taxonomies and phylogenies are also present in this tree in some
form, including Amphisbaenia, Anguimorpha, Gekkota, Iguania, Lacertoidea (but including
amphisbaenians), Scincoidea, Serpentes, and many families and subfamilies. In contrast, the
relationships among these groups differ strongly between molecular analyses [17-20] and
morphological analyses [14,15]. Our results demonstrate that this incongruence is not
explained by limited taxon sampling in the molecular data sets. In fact, our species-level
sampling is far more extensive than in any morphological analyses (e.g. [14,15]), by an order
of magnitude.
We find that the basal squamate relationships are strongly supported in our tree. The family
Dibamidae is the sister group to all other squamates, and Gekkota is the sister group to all
squamates excluding Dibamidae (Figure 1), as in some previous studies (e.g. [16,18]). Other
recent molecular analyses have also placed Dibamidae near the squamate root, but differed in
placing it as either the sister taxon to all squamates excluding Gekkota [17], or the sister-
group of Gekkota [19,20]. Our results also corroborate that the New World genus
Anelytropsis is nested within the Old World genus Dibamus [96], but the associated branches
are weakly supported (Figure 2).
Gekkota
Within Gekkota, we corroborate both earlier morphological [97] and recent molecular
estimates [55,56,59,98] in supporting a clade containing the Australian radiation of
"diplodactylid" geckos (Carphodactylidae and Diplodactylidae) and the snakelike pygopodids
(Figures 1, 2). As in previous studies [55], Carphodactylidae is the weakly supported sister
group to Pygopodidae, and this strongly supported clade is the sister group to Diplodactylidae
(Figures 1, 2). We recover clades within the former Gekkonidae that correspond to the
strongly supported families Eublepharidae, Sphaerodactylidae, Phyllodactylidae, and
Gekkonidae as in previous studies, and similar relationships among these groups [55-
57,59,60,98-100].
Within Gekkota, we find evidence for non-monophyly of many genera. Many relationships
among the New Caledonian diplodactylids are weakly supported (Figure 2), and there is
apparent non-monophyly of the genera Rhacodactylus, Bavayia, and Eurydactylodes with
respect to each other and Oedodera, Dierogekko, Paniegekko, Correlophus, and Mniarogekko
[101]. In the Australian diplodactylids, Strophurus taenicauda is strongly supported as
belonging to a clade that is only distantly related to the other sampled Strophurus species
(Figure 2). The two species of the North African sphaerodactylid genus Saurodactylus are
divided between the two major sphaerodactylid clades (Figure 3), but the associated branches
are weakly supported. The South American phyllodactylid genus Homonota is strongly
supported as being paraphyletic with respect to Phyllodactylus (Figure 3).
A number of gekkonid genera (Figure 4) also appear to be non-monophyletic, including the
Asian genera Cnemaspis (sampled species divided into two non-sister clades),
Lepidodactylus (with respect to Pseudogekko and some Luperosaurus), Gekko (with respect
to Ptychozoon and Lu. iskandari), Luperosaurus (with respect to Lepidodactylus and Gekko),
Mediodactylus (with respect to Pseudoceramodactylus, Tropiocolotes, Stenodactylus,
Cyrtopodion, Bunopus, Crossobamon, and Agamura), and Bunopus (with respect to
Crossobamon), and the African Afrogecko (with respect to Afroedura, Christinus,
Cryptactites, and Matoatoa), Afroedura (with respect to Afrogecko, Blaesodactylus,
Christinus, Geckolepis, Pachydactylus, Rhoptropus, and numerous other genera),
Chondrodactylus (with respect to Pachydactylus laevigatus), and Pachydactylus (with respect
to Chondrodactylus and Colopus). Many of these taxonomic problems in gekkotan families
have been identified in previous studies (e.g. [59,99,102]), and extensive changes will likely
be required to fix them.
Scincoidea
We strongly support (SHL = 100; Figures 1, 5, 6, 7, 8, 9, 10) the monophyly of Scincoidea
(Scincidae, Xantusiidae, Gerrhosauridae, and Cordylidae), as in other recent studies [16-20].
All four families are strongly supported (Figures 5, 6, 7, 8, 9, 10). A similar clade is also
recognized in morphological phylogenies [14], though without Xantusiidae in some [13].
Within the New World family Xantusiidae, we corroborate previous analyses [103,104] that
found strong support for a sister-group relationship between Xantusia and Lepidophyma,
excluding Cricosaura (Figure 5). These relationships support the subfamily Cricosaurinae for
Cricosaura [105]. We also recognize Xantusiinae for the North American genus Xantusia
and Lepidophyminae for the Central American genus Lepidophyma [106,107].
Within the African and Madagascan family Gerrhosauridae (Figure 5), the genus
Gerrhosaurus is weakly supported as being paraphyletic with respect to the clade comprising
Tetradactylus + Cordylosaurus, with G. major placed as the sister group to all other
gerrhosaurids. Within Cordylidae (Figure 5), we use the generic taxonomy from a recent
phylogenetic analysis and re-classification based on multiple nuclear and mitochondrial genes
[108]. This classification broke up the non-monophyletic Cordylus [109] into several smaller
genera, and we corroborate the non-monophyly of the former Cordylus and support the
monophyly of the newly recognized genera (Figure 5). We find support the distinctiveness of
Platysaurus (Figure 5) and recognition of the subfamily Platysaurinae [108].
We find strong support (SHL = 100) for the monophyly of Scincidae (Figure 6) as in previous
studies (e.g. [20,50,51]). We find strong support for the basal placement of the monophyletic
subfamily Acontiinae (Figure 6), as found in some previous studies (e.g. [20,51]) but not
others (e.g. [50]). Similar to earlier studies, we find that the subfamily Scincinae sensu [110]
is non-monophyletic, as Feylininae is nested within Scincinae (also found in [20,50,51,111]).
Based on these results, synonymizing Feylininae with Scincinae produces a monophyletic
Scincinae (SHL = 97), which is then sister to a monophyletic Lygosominae (SHL = 100
excluding Ateuchosaurus; see below) with 94% SHL support (Figures 6, 7, 8, 9, 10). This
yields a new classification in which all three subfamilies (Acontiinae, Lygosominae,
Scincinae) are strongly supported. Importantly, these definitions approximate the traditional
content of the three subfamilies [50,110], except for recognition of Feylininae.
We note that a recent revision of the New World genus Mabuya introduced a nontraditional
family-level classification for Scincidae [112]. These authors divided Scincidae into seven
families: Acontiidae, Egerniidae, Eugongylidae, Lygosomidae, Mabuyidae, Scincidae and
Sphenomorphidae. However, there was no phylogenetic need for considering these clades as
families (or another rank below family), since the family Scincidae is clearly monophyletic,
based on our results and others (see above). Thus, their new taxonomy changes the long-
standing definition of Scincidae unnecessarily (see [113]). Furthermore, these changes were
done without defining the full content (beyond a type genus) of any of these families other
than Scincidae (the former Scincinae + Feylininae), and Acontiidae (the former Acontiinae).
Most importantly, the new taxonomy proposed by these authors [112] is at odds with the
phylogeny estimated here, with respect to the familial and subfamilial classification of >1000
skink species (Figures 6, 7, 8, 9, 10). For instance, Sphenomorphus stellatus is found in a
strongly supported clade containing Lygosoma (presumably Lygosomidae; Figure 10), which
is separate from the other clade (presumably Sphenomorphidae) containing the other sampled
Sphenomorphus species (Figure 7; but note that these Sphenomorphus species are divided
among several subclades within this latter clade). An additional problem is that Egernia,
Lygosoma, and Sphenomorphus are the type genera of Egerniidae, Lygosomidae, and
Sphenomorphidae, but are paraphyletic as currently defined (Figures 7, 8, 9, 10), leading to
further uncertainty in the content and definition of these putative families.
Furthermore, Mabuyidae apparently refers to the clade (Figure 9) containing Chioninia,
Dasia, Mabuya, Trachylepis, with each of these genera placed in its own subfamily
(Chioniniinae, Dasiinae, Mabuyinae, and Trachylepidinae). However, several other genera
are strongly placed in this group, such as Eumecia, Eutropis, Lankaskincus, and Ristella
(Figure 9). These other genera cannot be readily fit into these subfamilial groups (i.e. they are
not the sister group of any genera in those subfamilies), and Trachylepis is paraphyletic with
respect to Eumecia, Chioninia, and Mabuya (Figure 9). Also, we find that Emoia is divided
between clades containing Lygosoma (Lygosomidae) and Eugongylus (Eugongylidae), and
many of these relationships have strong support (Figure 10). Finally, Ateuchosaurus is
apparently not accounted for in their classification, and here is weakly placed as the sister-
group to a clade comprising their Sphenomorphidae, Egerniidae, Mabuyidae, and
Lygosomidae (i.e. Lygosominae as recognized here; Figures 7, 8, 9, 10).
These authors [112] argued that a more heavily subdivided classification for skinks may be
desirable for facilitating future taxonomic revisions and species descriptions. However, this
classification seems likely to only exacerbate existing taxonomic problems (e.g. placing
congeneric species in different families without revising the genus-level taxonomy). Here, we
retain the previous definition of Mabuya (restricted to the New World clade; sensu [114]),
and we support the traditional definitions of Scincidae, Acontiinae, Scincinae (but including
Feylininae), and Lygosominae (Figures 6, 7, 8, 9, 10; note that we leave Ateuchosaurus as
incertae sedis). The other taxonomic issues in Scincidae identified here and elsewhere should
be resolved in future studies. Our phylogeny provides a framework in which these analyses
can take place (i.e. identifying major subclades within skinks), which we think may be more
useful than a classification lacking clear taxon definitions.
Of the 133 scincid genera [1], we can assign the 113 sampled in our tree to one of the three
subfamilies in our classification (Acontiinae, Lygosominae, and Scincinae; Appendix I). We
place 19 of the remaining genera into one of the three subfamilies based on previous
classifications (e.g. [110]), with Ateuchosaurus as incertae sedis in Scincidae. Below, we
review the non-monophyletic genera in our tree. Many of these problems have been reported
by previous authors [51,111,115-118], and for brevity we do not distinguish between cases
reported in previous studies, and potentially new instances found here.
Within Acontiinae, we find that the two genera are both strongly supported as monophyletic
(Figure 6). Within Scincinae, many genera are now strongly monophyletic (thanks in part to
the dismantling of Eumeces; [49,50,119]), but some problems remain (Figure 6). The genera
Scincus and Scincopus are strongly supported as being nested inside of the remaining
Eumeces. Among Malagasy scincines (see [49,120]), Pseudacontias is nested inside
Madascincus, and the genera Androngo, Pygomeles, and Voeltzkowia are all nested in
Amphiglossus (Figure 6).
We also find numerous taxonomic problems with lygosomines (Figures 7, 8, 9, 10). Species
of Sphenomorphus are widely dispersed among other lygosomine genera. The genus
Tropidophorus is paraphyletic with respect to a clade containing many other genera (Figure
7). The sampled species of Asymblepharus are only distantly related to each other, including
one species (A. sikimmensis) nested inside of Scincella (Figure 7). The genus Lipinia is
polyphyletic, with one species (L. vittigera) strongly placed as the sister taxon to Isopachys,
and with two other species (L. pulchella and L. noctua) forming a well-supported clade that
also includes Papuascincus (Figure 7).
Among Australian skinks, the genus Eulamprus is polyphyletic with respect to Nangura,
Calyptotis, Gnypetoscincus, Coggeria, Coeranoscincus, Ophioscincus, Saiphos, Anomalopus,
Eremiascincus, Hemiergis, Glaphyromorphus, Notoscincus, Ctenotus, and Lerista, and most
of the relevant nodes are strongly supported (Figure 8). The genera Coeranoscincus and
Ophioscincus are polyphyletic with respect to each other and to Saiphos and Coggeria
(Figure 8). The genus Glaphyromorphus is paraphyletic with respect to a clade of Eulamprus
(Figure 8). The genus Egernia is paraphyletic with respect to Bellatorias (which is
paraphyletic with respect to Egernia and Lissolepis) and Lissolepis, although many of the
relevant nodes are not strongly supported (Figure 9). The genera Cyclodomorphus and
Tiliqua are paraphyletic with respect to each other (Figure 9).
Among other lygosomines, Trachylepis is non-monophyletic [121], with two species (T.
aurata and T. vittata) that fall outside the strongly supported clade containing the other
species (Figure 9). The latter clade is weakly supported as the sister group to a clade
containing Chioninia, Eumecia, and Mabuya. In Mabuya, a few species (M. altamazonica, M.
bistriata, and M. nigropuncata) have unorthodox placements within a monophyletic Mabuya,
potentially due to uncertain taxonomic assignment of specimens by previous authors
[51,122]. The genus Lygosoma is paraphyletic with respect to Lepidothyris and Mochlus, and
many of the relevant nodes are strongly supported (Figure 10). Among New Caledonian
skinks, the genus Lioscincus is polyphyletic with respect to Marmorosphax, Celatiscincus,
and Tropidoscincus, and both Lioscincus and Tropidoscincus are paraphyletic with respect to,
Kanakysaurus, Lacertoides, Phoboscincus, Sigaloseps, Tropidoscincus, Graciliscincus,
Simiscincus, and Caledoniscincus, with strong support for most relevant nodes (Figure 10).
The genera Emoia and Bassiana are massively polyphyletic and divided across multiple
lygosomine clades (Figure 10). The genus Lygisaurus appears to be nested inside of Carlia,
although many of the relevant branches are only weakly supported (Figure 10).
Lacertoidea
Within Lacertoidea (Figure 1), we corroborate recent molecular analyses (e.g. [16,17,19,20])
and morphology-based phylogenies and classifications (e.g. [13,15]) in supporting the clade
including the New World families Gymnophthalmidae and Teiidae (Figure 11). Within a
weakly supported Teiidae (Figure 11), the subfamilies Tupinambinae and Teiinae are each
strongly supported as monophyletic, as in previous studies [61]. In Tupinambinae,
Callopistes is the sister group to a clade containing Tupinambis, Dracaena, and
Crocodilurus. The clade Dracaena + Crocodilurus is nested within Tupinambis, and the
associated clades have strong support (Figure 11). We find that the teiine genera Ameiva and
Cnemidophorus are non-monophyletic (Figure 11), interdigitating with each other and the
monophyletic genera Aspidoscelis, Dicrodon (monotypic), and Kentropyx, as in previous
phylogenies [62].
A recent study [123] proposed a re-classification of the family Teiidae based on analysis of
137 morphological characters for 101 terminal species (with ~150 species in the family).
Those authors erected several new genera and subfamilies in an attempt to deal with the
apparent non-monophyly of currently recognized taxa in their tree. However, in our tree,
some of these new taxa conflict strongly with the phylogeny or are rendered unnecessary.
First, they recognize Callopistinae as a distinct subfamily for Callopistes, arguing that failure
to do so would produce a taxonomy inconsistent with teiid phylogeny. However, we find
strong support for Callopistes in its traditional placement as part of Tupinambinae (Figure
11), and this change is thus not needed based on our results. The genus Ameiva is
paraphyletic under traditional definitions [62]. In our tree, their conception of Ameiva is also
non-monophyletic, with species found in three distinct clades (Figure 11). We also find non-
monophyly of many of their species groups within Ameiva, including the ameiva, bifrontata,
dorsalis, and erythrocephala groups (Figure 11). Their genera Aurivela (Cnemidophorus
longicaudus) and Contomastyx (Cnemidophorus lacertoides) are strongly supported as sister
taxa in our tree, and are nested within Ameiva in their erythrocephala species group, along
with Dicrodon (Figure 11).
On the positive side, many of the genera they recognize are monophyletic and are not nested
in other genera in our tree, including their Ameivula (Cnemidophorus ocellifer), Aspidoscelis
(unchanged from previous definitions), Cnemidophorus (excluding C. ocellifer, C.
lacertoides, and C. longicaudus), Holcosus (Ameiva undulata, A. festiva, and A.
quadrilineatus), Kentropyx (unchanged from previous definitions), Salvator (Tupinambis
rufescens, T. duseni, and T. merianae), and Teius (unchanged from previous definitions). We
did not sample Ameiva edracantha (their Medopheos).
Given our results, major taxonomic rearrangements within Teiidae seem problematic at
present, especially with the extensive paraphyly of many traditional and re-defined teiid
genera, the lack of strong resolution of many of these relationships based on molecular and
morphological data, and incomplete taxon sampling in all studies so far. Thus, we
provisionally retain the traditional taxonomy of Teiidae, pending additional data and
analyses. However, we note that Ameiva, Cnemidophorus, and Tupinambis are clearly non-
monophyletic based on both our results and those of recent authors [123], and will require
taxonomic changes in the future. We anticipate that many of these newly proposed genera
[123] will be useful in such revisions.
We find strong support (SHL = 100) for monophyly of Gymnophthalmidae (Figure 11).
Within Gymnophthalmidae, we find strong support for the monophyly of the previously
recognized subfamilies [63,64,124], with the exception of Cercosaurinae (Figure 11).
Previous researchers considered the genus Bachia a distinct tribe (Bachiini) within
Cercosaurinae, based on a poorly supported sister-group relationship with the tribe
Cercosaurini [63,64]. Here, we find a moderately well supported relationship (SHL = 84)
between Bachia and Gymnophthalminae + Rhachisaurinae, and we find that this clade is only
distantly related to other Cercosaurinae. Therefore, we restrict Cercosaurinae to the tribe
Cercosaurini, and elevate the tribe Bachiini [64] to the subfamily level. The subfamily
Bachiinae contains only the genus Bachia (Figure 11), identical in content to the previously
recognized tribe [64]. Within Cercosaurinae, we find that the genus Petracola is nested
within Proctoporus (Figure 11). In Ecpleopinae, Leposoma is divided into two clades,
separated by Anotosaura, Colobosauroides, and Arthrosaura (Figure 11), and many of the
relevant nodes are very strongly supported. These issues should be addressed in future
studies.
Our results show strong support for a clade uniting Lacertidae and Amphisbaenia
(Lacertoidea; Figure 1), as in many previous studies [16-20,23]. We also find strong support
for monophyly of amphisbaenians (SHL = 99), in contrast to some molecular analyses
[19,20]. Relationships among amphisbaenian families (Figure 12) are generally strongly
supported and similar to those in earlier molecular studies (Figure 12), including the
placement of the New World family Rhineuridae as sister group to all other amphisbaenians
[70,71,125]. The family Cadeidae is placed as the sister-group to Amphisbaenidae +
Trogonophiidae (Figures 1 and Figure 12) with weak support, but has been placed with
Blanidae in previous studies, with strong support but less extensive taxon sampling
[125,126].
We find strong support for monophyly of the Old World family Lacertidae (Figure 13).
Within Lacertidae, branch support for the monophyly of most genera and for the subfamilies
Gallotiinae and Lacertinae is very high (Figure 13). However, we find that relationships
among many genera are poorly supported, as in previous studies [65,67,68]. Our results
(Figure 13) also indicate that several lacertid genera are non-monophyletic with strong
support for the associated nodes, including Algyroides (paraphyletic with respect to
Dinarolacerta), Ichnotropis (paraphyletic with respect to Meroles), Meroles (paraphyletic
with respect to Ichnotropis), Nucras (polyphyletic with respect to several genera, including
Pedioplanis, Poromera, Latastia, Philocortus, Pseuderemias, and Heliobolus), and
Pedioplanis (paraphyletic with respect to Nucras).
Higher-level phylogeny of Toxicofera
We find strong support (SHL = 96) for monophyly of Toxicofera (Anguimorpha, Iguania,
and Serpentes; Figure 1), and moderate support for a sister-group relationship between
Iguania and Anguimorpha (SHL = 79). Relationships among Anguimorpha, Iguania, and
Serpentes were weakly supported in some Bayesian and likelihood analyses [16-19], but
strongly supported in others [20]. We further corroborate previous studies in also placing
Anguimorpha with Iguania [16-20]. In contrast, some other studies have placed anguimorphs
with snakes as the sister group to iguanians [127,128].
Anguimorpha
Our hypothesis for family-level anguimorphan relationships (Figures 1, 14) is generally
similar to that of other recent studies [17,19,20,129], and is strongly supported. Our results
differ from some analyses based only on morphology, which place Anguidae near the base of
Anguimorpha [130]. Here, Shinisauridae is strongly supported as the sister taxon to a well-
supported clade of Varanidae + Lanthanotidae (Figures 1, 14). Varanid relationships are
similar to previous estimates (e.g. [131]). Xenosauridae is here strongly supported as the
sister-group to a strongly supported clade containing Helodermatidae and the strongly
supported Anniellidae + Anguidae clade (Figures 1, 14). However, previous molecular
analyses have placed Helodermatidae as the sister to Xenosauridae (Anniellidae + Anguidae),
typically with strong support [16,17,19,20].
Within Anguidae (Figure 14), our phylogeny indicates non-monophyly of genera within
every subfamily, including Diploglossinae (Diploglossus and Celestus are strongly supported
as paraphyletic with respect to each other and to Ophiodes), Anguinae (Ophisaurus is
strongly supported as paraphyletic with respect to Anguis, Dopasia, and Pseudopus), and
Gerrhonotinae (Abronia and Mesaspis are non-monophyletic, and Coloptychon is nested
inside Gerrhonotus). Some of these problems were not reported previously (e.g.
Coloptychon, Abronia, and Mesaspis), due to incomplete taxon sampling in previous studies
[129,132,133], but relationships within Gerrhonotinae are under detailed investigation by
other researchers, so these issues are likely to be resolved in the near future.
Iguania
We find strong support (SHL = 100) for the monophyly of Iguania (Figure 1). This clade is
strongly supported by nuclear data [16,17,19,20], but an apparent episode of convergent
molecular evolution in several mitochondrial genes has seemingly misled some analyses of
mtDNA, leading to weak support for Iguania [134], or even separation of the acrodonts and
pleurodonts [17,135] in previous studies. Within Iguania (Figure 1), we find strong support
(SHL = 100) for a sister-group relationship between Chamaeleonidae and Agamidae
(Acrodonta), and for a clade of mostly New World families (Pleurodonta; SHL = 100).
We find strong support for the monophyly of Chamaeleonidae and the subfamily
Chamaeleoninae, and weak support for the paraphyly of Brookesiinae (Figures 1, 15). The
sampled species of the Brookesia nasus group appear as the sister group to all other
chamaeleonids (the latter clade weakly supported) as found by some previous authors [136],
though other studies have recovered a monophyletic Brookesia [137,138]. Within
Chamaeleoninae (Figure 15), we find strong support for the monophyly of most genera and
species-level relationships. However, we find strong support for the non-monophyly of
Calumma, with some species strongly placed with Chamaeleo, others strongly placed with
Rieppeleon, and a third set weakly placed with Nadzikambia + Rhampoleon. While non-
monophly of Calumma has also been found in previous studies [138], a recent study strongly
supports monophyly of Brookesia and weakly supports monophyly of Calumma [139].
Monophyly of Agamidae is strongly supported (Figure 16; SHL = 100), contrary to some
previous estimates [15,31]. Most relationships among agamid subfamilies and genera are
strongly supported (Figure 16), and largely congruent with earlier studies [17,29,34,140].
There are some differences with earlier studies. For example, previous studies based on 29
44 loci [20,29,34] placed Hydrosaurinae as sister to Amphibolurinae + (Agaminae +
Draconinae) with strong support, whereas we place Hydrosaurinae as the sister-group to
Amphibolurinae with weak support. Other authors [140] placed Leiolepiedinae with
Uromastycinae, but we (and most other studies) place Uromastycinae as the sister group to all
other agamids.
Our phylogeny indicates several taxonomic problems within amphibolurine agamids (Figure
16). The genera Moloch and Chelosania render Hypsilurus paraphyletic, although the support
for the relevant clades is weak. The species Lophognathus gilberti is placed in a strongly
supported clade with Chlamydosaurus and some Amphibolurus (including the type species,
A. muricatus), a clade that is not closely related to the other Lophognathus. Many of these
taxonomic problems were also noted by previous authors [141].
Within agamine agamids (Figure 16), most relationships are well supported and monophyly
of all sampled genera is strongly supported. In contrast, within draconine agamids (Figure
16), many intergeneric relationships are weakly supported, and some genera are non-
monophyletic (Figure 16; see also [142]), including Gonocephalus (G. robinsonii is only
distantly related to other Gonocephalus) and Japalura (with species distributed among three
distantly related clades, including one allied with Ptyctolaemus, another with G. robinsonii,
and a third with Pseudocalotes).
Recent authors suggested dividing Laudakia into three genera (Stellagama, Paralaudakia,
and Laudakia) based on a non-phylogenetic analysis of morphology [143]. Here, Laudakia
(as previously defined) is strongly supported as monophyletic (Figure 16), and this change is
not necessitated by the phylogeny. Similarly, based on genetic and morphological data, recent
authors [144] suggested resurrecting the genus Saara for the basal clade of Uromastyx (U.
asmussi, U. hardwickii, and U. loricata). However, Uromastyx (as previously defined) is
strongly supported as monophyletic in our results (Figure 16) and in those of the recent
revision [144], and this change is not needed. We therefore retain Laudakia and Uromastyx as
previously defined, to preserve taxonomic stability in these groups [113]. We note that recent
studies have also begun to revise species limits in other groups such as Trapelus [145], and
taxa such as T. pallidus (Figure 16) may represent populations within other species.
Within Pleurodonta we generally confirm the monophyly and composition of the clades that
were ranked as families (or subfamilies) within the group (e.g. Phrynosomatidae, Opluridae,
Leiosauridae, Leiocephalidae, and Corytophanidae; Figures 1, 17, 18, 19) based on previous
molecular studies [31,33,34] and earlier morphological studies [146,147].
One important exception is the previously recognized Polychrotidae. Our results confirm that
Anolis and Polychrus are not sister taxa (Figures 1, 18, 19), as also found in some previous
molecular studies [31,33,34], but not others [20,29]. Our results provide strong support for
non-monophyly of Polychrotidae, placing Polychrus with Hoplocercidae (SHL = 99) and
Anolis with Corytophanidae (SHL = 99; the latter also found by [34]). Recent analyses
placing Anolis with Polychrus showed only weak support for this relationship [20,29], despite
many loci (3044). We support continued recognition of Dactyloidae for Anolis and
Polychrotidae for Polychrus [34], based on a limited number of loci but extensive taxon
sampling. We note that these families are still monophlyetic, even if they prove to be sister
taxa.
Interestingly, our results for relationships among pleurodont families differ from most
previous studies, and are surprisingly well-supported in some cases by SHL values (but see
below). In previous studies, many relationships among pleurodont families were poorly
supported by Bayesian posterior probabilities and by parsimony and likelihood bootstrap
values, though typically sampling fewer taxa or characters [17,31,33,148-151]. Studies
including 29 nuclear loci found strong concatenated Bayesian support for many relationships
but weak support from ML bootstrap analyses for many of the same relationships [34]. The
latter pattern (typically weak ML support) was also found in an analysis including those same
29 loci and mitochondrial data for >150 species [29]. We also find a mixture of strongly and
weakly supported clades, but with many relationships that are incongruent with these
previous studies. First, we find that Tropiduridae is weakly supported as the sister group to all
other pleurodonts (also found by [29]), followed successively (Figures 1, 17, 18, 19) by
Iguanidae, Leiocephalidae, Crotaphytidae + Phrynosomatidae, Polychrotidae +
Hoplocercidae, and Corytophanidae + Dactyloidae.
The relatively strong support for the clades Crotaphytidae + Phrynosomatidae (SHL = 87),
Polychrotidae + Hoplocercidae (SHL = 99), and Corytophanidae + Dactyloidae (SHL = 99) is
largely unprecedented in previous studies (although Corytophanidae + Dactyloidae is
strongly supported in some Bayesian analyses [34]). As in many previous analyses, deeper
relationships among the families remain weakly supported. We also find a strongly supported
clade containing Liolaemidae, Opluridae, and Leiosauridae (SHL = 95), with Opluridae +
Leiosauridae also strongly supported (SHL = 99). Both clades have also been found in
previous studies [149,151], including studies based on 29 or more nuclear loci [20,29,34].
We note that previous studies have shown strong support for some pleurodont relationships
(e.g. basal placement of phrynosomatids; see [34]), only to be strongly overturned with
additional data [20,29]. Therefore, the relationships found here should be taken with some
caution (even if strongly supported), with the possible exception of the recurring clade of
Liolaemidae + (Opluridae + Leiosauridae).
All pleurodont families are strongly supported as monophyletic (SHL > 85). Within the
pleurodont families, our results generally support the current generic-level taxonomy (Figures
17, 18, 19). However, there are some exceptions. Within Tropiduridae (Figure 17),
Tropidurus is paraphyletic with respect to Eurolophosaurus, Strobilurus, Uracentron, and
Plica. Within Opluridae (Figure 18), the monotypic genus Chalarodon renders Oplurus
paraphyletic. Two leiosaurid genera are also problematic (Figure 18). In Enyaliinae,
Anisolepis is paraphyletic with respect to Urostrophus, and this clade is nested within
Enyalius. In Leiosaurinae, Pristidactylus is rendered paraphyletic by Leiosaurus and
Diplolaemus (Figure 18).
Within Dactyloidae, a recent study re-introduced a more subdivided classification of anoles
[152], an issue that has been debated extensively in the past [153-156]. Our results support
the monophyly of all the genera recognized by recent authors [152], including Anolis,
Audantia, Chamaelinorops, Dactyloa, Deiroptyx, Norops, and Xiphosurus (see Figure 19).
However, since Anolis is monophyletic as previously defined, we retain that definition here
(including the seven listed genera) for continuity with the recent literature [113,157].
Serpentes
Relationships among the major serpent groups (Figure 1) are generally similar to other recent
studies [20,35,36,38,41,44,47,158-160]. We find that the blindsnakes, Scolecophidia (Figures
1, 20) are not monophyletic, as in previous studies [19,20,36,44,159,160]. Similar to some
previous studies [44,159], our data weakly place Anomalepididae as the sister taxon to all
snakes, and the scolecophidian families Gerrhopilidae, Leptotyphlopidae, Typhlopidae, and
Xenotyphlopidae as the sister-group to all other snakes excluding Anomalepididae (Figures 1,
20). Previous studies have also placed Anomalepididae as the sister-group to all non-
scolecophidian snakes [19,20,35,36,158,160], in some cases with strong support [20].
Although it might appear that recent analyses of scolecophidian relationships [38] support
monophyly of Scolecophidia (e.g. Figure 1 of [38]), the tree including non-snake outgroups
from that study shows weak support for placing anomalepidids with alethinophidians, as in
other studies [19,20,36,160].
We follow recent authors [38] in recognizing Xenotyphlopidae (strongly placed as the sister
taxon of Typhlopidae) and Gerrhopilidae (strongly placed as the sister group of
Xenotyphlopidae + Typhlopidae) as distinct families (Figure 20). Leptotyphlopidae is
strongly supported as the sister group of a clade comprising Gerrhopilidae, Xenotyphlopidae,
and Typhlopidae (Figure 20). As in previous studies [38,44], we find strong support for non-
monophyly of several typhlopid genera (Afrotyphlops, Austrotyphlops, Ramphotyphlops,
Letheobia, and Typhlops; Figure 20). There are also undescribed taxa (e.g. Typhlopidae sp.
from Sri Lanka; [44]) of uncertain placement within this group (Figure 20). The systematics
of typhlopoid snakes will thus require extensive revision in the future, with additional taxon
and character sampling.
Within Alethinophidia (SHL = 100), Aniliidae is strongly supported (SHL = 98) as the sister
taxon of Tropidophiidae (together comprising Anilioidea), and all other alethinophidians
form a strongly supported sister group to this clade (SHL = 97; Figures 1, 21). The enigmatic
family Xenophidiidae is weakly placed as the sister-group to all alethinophidians exclusive of
Anilioidea (Figures 1, 21). The family Bolyeriidae is weakly placed as the sister-group to
pythons, boas, and relatives (Booidea), which are strongly supported (SHL = 88).
Relationships in this group are generally consistent with other recent molecular studies
[20,35-37,47,159].
Relationships among other alethinophidians are a mixture of strongly and weakly supported
nodes (Figures 1, 21). We find strong support (SHL = 100) for a clade containing
Anomochilidae + Cylindrophiidae + Uropeltidae. This clade of three families is strongly
supported (SHL = 89) as the sister taxon to Xenopeltidae + (Loxocemidae + Pythonidae).
Together, these six families form a strongly supported clade (SHL = 89; Figures 1, 21) that is
weakly supported as the sister group to the strongly supported clade of Boidae +
Calabariidae. Within the clade of Anomochilidae, Cylindrophiidae, and Uropeltidae (Figure
21), we weakly place Anomochilus as the sister group to Cylindrophiidae [44], in contrast to
previous studies which placed Anomochilus within Cylindrophis [161]. However, support for
monophyly of Cylindrophis excluding Anomochilus is weak (Figure 21). As in previous
studies [44,162], we find several taxonomic problems within Uropeltidae (Figure 21).
Specifically, Rhinophis and Uropeltis are paraphyletic with respect to each other and to
Pseudotyphlops. The problematic taxa are primarily Sri Lankan [44], and forthcoming
analyses will address these issues.
Within Pythonidae (Figure 21), the genus Python is the sister group to all other genera. Some
species that were traditionally referred to as Python (P. reticulatus and P. timoriensis) are
instead sister to an Australasian clade consisting of Antaresia, Apodora, Aspidites,
Bothrochilus, Leiopython, Liasis, and Morelia (Figure 21). These taxa (P. reticulatus and P.
timoriensis) have been referred to as Broghammerus, a name originating from an act of
"taxonomic vandalism" (i.e. an apparently intentional attempt to disrupt stable taxonomy) in a
non-peer reviewed organ without data or analyses [163,164]. However, this name was,
perhaps inadvertently, subsequently used by researchers in peer-reviewed work [165] and has
entered into somewhat widespread usage [1]. This name should be ignored and replaced with
a suitable substitute. Within the Australasian clade (Figure 21), Morelia is paraphyletic with
respect to all other genera, and Liasis is non-monophyletic with respect to Apodora, although
many of the relevant relationships are weakly supported.
Within Boidae (Figure 21), our results and those of other recent studies
[20,36,47,48,150,166] have converged on estimated relationships that are generally similar to
each other but which differ from traditional taxonomy [167]. However, the classification has
yet to be modified to reflect this, and we rectify this situation here. We find that Calabariidae
is nested within Boidae [150], but this is poorly supported, and contrary to most previous
studies [47,48]. While Calabaria has been classified as an erycine boid in the past, this
placement is strongly rejected here and in other studies [47,48]. If the current placement of
Calabaria is supported in the future, it would require recognition as the subfamily
Calabariinae.
The Malagasy boine genera Acrantophis and Sanzinia are placed as the sister taxa to a
weakly-supported clade containing Calabariidae and a strongly supported clade (SHL = 99)
comprising the currently recognized subfamilies Erycinae, Ungaliophiinae, and other boines
(Figure 21). Regardless of the position of Calabariidae, this placement of Malagasy boines
renders Boinae paraphyletic. We therefore resurrect the subfamily Sanziniinae [168] for
Acrantophis and Sanzinia. This subfamily could be recognized as a distinct family if future
studies also support placement of this clade as distinct from other Boidae + Calabariidae.
The genera Lichanura and Charina are currently classified as erycines [1], but are strongly
supported as the sister group to Ungaliophiinae, as in previous studies [20,36,47,166]. We
expand Ungaliophiinae to include these two genera (Figure 21), rather than erect a new
subfamily for these taxa. The subfamily Ungaliophiinae is placed as the sister group to a
well-supported clade (SHL = 87) containing the rest of the traditionally recognized Erycinae
and Boinae. We restrict Erycinae to the Old World genus Eryx.
The genus Candoia (Boinae) from Oceania and New Guinea [1], is placed as the sister taxon
to a moderately supported clade (SHL = 83) consisting of Erycinae (Eryx) and the remaining
genera of Boinae (Boa, Corallus, Epicrates, and Eunectes). To solve the non-monophyly of
Boinae with respect to Erycinae (due to Candoia), we place Candoia in a new subfamily
(Candoiinae, subfam. nov.; see Appendix I). Boinae then comprises the four Neotropical
genera that have traditionally been classified in this group (Boa, Corallus, Epicrates, and
Eunectes). We acknowledge that non-monophyly of Boinae could be resolved in other ways
(e.g. expanding it to include Erycinae). However, our taxonomy maintains the traditionally
used subfamilies Boinae, Erycinae, and Ungaliophiinae, modifies them to reflect the
phylogeny, and recognizes the phylogenetically distinct boine clades as separate subfamilies
(Candoiinae, Sanziniinae). Within Boinae, Eunectes renders Epicrates paraphyletic, but this
is not strongly supported see also ([48]).
Our results for advanced snakes (Caenophidia) are generally similar to those of other recent
studies [41,42,169], and will only be briefly described. However, in contrast to most recent
studies [20,36,41,42,81,159,160], Acrochordidae is here strongly placed (SHL = 95) as the
sister group to Xenodermatidae. This clade is then the sister group to the remaining
Colubroidea, which form a strongly supported clade (SHL = 100; Figures 1, 22). This
relationship has been found in some previous studies [169,170], and was hypothesized by
early authors [171]. Further evidence will be required to resolve this conclusively. Analyses
based on concatenation of 2044 loci do not support this grouping [20,36], though
preliminary species-tree analyses of >400 loci do (Pyron et al., in prep.). Relationships in
Pareatidae are similar to recent studies [172], and the group is strongly placed as the sister
taxon to colubroids excluding xenodermatids (SHL = 100; Figures 1 , 22), as in most recent
analyses (e.g. [41,43,44]).
The family Viperidae is the sister group to all colubroids excluding xenodermatids and
pareatids (Figure 1), as in other recent studies. The family Viperidae is strongly supported
(Figure 22), as is the subfamily Viperinae, and the sister-group relationship between
Azemiopinae and Crotalinae (SHL = 100). Our results generally support the existing generic-
level taxonomy within Viperinae (Figure 22). However, we recover a strongly supported
clade within Viperinae consisting of Daboia russelii, D. palaestinae, Macrovipera
mauritanica, and M. deserti (Figure 22), as in previous studies [173]. We corroborate
previous suggestions that these taxa be included in Daboia [174], though this has not been
widely adopted [1]. The other Macrovipera species (including the type species) remain in that
genus (Figure 22).
Within Crotalinae (Figure 22), a number of genera appear to be non-monophyletic. The
species Trimeresurus gracilis is strongly supported as the sister taxon to Ovophis okinavensis
and distantly related to other Trimeresurus, whereas the other Ovophis are strongly placed as
the sister group to Protobothrops. A well-supported clade (SHL = 90) containing Atropoides
picadoi, Cerrophidion, and Porthidium renders Atropoides paraphyletic (see also [175]). The
species Bothrops pictus, considered incertae sedis in previous studies [176], is here strongly
supported as the sister taxon to a clade containing Rhinocerophis, Bothropoides, Bothriopsis,
and Bothrops (Figure 22). Most of these relationships are strongly supported.
Viperidae is strongly placed (SHL = 95) as the sister taxon to a well-supported clade (SHL =
100) containing Colubridae, Elapidae, Homalopsidae, and Lamprophiidae (Figure 1).
Monophyly of Homalopsidae is also strongly supported (Figure 23). Within Homalopsidae,
the non-monophyly of the genus Enhydris is strongly supported (Figure 23), and should
likely be split into multiple genera. Homalopsidae is weakly supported (SHL = 58) as the
sister group of Elapidae + Lamprophiidae (Figure 1). This same relationship was also weakly
supported by previous analyses [41,44], but other studies have found strong support for
placing Homalopsidae as the sister group of a strongly supported clade including Elapidae,
Lamprophiidae, and Colubridae [20,36], including data from >400 loci (Pyron et al., in
prep.).
Support for the monophyly of Lamprophiidae is strong (but excluding Micrelaps; see below),
and most of its subfamilies are well-supported [40,41,177,178] including Atractaspidinae,
Aparallactinae, Lamprophiinae, Prosymninae (weakly placed as the sister-group to
Oxyrhabdium), Pseudaspidinae, Psammophiinae, and Pseudoxyrhophiinae (Figure 23). In
Lamprophiidae, most genera are monophyletic based on our sampling (Figure 23). However,
within Aparallactinae, Xenocalamus is strongly placed within Amblyodipsas, and in
Atractaspidinae, Homoroselaps is weakly placed in Atractaspis. In Lamprophiinae,
Lamprophis is paraphyletic with respect to Lycodonomorphus but support for the relevant
clades is weak.
The enigmatic genera Buhoma from Africa and Psammodynastes from Asia were both
previously considered incertae sedis within Lamprophiidae [41]. Here they are weakly placed
as sister taxa, and more importantly, they form a strongly supported clade with the African
genus Pseudaspis (Pseudaspidinae; SHL = 95; Figure 23). Therefore, we expand
Pseudaspidinae to include these two genera.
The genus Micrelaps (putatively an aparallactine; [1]) is weakly placed as the sister taxon to
Lamprophiidae + Elapidae. Along with Oxyrhabdium (see above) and Montaspis [40], this
genus is treated as incertae sedis in our classification (Appendix I). If future studies strongly
support these relationships, they may require a new family for Micrelaps and possibly a new
subfamily for Oxyrhabdium, though placement of these taxa has been highly variable in
previous studies [40,41,44,81].
Monophyly of Elapidae is strongly supported (Figure 24), and Calliophis melanurus is
strongly supported as the sister group to all other elapids (see also [44]). Within Elapidae
(Figure 24), relationships are generally concordant with previous taxonomy, with some
exceptions. The genera Toxicocalamus, Simoselaps, and Echiopsis are all divided across
multiple clades, with strong support for many of the relevant branches. A recent study has
provided a generic re-classification of the sea snakes (Hydrophis group) to resolve the
extensive paraphyly of genera found in previous studies (e.g. [46,179,180]). Our results
support this classification.
Monophyly of Colubridae and most of its subfamilies (sensu [41,44]) are strongly supported
(Figures 1, 25, 26, 27, 28). However, relationships among many of these subfamilies are
weakly supported (Figure 1), as in most previous studies [41,43,45,181]. The subfamilies
Calamariinae and Pseudoxenodontinae are strongly supported as sister taxa, and weakly
placed as the sister-group to the rest of Colubridae (Figure 25). There is a weakly supported
clade (Figure 1) comprising Natricinae + (Dipsadinae + Thermophis), but the clade uniting
the New World Dipsadinae with the Asian genus Thermophis is strongly supported (SHL =
100; Figure 28). Here, we place Thermophis (recently in Pseudoxenodontinae [41]) in
Dipsadinae (following [182]), making it the first and only Asian member of this otherwise
exclusively New World subfamily. However, despite the strong support for its placement
here, placement of this taxon has been variable in previous analyses [41,182,183], and we
acknowledge that future analyses may support recognition of a distinct subfamily
(Thermophiinae).
The clade of Natricinae and Dipsadinae is weakly supported as the sister group (Figures 1,
25, 26, 27, 28) to a clade containing Sibynophiinae [181] + (Colubrinae + Grayiinae). The
subfamily Colubrinae is weakly supported; we find that the colubrine genera Ahaetulla,
Chrysopelea, and Dendrelaphis form a strongly supported clade that is weakly placed as the
sister group to the rest of Colubrinae, which form a strongly supported clade (Figure 25).
This clade was also placed with Grayiinae or Sibynophiinae in many preliminary analyses,
rendering Colubrinae paraphyletic. This group of three genera has been strongly supported in
the past, and only weakly placed with Colubrinae [41,44]. It is possible that future analyses
will reveal that the clade of Ahaetulla, Chrysopelea, and Dendrelaphis is placed elsewhere in
Colubridae with strong support, and thus merits recognition as a distinct subfamily
(Ahaetuliinae). A notable feature of this clade is the presence of gliding flight in most species
of Chrysopelea, less-developed non-flight jumping with similar locomotor origins in
Dendrelaphis, and homologous glide-related traits in Ahaetulla [184].
Numerous colubroid genera are not included in our tree and are not clearly placed in
subfamilies based on previous morphological evidence. In our classification, these genera are
also considered incertae sedis within Colubridae, including Blythia, Cyclocorus, Elapoidis,
Gongylosoma, Helophis, Myersophis, Oreocalamus, Poecilopholis, Rhabdops, and
Tetralepis, as in previous classifications [1].
Our phylogeny reveals numerous taxonomic problems within Colubrinae (Figures 25, 26).
The genus Boiga is paraphyletic with respect to Crotaphopeltis, Dipsadoboa, Telescopus,
Toxicodryas, and Dasypeltis, with strong support (Figure 25). The genus Philothamnus is
paraphyletic with respect to Hapsidophrys (Figure 25). The genus Coluber is split between
Old World and New World clades (Figures 25, 26). The species Hierophis spinalis is sister to
Eirenis to the exclusion of the other Hierophis species (Figure 25). The genus Dryocalamus
is nested within Lycodon (Figure 26). The species Chironius carinatus and C.
quadricarinatus are weakly placed in a clade of Neotropical colubrines only distantly related
to the other Chironius species (Figure 26). The genus Drymobius renders Dendrophidion
paraphyletic (Figure 26). The monotypic genus Rhynchophis renders the two species of
Rhadinophis paraphyletic (Figure 26). The genus Coronella is rendered paraphyletic (Figure
26) by Oocatochus with weak support see also [185]. Finally, the genus Rhinechis is nested
within Zamenis (Figure 26).
We find numerous non-monophyletic genera within Natricinae (Figure 27), as in previous
studies [41,44,78,186]. These non-monophyletic genera include the Asian genera
Amphiesma, Atretium, and Xenocrophis. Among New World genera, we find Regina to be
non-monophyletic with respect to most other genera, as in previous phylogenetic studies (e.g.
[41,186]). Also, as in previous studies (e.g. [41,187]), we find that Adelophis [188] is nested
deep within Thamnophis [189].
Finally, within a weakly supported Dipsadinae (Figure 28), we find non-monophyly of
numerous genera, as in many earlier studies (e.g. [41-43,190]). These problems of non-
monophyly include Leptodeira (with respect to Imantodes), Geophis (with respect to
Atractus), Atractus (with respect to Geophis), Sibynomorphus (with respect to Dipsas),
Dipsas (with respect to Sibynomorphus), Taeniophallus (with respect to Echinanthera), and
Echinanthera (with respect to Taeniophallus). Recent revisions have begun to tackle these
problems [42,43,190], but additional taxon and character sampling will be crucial to resolve
relationships and taxonomy.
Discussion
In this study, we provide a phylogenetic estimate for 4161 species of squamates based on
molecular data from up to 12 genes per species, combining much of the relevant data used in
previous molecular phylogenetic analyses. This tree provides a framework for future
evolutionary studies, spanning from the species level to relationships among families,
utilizing a common set of branch lengths. These estimated branch lengths are critically
important for most phylogenetic comparative methods. To further facilitate use of this
phylogeny in comparative studies, we provide the Newick version of this tree (with estimated
branch lengths) in DataDryad repository 10.5061/dryad.82h0m and Additional file 1 Data
File S1. Our results also suggest that the branch lengths in this tree should not generally be
compromised by missing data for some genes in some taxa.
Our results also reveal many problems in squamate classification at nearly all phylogenetic
levels. We make several changes to higher-level taxonomy based on this phylogeny,
including changes to the traditionally recognized subfamilies of boid snakes (i.e. resurrecting
Sanziniinae for the boine genera Acrantophis and Sanzinia, erecting Candoiinae for the boine
genus Candoia, and moving Lichanura and Charina from Erycinae to Ungaliophiinae),
lamprophiid snakes (expansion of Pseudaspidinae to include the formerly incertae sedis
genera Buhoma and Psammodynastes), colubrid snakes (expansion of Dipsadinae to include
the Asian pseudoxenodontine genus Thermophis), and gymnophthalmid lizards (recognition
of Bachiinae for the tribe cercosaurine Bachiini, containing Bachia) and scincid lizards
(synonymizing Feylininae with Scincinae to yield a total of three scincid subfamilies:
Acontiinae, Lygosominae, and Scincinae). In Appendix I, we list the generic content of all
families and subfamilies. We also find dozens of problems at the genus level, many of which
have been identified previously, and which we defer the resolution of to future studies. Our
results also highlight potential problems in recent proposals to modify the classification of
scincid [112] and teiid lizards [123].
In addition to synthesizing existing molecular data for squamate phylogeny, our analyses also
reveal several apparently novel findings (Figures 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28). Given space constraints, we cannot detail
every deviation from previous phylogenetic hypotheses (especially pre-molecular studies).
Nevertheless, we focus on three sets of examples. First, we find some relatively novel,
strongly-supported relationships at the family level. These include the placement of
Helodermatidae (as sister to Xenosauridae, Anguidae, and Anniellidae) and the placement of
Xenodermatidae as the sister taxon to Acrochordidae (rendering Colubroidea paraphyletic),
in contrast to most recent analyses of anguimorphs and snakes (see above). We also find
some novel, strongly supported relationships among pleurodont families, but we
acknowledge that these may be overturned in future studies.
The second example is the higher-level relationships within Scincidae, the largest family of
lizards [1]. No previous studies examining higher-level relationships within the group
included more than ~50 species [50,51]. In this study, we sample 683 skink species (Figures
6, 7, 8, 9, 10), and our phylogeny provides a unique resolution of higher-level skink
relationships. Previous researchers [51] placed acontiines as the sister group to all other
skinks, but suggested that scincines and lygosomines were paraphyletic with respect to each
other (with feyliniines placed with scincines). In contrast, others [50] suggested that
acontiines, feyliniines, and lygosomines were all nested inside scincines (but with each of
those three subfamilies as monophyletic), although many clades were only weakly supported.
Here (Figures 1, 6, 7, 8, 9, 10), we find that acontiines are the sister group to a strongly
supported clade consisting of a monophyletic Scincinae and a monophyletic Lygosominae
(excepting the weakly supported placement of Ateuchosaurus and placement of Feyliniinae in
Scincinae).
Third, our phylogeny reveals numerous genera that appear to be non-monophyletic, with
many of these cases having strong support for the associated nodes. Our examples include
genera in many families, including dibamids, diplodactylids, gekkonids, phyllodactylids,
gerrhosaurids, scincids, teiids, gymnophthalmids, lacertids, anguids, chamaeleonids, agamids,
tropidurids, oplurids, leiosaurids, typhlopids, pythonids, uropeltids, boids, viperids,
lamprophiids, elapids, and colubrids (see Results). Although many problems noted here were
found in previous studies, some seem to be new, such as placement of Crocodilurus and
Draceana within Tupinambis (in Teiidae; Figure 11) and Coloptychon within Gerrhonotus
(in Anguidae; Figure 14).
Our study also offers an important test of higher-level squamate relationships using a very
different sampling strategy than that used in most previous analyses. Squamates have
traditionally been divided into two clades based on morphology, Iguania and Scleroglossa
(e.g. [13,21]). Despite considerable disagreement among morphology-based hypotheses, this
basic division is supported by nearly all phylogenetic analyses based on morphological data
[13-15,19,22,95,191]. In contrast, our results and those of most previous molecular analyses
strongly support placement of iguanians with anguimorphs and snakes [16-20,23,24]. The
causes of this conflict remain unclear, but may be related to morphological traits associated
with different feeding strategies of iguanian and (traditional) scleroglossan squamates [3,17].
Additionally, analyses of morphology often place dibamids, amphisbaenians, snakes, and (in
some cases) some scincids and anguids in a single clade [13-15]. Our analyses do not support
such a clade (Figure 1), nor do other analyses of molecular data alone [17-20], or analyses of
combined molecular and morphological data [19]. Instead, these morphological results seem
to be explained by convergence associated with burrowing (e.g. [19]). Overall, molecular
datasets have shown overwhelmingly strong support for placement of dibamids and
gekkonids at the base of the tree, amphisbaenians with lacertoids, and iguanians with snakes
and anguimorphs [17-20,23]. These results have now been corroborated with up to 22 genes
(15794 bp) for 45 taxa [19], 25 genes (19020 bp) for 64 taxa [16], and 44 genes (33717 bp)
for 161 taxa [20]. We now support this basic topology with 4161 species sampled for up to 12
genes each (up to 12896 bp).
Nevertheless, despite the overall strong support for most of the tree (i.e. 70% of all nodes
have SHL > 85), certain clades remain poorly supported (e.g. relationships among many
pleurodont iguanian families; Figures 1, 17, 18, 19). A potential criticism of the supermatrix
approach used here is that this weak support may occur due to missing data. However,
previous studies of 8 datasets have shown explicitly that there is typically little relationship
between branch support for terminal taxa and the amount of missing data [85]. Instead, these
patterns of weak support are more likely to reflect short underlying branch lengths [20,36,41],
and may be difficult to resolve even with more complete taxonomic and genomic sampling.
Indeed, as noted above, many of the weakly supported nodes in our phylogeny are also
weakly supported in analyses with little missing data (<20%) and large numbers of genes
(e.g. 44 genes as in [20]), such as the relationships of many pleurodont lizard families and
colubroid snake families and subfamilies.
We acknowledge that the differences between our results and previous studies (noted above)
do not necessarily mean that our results are right and those of previous studies are wrong. In
some cases, we provide strong support for novel relationships when previous, conflicting
studies showed only weak support (as in scincids, see above). In other cases, our results
disagree with other studies for clades that were strongly supported (e.g. placement of
xenodermatids). In the best-case scenario, these conflicts may be resolved because our results
are correct, possibly reflecting the beneficial effects of adding taxa and the associated
subdivision of long branches [25,26,28,87,192-194]. Furthermore, in many cases, we are
including more genes than used in previous studies of particular clades, increasing sampling
of characters and loci. This should generally reduce spurious results caused by sampling few
characters and by incongruence between gene and species trees.
However, other explanations for incongruence between our results and previous studies are
also possible. Adding taxa can potentially lead to incorrect results in some cases (e.g. [195]),
such as when a long terminal branch is added that further subdivides a short internal branch.
In other cases, conflicts with our results might reflect the impact of our sampling fewer
nuclear genes and a correspondingly increased influence of mitochondrial data.
Mitochondrial genes have relatively fast evolutionary rates (potentially exacerbating the
impacts of long branches), and their phylogenetic resolution for a particular node may also
reflect introgression or incomplete lineage sorting rather than the species phylogeny (review
in [196]). Many taxa in the matrix are represented only by mitochondrial data, and highly
variable mitochondrial genes might also overcome the influence of less variable nuclear
genes in combined analyses (although this scenario does not seem to be common [196]).
Such cases might explain some strongly supported conflicts between our results and those
based on multiple nuclear loci. Another possibility is that some cases may represent failure to
find the optimal tree (although we assume that these cases will likely show only weak
support). We acknowledge that there are many reasons why our results may differ from
previous studies, and the ultimate test of these novel findings will be corroboration in future
studies that include more taxa and characters.
This analysis also corroborates several recent studies suggesting that the supermatrix
approach is a powerful strategy for large-scale phylogenetic inference [41,72,73,75,76,197].
For example, even though each species had 81% missing data on average, we found that most
species were placed in the families and genera expected based on previous taxonomy, often
with very strong support. Furthermore, we found that incompleteness of terminal taxa is not
related to branch lengths (at least not terminal branch lengths), suggesting that missing data
are not significantly biasing branch-length estimates (see also [84,86,87]). Also, the CAT-
based models we used have been shown to be robust to missing data in large, sparse
supermatrices [84].
Even though we did find some subfamilies and genera to be non-monophyletic, similar
relationships were often found in previous studies based on data matrices with only limited
missing data (e.g. non-monophyly of boid snake subfamilies [47], lacertid and scincid lizard
genera [67,111], and scolecophidian, dipsadine, and natricine snake genera [38,43,186]). We
suggest that further resolution of the squamate tree will be greatly facilitated if researchers
deliberately sample mitochondrial genes and nuclear genes that include the set of genes used
here and in recent phylogenomic studies (e.g. [20]), to increase overlap between genes and
taxa, and decrease missing data.
With over 5000 species remaining to be included and only 12 genes sampled, our study is far
from the last word on squamate phylogeny. We note that new data can easily be added to this
matrix, in terms of both new taxa and new genes. Increased sampling of other nuclear genes
is likely to be advantageous as well. Next-generation sequencing strategies and phylogenomic
methods should help resolve difficult nodes [16,20,36,198-200], as should application of
species-tree methods [201,202]. Species-tree analyses of 44 nuclear loci support many of
these same clades across squamates [20], and data from >400 nuclear loci reinforces many of
the relationships found here among the colubroid snake subfamilies (Pyron et al., in prep.). In
addition, it would be useful to incorporate fossil taxa in future studies [15,19,22,86], utilizing
the large morphological datasets that are now available [14,15]. Despite these areas for future
studies, the present tree provides a framework for researchers analyzing patterns of squamate
evolution at both lower and higher taxonomic levels (e.g. [10,11,203,204]), and for building a
more complete picture of squamate phylogeny.
Conclusions
In this study, we provide a phylogenetic estimate for 4161 squamate species, based on a
supermatrix approach. Our results provide important confirmation for previous studies based
on more limited taxon sampling, and reveal new relationships at the level of families, genera,
and species. We also provide a phylogenetic framework for future comparative studies, with
a large-scale tree including a common set of estimated branch lengths. Finally, we provide a
revised classification for squamates based on this tree, including changes in the higher-level
taxonomy of gymnophthalmid and scincid lizards and boid, colubrid, and lamprophiid
snakes.
Methods
Initial classification
Our initial squamate classification is based on the June 2009 version of the Reptile Database
(http://www.reptile-database.org/), accessed in September of 2009 when this research was
begun. Minor modifications to this scheme were made, primarily to update changes in
colubroid snake taxonomy [41-44,205]. This initial taxonomic database consists of 8650
species (169 amphisbaenians, 5270 lizards, 3209 snakes, and 2 tuataras), against which the
classification of species in the molecular sequence database was fixed. While modifications
and updates (i.e. new species, revisions) have been made to squamate taxonomy
subsequently, these are minor and should have no impact on our phylogenetic results. This
database represents ~92% of the current estimated diversity of squamates (~9400 species as
of December 2012).
Throughout the paper, we refer to the updated version of squamate taxonomy from the
December 2012 update of the Reptile Database, incorporating major, well-accepted changes
from recent studies (summarized in [1]). However, for large, taxonomic groups that have
recently been broken up for reasons other than resolving paraphyly or matters of priority (e.g.
in dactyloid and scincid lizards; see Results), we generally retain the older, more inclusive
name in the interest of clarity, while providing references to the recent revision. We attempt
to alter existing classifications as little as possible (see also [113]). Therefore, we generally
only make changes when there is strong support for non-monophyly of currently recognized
taxa and our proposed changes yield strongly supported monophyletic groups. Similarly, we
only erect new taxa if they are strongly supported. Finally, although numerous genera are
identified as being non-monophyletic in our tree, we refrain from changing genus-level
taxonomy, given that our taxon sampling within many genera is limited.
Molecular data
Preliminary literature searches were conducted to identify candidate genes for which a
substantial number of squamate species were sequenced and available on GenBank (with the
sampled species spread across multiple families), and which were demonstrably useful in
previous phylogenetic studies of squamates (see Introduction for references). Twelve genes
were identified as meeting these criteria: seven nuclear genes (brain-derived neurotrophic
factor [BDNF], oocyte maturation factor [c-mos], neurotrophin-3 [NT3], phosducin [PDC], G
protein-coupled receptor 35 [R35], and recombination-activating genes 1 [RAG-1] and 2
[RAG-2]), and five mitochondrial genes (12S/16S long and short subunit RNAs, cytochrome
b [cyt-b], and nicotinamide adenine dehydrogenase subunits 2 [ND2] and 4 [ND4]). This
sampling of genes does not include all available markers. For example, we omitted several
nuclear and mitochondrial genes because they were available only for a limited subset of
taxa. We also excluded tRNAs associated with the protein-coding sequences, given their
short lengths and difficulty in alignment across the large time scales considered here.
To ensure maximal taxonomic coverage from the available data, searches were conducted on
GenBank by family (stopping in October 2012), and the longest sequence for every species
was gathered. Sequences totaling less than 250 bp for any species were not included. Only
species in the taxonomic database were included in the sequence matrix, which resulted in the
exclusion of numerous named taxa of ambiguous status, a few taxa described very recently,
and many sequences labeled 'sp.' Some recently described phylogeographic lineages were
also omitted. Species and GenBank accession numbers are available in Additional file 2
Table S1.
With respect to the December 2012 update of the Reptile Database, we sampled 52 of 183
amphisbaenian species (28%) from 11 of 19 (58%) genera; 2847 of 5799 lizard species (49%)
from 448 of 499 genera (90%); and 1262 of 3434 snake species (39%) in 396 of 500 genera
(80%). This yielded a total of 4161 species in 855 genera in the final matrix, 44% of the 9416
known, extant squamate species in 84% of 1018 genera [1]. The species-level classification
of squamates is in constant flux, and the numbers of species and genera changed even as this
paper was under review. The extant species of tuatara (Sphenodon punctatus) was included as
a non-squamate outgroup taxon (see below). We acknowledge that our sampling of outgroup
taxa is not extensive. However, placement of Sphenodon as the sister group to squamates is
well-established by molecular analyses with extensive taxon sampling (e.g. [16,128,206]) and
morphological data (e.g. [13]).
Alignment for protein-coding sequences was relatively straightforward. We converted them
to amino acids, and then used 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). Alignments were relatively unambiguous after being trimmed for
quality and maximum coverage (i.e. ambiguous end regions were removed, and most
sequences began and ended at the same point).
For the ribosomal RNA sequences (12S and 16S sequences), alignment was more
challenging. Preliminary global alignments using the algorithms MUSCLE [207] and
CLUSTAL [208] under a variety of gap-cost parameters yielded low-quality results (i.e.
alignments with large numbers of gaps and little overlap of potentially homologous
characters). We subsequently employed a two-step strategy for these data. We first grouped
sequences by higher taxa (i.e. Amphisbaenia, Anguimorpha, Gekkota, Iguania,
Scincomorpha, and Serpentes, though these are not all monophyletic as previously defined),
for which alignments were relatively straightforward under the default MUSCLE parameters.
These were then combined using the profile alignment feature of MUSCLE, and the global
alignment was subsequently updated using the "refine alignment" option. Minor adjustments
were then made by eye, and ambiguously aligned end-regions were trimmed for maximum
coverage and quality. We did not include partitions for stems and loops for the ribosomal
sequences, although this has been shown to improve model fit in previous squamate studies
(e.g. [82]). Although it is possible to assign individual nucleotide positions to these partitions,
this would have been challenging given the large number of sequences, and the potential for
stems and loops to shift across the many species and large time scales involved.
Each species was represented by a single terminal taxon in the matrix. In many cases,
sequences from multiple individuals of the same species were combined, to allow us to
combine data from different genes for the same species. We acknowledge the possibility that
in some cases this approach may cause us to combine genes from different species in the
same terminal taxon (e.g. due to changing taxonomy or incorrect identifications).
Additionally, many sequences are not from vouchered specimens, and it is possible that
misidentified species are present on GenBank and in our matrix. However, most of our data
came from lower-level phylogenetic studies, in which the identification of species by
previous authors should be highly accurate. In addition, any such mistakes should be among
closely related species, and lead to minimal phylogenetic distortion, as the grossest errors are
easily identified.
Some species were removed after preliminary analyses, due either to obvious sequencing
errors (e.g. high BLAST homology with unrelated families or non-squamates, excessive
ambiguities) or a lack of overlap in genes sampled with other members of the same genus
(leading to seemingly artificial paraphyly). We also excluded species with identical
sequences between taxa across all genes, arbitrarily choosing the first taxon in alphabetical
order to remain in the matrix. Additionally, we also removed a few apparent "rogue taxa"
[75,77]. These were identified by their poor support and suspect placement (e.g. in a clearly
incorrect family), and were typically represented in the matrix by short fragments of single
genes (e.g. an ND4 fragment from the enigmatic colubroid snake Oreocalamus hanitchsi).
The final combined matrix contained sequence data for: 2335 species for 12S (including 56%
of all 4162 taxa, 1395 bp), 2377 for 16S (57%, 1970 bp), 730 for BDNF (18%, 714 bp), 1671
for c-mos (40%, 903 bp), 1985 for cyt-b (48%, 1000 bp), 437 for NT3 (10%, 675 bp), 1860
for ND2 (45%, 960 bp), 1556 for ND4 (37%, 696 bp), 393 for PDC (9%, 395 bp), 401 for
R35 (10%, 768 bp), 1379 for RAG-1 (33%, 2700 bp), and 471 for RAG2 (11%, 720 bp). The
total alignment consists of 12896 bp for 4162 taxa (4161 squamates and 1 outgroup). The
mean length is 2497 bp of sequence data present per species from 3.75 genes (19% of the
total matrix length of 12896 bp, or 81% missing data), and ranges from 27011153 bp (2
86% complete). The matrix and phylogeny (see below) are available in DataDryad repository
10.5061/dryad.82h0m.
Clearly, many taxa had large amounts of missing data (some >95%), and on average each
species had 81% missing cells. However, several lines of evidence suggest that these missing
data are not generally problematic. First, a large body of empirical and theoretical studies has
shown 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 reviews in [84,85]). Second, 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 generally congruent with previous
taxonomies and phylogenetic estimates (e.g. [41,48,72,73,75,76,197]). Third, recent studies
have also shown that there is generally little relationship between the amount of missing data
in individual taxa and the support for their placement on the tree [41,73,85]. Finally, we note
that some highly incomplete taxa were unstable in their placement (rogue taxa;[ 75]), but
these were removed prior to the analysis of the final matrix (see above).
Our sampling design should be especially robust to the impacts of missing data for several
reasons. Most importantly, most terminal taxon (species) had substantial data present (mean
of 2497 bp per species) regardless of the number of missing data cells. Simulations (see
reviews in [84,85]) suggest that the amount of data present is a key parameter in determining
the accuracy with which incomplete taxa are placed in phylogenies, not the amount of data
absent. Additionally, several genes (e.g. 12S/16S, cyt-b, and c-mos) were shared by many
(>40%) of taxa. Thus, there was typically extensive overlap among the genes present for each
taxon (as also indicated by the mean bp per species being much greater than the length of
most genes). Limited overlap in gene sampling among taxa could be highly problematic,
irrespective of the amount of missing data per se, but this does not appear to be a problem in
our dataset. Finally, several nuclear genes (e.g. BDNF, c-mos, R35, and RAG-1) were
congruently sampled in previous studies to represent most (>80%) squamate families and
subfamilies (e.g. [20]), providing a scaffold of well-sampled taxa spanning all major clades,
as recommended by recent authors [84].
Phylogenetic analyses
We performed phylogenetic analyses of the 12-gene concatenated matrix using Maximum
Likelihood (ML). We assessed node support using the non-parametric Shimodaira-
Hasegawa-Like (SHL) implementation of the approximate likelihood-ratio test (aLRT; [94]).
This involved a two-stage strategy. We first performed initial ML tree inference using the
program RAxML-Light v1.0.7 [209], a modification of the original RAxML algorithm [210].
This program uses the GTRCAT strategy for all genes and partitions, a high-speed
approximation of the GTR+ model (general time-reversible with gamma-distribution of rate
heterogeneity among sites). The GTR model is the only substitution model implemented in
RAxML [210], and all other substitution models are simply special cases of the GTR model
[211]. Previous analyses suggest that GTR is generally the best-fitting model for these genes
and that they should be partitioned by gene and codon position [16,17,19,20,36,81].
To generate an initial ML estimate for final optimization and support estimation, we
performed 11 ML searches from 11 parsimony starting trees generated under the default
parsimony model in RAxMLv7.2.8. This number is likely to be sufficient when datasets
contain many characters that have strong phylogenetic signal (A. Stamatakis, pers. comm.).
Additionally, the dataset was analyzed with these settings (GTRCAT search from a
randomized parsimony starting tree) numerous times (>20) as the final matrix was assembled
and tested, representing hundreds of independent searches from random starting points. All of
the estimated trees from these various analyses showed high overall congruence with the final
topology. The concordance between the preliminary and final results suggests that the tree
was not strongly impacted by searches stuck on local optima, and that it should be a good
approximation of the ML tree.
We then performed a final topology optimization and assessed support. We passed our best
ML estimate of the phylogeny (based on GTRCAT) from RAxML-Light to RAxMLv7.2.8,
which does an additional search (using the GTRGAMMA model) to produce a nearest-
neighbor interchange (NNI)-optimized estimate of the ML tree. This optimization is needed
to calculate the SHL version of the aLRT for estimating support values [94]. The SHL-aLRT
strategy approximates a test of the null hypothesis that the branch length subtending each
node equals 0 (i.e. that the node can be resolved, rather than estimated as a polytomy) with a
test of the more general null hypothesis that "the branch is incorrect" relative to the four next
suboptimal arrangements of that node relative to the NNI-optimal arrangement [94]. Based
on initial analyses, generating sufficient ML bootstrap replicates for a tree of this size proved
computationally intractable, so we rely on SHL values alone to assess support.
The SHL approach has at least two major advantages over non-parametric bootstrapping for
large ML trees: (i) values are apparently robust to many potential model violations and have
the same properties as bootstrap proportions for all but the shortest branches [41,94,212], and
(ii) values for short branches may be more accurate than bootstrap proportions, as support is
evaluated based on whole-alignment likelihoods, rather than the frequency of re-sampled
characters [94,213]. Additionally, the SHL approach is orders of magnitude faster than
traditional bootstrapping [94,212,213], and it appears to be similarly robust to matrices with
extensive missing data [41]. As in previous studies, we take a conservative view, considering
SHL values of 85 or greater (i.e. a 15% chance that a branch is "incorrect") as strong support
[41,212,213].
These analyses were performed on a 360-core SGI ICE supercomputing system ("ANDY") at
the High Performance Computing Center at the City University of New York (CUNY). The
final analysis was completed in 8.8 days of computer time using 188 nodes of the CUNY
supercomputing cluster.
Finally, we assessed the potential impact of missing data on our branch-length estimates. We
performed linear regression (in R) of the proportional completeness of each terminal taxa
(non-missing data in bp / maximum amount of non-missing data, 12896 bp) against the
length of its terminal branch. This test addresses whether incomplete taxa have branch-length
estimates that are consistently biased in one direction (shorter vs. longer) relative to more
complete terminals. However, it does not directly test whether branch length estimates are
correct or not, nor how branch length estimates are impacted by replacing non-missing data
with missing data (see [87] for results suggesting that such replacements have little effect in
real data sets).
Authors' contributions
RAP and JJW conceived the study. RAP, FTB, and JJW conducted analyses and checked
results. RAP, FTB, and JJW wrote the MS. All authors read and approved the final
manuscript.
Acknowledgements
We thank the many researchers who made this study possible through their detailed studies of
squamate phylogeny with a (mostly) shared set of molecular markers, and uploading their
sequence data to GenBank. We thank E. Paradis, J. Lombardo T. Guiher, R. Walsh, and P.
Muzio for computational assistance, T. Gamble, D. Frost, D. Cannatella, H. Zaher, F.
Grazziotin, P. Uetz, T. Jackman, and A. Bauer for taxonomic advice, and A. Larson, M.
Vences, and five anonymous reviewers for comments on this manuscript. The research was
supported in part by the U.S. National Science Foundation, including a Bioinformatics
Postdoctoral grant to R.A.P. (DBI-0905765), an AToL grant to J.J.W. (EF-0334923), and
grants to the CUNY HPCC (CNS-0958379 and CNS-0855217).
Appendix I
Note that we only provide here an account for the one subfamily newly erected in this study.
We do not provide accounts for subfamilies with changes in content (Boinae, Erycinae,
Dipsadinae, Pseudaspidinae, Scincinae, Ungaliophiinae), that have been resurrrected
(Sanziniinae), or that represent elevation of lower-ranked taxa (tribe Bachiini here recognized
as Bachiinae).
Candoiinae subfam. nov. (family Boidae)
Type: genus and species Candoia carinata [214].
Content: one genus, 4 species; C. aspera, C. bibroni, C. carinata, C. paulsoni.
Definition: this subfamily consists of the most recent common ancestor of the extant species
of Candoia, and all its descendants. These species are morphologically distinguished in part
from other boid snakes by a flattened rostrum leading to an angular snout [215] and a wide
premaxillary floor [167].
Distribution: these snakes are primarily restricted to the South Pacific islands of New Guinea
and Melanesia, and the eastern Indonesian archipelago [150].
Remarks: the three species from this subfamily that are sampled in our tree are strongly
supported as monophyletic (SHL = 100), and are well supported (SHL = 87) as the sister
taxon to a moderately supported clade consisting of Erycinae + Boinae (SHL = 83).
Proposed Generic Composition of Higher Taxa
Below, we list the familial and subfamilial assignment of all squamate genera from the
December, 2012 update of the Reptile Database, updated to reflect some recent changes and
the proposed subfamily level changes listed above. As this classification includes numerous
taxa not sampled in our tree, we deal with this conservatively. For traditionally recognized
families and subfamilies that we found to be monophyletic, we include all taxa traditionally
assigned to them. Taxa are denoted incertae sedis if they are of ambiguous familial or
subfamilial assignment due to uncertain placement in our tree, or due to absence from our
tree and lack of assignment by previous authors. This classification includes 67 families and
56 subfamilies, and accounts for >9400 squamate species in 1018 genera [1]. Higher taxa are
listed (more-or-less) phylogenetically (starting closest to the root; Figure 1), families are
listed alphabetically within higher taxa, and subfamilies and genera are listed alphabetically
within families.
Dibamidae (Anelytropsis, Dibamus)
Gekkota
Carphodactylidae (Carphodactylus, Nephrurus, Orraya, Phyllurus, Saltuarius,
Underwoodisaurus, Uvidicolus); Diplodactylidae (Amalosia, Bavayia, Correlophus,
Crenadactylus, Dactylocnemis, Dierogekko, Diplodactylus, Eurydactylodes, Hesperoedura,
Hoplodactylus, Lucasium, Mniarogekko, Mokopirirakau, Naultinus, Nebulifera, Oedodera,
Oedura, Paniegekko, Pseudothecadactylus, Rhacodactylus, Rhynchoedura, Strophurus,
Toropuku, Tukutuku, Woodworthia); Eublepharidae (Aeluroscalabotes, Coleonyx,
Eublepharis, Goniurosaurus, Hemitheconyx, Holodactylus); Gekkonidae (Afroedura,
Afrogecko, Agamura, Ailuronyx, Alsophylax, Asiocolotes, Blaesodactylus, Bunopus,
Calodactylodes, Chondrodactylus, Christinus, Cnemaspis, Colopus, Crossobamon,
Cryptactites, Cyrtodactylus, Cyrtopodion, Dixonius, Ebenavia, Elasmodactylus, Geckolepis,
Gehyra, Gekko, Goggia, Hemidactylus, Hemiphyllodactylus, Heteronotia, Homopholis,
Lepidodactylus, Luperosaurus, Lygodactylus, Matoatoa, Mediodactylus, Nactus, Narudasia,
Pachydactylus, Paragehyra, Paroedura, Perochirus, Phelsuma, Pseudoceramodactylus,
Pseudogekko, Ptenopus, Ptychozoon, Rhinogecko, Rhoptropella, Rhoptropus, Stenodactylus,
Tropiocolotes, Urocotyledon, Uroplatus); Phyllodactylidae (Asaccus, Gymnodactylus,
Haemodracon, Homonota, Phyllodactylus, Phyllopezus, Ptyodactylus, Tarentola,
Thecadactylus); Pygopodidae (Aprasia, Delma, Lialis, Ophidiocephalus, Paradelma,
Pletholax, Pygopus); Spha (Aristelliger, Chatogekko, Coleodactylus, Euleptes, Gonatodes,
Lepidoblepharis, Pristurus, Pseudogonatodes, Quedenfeldtia, Saurodactylus,
Sphaerodactylus, Teratoscincus)
Scincoidea
Cordylidae, Cordylinae (Chamaesaura, Cordylus, Hemicordylus, Karusasaurus,
Namazonurus, Ninurta, Ouroborus, Pseudocordylus, Smaug), Platysaurinae (Platysaurus);
Gerrhosauridae, Gerrhosaurinae (Cordylosaurus, Gerrhosaurus, Tetradactylus),
Zonosaurinae (Tracheloptychus, Zonosaurus); Scincidae, Acontiinae (Acontias,
Typhlosaurus), Lygosominae (Ablepharus, Afroablepharus, Anomalopus, Asymblepharus,
Ateuchosaurus, Bartleia, Bassiana, Bellatorias, Caledoniscincus, Calyptotis, Carlia,
Cautula, Celatiscincus, Chioninia, Coeranoscincus, Coggeria, Cophoscincopus, Corucia,
Cryptoblepharus, Ctenotus, Cyclodomorphus, Dasia, Egernia, Emoia, Eremiascincus,
Eroticoscincus, Eugongylus, Eulamprus, Eumecia, Eutropis, Fojia, Geomyersia, Geoscincus,
Glaphyromorphus, Gnypetoscincus, Graciliscincus, Haackgreerius, Hemiergis,
Hemisphaeriodon, Insulasaurus, Isopachys, Kaestlea, Kanakysaurus, Lacertaspis,
Lacertoides, Lamprolepis, Lampropholis, Lankascincus, Larutia, Leiolopisma, Lepidothyris,
Leptoseps, Leptosiaphos, Lerista, Liburnascincus, Liopholis, Lioscincus, Lipinia, Lissolepis,
Lobulia, Lygisaurus, Lygosoma, Mabuya, Marmorosphax, Menetia, Mochlus, Morethia,
Nangura, Nannoscincus, Niveoscincus, Notoscincus, Oligosoma, Ophioscincus, Otosaurus,
Panaspis, Papuascincus, Parvoscincus, Phoboscincus, Pinoyscincus, Prasinohaema,
Proablepharus, Pseudemoia, Ristella, Saiphos, Saproscincus, Scincella, Sigaloseps,
Simiscincus, Sphenomorphus, Tachygyia, Tiliqua, Trachylepis, Tribolonotus, Tropidophorus,
Tropidoscincus, Tytthoscincus, Vietnascincus), Scincinae (Amphiglossus, Androngo,
Barkudia, Brachymeles, Chabanaudia, Chalcides, Chalcidoseps, Eumeces, Eurylepis,
Feylinia, Gongylomorphus, Hakaria, Janetaescincus, Jarujinia, Madascincus, Melanoseps,
Mesoscincus, Nessia, Ophiomorus, Pamelaescincus, Paracontias, Plestiodon, Proscelotes,
Pseudoacontias, Pygomeles, Scelotes, Scincopus, Scincus, Scolecoseps, Sepsina, Sepsophis,
Sirenoscincus, Typhlacontias, Voeltzkowia); Xantusiidae, Cricosaurinae (Cricosaura),
Lepidophyminae (Lepidophyma), Xantusiinae (Xantusia)
Lacertoidea (including Amphisbaenia)
Amphisbaenidae (Amphisbaena, Ancylocranium, Baikia, Chirindia, Cynisca, Dalophia,
Geocalamus, Loveridgea, Mesobaena, Monopeltis, Zygaspis); Bipedidae (Bipes); Blanidae
(Blanus); Cadeidae (Cadea); Gymnophthalmidae, Alopoglossinae (Alopoglossus,
Ptychoglossus), Bachiinae (Bachia), Cercosaurinae (Anadia, Cercosaura, Echinosaura,
Euspondylus, Macropholidus, Neusticurus, Opipeuter, Petracola, Pholidobolus, Placosoma,
Potamites, Proctoporus, Riama, Riolama, Teuchocercus), Ecpleopinae (Adercosaurus,
Amapasaurus, Anotosaura, Arthrosaura, Colobosauroides, Dryadosaura, Ecpleopus,
Kaieteurosaurus, Leposoma, Marinussaurus, Pantepuisaurus), Gymnophthalminae
(Acratosaura, Alexandresaurus, Calyptommatus, Caparaonia, Colobodactylus, Colobosaura,
Gymnophthalmus, Heterodactylus, Iphisa, Micrablepharus, Nothobachia, Procellosaurinus,
Psilophthalmus, Scriptosaura, Stenolepis, Tretioscincus, Vanzosaura), Rhachisaurinae
(Rhachisaurus); Lacertidae, Gallotiinae (Gallotia, Psammodromus), Lacertinae
(Acanthodactylus, Adolfus, Algyroides, Anatololacerta, Apathya, Archaeolacerta,
Atlantolacerta, Australolacerta, Congolacerta, Dalmatolacerta, Darevskia, Dinarolacerta,
Eremias, Gastropholis, Heliobolus, Hellenolacerta, Holaspis, Iberolacerta, Ichnotropis,
Iranolacerta, Lacerta, Latastia, Meroles, Mesalina, Nucras, Omanosaura, Ophisops,
Parvilacerta, Pedioplanis, Philochortus, Phoenicolacerta, Podarcis, Poromera,
Pseuderemias, Scelarcis, Takydromus, Teira, Timon, Tropidosaura, Zootoca); Rhineuridae
(Rhineura); Teiidae, Teiinae (Ameiva, Aspidoscelis, Cnemidophorus, Dicrodon, Kentropyx,
Teius), Tupinambinae (Callopistes, Crocodilurus, Dracaena, Tupinambis); Trogonophiidae
(Agamodon, Diplometopon, Pachycalamus, Trogonophis)
Iguania
Agamidae, Agaminae (Acanthocercus, Agama, Brachysaura, Bufoniceps, Laudakia,
Phrynocephalus, Pseudotrapelus, Trapelus, Xenagama), Amphibolurinae (Amphibolurus,
Chelosania, Chlamydosaurus, Cryptagama, Ctenophorus, Diporiphora, Hypsilurus,
Intellagama, Lophognathus, Moloch, Physignathus, Pogona, Rankinia, Tympanocryptis),
Draconinae (Acanthosaura, Aphaniotis, Bronchocela, Calotes, Ceratophora, Complicitus,
Cophotis, Coryphophylax, Dendragama, Draco, Gonocephalus, Harpesaurus, Hypsicalotes,
Japalura, Lophocalotes, Lyriocephalus, Mantheyus, Oriocalotes, Otocryptis, Phoxophrys,
Psammophilus, Pseudocalotes, Pseudocophotis, Ptyctolaemus, Salea, Sitana,
Thaumatorhynchus), Hydrosaurinae (Hydrosaurus), Leiolepidinae (Leiolepis),
Uromastycinae (Uromastyx); Chamaeleonidae, Brookesiinae (Brookesia), Chamaeleoninae
(Archaius, Bradypodion, Calumma, Chamaeleo, Furcifer, Kinyongia, Nadzikambia,
Rhampholeon, Rieppeleon, Trioceros); Corytophanidae (Basiliscus, Corytophanes,
Laemanctus); Crotaphytidae (Crotaphytus, Gambelia); Dactyloidae (Anolis);
Hoplocercidae (Enyalioides, Hoplocercus, Morunasaurus); Iguanidae (Amblyrhynchus,
Brachylophus, Conolophus, Ctenosaura, Cyclura, Dipsosaurus, Iguana, Sauromalus);
Leiocephalidae (Leiocephalus); Leiosauridae, Enyaliinae (Anisolepis, Enyalius,
Urostrophus), Leiosaurinae (Diplolaemus, Leiosaurus, Pristidactylus); Liolaemidae
(Ctenoblepharys, Liolaemus, Phymaturus); Opluridae (Chalarodon, Oplurus);
Phrynosomatidae (Callisaurus, Cophosaurus, Holbrookia, Petrosaurus, Phrynosoma,
Sceloporus, Uma, Urosaurus, Uta); Polychrotidae (Polychrus); Tropiduridae
(Eurolophosaurus, Microlophus, Plica, Stenocercus, Strobilurus, Tropidurus, Uracentron,
Uranoscodon)
Anguimorpha
Anguidae, Anguinae (Anguis, Dopasia, Ophisaurus, Pseudopus), Diploglossinae (Celestus,
Diploglossus, Ophiodes), Gerrhonotinae (Abronia, Barisia, Coloptychon, Elgaria,
Gerrhonotus, Mesaspis); Anniellidae (Anniella); Helodermatidae (Heloderma);
Lanthanotidae (Lanthanotus); Shinisauridae (Shinisaurus); Varanidae (Varanus);
Xenosauridae (Xenosaurus)
Serpentes
Acrochordidae (Acrochordus); Aniliidae (Anilius); Anomalepididae (Anomalepis,
Helminthophis, Liotyphlops, Typhlophis); Anomochilidae (Anomochilus); Boidae, Boinae
(Boa, Corallus, Epicrates, Eunectes), Candoiinae (Candoia), Erycinae (Eryx), Sanziniinae
(Acrantophis, Sanzinia), Ungaliophiinae (Charina, Exiliboa, Lichanura, Ungaliophis);
Bolyeriidae (Bolyeria, Casarea); Calabariidae (Calabaria); Colubridae incertae sedis
(Blythia, Cyclocorus, Elapoidis, Gongylosoma, Helophis, Myersophis, Oreocalamus,
Poecilopholis, Rhabdops, Tetralepis), Calamariinae (Calamaria, Calamorhabdium,
Collorhabdium, Etheridgeum, Macrocalamus, Pseudorabdion, Rabdion), Colubrinae
(Aeluroglena, Ahaetulla, Aprosdoketophis, Archelaphe, Argyrogena, Arizona, Bamanophis,
Bogertophis, Boiga, Cemophora, Chilomeniscus, Chionactis, Chironius, Chrysopelea,
Coelognathus, Coluber, Colubroelaps, Conopsis, Coronella, Crotaphopeltis, Cyclophiops,
Dasypeltis, Dendrelaphis, Dendrophidion, Dipsadoboa, Dispholidus, Dolichophis,
Drymarchon, Drymobius, Drymoluber, Dryocalamus, Dryophiops, Eirenis, Elachistodon,
Elaphe, Euprepiophis, Ficimia, Geagras, Gonyophis, Gonyosoma, Gyalopion, Hapsidophrys,
Hemerophis, Hemorrhois, Hierophis, Lampropeltis, Leptodrymus, Leptophis, Lepturophis,
Limnophis, Liopeltis, Lycodon, Lytorhynchus, Macroprotodon, Mastigodryas, Meizodon,
Oligodon, Oocatochus, Opheodrys, Oreocryptophis, Orthriophis, Oxybelis, Pantherophis,
Philothamnus, Phyllorhynchus, Pituophis, Platyceps, Pseudelaphe, Pseudoficimia, Pseustes,
Ptyas, Rhadinophis, Rhamnophis, Rhinechis, Rhinobothryum, Rhinocheilus,
Rhynchocalamus, Rhynchophis, Salvadora, Scaphiophis, Scolecophis, Senticolis, Simophis,
Sonora, Spalerosophis, Spilotes, Stegonotus, Stenorrhina, Symphimus, Sympholis, Tantilla,
Tantillita, Telescopus, Thelotornis, Thrasops, Toxicodryas, Trimorphodon, Xenelaphis,
Xyelodontophis, Zamenis), Dipsadinae (Adelphicos, Alsophis, Amastridium, Amnesteophis,
Antillophis, Apostolepis, Arrhyton, Atractus, Boiruna, Borikenophis, Caaeteboia,
Calamodontophis, Caraiba, Carphophis, Cercophis, Chapinophis, Chersodromus, Clelia,
Coniophanes, Conophis, Contia, Coronelaps, Crisantophis, Cryophis, Cubophis,
Darlingtonia, Diadophis, Diaphorolepis, Dipsas, Ditaxodon, Drepanoides, Echinanthera,
Elapomorphus, Emmochliophis, Enuliophis, Enulius, Erythrolamprus, Farancia, Geophis,
Gomesophis, Haitiophis, Helicops, Heterodon, Hydrodynastes, Hydromorphus, Hydrops,
Hypsiglena, Hypsirhynchus, Ialtris, Imantodes, Leptodeira, Lioheterophis, Lygophis,
Magliophis, Manolepis, Mussurana, Ninia, Nothopsis, Ocyophis, Omoadiphas, Oxyrhopus,
Paraphimophis, Phalotris, Philodryas, Phimophis, Plesiodipsas, Pliocercus, Pseudalsophis,
Pseudoboa, Pseudoeryx, Pseudoleptodeira, Pseudotomodon, Psomophis, Ptychophis,
Rhachidelus, Rhadinaea, Rhadinella, Rhadinophanes, Rodriguesophis, Saphenophis,
Schwartzophis, Sibon, Sibynomorphus, Siphlophis, Sordellina, Synophis, Tachymenis,
Taeniophallus, Tantalophis, Thamnodynastes, Thermophis, Tomodon, Tretanorhinus,
Trimetopon, Tropidodipsas, Tropidodryas, Uromacer, Uromacerina, Urotheca, Xenodon,
Xenopholis), Grayiinae (Grayia), Natricinae (Adelophis, Afronatrix, Amphiesma,
Amphiesmoides, Anoplohydrus, Aspidura, Atretium, Balanophis, Clonophis, Hologerrhum,
Hydrablabes, Hydraethiops, Iguanognathus, Lycognathophis, Macropisthodon, Natriciteres,
Natrix, Nerodia, Opisthotropis, Parahelicops, Pararhabdophis, Paratapinophis, Regina,
Rhabdophis, Seminatrix, Sinonatrix, Storeria, Thamnophis, Trachischium, Tropidoclonion,
Tropidonophis, Virginia, Xenochrophis), Pseudoxenodontinae (Plagiopholis,
Pseudoxenodon), Sibynophiinae (Scaphiodontophis, Sibynophis); Cylindrophiidae
(Cylindrophis); Elapidae (Acanthophis, Aipysurus, Aspidelaps, Aspidomorphus, Austrelaps,
Bungarus, Cacophis, Calliophis, Cryptophis, Demansia, Dendroaspis, Denisonia, Drysdalia,
Echiopsis, Elapognathus, Elapsoidea, Emydocephalus, Ephalophis, Furina, Hemachatus,
Hemiaspis, Hemibungarus, Hoplocephalus, Hydrelaps, Hydrophis, Kolpophis, Laticauda,
Loveridgelaps, Maticora, Micropechis, Micruroides, Micrurus, Naja, Notechis, Ogmodon,
Ophiophagus, Oxyuranus, Parahydrophis, Parapistocalamus, Parasuta, Pseudechis,
Pseudohaje, Pseudolaticauda, Pseudonaja, Rhinoplocephalus, Salomonelaps, Simoselaps,
Sinomicrurus, Suta, Thalassophis, Toxicocalamus, Tropidechis, Vermicella, Walterinnesia);
Gerrhopilidae (Gerrhopilus); Homalopsidae (Bitia, Brachyorrhos, Cantoria, Cerberus,
Djokoiskandarus, Enhydris, Erpeton, Fordonia, Gerarda, Heurnia, Homalopsis, Myron,
Pseudoferania); Lamprophiidae incertae sedis (Micrelaps, Montaspis, Oxyrhabdium),
Aparallactinae (Amblyodipsas, Aparallactus, Brachyophis, Chilorhinophis, Elapotinus,
Hypoptophis, Macrelaps, Polemon, Xenocalamus), Atractaspidinae (Atractaspis,
Homoroselaps), Lamprophiinae (Boaedon, Bothrophthalmus, Chamaelycus, Dendrolycus,
Gonionotophis, Hormonotus, Inyoka, Lamprophis, Lycodonomorphus, Lycophidion,
Pseudoboodon), Prosymninae (Prosymna), Psammophiinae (Dipsina, Hemirhagerrhis,
Malpolon, Mimophis, Psammophis, Psammophylax, Rhagerhis, Rhamphiophis),
Pseudaspidinae (Buhoma, Psammodynastes, Pseudaspis, Pythonodipsas), Pseudoxyrhophiine
(Alluaudina, Amplorhinus, Bothrolycus, Brygophis, Compsophis, Ditypophis, Dromicodryas,
Duberria, Exallodontophis, Heteroliodon, Ithycyphus, Langaha, Leioheterodon, Liophidium,
Liopholidophis, Lycodryas, Madagascarophis, Micropisthodon, Pararhadinaea,
Parastenophis, Phisalixella, Pseudoxyrhopus, Thamnosophis); Leptotyphlopidae
(Epacrophis, Epictia, Leptotyphlops, Mitophis, Myriopholis, Namibiana, Rena, Rhinoleptus,
Siagonodon, Tetracheilostoma, Tricheilostoma, Trilepida); Loxocemidae (Loxocemus);
Pareatidae (Aplopeltura, Asthenodipsas, Pareas); Pythonidae (Antaresia, Apodora,
Aspidites, Bothrochilus, Broghammerus, Leiopython, Liasis, Morelia, Python);
Tropidophiidae (Trachyboa, Tropidophis); Typhlopidae (Acutotyphlops, Afrotyphlops,
Austrotyphlops, Cyclotyphlops, Grypotyphlops, Letheobia, Megatyphlops, Ramphotyphlops,
Rhinotyphlops, Typhlops); Uropeltidae (Brachyophidium, Melanophidium, Platyplectrurus,
Plectrurus, Pseudotyphlops, Rhinophis, Teretrurus, Uropeltis); Viperidae, Azemiopinae
(Azemiops), Crotalinae (Agkistrodon, Atropoides, Bothriechis, Bothriopsis, Bothrocophias,
Bothropoides, Bothrops, Calloselasma, Cerrophidion, Crotalus, Deinagkistrodon, Garthius,
Gloydius, Hypnale, Lachesis, Mixcoatlus, Ophryacus, Ovophis, Porthidium, Protobothrops,
Rhinocerophis, Sistrurus, Trimeresurus, Tropidolaemus), Viperinae (Atheris, Bitis, Causus,
Cerastes, Daboia, Echis, Eristicophis, Macrovipera, Montatheris, Montivipera, Proatheris,
Pseudocerastes, Vipera); Xenodermatidae (Achalinus, Fimbrios, Stoliczkia, Xenodermus,
Xylophis); Xenopeltidae (Xenopeltis); Xenophidiidae (Xenophidion); Xenotyphlopidae
(Xenotyphlops)
Additional files
Additional_file_1 as TXT
Additional file 1: Data File S1 The 4162-species ML phylogeny in Newick format;
taxonomic changes are given in Additional file 2: Table S1.
Additional_file_2 as DOCX
Additional file 2: Table S1 GenBank accession numbers for all taxa included in this
analysis.
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0.2 subst./site
Scincidae
Xantusiidae
Gerrhosauridae
Teiidae
Gymnophthalmidae
Lacertidae
Anguidae
Chamaeleonidae
Agamidae
Leiosauridae
Boidae
Viperidae
Colubridae
Lamprophiidae
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G
A) Gekkota
B) Scincoidea
C) Episquamata
D) Lacertoidea
E) Toxicofera
F) Anguimorpha
G) Iguania
H) Serpentes
H
Dipsadinae
Gekkonidae
Cercosaurinae
Acontiinae
Lacertinae
Hydrosaurinae
Xenodermatidae
Anniellidae
Crotaphytidae
Hoplocercidae
Sphenodontidae
Leiolepidinae
Polychrotidae
Pseudoxyrhophiinae
Loxocemidae
Dibamidae
Prosymninae
Lygosominae
Natricinae
Xantusiinae
Tropiduridae
Corytophanidae
Ecpleopinae
Anomochilidae
Amphisbaenidae
Leiosaurinae
Xenophiidae
Scincinae
Draconinae
Bipedidae
Gerrhosaurinae
Rhineuridae
Anomalepididae
Trogonophiidae
Aniliidae
Azemiopinae
Alopoglossinae
Lanthanotidae
Pseudaspidinae
Tupinambinae
Xenotyphlopidae
Blanidae
Gerrhopilidae
Liolaemidae
Candoiinae
Gallotiinae
Leptotyphlopidae
Platysaurinae
Pythonidae
Boinae
Colubrinae
Opluridae
Elapidae
Typhlopidae
Pareatidae
Cadeidae
Crotalinae
Sibynophiinae
Chamaeleoninae
Rhachisaurinae
Grayiinae
Ungaliophiinae
Erycinae
Phyllodactylidae
Anguinae
Helodermatidae
Phrynosomatidae
Sanziniinae
Tropidophiidae
Viperinae
Cricosaurinae
Shinisauridae
Teiinae
Diplodactylidae
Cylindrophiidae
Brookesiinae
Lepidophyminae
Enyaliinae
Varanidae
Bachiinae
Aparallactinae
Sphaerodactylidae
Atractaspidinae
Uropeltidae
Leiocephalidae
Iguanidae
Homalopsidae
Amphibolurinae
Xenopeltidae
Diploglossinae
Calamariinae
Xenosauridae
Uromasticinae
Agaminae
Acrochordidae
Pygopodidae
Calabariidae
Psammophiinae
Carphodactylidae
Cordylinae
Gymnophthalminae
Pseudoxenodontinae
Bolyeriidae
Dactyloidae
Gerrhonotinae
Eublepharidae
Lamprophiinae
Zonosaurinae
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98
99
100
99
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99
83
54
98
99
84
100
68
100
100
95
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94
63
84
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90
100
100
100
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81
100
100
100
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87
99
69
90
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100
88
65
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96
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100
Squamata
Cordylidae
Figure 1

Dibamu bourreti
Dibamu greeri
Dibamu montanu
Aneltropi papillou
Dibamu tiomaneni
Dibamu noaeguineae
Dibamu celebeni
Dibamu erameni
Phlluru kabikabi
Phlluru amnicola
Phlluru platuru
Saltuariu alebrou
Saltuariu cornutu
Saltuariu wberba
Saltuariu kateae
Saltuariu moritzi
Saltuariu waini
Orraa occultu
Carphodactlu laei
Uidicolu phruru
Underwoodiauru milii
Nephruru wheeleri
Nephruru aper
Nephruru heai
Nephruru amae
Nephruru lei
Nephruru tellatu
Nephruru ertebrali
Nephruru deleani
Nephruru laeiimu
Delma autrali
Delma toruata
Delma concinna
Delma labiali
Delma borea
Delma tincta
Delma pax
Delma mitella
Delma impar
Delma molleri
Delma butleri
Delma nauta
Delma inornata
Delma graii
Delma fraeri
Ophidiocephalu taeniatu
Liali jicari
Liali burtoni
Pletholax gracili
Paradelma orientali
Pgopu lepidopodu
Pgopu nigricep
Apraia picturata
Apraia pulchella
Apraia fuca
Apraia repen
Apraia mithi
Apraia aurita
Apraia peudopulchella
Apraia parapulchella
Apraia inaurita
Apraia triolata
Peudothecadactlu lindneri
Rhacodactlu trachrhnchu
Oedodera marmorata
Dierogekko poumeni
Dierogekko inexpectatu
Dierogekko nehoueeni
Dierogekko alidiclai
Dierogekko inulari
Dierogekko koniambo
Dierogekko kaalaeni
Dierogekko thomawhitei
Baaia pulchella
Baaia geitaina
Baaia auagii
Paniegekko madjo
Rhacodactlu leachianu
Baaia ornata
Baaia goroeni
Baaia cclura
Baaia montana
Rhacodactlu auriculatu
Correlophu arainorum
Correlophu ciliatu
Eurdactlode mmetricu
Mniarogekko chahoua
Eurdactlode occidentali
Eurdactlode agricolae
Eurdactlode ieillardi
Crenadactlu ocellatu
Hoplodactlu duaucelii
Woodworthia chroireticu
Woodworthia maculatu
Toropuku tepheni
Dactlocnemi pacificu
Mokopirirakau crptozoicu
Mokopirirakau nebulou
Mokopirirakau granulatu
Mokopirirakau kahutarae
Tukutuku rakiurae
Naultinu gemmeu
Naultinu elegan
Naultinu graii
Naultinu tuberculatu
Naultinu tellatu
Naultinu manukanu
Naultinu poecilochloru
Naultinu rudi
Strophuru taenicauda
Nebulifera robuta
Amaloia leueurii
Amaloia rhombifer
Amaloia obcura
Heperoedura reticulata
Oedura gemmata
Oedura marmorata
Oedura filicipoda
Oedura gracili
Oedura catelnaui
Oedura coggeri
Oedura troni
Oedura monili
Strophuru mcmillani
Strophuru taeniatu
Strophuru elderi
Strophuru jeanae
Strophuru trophuru
Strophuru aimili
Strophuru krial
Strophuru ciliari
Strophuru wellingtonae
Strophuru williami
Strophuru intermediu
Strophuru rankini
Strophuru pinigeru
Rhnchoedura ornata
Lucaium brnei
Lucaium alboguttatum
Lucaium maini
Lucaium damaeum
Lucaium immaculatum
Lucaium teindachneri
Lucaium wombei
Lucaium tenodactlum
Lucaium uarroum
Diplodactlu granarieni
Diplodactlu fulleri
Diplodactlu ittatu
Diplodactlu galeatu
Diplodactlu teellatu
Diplodactlu ornatu
Diplodactlu polophthalmu
Diplodactlu conpicillatu
Diplodactlu mitchelli
Diplodactlu capeni
Diplodactlu aagei
Diplodactlu klugei
Diplodactlu pulcher
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Dibamidae
CarphodactyIidae
Pygopodidae
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Figure 2
B
Tarentola gigas
Tarentola caboverdiana
Tarentola rudis
Tarentola darwini
Tarentola chazaliae
Tarentola delalandii
Tarentola gomerensis
Tarentola annularis
Tarentola ephippiata
Tarentola boettgeri
Tarentola mindiae
Tarentola neglecta
Tarentola angustimentalis
Tarentola mauritanica
Tarentola deserti
Tarentola boehmei
Tarentola americana
Phyllopezus maranjonensis
Phyllopezus lutzae
Phyllopezus pollicaris
Phyllopezus periosus
Phyllodactylus homolepidurus
Phyllodactylus davisi
Phyllodactylus duellmani
Phyllodactylus delcampoi
Phyllodactylus paucituberculatus
Phyllodactylus nocticolus
Phyllodactylus bugastrolepis
Phyllodactylus unctus
Phyllodactylus xanti
Phyllodactylus bordai
Phyllodactylus lanei
Phyllodactylus tuberculosus
Phyllodactylus reissii
Phyllodactylus wirshingi
Homonota andicola
Homonota darwinii
Homonota borellii
Homonota underwoodi
Homonota fasciata
Homonota gaudichaudii
Ptyodactylus guttatus
Ptyodactylus hasselquistii
Ptyodactylus oudrii
Ptyodactylus ragazzii
Asaccus platyrhynchus
Haemodracon riebeckii
Thecadactylus rapicauda
Thecadactylus solimoensis
Sphaerodactylus nicholsi
Sphaerodactylus ocoae
Sphaerodactylus gaigeae
Sphaerodactylus klauberi
Sphaerodactylus semasiops
Sphaerodactylus goniorhynchus
Sphaerodactylus townsendi
Sphaerodactylus armstrongi
Sphaerodactylus macrolepis
Sphaerodactylus argus
Sphaerodactylus roosevelti
Sphaerodactylus altavelensis
Sphaerodactylus notatus
Sphaerodactylus darlingtoni
Sphaerodactylus cryphius
Sphaerodactylus shrevei
Sphaerodactylus elegans
Sphaerodactylus leucaster
Sphaerodactylus copei
Sphaerodactylus nigropunctatus
Sphaerodactylus intermedius
Sphaerodactylus torrei
Sphaerodactylus cinereus
Sphaerodactylus thompsoni
Sphaerodactylus glaucus
Sphaerodactylus molei
Sphaerodactylus oliveri
Sphaerodactylus richardi
Sphaerodactylus cricoderus
Sphaerodactylus ramsdeni
Sphaerodactylus schwartzi
Sphaerodactylus kirbyi
Sphaerodactylus vincenti
Sphaerodactylus microlepis
Sphaerodactylus parvus
Sphaerodactylus sabanus
Sphaerodactylus elegantulus
Sphaerodactylus sputator
Sphaerodactylus fantasticus
Pseudogonatodes guianensis
Pseudogonatodes lunulatus
Pseudogonatodes manessi
Coleodactylus natalensis
Coleodactylus meridionalis
Coleodactylus brachystoma
Coleodactylus septentrionalis
Gonatodes ocellatus
Gonatodes ceciliae
Gonatodes seigliei
Gonatodes concinnatus
Gonatodes antillensis
Gonatodes humeralis
Gonatodes falconensis
Gonatodes taniae
Gonatodes purpurogularis
Gonatodes alexandermendesi
Gonatodes superciliaris
Gonatodes annularis
Gonatodes hasemani
Gonatodes infernalis
Gonatodes vittatus
Gonatodes petersi
Gonatodes albogularis
Gonatodes daudini
Gonatodes caudiscutatus
Gonatodes eladioi
Lepidoblepharis festae
Lepidoblepharis xanthostigma
Chatogekko amazonicus
Saurodactylus mauritanicus
Teratoscincus roborowskii
Teratoscincus przewalskii
Teratoscincus scincus
Teratoscincus microlepis
Euleptes europaea
Saurodactylus fasciatus
Aristelliger georgeensis
Aristelliger praesignis
Aristelliger lar
Quedenfeldtia moerens
Quedenfeldtia trachyblepharus
Pristurus somalicus
Pristurus crucifer
Pristurus carteri
Pristurus minimus
Pristurus rupestris
Pristurus flavipunctatus
Pristurus abdelkuri
Pristurus guichardi
Pristurus sokotranus
Pristurus insignis
Pristurus celerrimus
Goniurosaurus araneus
Goniurosaurus luii
Goniurosaurus catbaensis
Goniurosaurus lichtenfelderi
Goniurosaurus kuroiwae
Hemitheconyx taylori
Hemitheconyx caudicinctus
Holodactylus africanus
Eublepharis turcmenicus
Eublepharis macularius
Coleonyx elegans
Coleonyx mitratus
Coleonyx variegatus
Coleonyx brevis
Aeluroscalabotes felinus
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Phyllodactylidae
Eublepharidae
Sphaerodactylidae
C
Figure 3
C
Phelsuma kely
Phelsuma lineata
Phelsuma comorensis
Phelsuma pusilla
Phelsuma quadriocellata
Phelsuma antanosy
Phelsuma klemmeri
Phelsuma robertmertensi
Phelsuma laticauda
Phelsuma serraticauda
Phelsuma malamakibo
Phelsuma berghofi
Phelsuma hielscheri
Phelsuma flavigularis
Phelsuma ravenala
Phelsuma dubia
Phelsuma modesta
Phelsuma nigristriata
Phelsuma inexpectata
Phelsuma ornata
Phelsuma guimbeaui
Phelsuma cepediana
Phelsuma borbonica
Phelsuma guentheri
Phelsuma gigas
Phelsuma edwardnewtoni
Phelsuma standingi
Phelsuma andamanense
Phelsuma mutabilis
Phelsuma breviceps
Phelsuma pronki
Phelsuma barbouri
Phelsuma seippi
Phelsuma parkeri
Phelsuma abbotti
Phelsuma madagascariensis
Phelsuma guttata
Phelsuma sundbergi
Phelsuma astriata
Phelsuma vanheygeni
Lygodactylus keniensis
Lygodactylus kimhowelli
Lygodactylus luteopicturatus
Lygodactylus picturatus
Lygodactylus williamsi
Lygodactylus chobiensis
Lygodactylus gutturalis
Lygodactylus angularis
Lygodactylus thomensis
Lygodactylus conraui
Lygodactylus klugei
Lygodactylus bradfieldi
Lygodactylus capensis
Lygodactylus stevensoni
Lygodactylus lawrencei
Lygodactylus pictus
Lygodactylus mirabilis
Lygodactylus tuberosus
Lygodactylus montanus
Lygodactylus gravis
Lygodactylus pauliani
Lygodactylus arnoulti
Lygodactylus blancae
Lygodactylus verticillatus
Lygodactylus heterurus
Lygodactylus tolampyae
Lygodactylus guibei
Lygodactylus miops
Lygodactylus madagascariensis
Lygodactylus rarus
Lygodactylus expectatus
Rhoptropella ocellata
Cnemaspis tropidogaster
Cnemaspis kandiana
Cnemaspis podihuna
Pachydactylus affinis
Pachydactylus vansoni
Pachydactylus capensis
Pachydactylus oshaughnessyi
Pachydactylus tigrinus
Pachydactylus montanus
Pachydactylus vanzyli
Pachydactylus rangei
Pachydactylus austeni
Pachydactylus mariquensis
Pachydactylus mclachlani
Pachydactylus monicae
Pachydactylus weberi
Pachydactylus serval
Pachydactylus griffini
Pachydactylus carinatus
Pachydactylus fasciatus
Pachydactylus tsodiloensis
Pachydactylus waterbergensis
Pachydactylus purcelli
Pachydactylus oculatus
Pachydactylus maculatus
Pachydactylus geitje
Pachydactylus labialis
Pachydactylus barnardi
Pachydactylus formosus
Pachydactylus rugosus
Pachydactylus punctatus
Pachydactylus scherzi
Pachydactylus sansteynae
Pachydactylus caraculicus
Pachydactylus bicolor
Pachydactylus oreophilus
Pachydactylus gaiasensis
Pachydactylus reconditus
Pachydactylus parascutatus
Pachydactylus scutatus
Pachydactylus namaquensis
Pachydactylus kladaroderma
Pachydactylus haackei
Colopus kochii
Colopus wahlbergii
Pachydactylus robertsi
Chondrodactylus bibronii
Chondrodactylus fitzsimonsi
Chondrodactylus turneri
Pachydactylus laevigatus
Chondrodactylus angulifer
Elasmodactylus tuberculosus
Elasmodactylus tetensis
Rhoptropus barnardi
Rhoptropus biporosus
Rhoptropus boultoni
Rhoptropus bradfieldi
Rhoptropus afer
Goggia lineata
Blaesodactylus sakalava
Blaesodactylus antongilensis
Blaesodactylus boivini
Homopholis mulleri
Homopholis walbergii
Homopholis fasciata
Geckolepis maculata
Geckolepis typica
Afroedura karroica
Afroedura pondolia
Afrogecko porphyreus
Matoatoa brevipes
Cryptactites peringueyi
Afrogecko swartbergensis
Christinus marmoratus
Paragehyra gabriellae
Uroplatus fimbriatus
Uroplatus giganteus
Uroplatus henkeli
Uroplatus sikorae
Uroplatus lineatus
Uroplatus pietschmanni
Uroplatus alluaudi
Uroplatus phantasticus
Uroplatus ebenaui
Uroplatus malama
Uroplatus malahelo
Uroplatus guentheri
Cnemaspis africana
Cnemaspis dickersonae
Cnemaspis uzungwae
Narudasia festiva
Ptenopus carpi
Calodactylodes aureus
Calodactylodes illingworthorum
Ailuronyx trachygaster
Ailuronyx seychellensis
Ailuronyx tachyscopaeus
Paroedura bastardi
Paroedura tanjaka
Paroedura vazimba
Paroedura androyensis
Paroedura picta
Paroedura sanctijohannis
Paroedura stumpffi
Paroedura lohatsara
Paroedura karstophila
Paroedura oviceps
Paroedura homalorhina
Paroedura gracilis
Paroedura masobe
Ebenavia inunguis
Urocotyledon inexpectata
Perochirus ateles
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(ii)
Hemidactylus homoeolepis
Hemidactylus forbesii
Hemidactylus oxyrhinus
Hemidactylus macropholis
Hemidactylus mindiae
Hemidactylus lemurinus
Hemidactylus turcicus
Hemidactylus robustus
Hemidactylus yerburii
Hemidactylus persicus
Hemidactylus granti
Hemidactylus dracaenacolus
Hemidactylus pumilio
Hemidactylus foudaii
Hemidactylus citernii
Hemidactylus modestus
Hemidactylus agrius
Hemidactylus palaichthus
Hemidactylus bouvieri
Hemidactylus brasilianus
Hemidactylus greeffii
Hemidactylus platycephalus
Hemidactylus longicephalus
Hemidactylus mercatorius
Hemidactylus mabouia
Hemidactylus haitianus
Hemidactylus angulatus
Hemidactylus gracilis
Hemidactylus reticulatus
Hemidactylus albofasciatus
Hemidactylus imbricatus
Hemidactylus sataraensis
Hemidactylus brookii
Hemidactylus frenatus
Hemidactylus flaviviridis
Hemidactylus leschenaultii
Hemidactylus maculatus
Hemidactylus prashadi
Hemidactylus triedrus
Hemidactylus depressus
Hemidactylus giganteus
Hemidactylus aaronbaueri
Hemidactylus fasciatus
Hemidactylus platyurus
Hemidactylus karenorum
Hemidactylus garnotii
Hemidactylus bowringii
Cyrtodactylus louisiadensis
Cyrtodactylus epiroticus
Cyrtodactylus tripartitus
Cyrtodactylus robustus
Cyrtodactylus klugei
Cyrtodactylus tuberculatus
Cyrtodactylus novaeguineae
Cyrtodactylus loriae
Cyrtodactylus sermowaiensis
Cyrtodactylus pulchellus
Cyrtodactylus intermedius
Cyrtodactylus agusanensis
Cyrtodactylus philippinicus
Cyrtodactylus annulatus
Cyrtodactylus consobrinus
Cyrtodactylus irregularis
Cyrtodactylus marmoratus
Cyrtodactylus triedrus
Cyrtodactylus jarujini
Cyrtodactylus angularis
Cyrtodactylus ayeyarwadyensis
Cyrtodactylus oldhami
Cyrtopodion gastrophole
Cyrtopodion agamuroides
Cyrtopodion caspium
Cyrtopodion longipes
Cyrtopodion scabrum
Cyrtopodion sistanensis
Agamura persica
Bunopus crassicauda
Crossobamon orientalis
Bunopus tuberculatus
Mediodactylus heteropholis
Mediodactylus heterocercum
Mediodactylus sagittiferum
Mediodactylus kotschyi
Stenodactylus sthenodactylus
Stenodactylus yemenensis
Stenodactylus doriae
Stenodactylus leptocosymbotus
Stenodactylus petrii
Stenodactylus arabicus
Tropiocolotes tripolitanus
Pseudoceramodactylus khobarensis
Mediodactylus russowii
Mediodactylus spinicaudum
Cnemaspis kendallii
Cnemaspis limi
Tropiocolotes helenae
Alsophylax pipiens
Gehyra minuta
Gehyra montium
Gehyra pilbara
Gehyra punctata
Gehyra variegata
Gehyra purpurascens
Gehyra nana
Gehyra xenopus
Gehyra australis
Gehyra occidentalis
Gehyra koira
Gehyra robusta
Gehyra borroloola
Gehyra pamela
Gehyra catenata
Gehyra dubia
Gehyra membranacruralis
Gehyra oceanica
Gehyra marginata
Gehyra barea
Gehyra baliola
Gehyra brevipalmata
Gehyra lacerata
Gehyra mutilata
Gehyra fehlmanni
Hemiphyllodactylus aurantiacus
Hemiphyllodactylus yunnanensis
Hemiphyllodactylus typus
Nactus pelagicus
Nactus multicarinatus
Nactus cheverti
Nactus galgajuga
Nactus vankampeni
Nactus eboracensis
Nactus acutus
Heteronotia spelea
Heteronotia binoei
Heteronotia planiceps
Dixonius siamensis
Dixonius vietnamensis
Dixonius melanostictus
Gekko grossmanni
Gekko badenii
Gekko petricolus
Gekko vittatus
Luperosaurus iskandari
Ptychozoon lionotum
Ptychozoon kuhli
Ptychozoon rhacophorus
Gekko porosus
Gekko crombota
Gekko romblon
Gekko mindorensis
Gekko monarchus
Gekko athymus
Gekko swinhonis
Gekko auriverrucosus
Gekko hokouensis
Gekko japonicus
Gekko chinensis
Gekko gecko
Gekko smithii
Lepidodactylus moestus
Lepidodactylus lugubris
Luperosaurus joloensis
Luperosaurus cumingii
Luperosaurus macgregori
Lepidodactylus orientalis
Pseudogekko compressicorpus
Pseudogekko smaragdinus
Lepidodactylus novaeguineae
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Figure 4
D
Cordylus cordylus
Cordylus tasmani
Cordylus oelofseni
Cordylus mclachlani
Cordylus niger
Cordylus minor
Cordylus aridus
Cordylus imkeae
Cordylus macropholis
Cordylus rhodesianus
Cordylus jonesii
Cordylus beraduccii
Cordylus ukingensis
Cordylus vittifer
Cordylus meculae
Cordylus tropidosternum
Hemicordylus capensis
Hemicordylus nebulosus
Ninurta coeruleopunctatus
Pseudocordylus melanotus
Pseudocordylus spinosus
Pseudocordylus microlepidotus
Pseudocordylus langi
Chamaesaura anguina
Chamaesaura aenea
Smaug giganteus
Smaug warreni
Namazonurus peersi
Namazonurus lawrenci
Namazonurus namaquensis
Namazonurus pustulatus
Namazonurus campbelli
Karusasaurus polyzonus
Karusasaurus jordani
Ouroborus cataphractus
Platysaurus monotropis
Platysaurus minor
Platysaurus intermedius
Platysaurus capensis
Platysaurus broadleyi
Platysaurus mitchelli
Platysaurus pungweensis
Zonosaurus rufipes
Zonosaurus aeneus
Zonosaurus bemaraha
Zonosaurus subunicolor
Zonosaurus brygooi
Zonosaurus tsingy
Zonosaurus boettgeri
Zonosaurus laticaudatus
Zonosaurus anelanelany
Zonosaurus karsteni
Zonosaurus quadrilineatus
Zonosaurus trilineatus
Zonosaurus ornatus
Zonosaurus madagascariensis
Zonosaurus haraldmeieri
Tracheloptychus petersi
Tracheloptychus madagascariensis
Gerrhosaurus flavigularis
Gerrhosaurus multilineatus
Gerrhosaurus nigrolineatus
Gerrhosaurus typicus
Gerrhosaurus skoogi
Gerrhosaurus validus
Tetradactylus tetradactylus
Tetradactylus africanus
Tetradactylus seps
Cordylosaurus subtessellatus
Gerrhosaurus major
Lepidophyma dontomasi
Lepidophyma radula
Lepidophyma lowei
Lepidophyma cuicateca
Lepidophyma smithii
Lepidophyma lineri
Lepidophyma gaigeae
Lepidophyma sylvaticum
Lepidophyma micropholis
Lepidophyma occulor
Lepidophyma pajapanensis
Lepidophyma reticulatum
Lepidophyma flavimaculatum
Lepidophyma lipetzi
Lepidophyma tuxtlae
Lepidophyma mayae
Xantusia wigginsi
Xantusia bezyi
Xantusia vigilis
Xantusia arizonae
Xantusia riversiana
Xantusia sanchezi
Xantusia bolsonae
Xantusia henshawi
Xantusia gracilis
Cricosaura typica
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Platysaurinae
Cordylinae
Cordylidae
Gerrhosauridae
Gerrhosaurinae
Zonosaurinae
Lepidophyminae
Xantusiinae
Cricosaurinae
Xantusiidae
Figure 5
E
Amphiglossus frontoparietalis
Amphiglossus punctatus
Amphiglossus macrocercus
Amphiglossus anosyensis
Amphiglossus splendidus
Voeltzkowia rubrocaudata
Voeltzkowia lineata
Voeltzkowia fierinensis
Amphiglossus astrolabi
Amphiglossus reticulatus
Amphiglossus tsaratananensis
Androngo trivittatus
Pygomeles braconnieri
Amphiglossus tanysoma
Amphiglossus mandokava
Amphiglossus ornaticeps
Amphiglossus melanurus
Madascincus intermedius
Madascincus polleni
Madascincus stumpffi
Madascincus nanus
Madascincus mouroundavae
Madascincus igneocaudatus
Pseudoacontias menamainty
Madascincus melanopleura
Paracontias rothschildi
Paracontias hildebrandti
Paracontias manify
Paracontias brocchii
Paracontias holomelas
Scelotes kasneri
Scelotes montispectus
Scelotes gronovii
Scelotes sexlineatus
Scelotes bipes
Scelotes arenicolus
Scelotes mirus
Scelotes anguineus
Scelotes caffer
Proscelotes eggeli
Hakaria simonyi
Melanoseps loveridgei
Melanoseps ater
Melanoseps occidentalis
Feylinia currori
Feylinia polylepis
Feylinia grandisquamis
Typhlacontias punctatissimus
Typhlacontias brevipes
Sepsina angolensis
Chalcides montanus
Chalcides polylepis
Chalcides manueli
Chalcides mionecton
Chalcides sphenopsiformis
Chalcides viridanus
Chalcides coeruleopunctatus
Chalcides sexlineatus
Chalcides lanzai
Chalcides parallelus
Chalcides boulengeri
Chalcides bedriagai
Chalcides colosii
Chalcides sepsoides
Chalcides ocellatus
Chalcides striatus
Chalcides pseudostriatus
Chalcides chalcides
Chalcides guentheri
Chalcides minutus
Chalcides mauritanicus
Gongylomorphus bojerii
Janetaescincus braueri
Janetaescincus veseyfitzgeraldi
Pamelaescincus gardineri
Scincus mitranus
Scincus scincus
Eumeces algeriensis
Scincopus fasciatus
Eumeces schneideri
Eurylepis taeniolatus
Plestiodon dugesii
Plestiodon brevirostris
Plestiodon copei
Plestiodon parvulus
Plestiodon ochoterenae
Plestiodon lynxe
Plestiodon sumichrasti
Plestiodon parviauriculatus
Plestiodon skiltonianus
Plestiodon lagunensis
Plestiodon gilberti
Plestiodon longirostris
Plestiodon septentrionalis
Plestiodon multivirgatus
Plestiodon fasciatus
Plestiodon obsoletus
Plestiodon callicephalus
Plestiodon tetragrammus
Plestiodon laticeps
Plestiodon inexpectatus
Plestiodon anthracinus
Plestiodon egregius
Plestiodon reynoldsi
Plestiodon stimpsonii
Plestiodon marginatus
Plestiodon elegans
Plestiodon latiscutatus
Plestiodon japonicus
Plestiodon barbouri
Plestiodon capito
Plestiodon tunganus
Plestiodon quadrilineatus
Plestiodon chinensis
Plestiodon kishinouyei
Plestiodon tamdaoensis
Brachymeles pathfinderi
Brachymeles gracilis
Brachymeles bicolor
Brachymeles boulengeri
Brachymeles schadenbergi
Brachymeles elerae
Brachymeles talinis
Brachymeles samarensis
Brachymeles cebuensis
Brachymeles minimus
Brachymeles bonitae
Brachymeles tridactylus
Brachymeles miriamae
Brachymeles apus
Ophiomorus latastii
Ophiomorus punctatissimus
Mesoscincus managuae
Mesoscincus schwartzei
Acontias poecilus
Acontias plumbeus
Acontias gracilicauda
Acontias breviceps
Acontias rieppeli
Acontias percivali
Acontias meleagris
Acontias kgalagadi
Acontias litoralis
Acontias lineatus
Acontias gariepensis
Typhlosaurus lomiae
Typhlosaurus vermis
Typhlosaurus caecus
Typhlosaurus meyeri
Typhlosaurus braini
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Scincidae
Acontiinae
Scincinae
F-I
Figure 6
Lygosominae
Lygosominae
cont.
F
Papuascincus stanleyanus
Lipinia noctua
Lipinia pulchella
Insulasaurus victoria
Insulasaurus wrighti
Insulasaurus arborens
Prasinohaema virens
Sphenomorphus buenloicus
Scincella assatus
Scincella cherriei
Scincella gemmingeri
Scincella lateralis
Asymblepharus sikimmensis
Scincella reevesii
Sphenomorphus sabanus
Sphenomorphus cyanolaemus
Sphenomorphus variegatus
Sphenomorphus multisquamatus
Sphenomorphus indicus
Sphenomorphus maculatus
Larutia seribuatensis
Parvoscincus lawtoni
Parvoscincus kitangladensis
Parvoscincus luzonense
Parvoscincus laterimaculatus
Parvoscincus beyeri
Parvoscincus sisoni
Parvoscincus tagapayo
Parvoscincus leucospilos
Parvoscincus decipiens
Parvoscincus steerei
Sphenomorphus acutus
Sphenomorphus diwata
Pinoyscincus llanosi
Pinoyscincus abdictus
Pinoyscincus coxi
Pinoyscincus jagori
Pinoyscincus mindanensis
Otosaurus cumingi
Sphenomorphus maindroni
Sphenomorphus cranei
Sphenomorphus leptofasciatus
Sphenomorphus fasciatus
Sphenomorphus solomonis
Sphenomorphus scutatus
Sphenomorphus concinnatus
Tytthoscincus atrigularis
Tytthoscincus hallieri
Tytthoscincus parvus
Tytthoscincus aesculeticola
Sphenomorphus muelleri
Sphenomorphus jobiensis
Sphenomorphus melanopogon
Isopachys anguinoides
Lipinia vittigera
Tropidophorus misaminius
Tropidophorus partelloi
Tropidophorus brookei
Tropidophorus beccarii
Tropidophorus baconi
Tropidophorus grayi
Tropidophorus microlepis
Tropidophorus cocincinensis
Tropidophorus thai
Tropidophorus robinsoni
Tropidophorus sinicus
Tropidophorus baviensis
Tropidophorus hainanus
Tropidophorus murphyi
Tropidophorus noggei
Tropidophorus latiscutatus
Tropidophorus matsuii
Tropidophorus berdmorei
Sphenomorphus si mus
Sphenomorphus praesignis
Ablepharus pannonicus
Asymblepharus alaicus
Ateuchosaurus pellopleurus
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93
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60
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100
H-I G Figure 7
Lerista kennedyensis
Lerista onsloviana
Lerista uniduo
Lerista connivens
Lerista varia
Lerista lineopunctulata
Lerista yuna
Lerista kendricki
Lerista nichollsi
Lerista gascoynensis
Lerista petersoni
Lerista humphriesi
Lerista praepedita
Lerista bougainvillii
Lerista viduata
Lerista muelleri
Lerista haroldi
Lerista allochira
Lerista stictopleura
Lerista planiventralis
Lerista lineata
Lerista christinae
Lerista distinguenda
Lerista elegans
Lerista emmotti
Lerista punctatovittata
Lerista dorsalis
Lerista terdigitata
Lerista tridactyla
Lerista elongata
Lerista speciosa
Lerista zietzi
Lerista flammicauda
Lerista picturata
Lerista baynesi
Lerista edwardsae
Lerista arenicola
Lerista microtis
Lerista macropisthopus
Lerista axillaris
Lerista gerrardii
Lerista eupoda
Lerista desertorum
Lerista puncticauda
Lerista neander
Lerista zonulata
Lerista ingrami
Lerista orientalis
Lerista taeniata
Lerista aericeps
Lerista xanthura
Lerista chordae
Lerista fragilis
Lerista frosti
Lerista borealis
Lerista walkeri
Lerista simillima
Lerista vermicularis
Lerista robusta
Lerista greeri
Lerista labialis
Lerista bipes
Lerista ips
Lerista griffini
Lerista apoda
Lerista kalumburu
Lerista wilkinsi
Lerista cinerea
Lerista ameles
Lerista carpentariae
Lerista karlschmidti
Lerista stylis
Ctenotus pulchellus
Ctenotus gagudju
Ctenotus hilli
Ctenotus hebetior
Ctenotus essingtonii
Ctenotus piankai
Ctenotus hanloni
Ctenotus angusticeps
Ctenotus grandis
Ctenotus atlas
Ctenotus maryani
Ctenotus olympicus
Ctenotus regius
Ctenotus septenarius
Ctenotus astarte
Ctenotus mimetes
Ctenotus tanamiensis
Ctenotus greeri
Ctenotus serventyi
Ctenotus quattuordecimlineatus
Ctenotus leonhardii
Ctenotus leae
Ctenotus australis
Ctenotus uber
Ctenotus rutilans
Ctenotus taeniolatus
Ctenotus robustus
Ctenotus spaldingi
Ctenotus inornatus
Ctenotus saxatilis
Ctenotus fallens
Ctenotus rawlinsoni
Ctenotus calurus
Ctenotus schomburgkii
Ctenotus youngsoni
Ctenotus strauchii
Ctenotus pantherinus
Ctenotus nasutus
Ctenotus rubicundus
Ctenotus brooksi
Ctenotus labillardieri
Notoscincus ornatus
Eulamprus tympanum
Eulamprus heatwolei
Eulamprus kosciuskoi
Eulamprus leuraensis
Eulamprus quoyii
Glaphyromorphus darwiniensis
Glaphyromorphus cracens
Glaphyromorphus pumilus
Glaphyromorphus fuscicaudis
Glaphyromorphus mjobergi
Glaphyromorphus punctulatus
Hemiergis decresiensis
Hemiergis millewae
Hemiergis gracilipes
Hemiergis quadrilineatum
Hemiergis peronii
Hemiergis initialis
Eremiascincus isolepis
Eremiascincus douglasi
Eremiascincus richardsonii
Eremiascincus pardalis
Eremiascincus fasciolatus
Anomalopus leuckartii
Anomalopus verreauxi
Anomalopus mackayi
Anomalopus swansoni
Ophioscincus truncatus
Coeranoscincus reticulatus
Saiphos equalis
Ophioscincus ophioscincus
Coeranoscincus frontalis
Coggeria naufragus
Eulamprus murrayi
Eulamprus tryoni
Eulamprus luteilateralis
Eulamprus brachyosoma
Eulamprus sokosoma
Eulamprus martini
Eulamprus tigrinus
Eulamprus tenuis
Eulamprus amplus
Gnypetoscincus queenslandiae
Calyptotis ruficauda
Calyptotis scutirostrum
Calyptotis lepidorostrum
Nangura spinosa
Eulamprus frerei
100
95
55
100
85
82
87
90
93
93
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98
84
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100
81
77
56
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90
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87
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51
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63
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95
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96
88
100
100
77
G
Lygosominae
cont.
Figure 8
Mabuya heathi
Mabuya caissara
Mabuya agilis
Mabuya guaporicola
Mabuya macrorhyncha
Mabuya agmosticha
Mabuya frenata
Mabuya bistriata
Mabuya falconensis
Mabuya unimarginata
Mabuya mabouya
Mabuya meridensis
Mabuya dorsivittata
Mabuya cochabambae
Mabuya nigropunctata
Mabuya altamazonica
Mabuya sloanii
Mabuya nigropalmata
Mabuya croizati
Mabuya carvalhoi
Chioninia stangeri
Chioninia fogoensis
Chioninia spinalis
Chioninia coctei
Chioninia delalandii
Chioninia vaillantii
Eumecia anchietae
Trachylepis dumasi
Trachylepis aureopunctata
Trachylepis vato
Trachylepis boettgeri
Trachylepis madagascariensis
Trachylepis elegans
Trachylepis gravenhorstii
Trachylepis acutilabris
Trachylepis homalocephala
Trachylepis sulcata
Trachylepis variegata
Trachylepis hoeschi
Trachylepis striata
Trachylepis spilogaster
Trachylepis occidentalis
Trachylepis capensis
Trachylepis varia
Trachylepis atlantica
Trachylepis margaritifera
Trachylepis quinquetaeniata
Trachylepis perrotetii
Trachylepis affinis
Trachylepis sechellensis
Trachylepis wrightii
Trachylepis maculilabris
Trachylepis socotrana
Trachylepis brevicollis
Trachylepis vittata
Trachylepis aurata
Dasia olivacea
Dasia grisea
Dasia vittata
Eutropis trivittata
Eutropis nagarjuni
Eutropis beddomii
Eutropis bibronii
Eutropis clivicola
Eutropis multicarinata
Eutropis cumingi
Eutropis multifasciata
Eutropis macrophthalma
Eutropis rudis
Eutropis macularia
Eutropis longicaudata
Lankascincus fallax
Ristella rurkii
Liopholis montana
Liopholis guthega
Liopholis whitii
Liopholis margaretae
Liopholis modesta
Liopholis pulchra
Liopholis kintorei
Liopholis multiscutata
Liopholis inornata
Liopholis striata
Tiliqua scincoides
Tiliqua gigas
Tiliqua nigrolutea
Tiliqua occipitalis
Tiliqua rugosa
Tiliqua adelaidensis
Cyclodomorphus branchialis
Cyclodomorphus casuarinae
Cyclodomorphus michaeli
Egernia hosmeri
Egernia stokesii
Lissolepis luctuosa
Egernia napoleonis
Egernia richardi
Bellatorias frerei
Egernia kingii
Egernia depressa
Bellatorias major
Egernia saxatilis
Corucia zebrata
Tribolonotus pseudoponceleti
Tribolonotus ponceleti
Tribolonotus brongersmai
Tribolonotus schmidti
Tribolonotus blanchardi
Tribolonotus gracilis
Tribolonotus novaeguineae
83
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87
100
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80
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100
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100
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100
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100
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52
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97
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71
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81
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66
86
74
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100
Lygosominae
cont.
H
Figure 9
Carlia vivax
Carlia dogare
Carlia rostralis
Carlia amax
Carlia tetradactyla
Carlia rubrigularis
Carlia rhomboidalis
Carlia rufilatus
Carlia pectoralis
Carlia munda
Carlia mysi
Carlia longipes
Carlia fusca
Carlia storri
Carlia schmeltzii
Lygisaurus malleolus
Lygisaurus tanneri
Lygisaurus abscondita
Lygisaurus foliorum
Lygisaurus laevis
Lygisaurus aeratus
Lygisaurus novaeguineae
Lygisaurus macfarlani
Lygisaurus parrhasius
Lygisaurus sesbrauna
Carlia gracilis
Carlia bicarinata
Carlia jarnoldae
Carlia johnstonei
Carlia triacantha
Menetia timlowi
Liburnascincus mundivensis
Liburnascincus scirtetis
Liburnascincus coensis
Cautula zia
Niveoscincus metallicus
Niveoscincus pretiosus
Niveoscincus ocellatus
Niveoscincus greeni
Proablepharus reginae
Lampropholis robertsi
Lampropholis coggeri
Lampropholis delicata
Lampropholis guichenoti
Saproscincus spectabilis
Saproscincus rosei
Saproscincus challengeri
Saproscincus mustelinus
Saproscincus oriarus
Saproscincus hannahae
Saproscincus tetradactylus
Saproscincus czechurai
Saproscincus lewisi
Saproscincus basiliscus
Bartleia jigurru
Morethia adelaidensis
Morethia butleri
Morethia ruficauda
Bassiana trilineata
Emoia isolata
Emoia pseudocyanura
Emoia cyanura
Emoia impar
Emoia physicae
Emoia jakati
Emoia atrocostata
Emoia caeruleocauda
Emoia cyanogaster
Emoia schmidti
Menetia alanae
Menetia greyii
Cryptoblepharus novocaledonicus
Cryptoblepharus boutonii
Cryptoblepharus nigropunctatus
Caledoniscincus terma
Caledoniscincus aquilonius
Caledoniscincus chazeaui
Caledoniscincus atropunctatus
Caledoniscincus haplorhinus
Caledoniscincus austrocaledonicus
Caledoniscincus festivus
Caledoniscincus auratus
Caledoniscincus renevieri
Caledoniscincus orestes
Simiscincus aurantiacus
Graciliscincus shonae
Tropidoscincus variabilis
Tropidoscincus boreus
Tropidoscincus aubrianus
Lioscincus tillieri
Lioscincus maruia
Lioscincus novaecaledoniae
Sigaloseps deplanchei
Sigaloseps ruficauda
Phoboscincus garnieri
Lacertoides pardalis
Lioscincus nigrofasciolatum
Kanakysaurus viviparus
Lioscincus steindachneri
Lioscincus vivae
Celatiscincus euryotis
Celatiscincus similis
Marmorosphax tricolor
Marmorosphax montana
Nannoscincus humectus
Nannoscincus hanchisteus
Nannoscincus greeri
Nannoscincus mariei
Nannoscincus gracilis
Nannoscincus slevini
Nannoscincus garrulus
Oligosoma whitakeri
Oligosoma oliveri
Oligosoma townsi
Oligosoma ornatum
Oligosoma macgregori
Oligosoma moco
Oligosoma alani
Oligosoma fallai
Oligosoma hardyi
Oligosoma levidensum
Oligosoma aeneum
Oligosoma microlepis
Oligosoma smithi
Oligosoma striatum
Oligosoma homalonotum
Oligosoma zelandicum
Oligosoma notosaurus
Oligosoma inconspicuum
Oligosoma maccanni
Oligosoma stenotis
Oligosoma grande
Oligosoma nigriplantare
Oligosoma longipes
Oligosoma lineoocellatum
Oligosoma chloronoton
Oligosoma otagense
Oligosoma waimatense
Oligosoma infrapunctatum
Oligosoma acrinasum
Oligosoma taumakae
Oligosoma pikitanga
Oligosoma suteri
Oligosoma lichenigera
Pseudemoia entrecasteauxii
Bassiana duperreyi
Pseudemoia pagenstecheri
Leptosiaphos vigintiserierum
Leptosiaphos kilimensis
Leptosiaphos amieti
Leptosiaphos graueri
Leptosiaphos hackarsi
Lacertaspis lepesmei
Lacertaspis gemmiventris
Lacertaspis chriswildi
Lacertaspis rohdei
Lacertaspis reichenowi
Afroablepharus africanus
Afroablepharus annobonensis
Afroablepharus wahlbergi
Panaspis togoensis
Panaspis breviceps
Leiolopisma mauritiana
Leiolopisma telfairii
Emoia loyaltiensis
Eugongylus albofasciolatus
Eugongylus rufescens
Lygosoma bowringii
Mochlus brevicaudis
Lygosoma punctata
Lygosoma sundevalli
Mochlus afer
Lygosoma lineolatum
Lepidothyris fernandi
Lygosoma albopunctata
Lygosoma koratense
Lygosoma quadrupes
Lamprolepis smaragdina
Emoia tongana
Emoia concolor
Sphenomorphus stellatus
Ablepharus kitaibelii
Ablepharus chernovi
Ablepharus budaki
90
100
100
84
52
79
100
72
87
88
98
90
88
68
80
85
76
53
62
92
100
93
98
100
73
91
75
98
85
78
89
100
100
100
99
79
100
96
91
76
100
92
100
72
76
71
100
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100
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98
96
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93
91
100
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98 71 98
98
100
100
93
100
79
61
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98
87
97
95
83
53
87
95
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95
97
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100
100
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85
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100
80
90
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96
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100
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93
94
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89
100
98
90
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97
96
63
93
99
100
100
100
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85
98
100
98
99
100
99
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91
100
95
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80
75
84
85
100
81
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99
95
93
96
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90
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99
85
100
100
100
100
63
60
95
93
76
70
92
100
98
96
I
Lygosominae
cont.
Figure 10
Gymnophthalmus cryptus
Gymnophthalmus underwoodi
Gymnophthalmus speciosus
Gymnophthalmus vanzoi
Gymnophthalmus leucomystax
Gymnophthalmus pleei
Psilophthalmus paeminosus
Calyptommatus nicterus
Calyptommatus leiolepis
Calyptommatus confusionibus
Calyptommatus sinebrachiatus
Nothobachia ablephara
Procellosaurinus tetradactylus
Procellosaurinus erythrocercus
Vanzosaura rubricauda
Micrablepharus maximiliani
Micrablepharus atticolus
Tretioscincus oriximinensis
Tretioscincus agilis
Acratosaura mentalis
Stenolepis ridleyi
Colobosaura modesta
Iphisa elegans
Colobodactylus taunayi
Colobodactylus dalcyanus
Heterodactylus imbricatus
Rhachisaurus brachylepis
Bachia heteropa
Bachia intermedia
Bachia barbouri
Bachia bicolor
Bachia peruana
Bachia panoplia
Bachia trisanale
Bachia scolecoides
Bachia huallagana
Bachia dorbignyi
Bachia bresslaui
Bachia flavescens
Petracola ventrimaculatus
Proctoporus bolivianus
Proctoporus unsaacae
Proctoporus guentheri
Proctoporus pachyurus
Proctoporus subsolanus
Proctoporus sucullucu
Cercosaura eigenmanni
Cercosaura schreibersii
Cercosaura ocellata
Cercosaura argulus
Cercosaura oshaughnessyi
Cercosaura quadrilineata
Potamites juruazensis
Potamites ecpleopus
Pholidobolus macbrydei
Pholidobolus montium
Placosoma glabellum
Placosoma cordylinum
Neusticurus bicarinatus
Neusticurus rudis
Riama simoterus
Riama colomaromani
Riama unicolor
Leposoma guianense
Leposoma southi
Leposoma parietale
Leposoma osvaldoi
Leposoma percarinatum
Arthrosaura kockii
Arthrosaura reticulata
Anotosaura collaris
Colobosauroides cearensis
Leposoma annectans
Leposoma scincoides
Leposoma puk
Leposoma baturitensis
Leposoma nanodactylus
Ecpleopus gaudichaudii
Alopoglossus angulatus
Alopoglossus copii
Alopoglossus atriventris
Ptychoglossus brevifrontalis
Cnemidophorus lacertoides
Cnemidophorus longicaudus
Dicrodon guttulatum
Ameiva fuscata
Ameiva erythrocephala
Ameiva griswoldi
Ameiva pluvianotata
Ameiva corax
Ameiva plei
Ameiva maynardi
Ameiva lineolata
Ameiva taeniura
Ameiva chrysolaema
Ameiva leberi
Ameiva wetmorei
Ameiva exsul
Ameiva polops
Ameiva dorsalis
Ameiva auberi
Aspidoscelis ceralbensis
Aspidoscelis hyperythra
Aspidoscelis tigris
Aspidoscelis marmorata
Aspidoscelis lineattissima
Aspidoscelis guttata
Aspidoscelis deppei
Aspidoscelis velox
Aspidoscelis laredoensis
Aspidoscelis gularis
Aspidoscelis costata
Aspidoscelis communis
Aspidoscelis burti
Aspidoscelis sexlineata
Aspidoscelis inornata
Cnemidophorus arenivagus
Cnemidophorus lemniscatus
Cnemidophorus gramivagus
Cnemidophorus vanzoi
Ameiva festiva
Ameiva quadrilineata
Ameiva undulata
Kentropyx viridistriga
Kentropyx vanzoi
Kentropyx paulensis
Kentropyx pelviceps
Kentropyx altamazonica
Kentropyx striata
Kentropyx calcarata
Cnemidophorus ocellifer
Ameiva bifrontata
Ameiva ameiva
Teius teyou
Dracaena guianensis
Crocodilurus amazonicus
Tupinambis teguixin
Tupinambis longilineus
Tupinambis quadrilineatus
Tupinambis duseni
Tupinambis merianae
Tupinambis rufescens
Callopistes maculatus
Callopistes flavipunctatus
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J
Teiidae
Gymnophthalmidae
Tupinambinae
Teiinae
Alopoglossinae
Ecpleopinae
Cercosaurinae
Bachiinae
Rhachisaurinae
Gymnophthalminae
Figure 11
Amphisbaena xera
Amphisbaena bakeri
Amphisbaena caeca
Amphisbaena fenestrata
Amphisbaena manni
Amphisbaena schmidti
Amphisbaena carlgansi
Amphisbaena cubana
Amphisbaena barbouri
Amphisbaena anaemariae
Amphisbaena silvestrii
Amphisbaena leeseri
Amphisbaena angustifrons
Amphisbaena darwini
Amphisbaena munoai
Amphisbaena kingii
Amphisbaena cuiabana
Amphisbaena hastata
Amphisbaena infraorbitale
Amphisbaena microcephalum
Amphisbaena polystegum
Amphisbaena anomala
Amphisbaena bolivica
Amphisbaena camura
Amphisbaena alba
Amphisbaena vermicularis
Amphisbaena roberti
Amphisbaena kraoh
Amphisbaena saxosa
Amphisbaena ignatiana
Amphisbaena leali
Amphisbaena innocens
Amphisbaena hyporissor
Amphisbaena mertensii
Amphisbaena cunhai
Amphisbaena fuliginosa
Amphisbaena brasiliana
Monopeltis capensis
Geocalamus acutus
Chirindia swynnertoni
Cynisca leucura
Trogonophis wiegmanni
Diplometopon zarudnyi
Cadea blanoides
Blanus tingitanus
Blanus mettetali
Blanus cinereus
Blanus strauchi
Bipes canaliculatus
Bipes biporus
Bipes tridactylus
Rhineura floridana
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Blanidae
Cadeidae
Trogonophiidae
Amphisbaenidae
K
Bipedidae
Rhineuridae
Figure 12
Darevskia derjugini
Darevskia caucasica
Darevskia daghestanica
Darevskia mixta
Darevskia clarkorum
Darevskia armeniaca
Darevskia bendimahiensis
Darevskia sapphirina
Darevskia uzzelli
Darevskia raddei
Darevskia rostombekovi
Darevskia saxicola
Darevskia brauneri
Darevskia lindholmi
Darevskia alpina
Darevskia chlorogaster
Darevskia praticola
Darevskia valentini
Darevskia portschinskii
Darevskia rudis
Darevskia parvula
Iranolacerta zagrosica
Iranolacerta brandtii
Algyroides fitzingeri
Algyroides marchi
Dinarolacerta montenegrina
Dinarolacerta mosorensis
Algyroides nigropunctatus
Algyroides moreoticus
Anatololacerta danfordi
Anatololacerta oertzeni
Anatololacerta anatolica
Parvilacerta parva
Parvilacerta fraasii
Iberolacerta aranica
Iberolacerta bonnali
Iberolacerta aurelioi
Iberolacerta horvathi
Iberolacerta monticola
Iberolacerta cyreni
Iberolacerta galani
Apathya cappadocica
Archaeolacerta bedriagae
Hellenolacerta graeca
Dalmatolacerta oxycephala
Podarcis carbonelli
Podarcis bocagei
Podarcis hispanicus
Podarcis vaucheri
Podarcis liolepis
Podarcis peloponnesiacus
Podarcis erhardii
Podarcis raffoneae
Podarcis lilfordi
Podarcis pityusensis
Podarcis siculus
Podarcis muralis
Podarcis tiliguerta
Podarcis filfolensis
Podarcis gaigeae
Podarcis milensis
Podarcis tauricus
Podarcis melisellensis
Scelarcis perspicillata
Teira dugesii
Lacerta pamphylica
Lacerta trilineata
Lacerta media
Lacerta agilis
Lacerta schreiberi
Lacerta strigata
Lacerta bilineata
Lacerta viridis
Timon tangitanus
Timon lepidus
Timon pater
Timon princeps
Takydromus stejnegeri
Takydromus septentrionalis
Takydromus toyamai
Takydromus wolteri
Takydromus formosanus
Takydromus hsuehshanensis
Takydromus amurensis
Takydromus sylvaticus
Takydromus dorsalis
Takydromus intermedius
Takydromus sauteri
Takydromus smaragdinus
Takydromus tachydromoides
Takydromus sexlineatus
Takydromus kuehnei
Zootoca vivipara
Phoenicolacerta cyanisparsa
Phoenicolacerta laevis
Phoenicolacerta kulzeri
Acanthodactylus schreiberi
Acanthodactylus boskianus
Acanthodactylus opheodurus
Acanthodactylus gongrorhynchatus
Acanthodactylus masirae
Acanthodactylus cantoris
Acanthodactylus schmidti
Acanthodactylus longipes
Acanthodactylus scutellatus
Acanthodactylus aureus
Acanthodactylus maculatus
Acanthodactylus pardalis
Acanthodactylus beershebensis
Acanthodactylus busacki
Acanthodactylus erythrurus
Acanthodactylus blanci
Acanthodactylus tristrami
Acanthodactylus orientalis
Ophisops elegans
Ophisops occidentalis
Mesalina rubropunctata
Mesalina brevirostris
Mesalina adramitana
Mesalina balfouri
Mesalina guttulata
Mesalina bahaeldini
Mesalina olivieri
Mesalina simoni
Omanosaura jayakari
Omanosaura cyanura
Congolacerta vauereselli
Eremias grammica
Eremias pleskei
Eremias multiocellata
Eremias przewalskii
Eremias arguta
Eremias nigrolateralis
Eremias persica
Eremias montanus
Eremias velox
Eremias vermiculata
Eremias argus
Eremias brenchleyi
Adolfus jacksoni
Adolfus alleni
Adolfus africanus
Gastropholis prasina
Gastropholis vittata
Holaspis guentheri
Holaspis laevis
Pedioplanis gaerdesi
Pedioplanis inornata
Pedioplanis rubens
Pedioplanis undata
Pedioplanis husabensis
Pedioplanis namaquensis
Pedioplanis breviceps
Pedioplanis burchelli
Pedioplanis laticeps
Nucras tessellata
Pedioplanis lineoocellata
Meroles cuneirostris
Meroles micropholidotus
Meroles ctenodactylus
Meroles anchietae
Ichnotropis squamulosa
Meroles suborbitalis
Meroles knoxii
Meroles reticulatus
Ichnotropis capensis
Tropidosaura gularis
Australolacerta australis
Heliobolus spekii
Heliobolus lugubris
Pseuderemias smithii
Philochortus spinalis
Latastia longicaudata
Nucras lalandii
Poromera fordii
Atlantolacerta andreanskyi
Gallotia bravoana
Gallotia simonyi
Gallotia intermedia
Gallotia caesaris
Gallotia galloti
Gallotia atlantica
Gallotia stehlini
Psammodromus blanci
Psammodromus algirus
Psammodromus hispanicus
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Lacertidae
Gallotiinae
Lacertinae
L
Figure 13
Varanus baritji
Varanus acanthurus
Varanus storri
Varanus primordius
Varanus kingorum
Varanus bushi
Varanus gilleni
Varanus caudolineatus
Varanus eremius
Varanus brevicauda
Varanus semiremex
Varanus mitchelli
Varanus timorensis
Varanus scalaris
Varanus glauerti
Varanus tristis
Varanus pilbarensis
Varanus glebopalma
Varanus komodoensis
Varanus varius
Varanus salvadorii
Varanus gouldii
Varanus panoptes
Varanus rosenbergi
Varanus giganteus
Varanus spenceri
Varanus mertensi
Varanus bengalensis
Varanus flavescens
Varanus dumerilii
Varanus rudicollis
Varanus salvator
Varanus marmoratus
Varanus finschi
Varanus doreanus
Varanus yuwonoi
Varanus jobiensis
Varanus caerulivirens
Varanus cerambonensis
Varanus melinus
Varanus indicus
Varanus rainerguentheri
Varanus prasinus
Varanus macraei
Varanus boehmei
Varanus beccarii
Varanus keithhornei
Varanus olivaceus
Varanus yemenensis
Varanus albigularis
Varanus exanthematicus
Varanus niloticus
Varanus griseus
Lanthanotus borneensis
Shinisaurus crocodilurus
Abronia aurita
Abronia campbelli
Abronia anzuetoi
Abronia matudai
Abronia fimbriata
Abronia lythrochila
Abronia ornelasi
Abronia frosti
Abronia graminea
Abronia oaxacae
Abronia chiszari
Mesaspis gadovii
Mesaspis moreletii
Barisia rudicollis
Barisia herrerae
Barisia imbricata
Barisia levicollis
Abronia mixteca
Gerrhonotus infernalis
Gerrhonotus liocephalus
Coloptychon rhombifer
Gerrhonotus parvus
Elgaria multicarinata
Elgaria panamintina
Elgaria paucicarinata
Elgaria kingii
Elgaria coerulea
Dopasia harti
Dopasia gracilis
Ophisaurus attenuatus
Anguis fragilis
Pseudopus apodus
Ophisaurus koellikeri
Ophisaurus ventralis
Celestus haetianus
Celestus agasepsoides
Ophiodes striatus
Diploglossus pleii
Diploglossus bilobatus
Celestus enneagrammus
Anniella geronimensis
Anniella pulchra
Heloderma horridum
Heloderma suspectum
Xenosaurus grandis
Xenosaurus platyceps
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M
Xenosauridae
Helodermatidae
Anniellidae
Anguidae
Shinisauridae
Lanthanotidae
Varanidae
Gerrhonotinae
Anguinae
Diploglossinae
Figure 14
Trioceros sternfeldi
Trioceros rudis
Trioceros ellioti
Trioceros hoehnelii
Trioceros schubotzi
Trioceros narraioca
Trioceros jacksonii
Trioceros bitaeniatus
Trioceros fuelleborni
Trioceros goetzei
Trioceros tempeli
Trioceros werneri
Trioceros deremensis
Trioceros melleri
Trioceros johnstoni
Trioceros oweni
Trioceros pfefferi
Trioceros quadricornis
Trioceros wiedersheimi
Trioceros cristatus
Trioceros montium
Trioceros feae
Trioceros balebicornutus
Trioceros harennae
Trioceros affinis
Chamaeleo arabicus
Chamaeleo calyptratus
Chamaeleo zeylanicus
Chamaeleo chamaeleon
Chamaeleo calcaricarens
Chamaeleo africanus
Chamaeleo monachus
Chamaeleo senegalensis
Chamaeleo roperi
Chamaeleo dilepis
Chamaeleo quilensis
Chamaeleo gracilis
Chamaeleo necasi
Chamaeleo laevigatus
Chamaeleo namaquensis
Calumma globifer
Calumma parsonii
Calumma oshaughnessyi
Calumma capuroni
Rhampholeon chapmanorum
Rhampholeon platyceps
Rhampholeon nchisiensis
Rhampholeon beraduccii
Rhampholeon boulengeri
Rhampholeon acuminatus
Rhampholeon uluguruensis
Rhampholeon moyeri
Rhampholeon marshalli
Rhampholeon viridis
Rhampholeon spinosus
Rhampholeon temporalis
Rhampholeon spectrum
Nadzikambia mlanjensis
Calumma nasutum
Calumma boettgeri
Calumma fallax
Calumma gallus
Calumma malthe
Calumma guibei
Calumma hilleniusi
Calumma tsaratananense
Calumma brevicorne
Calumma crypticum
Calumma cucullatum
Rieppeleon brevicaudatus
Rieppeleon brachyurus
Rieppeleon kerstenii
Calumma gastrotaenia
Calumma furcifer
Bradypodion ventrale
Bradypodion karrooicum
Bradypodion taeniabronchum
Bradypodion gutturale
Bradypodion atromontanum
Bradypodion occidentale
Bradypodion setaroi
Bradypodion nemorale
Bradypodion dracomontanum
Bradypodion transvaalense
Bradypodion thamnobates
Bradypodion melanocephalum
Bradypodion caffer
Bradypodion damaranum
Bradypodion pumilum
Kinyongia fischeri
Kinyongia vosseleri
Kinyongia multituberculata
Kinyongia matschiei
Kinyongia boehmei
Kinyongia tavetana
Kinyongia uthmoelleri
Kinyongia carpenteri
Kinyongia xenorhina
Kinyongia excubitor
Kinyongia adolfifriderici
Kinyongia tenue
Kinyongia oxyrhina
Furcifer antimena
Furcifer labordi
Furcifer lateralis
Furcifer belalandaensis
Furcifer verrucosus
Furcifer oustaleti
Furcifer angeli
Furcifer pardalis
Furcifer polleni
Furcifer cephalolepis
Furcifer campani
Furcifer petteri
Furcifer willsii
Furcifer minor
Furcifer bifidus
Furcifer balteatus
Brookesia lineata
Brookesia betschi
Brookesia thieli
Brookesia vadoni
Brookesia ebenaui
Brookesia antakarana
Brookesia ambreensis
Brookesia stumpffi
Brookesia griveaudi
Brookesia valerieae
Brookesia superciliaris
Brookesia therezieni
Brookesia bonsi
Brookesia brygooi
Brookesia decaryi
Brookesia perarmata
Brookesia peyrierasi
Brookesia karchei
Brookesia tuberculata
Brookesia minima
Brookesia exarmata
Brookesia dentata
Brookesia nasus
Brookesia lolontany
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Chamaeleonidae
Brookesiinae
Chamaeleoninae
N
Figure 15
Pseudocalotes flavigula
Pseudocalotes brevipes
Pseudocalotes kakhienensis
Japalura splendida
Japalura flaviceps
Otocryptis wiegmanni
Sitana ponticeriana
Acanthosaura lepidogaster
Acanthosaura capra
Acanthosaura armata
Acanthosaura crucigera
Salea horsfieldii
Calotes htunwini
Calotes calotes
Calotes irawadi
Calotes versicolor
Calotes liolepis
Calotes nigrilabris
Calotes ceylonensis
Calotes liocephalus
Calotes emma
Calotes chincollium
Calotes mystaceus
Ceratophora erdeleni
Ceratophora stoddartii
Ceratophora karu
Ceratophora aspera
Cophotis ceylanica
Cophotis dumbara
Lyriocephalus scutatus
Gonocephalus kuhlii
Gonocephalus chamaeleontinus
Gonocephalus grandis
Bronchocela cristatella
Coryphophylax subcristatus
Aphaniotis fusca
Gonocephalus robinsonii
Japalura polygonata
Phoxophrys nigrilabris
Draco ornatus
Draco palawanensis
Draco spilopterus
Draco cornutus
Draco guentheri
Draco quadrasi
Draco cyanopterus
Draco reticulatus
Draco boschmai
Draco timorensis
Draco volans
Draco bimaculatus
Draco rhytisma
Draco bourouniensis
Draco beccarii
Draco biaro
Draco caerulhians
Draco spilonotus
Draco obscurus
Draco taeniopterus
Draco blanfordii
Draco indochinensis
Draco haematopogon
Draco melanopogon
Draco quinquefasciatus
Draco mindanensis
Draco maximus
Draco cristatellus
Draco fimbriatus
Draco maculatus
Draco lineatus
Draco dussumieri
Ptyctolaemus collicristatus
Ptyctolaemus gularis
Japalura tricarinata
Japalura variegata
Mantheyus phuwuanensis
Agama paragama
Agama planiceps
Agama finchi
Agama agama
Agama doriae
Agama sankaranica
Agama mwanzae
Agama kaimosae
Agama lionotus
Agama rueppelli
Agama caudospinosa
Agama aculeata
Agama armata
Agama hispida
Agama atra
Agama anchietae
Agama weidholzi
Agama gracilimembris
Agama insularis
Agama boulengeri
Agama castroviejoi
Agama impalearis
Agama boueti
Agama spinosa
Trapelus savignii
Trapelus flavimaculatus
Trapelus pallidus
Trapelus ruderatus
Trapelus agilis
Trapelus mutabilis
Trapelus sanguinolentus
Bufoniceps laungwalaensis
Xenagama taylori
Acanthocercus atricollis
Pseudotrapelus sinaitus
Phrynocephalus guttatus
Phrynocephalus albolineatus
Phrynocephalus melanurus
Phrynocephalus przewalskii
Phrynocephalus versicolor
Phrynocephalus raddei
Phrynocephalus mystaceus
Phrynocephalus helioscopus
Phrynocephalus axillaris
Phrynocephalus lidskii
Phrynocephalus vlangalii
Phrynocephalus putjatai
Phrynocephalus theobaldi
Phrynocephalus forsythii
Phrynocephalus interscapularis
Phrynocephalus scutellatus
Laudakia erythrogaster
Laudakia caucasia
Laudakia microlepis
Laudakia stoliczkana
Laudakia himalayana
Laudakia lehmanni
Laudakia nupta
Laudakia tuberculata
Laudakia sacra
Laudakia stellio
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Diporiphora lalliae
Diporiphora arnhemica
Diporiphora albilabris
Diporiphora bennettii
Diporiphora nobbi
Diporiphora australis
Diporiphora amphiboluroides
Diporiphora valens
Diporiphora pindan
Diporiphora bilineata
Diporiphora magna
Diporiphora reginae
Diporiphora winneckei
Diporiphora linga
Diporiphora superba
Pogona vitticeps
Pogona minor
Pogona minima
Pogona henrylawsoni
Pogona nullarbor
Pogona barbata
Rankinia diemensis
Tympanocryptis lineata
Tympanocryptis pinguicolla
Tympanocryptis cephalus
Tympanocryptis tetraporophora
Tympanocryptis intima
Tympanocryptis uniformis
Amphibolurus norrisi
Amphibolurus muricatus
Lophognathus gilberti
Chlamydosaurus kingii
Lophognathus longirostris
Lophognathus temporalis
Ctenophorus femoralis
Ctenophorus fordi
Ctenophorus maculatus
Ctenophorus pictus
Ctenophorus mckenziei
Ctenophorus scutulatus
Ctenophorus isolepis
Ctenophorus ornatus
Ctenophorus caudicinctus
Ctenophorus fionni
Ctenophorus decresii
Ctenophorus vadnappa
Ctenophorus tjantjalka
Ctenophorus rufescens
Ctenophorus reticulatus
Ctenophorus nuchalis
Ctenophorus cristatus
Ctenophorus salinarum
Ctenophorus gibba
Ctenophorus clayi
Ctenophorus adelaidensis
Ctenophorus maculosus
Intellagama lesueurii
Hypsilurus bruijnii
Hypsilurus nigrigularis
Hypsilurus papuensis
Hypsilurus modestus
Chelosania brunnea
Moloch horridus
Hypsilurus dilophus
Hypsilurus boydii
Hypsilurus spinipes
Physignathus cocincinus
Hydrosaurus amboinensis
Leiolepis guentherpetersi
Leiolepis guttata
Leiolepis reevesii
Leiolepis belliana
Uromastyx yemenensis
Uromastyx benti
Uromastyx ocellata
Uromastyx ornata
Uromastyx leptieni
Uromastyx aegyptia
Uromastyx thomasi
Uromastyx dispar
Uromastyx acanthinura
Uromastyx geyri
Uromastyx macfadyeni
Uromastyx princeps
Uromastyx asmussi
Uromastyx loricata
Uromastyx hardwickii
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Uromasticinae
Leiolepidinae
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Hydrosaurinae
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Draconinae
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Figure 16
Ctenosaura oaxacana
Ctenosaura quinquecarinata
Ctenosaura flavidorsalis
Ctenosaura palearis
Ctenosaura bakeri
Ctenosaura oedirhina
Ctenosaura melanosterna
Ctenosaura pectinata
Ctenosaura acanthura
Ctenosaura hemilopha
Ctenosaura similis
Conolophus pallidus
Conolophus subcristatus
Amblyrhynchus cristatus
Cyclura cychlura
Cyclura nubila
Cyclura rileyi
Cyclura collei
Cyclura carinata
Cyclura ricordi
Cyclura cornuta
Cyclura pinguis
Sauromalus varius
Sauromalus hispidus
Sauromalus klauberi
Sauromalus ater
Iguana delicatissima
Iguana iguana
Brachylophus vitiensis
Brachylophus fasciatus
Dipsosaurus dorsalis
Tropidurus torquatus
Tropidurus hispidus
Tropidurus oreadicus
Tropidurus insulanus
Tropidurus erythrocephalus
Tropidurus mucujensis
Tropidurus etheridgei
Tropidurus cocorobensis
Tropidurus itambere
Tropidurus psammonastes
Tropidurus montanus
Tropidurus hygomi
Eurolophosaurus nanuzae
Eurolophosaurus amathites
Eurolophosaurus divaricatus
Tropidurus spinulosus
Tropidurus callathelys
Plica plica
Plica lumaria
Plica umbra
Strobilurus torquatus
Tropidurus bogerti
Uracentron flaviceps
Uranoscodon superciliosus
Microlophus duncanensis
Microlophus albemarlensis
Microlophus pacificus
Microlophus grayii
Microlophus delanonis
Microlophus stolzmanni
Microlophus habelii
Microlophus bivittatus
Microlophus occipitalis
Microlophus koepckeorum
Microlophus yanezi
Microlophus theresioides
Microlophus atacamensis
Microlophus quadrivittatus
Microlophus peruvianus
Microlophus tigris
Microlophus heterolepis
Microlophus theresiae
Microlophus thoracicus
Stenocercus stigmosus
Stenocercus melanopygus
Stenocercus latebrosus
Stenocercus orientalis
Stenocercus ornatissimus
Stenocercus chrysopygus
Stenocercus cupreus
Stenocercus boettgeri
Stenocercus empetrus
Stenocercus eunetopsis
Stenocercus imitator
Stenocercus varius
Stenocercus torquatus
Stenocercus crassicaudatus
Stenocercus marmoratus
Stenocercus humeralis
Stenocercus angel
Stenocercus guentheri
Stenocercus festae
Stenocercus chota
Stenocercus rhodomelas
Stenocercus angulifer
Stenocercus iridescens
Stenocercus puyango
Stenocercus percultus
Stenocercus ornatus
Stenocercus caducus
Stenocercus limitaris
Stenocercus doellojuradoi
Stenocercus azureus
Stenocercus roseiventris
Stenocercus ochoai
Stenocercus formosus
Stenocercus apurimacus
Stenocercus scapularis
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Iguanidae
Tropiduridae
P
Q-R Figure 17
Sceloporus adleri
Sceloporus stejnegeri
Sceloporus formosus
Sceloporus subpictus
Sceloporus cryptus
Sceloporus lundelli
Sceloporus malachiticus
Sceloporus smaragdinus
Sceloporus taeniocnemis
Sceloporus spinosus
Sceloporus edwardtaylori
Sceloporus horridus
Sceloporus cautus
Sceloporus undulatus
Sceloporus consobrinus
Sceloporus woodi
Sceloporus virgatus
Sceloporus occidentalis
Sceloporus olivaceus
Sceloporus clarkii
Sceloporus cyanogenys
Sceloporus serrifer
Sceloporus ornatus
Sceloporus minor
Sceloporus dugesii
Sceloporus poinsettii
Sceloporus macdougalli
Sceloporus mucronatus
Sceloporus bulleri
Sceloporus torquatus
Sceloporus jarrovii
Sceloporus insignis
Sceloporus megalepidurus
Sceloporus goldmani
Sceloporus samcolemani
Sceloporus chaneyi
Sceloporus slevini
Sceloporus scalaris
Sceloporus bicanthalis
Sceloporus aeneus
Sceloporus heterolepis
Sceloporus palaciosi
Sceloporus grammicus
Sceloporus melanorhinus
Sceloporus hunsakeri
Sceloporus orcutti
Sceloporus licki
Sceloporus lineatulus
Sceloporus zosteromus
Sceloporus magister
Sceloporus arenicolus
Sceloporus graciosus
Sceloporus vandenburgianus
Sceloporus ochoterenae
Sceloporus jalapae
Sceloporus maculosus
Sceloporus gadoviae
Sceloporus nelsoni
Sceloporus pyrocephalus
Sceloporus merriami
Sceloporus siniferus
Sceloporus squamosus
Sceloporus carinatus
Sceloporus utiformis
Sceloporus angustus
Sceloporus grandaevus
Sceloporus cozumelae
Sceloporus smithi
Sceloporus variabilis
Sceloporus teapensis
Sceloporus chrysostictus
Sceloporus couchii
Sceloporus parvus
Urosaurus auriculatus
Urosaurus clarionensis
Urosaurus ornatus
Urosaurus graciosus
Urosaurus nigricaudus
Urosaurus lahtelai
Urosaurus bicarinatus
Urosaurus gadovi
Uta stejnegeri
Uta stansburiana
Uta palmeri
Uta squamata
Petrosaurus thalassinus
Petrosaurus repens
Petrosaurus mearnsi
Phrynosoma hernandesi
Phrynosoma douglassii
Phrynosoma ditmarsi
Phrynosoma orbiculare
Phrynosoma modestum
Phrynosoma taurus
Phrynosoma braconnieri
Phrynosoma asio
Phrynosoma wigginsi
Phrynosoma cerroense
Phrynosoma blainvillii
Phrynosoma coronatum
Phrynosoma platyrhinos
Phrynosoma mcallii
Phrynosoma solare
Phrynosoma cornutum
Holbrookia maculata
Holbrookia propinqua
Holbrookia lacerata
Cophosaurus texanus
Callisaurus draconoides
Uma notata
Uma inornata
Uma scoparia
Uma paraphygas
Uma exsul
Crotaphytus collaris
Crotaphytus nebrius
Crotaphytus bicinctores
Crotaphytus grismeri
Crotaphytus insularis
Crotaphytus vestigium
Crotaphytus reticulatus
Crotaphytus antiquus
Gambelia copeii
Gambelia sila
Gambelia wislizenii
Leiocephalus barahonensis
Leiocephalus schreibersii
Leiocephalus personatus
Leiocephalus psammodromus
Leiocephalus raviceps
Leiocephalus carinatus
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Crotaphytidae
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Liolaemus lavillai
Liolaemus ornatus
Liolaemus calchaqui
Liolaemus albiceps
Liolaemus irregularis
Liolaemus crepuscularis
Liolaemus abaucan
Liolaemus espinozai
Liolaemus quilmes
Liolaemus koslowskyi
Liolaemus laurenti
Liolaemus darwinii
Liolaemus grosseorum
Liolaemus olongasta
Liolaemus chacoensis
Liolaemus uspallatensis
Liolaemus hermannunezi
Liolaemus xanthoviridis
Liolaemus fitzingerii
Liolaemus chehuachekenk
Liolaemus morenoi
Liolaemus canqueli
Liolaemus melanops
Liolaemus donosobarrosi
Liolaemus cuyanus
Liolaemus telsen
Liolaemus inacayali
Liolaemus boulengeri
Liolaemus rothi
Liolaemus wiegmannii
Liolaemus azarai
Liolaemus scapularis
Liolaemus multimaculatus
Liolaemus riojanus
Liolaemus salinicola
Liolaemus lutzae
Liolaemus occipitalis
Liolaemus pseudoanomalus
Liolaemus andinus
Liolaemus multicolor
Liolaemus molinai
Liolaemus dorbignyi
Liolaemus huacahuasicus
Liolaemus fabiani
Liolaemus audituvelatus
Liolaemus ruibali
Liolaemus vallecurensis
Liolaemus famatinae
Liolaemus orientalis
Liolaemus stolzmanni
Liolaemus archeforus
Liolaemus tristis
Liolaemus zullyae
Liolaemus scolaroi
Liolaemus sarmientoi
Liolaemus gallardoi
Liolaemus kingii
Liolaemus escarchadosi
Liolaemus tari
Liolaemus baguali
Liolaemus somuncurae
Liolaemus uptoni
Liolaemus magellanicus
Liolaemus kolengh
Liolaemus silvanae
Liolaemus lineomaculatus
Liolaemus hatcheri
Liolaemus saxatilis
Liolaemus gracilis
Liolaemus robertmertensi
Liolaemus ramirezae
Liolaemus yanalcu
Liolaemus walkeri
Liolaemus puna
Liolaemus chaltin
Liolaemus bitaeniatus
Liolaemus pagaburoi
Liolaemus bibronii
Liolaemus hernani
Liolaemus pictus
Liolaemus cyanogaster
Liolaemus chiliensis
Liolaemus schroederi
Liolaemus gravenhorstii
Liolaemus bellii
Liolaemus coeruleus
Liolaemus elongatus
Liolaemus kriegi
Liolaemus leopardinus
Liolaemus ceii
Liolaemus buergeri
Liolaemus petrophilus
Liolaemus umbrifer
Liolaemus capillitas
Liolaemus heliodermis
Liolaemus dicktracyi
Liolaemus thermarum
Liolaemus austromendocinus
Liolaemus paulinae
Liolaemus platei
Liolaemus nigromaculatus
Liolaemus pseudolemniscatus
Liolaemus zapallarensis
Liolaemus atacamensis
Liolaemus fuscus
Liolaemus nigroviridis
Liolaemus nitidus
Liolaemus monticola
Liolaemus lemniscatus
Liolaemus tenuis
Phymaturus antofagastensis
Phymaturus mallimaccii
Phymaturus punae
Phymaturus palluma
Phymaturus dorsimaculatus
Phymaturus patagonicus
Phymaturus somuncurensis
Phymaturus indistinctus
Ctenoblepharys adspersa
Leiosaurus catamarcensis
Leiosaurus paronae
Leiosaurus bellii
Pristidactylus torquatus
Diplolaemus darwinii
Pristidactylus scapulatus
Urostrophus vautieri
Anisolepis longicauda
Urostrophus gallardoi
Enyalius leechii
Enyalius bilineatus
Oplurus fierinensis
Oplurus grandidieri
Oplurus saxicola
Oplurus quadrimaculatus
Oplurus cuvieri
Oplurus cyclurus
Chalarodon madagascariensis
Enyalioides praestabilis
Enyalioides microlepis
Enyalioides palpebralis
Enyalioides oshaughnessyi
Enyalioides heterolepis
Enyalioides laticeps
Morunasaurus annularis
Hoplocercus spinosus
Polychrus marmoratus
Polychrus femoralis
Polychrus acutirostris
Polychrus gutturosus
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Opluridae
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Leiosaurinae
Enyaliinae
(i)
(ii)
(i)
(ii)
Q
R
Figure 18
Anolis smaragdinus
Anolis allisoni
Anolis maynardi
Anolis brunneus
Anolis longiceps
Anolis porcatus
Anolis carolinensis
Anolis isolepis
Anolis oporinus
Anolis argillaceus
Anolis centralis
Anolis pumilus
Anolis loysiana
Anolis guazuma
Anolis garridoi
Anolis angusticeps
Anolis paternus
Anolis alayoni
Anolis sheplani
Anolis placidus
Anolis alutaceus
Anolis inexpectatus
Anolis vanidicus
Anolis alfaroi
Anolis macilentus
Anolis cupeyalensis
Anolis cyanopleurus
Anolis rejectus
Anolis clivicola
Anolis lucius
Anolis whitemani
Anolis cybotes
Anolis armouri
Anolis shrevei
Anolis haetianus
Anolis longitibialis
Anolis strahmi
Anolis marcanoi
Anolis barahonae
Anolis baleatus
Anolis ricordi
Anolis eugenegrahami
Anolis christophei
Anolis cuvieri
Anolis guamuhaya
Anolis chamaeleonides
Anolis porcus
Anolis barbatus
Anolis argenteolus
Anolis alumina
Anolis semilineatus
Anolis olssoni
Anolis barbouri
Anolis insolitus
Anolis fowleri
Anolis etheridgei
Anolis equestris
Anolis luteogularis
Anolis baracoae
Anolis noblei
Anolis smallwoodi
Anolis aliniger
Anolis singularis
Anolis chlorocyanus
Anolis coelestinus
Anolis hendersoni
Anolis dolichocephalus
Anolis bahorucoensis
Anolis darlingtoni
Anolis monticola
Anolis occultus
Anolis vermiculatus
Anolis bartschi
Anolis maculigula
Anolis casildae
Anolis frenatus
Anolis princeps
Anolis chocorum
Anolis fraseri
Anolis danieli
Anolis insignis
Anolis microtus
Anolis agassizi
Anolis neblininus
Anolis calimae
Anolis anatoloros
Anolis jacare
Anolis tigrinus
Anolis transversalis
Anolis punctatus
Anolis inderenae
Anolis vanzolinii
Anolis heterodermus
Anolis nicefori
Anolis euskalerriari
Anolis gemmosus
Anolis aequatorialis
Anolis ventrimaculatus
Anolis chloris
Anolis festae
Anolis peraccae
Anolis huilae
Anolis fitchi
Anolis extremus
Anolis roquet
Anolis aeneus
Anolis richardii
Anolis trinitatis
Anolis griseus
Anolis bonairensis
Anolis luciae
Anolis boettgeri
Basiliscus basiliscus
Basiliscus plumifrons
Basiliscus vittatus
Basiliscus galeritus
Corytophanes cristatus
Corytophanes percarinatus
Laemanctus longipes
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Anolis trachyderma
Anolis poecilopus
Anolis tropidogaster
Anolis lionotus
Anolis oxylophus
Anolis zeus
Anolis limifrons
Anolis lemurinus
Anolis bicaorum
Anolis carpenteri
Anolis ocelloscapularis
Anolis tropidonotus
Anolis capito
Anolis polylepis
Anolis cupreus
Anolis fuscoauratus
Anolis kemptoni
Anolis altae
Anolis humilis
Anolis pachypus
Anolis sericeus
Anolis isthmicus
Anolis intermedius
Anolis laeviventris
Anolis ortonii
Anolis quercorum
Anolis aquaticus
Anolis woodi
Anolis biporcatus
Anolis bitectus
Anolis uniformis
Anolis polyrhachis
Anolis sminthus
Anolis crassulus
Anolis utilensis
Anolis purpurgularis
Anolis loveridgei
Anolis chrysolepis
Anolis bombiceps
Anolis nitens
Anolis meridionalis
Anolis lineatus
Anolis onca
Anolis annectens
Anolis auratus
Anolis grahami
Anolis conspersus
Anolis garmani
Anolis opalinus
Anolis valencienni
Anolis reconditus
Anolis lineatopus
Anolis bremeri
Anolis quadriocellifer
Anolis sagrei
Anolis ophiolepis
Anolis mestrei
Anolis homolechis
Anolis jubar
Anolis confusus
Anolis guafe
Anolis ahli
Anolis allogus
Anolis rubribarbaris
Anolis imias
Anolis cristatellus
Anolis desechensis
Anolis ernestwilliamsi
Anolis scriptus
Anolis cooki
Anolis monensis
Anolis krugi
Anolis pulchellus
Anolis gundlachi
Anolis poncensis
Anolis evermanni
Anolis stratulus
Anolis acutus
Anolis caudalis
Anolis marron
Anolis brevirostris
Anolis websteri
Anolis distichus
Anolis marmoratus
Anolis sabanus
Anolis nubilus
Anolis lividus
Anolis ferreus
Anolis terraealtae
Anolis oculatus
Anolis gingivinus
Anolis bimaculatus
Anolis leachii
Anolis pogus
Anolis wattsi
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77
56
90
100
Corytophanidae
Dactyloidae
(i)
(ii)
(i)
(ii)
R
Figure 19
Austrotyphlops pilbarensis
Austrotyphlops hamatus
Austrotyphlops endoterus
Austrotyphlops australis
Austrotyphlops waitii
Austrotyphlops splendidus
Austrotyphlops pinguis
Ramphotyphlops bicolor
Austrotyphlops ligatus
Austrotyphlops ganei
Austrotyphlops troglodytes
Austrotyphlops kimberleyensis
Austrotyphlops ammodytes
Austrotyphlops unguirostris
Austrotyphlops leptosomus
Austrotyphlops longissimus
Austrotyphlops grypus
Austrotyphlops bituberculatus
Austrotyphlops guentheri
Austrotyphlops howi
Austrotyphlops diversus
Ramphotyphlops polygrammicus
Acutotyphlops kunuaensis
Acutotyphlops subocularis
Ramphotyphlops acuticaudus
Ramphotyphlops lineatus
Typhlopidae sp. (Sri Lanka)
Ramphotyphlops braminus
Typhlops pammeces
Ramphotyphlops albiceps
Typhlops ruber
Typhlops luzonensis
Typhlops arenarius
Typhlops vermicularis
Afrotyphlops punctatus
Afrotyphlops congestus
Afrotyphlops lineolatus
Afrotyphlops bibronii
Afrotyphlops fornasinii
Megatyphlops schlegelii
Afrotyphlops angolensis
Typhlops elegans
Letheobia obtusa
Letheobia newtoni
Letheobia feae
Rhinotyphlops lalandei
Typhlops catapontus
Typhlops richardi
Typhlops platycephalus
Typhlops hypomethes
Typhlops granti
Typhlops dominicanus
Typhlops monastus
Typhlops notorachius
Typhlops anousius
Typhlops anchaurus
Typhlops contorhinus
Typhlops arator
Typhlops caymanensis
Typhlops agoralionis
Typhlops sylleptor
Typhlops jamaicensis
Typhlops capitulatus
Typhlops rostellatus
Typhlops sulcatus
Typhlops titanops
Typhlops schwartzi
Typhlops lumbricalis
Typhlops eperopeus
Typhlops syntherus
Typhlops hectus
Typhlops pusillus
Typhlops biminiensis
Typhlops reticulatus
Typhlops brongersmianus
Xenotyphlops grandidieri
Gerrhopilus mirus
Gerrhopilus hedraeus
Leptotyphlops scutifrons
Leptotyphlops distanti
Leptotyphlops conjunctus
Leptotyphlops sylvicolus
Leptotyphlops nigricans
Leptotyphlops nigroterminus
Namibiana occidentalis
Myriopholis adleri
Myriopholis macrorhyncha
Myriopholis blanfordi
Myriopholis boueti
Myriopholis rouxestevae
Myriopholis algeriensis
Myriopholis longicauda
Mitophis leptipileptus
Mitophis pyrites
Mitophis asbolepis
Tetracheilostoma breuili
Tetracheilostoma carlae
Rena humilis
Rena dulcis
Trilepida macrolepis
Epictia columbi
Epictia goudotii
Epictia albifrons
Siagonodon septemstriatus
Tricheilostoma bicolor
Typhlophis squamosus
Liotyphlops albirostris
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Anomalepididae
Leptotyphlopidae
Gerrhopilidae
Xenotyphlopidae
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Figure 20
Antaresia childreni
Antaresia stimsoni
Antaresia perthensis
Antaresia maculosa
Morelia bredli
Morelia spilota
Morelia carinata
Morelia viridis
Bothrochilus boa
Leiopython albertisii
Liasis fuscus
Liasis mackloti
Apodora papuana
Liasis olivaceus
Aspidites melanocephalus
Aspidites ramsayi
Morelia amethistina
Morelia boeleni
Morelia oenpelliensis
Broghammerus timoriensis
Broghammerus reticulatus
Python molurus
Python sebae
Python curtus
Python regius
Python brongersmai
Loxocemus bicolor
Xenopeltis unicolor
Rhinophis blythii
Rhinophis homolepis
Pseudotyphlops philippinus
Rhinophis oxyrhynchus
Rhinophis philippinus
Rhinophis dorsimaculatus
Rhinophis drummondhayi
Uropeltis phillipsi
Uropeltis melanogaster
Rhinophis travancoricus
Uropeltis ceylanicus
Uropeltis liura
Brachyophidium rhodogaster
Melanophidium punctatum
Cylindrophis ruffus
Cylindrophis maculatus
Anomochilus leonardi
Epicrates striatus
Epicrates exsul
Epicrates chrysogaster
Epicrates subflavus
Epicrates fordi
Epicrates monensis
Epicrates inornatus
Epicrates angulifer
Eunectes notaeus
Eunectes murinus
Epicrates cenchria
Corallus annulatus
Corallus caninus
Corallus hortulanus
Boa constrictor
Eryx tataricus
Eryx miliaris
Eryx elegans
Eryx jaculus
Eryx johnii
Eryx conicus
Eryx colubrinus
Eryx jayakari
Candoia bibroni
Candoia carinata
Candoia aspera
Lichanura trivirgata
Charina bottae
Ungaliophis continentalis
Exiliboa placata
Calabaria reinhardtii
Acrantophis dumerili
Acrantophis madagascariensis
Sanzinia madagascariensis
Casarea dussumieri
Xenophidion schaeferi
Tropidophis melanurus
Tropidophis feicki
Tropidophis haetianus
Tropidophis greenwayi
Tropidophis wrighti
Tropidophis pardalis
Trachyboa boulengeri
Trachyboa gularis
Anilius scytale
100
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Aniliidae
Tropidophiidae
Xenophidiidae
Bolyeriidae
Boidae
Anomochilidae
Cylindrophiidae
Uropeltidae
Xenopeltidae
Loxocemidae
Pythonidae
Calabariidae
Sanziniinae
Ungaliophiinae
Candoiinae
Erycinae
Boinae
T
U-AA
Figure 21
Bitis rubida
Bitis cornuta
Bitis atropos
Bitis xeropaga
Bitis caudalis
Bitis peringueyi
Bitis gabonica
Bitis nasicornis
Bitis arietans
Bitis worthingtoni
Atheris desaixi
Atheris nitschei
Atheris squamigera
Atheris hispida
Atheris chlorechis
Atheris barbouri
Atheris ceratophora
Echis pyramidum
Echis leucogaster
Echis coloratus
Echis omanensis
Echis jogeri
Echis ocellatus
Echis carinatus
Causus defilippii
Causus rhombeatus
Causus resimus
Cerastes gasperettii
Cerastes cerastes
Cerastes vipera
Proatheris superciliaris
Vipera lotievi
Vipera renardi
Vipera dinniki
Vipera ursinii
Vipera eriwanensis
Vipera kaznakovi
Vipera barani
Vipera berus
Vipera nikolskii
Vipera seoanei
Vipera aspis
Vipera latastei
Vipera ammodytes
Macrovipera mauritanica
Macrovipera deserti
Daboia russelii
Daboia palaestinae
Montivipera wagneri
Montivipera albizona
Montivipera bornmuelleri
Montivipera raddei
Montivipera xanthina
Macrovipera schweizeri
Macrovipera lebetina
Pseudocerastes fieldi
Pseudocerastes persicus
Eristicophis macmahoni
Pareas nuchalis
Pareas carinatus
Pareas hamptoni
Pareas macularius
Pareas margaritophorus
Pareas formosensis
Pareas boulengeri
Pareas monticola
Aplopeltura boa
Asthenodipsas vertebralis
Achalinus rufescens
Achalinus meiguensis
Xenodermus javanicus
Stoliczkia borneensis
Acrochordus arafurae
Acrochordus granulatus
Acrochordus javanicus
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Crotalus adamanteus
Crotalus tigris
Crotalus mitchellii
Crotalus viridis
Crotalus oreganus
Crotalus scutulatus
Crotalus tortugensis
Crotalus atrox
Crotalus catalinensis
Crotalus ruber
Crotalus totonacus
Crotalus molossus
Crotalus basiliscus
Crotalus simus
Crotalus durissus
Crotalus horridus
Crotalus willardi
Crotalus ravus
Crotalus cerastes
Crotalus polystictus
Crotalus enyo
Crotalus aquilus
Crotalus lepidus
Crotalus pusillus
Crotalus triseriatus
Crotalus tancitarensis
Crotalus transversus
Crotalus intermedius
Crotalus pricei
Sistrurus miliarius
Sistrurus catenatus
Agkistrodon bilineatus
Agkistrodon taylori
Agkistrodon piscivorus
Agkistrodon contortrix
Bothriechis rowleyi
Bothriechis aurifer
Bothriechis bicolor
Bothriechis thalassinus
Bothriechis marchi
Bothriechis lateralis
Bothriechis nigroviridis
Bothriechis schlegelii
Lachesis muta
Lachesis stenophrys
Mixcoatlus melanurus
Mixcoatlus barbouri
Ophryacus undulatus
Bothrops leucurus
Bothrops moojeni
Bothrops atrox
Bothrops colombiensis
Bothrops marajoensis
Bothrops asper
Bothrops lanceolatus
Bothrops caribbaeus
Bothrops punctatus
Bothrops jararacussu
Bothrops brazili
Bothriopsis bilineata
Bothriopsis taeniata
Bothriopsis chloromelas
Bothriopsis pulchra
Bothropoides alcatraz
Bothropoides insularis
Bothropoides jararaca
Bothropoides neuwiedi
Bothropoides diporus
Bothropoides erythromelas
Rhinocerophis itapetiningae
Rhinocerophis alternatus
Rhinocerophis fonsecai
Rhinocerophis cotiara
Rhinocerophis ammodytoides
Bothrops pictus
Bothrocophias hyoprora
Bothrocophias microphthalmus
Bothrocophias campbelli
Porthidium lansbergii
Porthidium porrasi
Porthidium nasutum
Porthidium yucatanicum
Porthidium dunni
Porthidium ophryomegas
Cerrophidion petlalcalensis
Cerrophidion tzotzilorum
Cerrophidion godmani
Atropoides picadoi
Atropoides olmec
Atropoides nummifer
Atropoides occiduus
Gloydius saxatilis
Gloydius intermedius
Gloydius shedaoensis
Gloydius halys
Gloydius strauchi
Gloydius blomhoffii
Gloydius ussuriensis
Gloydius brevicaudus
Gloydius tsushimaensis
Trimeresurus gracilis
Ovophis okinavensis
Protobothrops tokarensis
Protobothrops flavoviridis
Protobothrops mucrosquamatus
Protobothrops elegans
Protobothrops jerdonii
Protobothrops xiangchengensis
Protobothrops cornutus
Protobothrops mangshanensis
Protobothrops sieversorum
Protobothrops kaulbacki
Ovophis tonkinensis
Ovophis zayuensis
Ovophis monticola
Trimeresurus purpureomaculatus
Trimeresurus erythrurus
Trimeresurus cantori
Trimeresurus albolabris
Trimeresurus andersonii
Trimeresurus septentrionalis
Trimeresurus insularis
Trimeresurus fasciatus
Trimeresurus macrops
Trimeresurus venustus
Trimeresurus kanburiensis
Trimeresurus vogeli
Trimeresurus stejnegeri
Trimeresurus gumprechti
Trimeresurus yunnanensis
Trimeresurus medoensis
Trimeresurus tibetanus
Trimeresurus popeiorum
Trimeresurus sumatranus
Trimeresurus schultzei
Trimeresurus flavomaculatus
Trimeresurus malcolmi
Trimeresurus hageni
Trimeresurus trigonocephalus
Trimeresurus gramineus
Trimeresurus malabaricus
Trimeresurus borneensis
Trimeresurus puniceus
Hypnale zara
Hypnale hypnale
Hypnale nepa
Calloselasma rhodostoma
Deinagkistrodon acutus
Tropidolaemus wagleri
Garthius chaseni
Azemiops feae
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Acrochordidae
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Azemiopinae
C
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U
V-AA
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(ii)
(i)
(ii)
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Figure 22
Liophidium chabaudi
Liophidium mayottensis
Liophidium torquatum
Liophidium therezieni
Liophidium vaillanti
Liophidium rhodogaster
Liopholidophis sexlineatus
Liopholidophis dolicocercus
Liopholidophis dimorphus
Heteroliodon occipitalis
Pseudoxyrhopus ambreensis
Thamnosophis lateralis
Thamnosophis stumpffi
Thamnosophis epistibes
Thamnosophis martae
Thamnosophis infrasignatus
Dromicodryas bernieri
Dromicodryas quadrilineatus
Lycodryas granuliceps
Lycodryas pseudogranuliceps
Lycodryas inopinae
Lycodryas sanctijohannis
Lycodryas citrinus
Lycodryas inornatus
Madagascarophis meridionalis
Madagascarophis colubrinus
Ithycyphus oursi
Ithycyphus miniatus
Micropisthodon ochraceus
Langaha madagascariensis
Leioheterodon modestus
Leioheterodon madagascariensis
Leioheterodon geayi
Parastenophis betsileanus
Alluaudina bellyi
Compsophis infralineatus
Compsophis laphystius
Compsophis albiventris
Compsophis boulengeri
Ditypophis vivax
Duberria lutrix
Duberria variegata
Amplorhinus multimaculatus
Lycodonomorphus whytii
Lycodonomorphus laevissimus
Lycodonomorphus rufulus
Lycodonomorphus inornatus
Lamprophis fiskii
Lamprophis aurora
Lamprophis fuscus
Lamprophis guttatus
Boaedon olivaceus
Boaedon fuliginosus
Boaedon lineatus
Boaedon virgatus
Bothrophthalmus lineatus
Bothrophthalmus brunneus
Bothrolycus ater
Pseudoboodon lemniscatus
Gonionotophis capensis
Gonionotophis poensis
Gonionotophis brussauxi
Gonionotophis nyassae
Gonionotophis stenophthalmus
Inyoka swazicus
Hormonotus modestus
Lycophidion ornatum
Lycophidion capense
Lycophidion laterale
Lycophidion nigromaculatum
Buhoma depressiceps
Buhoma procterae
Psammodynastes pictus
Psammodynastes pulverulentus
Pseudaspis cana
Pythonodipsas carinata
Aparallactus guentheri
Aparallactus capensis
Aparallactus werneri
Aparallactus modestus
Polemon acanthias
Polemon collaris
Polemon notatus
Amblyodipsas dimidiata
Xenocalamus transvaalensis
Amblyodipsas polylepis
Macrelaps microlepidotus
Atractaspis corpulenta
Atractaspis micropholis
Atractaspis bibronii
Atractaspis boulengeri
Atractaspis microlepidota
Atractaspis irregularis
Homoroselaps lacteus
Psammophis phillipsi
Psammophis mossambicus
Psammophis leopardinus
Psammophis sibilans
Psammophis rukwae
Psammophis orientalis
Psammophis sudanensis
Psammophis subtaeniatus
Psammophis lineatus
Psammophis biseriatus
Psammophis tanganicus
Psammophis praeornatus
Psammophis punctulatus
Psammophis schokari
Psammophis angolensis
Psammophis notostictus
Psammophis leightoni
Psammophis jallae
Psammophis trigrammus
Psammophis condanarus
Psammophis lineolatus
Psammophis crucifer
Psammophylax tritaeniatus
Psammophylax variabilis
Psammophylax rhombeatus
Psammophylax acutus
Hemirhagerrhis hildebrandtii
Hemirhagerrhis kelleri
Hemirhagerrhis viperina
Dipsina multimaculata
Mimophis mahfalensis
Rhagerhis moilensis
Malpolon monspessulanus
Rhamphiophis rubropunctatus
Rhamphiophis oxyrhynchus
Prosymna meleagris
Prosymna greigerti
Prosymna janii
Prosymna visseri
Prosymna ruspolii
Oxyrhabdium leporinum
Micrelaps bicoloratus
Cerberus rynchops
Cerberus microlepis
Cerberus australis
Homalopsis buccata
Enhydris punctata
Fordonia leucobalia
Gerarda prevostiana
Cantoria violacea
Bitia hydroides
Enhydris bocourti
Erpeton tentaculatum
Pseudoferania polylepis
Myron richardsonii
Enhydris innominata
Enhydris longicauda
Enhydris jagorii
Enhydris enhydris
Enhydris matannensis
Enhydris plumbea
Enhydris chinensis
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Homalopsidae
Prosymninae
Psammophiinae
Atractaspidinae
Aparallactinae
Pseudaspidinae
Lamprophiinae
Pseudoxyrhophiinae
Lamprophiidae
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Figure 23
Hydrophis ornata
Hydrophis peronii
Hydrophis kingii
Hydrophis macdowelli
Hydrophis schistosa
Hydrophis major
Hydrophis czeblukovi
Hydrophis caerulescens
Hydrophis brooki
Hydrophis atriceps
Hydrophis stokesii
Hydrophis platura
Hydrophis curtus
Hydrophis parviceps
Hydrophis melanocephala
Hydrophis cyanocincta
Hydrophis pacifica
Hydrophis semperi
Hydrophis spiralis
Hydrophis lapemoides
Hydrophis elegans
Hydrelaps darwiniensis
Ephalophis greyae
Parahydrophis mertoni
Aipysurus laevis
Aipysurus fuscus
Aipysurus apraefrontalis
Aipysurus duboisii
Aipysurus eydouxii
Emydocephalus annulatus
Hemiaspis damelii
Hemiaspis signata
Tropidechis carinatus
Notechis scutatus
Echiopsis atriceps
Hoplocephalus bitorquatus
Austrelaps superbus
Austrelaps labialis
Drysdalia coronoides
Drysdalia mastersii
Echiopsis curta
Pseudonaja textilis
Pseudonaja modesta
Oxyuranus scutellatus
Oxyuranus microlepidotus
Denisonia devisi
Simoselaps calonotus
Vermicella intermedia
Suta spectabilis
Suta suta
Suta monachus
Suta fasciata
Rhinoplocephalus bicolor
Cryptophis nigrescens
Elapognathus coronata
Cacophis squamulosus
Pseudechis guttatus
Pseudechis papuanus
Pseudechis colletti
Pseudechis australis
Pseudechis butleri
Pseudechis porphyriacus
Acanthophis antarcticus
Acanthophis praelongus
Aspidomorphus muelleri
Aspidomorphus lineaticollis
Aspidomorphus schlegeli
Simoselaps bertholdi
Simoselaps anomalus
Simoselaps semifasciatus
Furina diadema
Furina ornata
Toxicocalamus loriae
Demansia psammophis
Demansia papuensis
Demansia vestigiata
Toxicocalamus preussi
Micropechis ikaheka
Laticauda colubrina
Laticauda guineai
Laticauda saintgironsi
Laticauda laticaudata
Bungarus candidus
Bungarus multicinctus
Bungarus niger
Bungarus caeruleus
Bungarus ceylonicus
Bungarus sindanus
Bungarus fasciatus
Bungarus bungaroides
Bungarus flaviceps
Elapsoidea sundevallii
Elapsoidea semiannulata
Elapsoidea nigra
Naja ashei
Naja nigricollis
Naja mossambica
Naja katiensis
Naja pallida
Naja nubiae
Naja haje
Naja annulifera
Naja nivea
Naja annulata
Naja melanoleuca
Naja multifasciata
Naja sumatrana
Naja siamensis
Naja mandalayensis
Naja naja
Naja atra
Naja kaouthia
Hemachatus haemachatus
Aspidelaps scutatus
Walterinnesia aegyptia
Dendroaspis polylepis
Dendroaspis angusticeps
Ophiophagus hannah
Hemibungarus calligaster
Micrurus brasiliensis
Micrurus frontalis
Micrurus spixii
Micrurus ibiboboca
Micrurus altirostris
Micrurus pyrrhocryptus
Micrurus baliocoryphus
Micrurus decoratus
Micrurus lemniscatus
Micrurus hemprichii
Micrurus surinamensis
Micrurus dissoleucus
Micrurus mipartitus
Micrurus narduccii
Micrurus diastema
Micrurus fulvius
Micrurus psyches
Micrurus albicinctus
Micrurus corallinus
Sinomicrurus macclellandi
Sinomicrurus kelloggi
Sinomicrurus japonicus
Micruroides euryxanthus
Maticora bivirgata
Calliophis melanurus
100
98
95
90
100
92
85
67
89
75
99
91
100
98
72
100
95
67
83
93
88
74
100
83
77
98
54
94
100
97
100
75
94
96
100
94
90
100
97
100
78
97
98
99
98
98
100
100
71
100
97
100
94
88
98
100
90
88
95
68
100 100
100
100
100
100
99
100
82 100
100
100
91
100
98
100
98
100
100
99
100
97
97
100
99
87
100
91
90
83
92
99
96
96
76
78
100
88
69
58
100
99
87
63
84
84
100
61
85
100
91
94
98
88
89
59
97
97
98
100
90
99
100
95
Elapidae
W
Figure 24
Eirenis punctatolineatus
Eirenis barani
Eirenis collaris
Eirenis eiselti
Eirenis coronelloides
Eirenis rothii
Eirenis lineomaculatus
Eirenis thospitis
Eirenis medus
Eirenis levantinus
Eirenis decemlineatus
Eirenis persicus
Eirenis aurolineatus
Eirenis modestus
Hierophis spinalis
Hierophis gemonensis
Hierophis viridiflavus
Dolichophis caspius
Dolichophis schmidti
Dolichophis jugularis
Platyceps florulentus
Platyceps collaris
Platyceps najadum
Platyceps ventromaculatus
Platyceps karelini
Platyceps rogersi
Platyceps rhodorachis
Spalerosophis diadema
Spalerosophis microlepis
Hemorrhois ravergieri
Hemorrhois nummifer
Hemorrhois algirus
Hemorrhois hippocrepis
Hemerophis socotrae
Macroprotodon abubakeri
Macroprotodon cucullatus
Bamanophis dorri
Coluber zebrinus
Lytorhynchus diadema
Hapsidophrys principis
Hapsidophrys smaragdina
Hapsidophrys lineatus
Philothamnus hoplogaster
Philothamnus natalensis
Philothamnus thomensis
Philothamnus girardi
Philothamnus angolensis
Philothamnus semivariegatus
Philothamnus nitidus
Philothamnus heterodermus
Philothamnus carinatus
Thelotornis capensis
Dispholidus typus
Thrasops jacksonii
Coelognathus flavolineatus
Coelognathus subradiatus
Coelognathus erythrurus
Coelognathus helena
Coelognathus radiatus
Oligodon planiceps
Oligodon torquatus
Oligodon theobaldi
Oligodon cruentatus
Oligodon splendidus
Oligodon maculatus
Oligodon cinereus
Oligodon formosanus
Oligodon ocellatus
Oligodon chinensis
Oligodon taeniatus
Oligodon barroni
Oligodon cyclurus
Oligodon octolineatus
Oligodon taeniolatus
Oligodon sublineatus
Oligodon arnensis
Scaphiophis albopunctatus
Dasypeltis fasciata
Dasypeltis gansi
Dasypeltis sahelensis
Dasypeltis scabra
Dasypeltis atra
Dasypeltis confusa
Toxicodryas pulverulenta
Boiga multomaculata
Boiga beddomei
Boiga ceylonensis
Boiga trigonata
Boiga barnesii
Boiga cynodon
Boiga forsteni
Boiga dendrophila
Boiga irregularis
Telescopus fallax
Dipsadoboa unicolor
Crotaphopeltis tornieri
Boiga kraepelini
Dendrelaphis tristis
Dendrelaphis schokari
Dendrelaphis caudolineatus
Dendrelaphis caudolineolatus
Dendrelaphis bifrenalis
Chrysopelea paradisi
Chrysopelea ornata
Chrysopelea taprobanica
Ahaetulla nasuta
Ahaetulla pulverulenta
Ahaetulla fronticincta
Grayia smithii
Grayia ornata
Grayia tholloni
Sibynophis chinensis
Sibynophis collaris
Sibynophis triangularis
Sibynophis subpunctatus
Sibynophis bistrigatus
Scaphiodontophis annulatus
Pseudoxenodon karlschmidti
Pseudoxenodon macrops
Pseudoxenodon bambusicola
Plagiopholis styani
Calamaria yunnanensis
Calamaria pavimentata
Pseudorabdion oxycephalum
100
68
74
71
100
57
100
68
100
94
60
94
100
92
83
100
83
97
91
100
86
59
86
82
100
100
100
100
99
100
100
98
52
61
86
95
100
100
100
92
86
100
60
99
69
87
68
99
99
94
90
88
52
90
98
100
100
99
86
100
99
98
98
100
97
93
56
100
89
99
90
85
99
100
83
100
79
98
70
92
77
90
100
74
85
73
89
96
96
68
71
99
100
100
97
91
69
100
100
100
100
96
68
100
100
100
97
100
97
85
99
100
C
o
l
u
b
r
i
d
a
e
Calamariinae
Pseudoxenodontinae
Sibynophiinae
Grayiinae
C
o
l
u
b
r
i
n
a
e
X
Y
Z-AA
Colubrinae cont.
Figure 25
Lampropeltis californiae
Lampropeltis splendida
Lampropeltis holbrooki
Lampropeltis getula
Lampropeltis nigra
Lampropeltis alterna
Lampropeltis extenuatum
Lampropeltis triangulum
Lampropeltis ruthveni
Lampropeltis mexicana
Lampropeltis elapsoides
Lampropeltis zonata
Lampropeltis pyromelana
Lampropeltis webbi
Lampropeltis calligaster
Cemophora coccinea
Pseudelaphe flavirufa
Arizona elegans
Rhinocheilus lecontei
Bogertophis rosaliae
Bogertophis subocularis
Pantherophis bairdi
Pantherophis obsoletus
Pantherophis alleghaniensis
Pantherophis spiloides
Pantherophis slowinskii
Pantherophis emoryi
Pantherophis guttatus
Pantherophis vulpinus
Pituophis catenifer
Pituophis ruthveni
Pituophis melanoleucus
Pituophis lineaticollis
Pituophis vertebralis
Pituophis deppei
Senticolis triaspis
Oocatochus rufodorsatus
Coronella austriaca
Coronella girondica
Elaphe sauromates
Elaphe quatuorlineata
Elaphe quadrivirgata
Elaphe schrenckii
Elaphe climacophora
Elaphe dione
Elaphe bimaculata
Elaphe carinata
Elaphe davidi
Zamenis situla
Rhinechis scalaris
Zamenis lineatus
Zamenis longissimus
Zamenis persicus
Zamenis hohenackeri
Orthriophis cantoris
Orthriophis moellendorffi
Orthriophis hodgsoni
Orthriophis taeniurus
Oreocryptophis porphyraceus
Euprepiophis mandarinus
Euprepiophis conspicillata
Archelaphe bella
Lycodon aulicus
Lycodon zawi
Lycodon osmanhilli
Lycodon capucinus
Lycodon carinatus
Dryocalamus nympha
Lycodon semicarinatum
Lycodon rufozonatum
Lycodon paucifasciatus
Lycodon fasciatus
Lycodon laoensis
Lycodon ruhstrati
Rhadinophis frenatus
Rhynchophis boulengeri
Rhadinophis prasinus
Gonyosoma jansenii
Gonyosoma oxycephalum
Sympholis lippiens
Pseudoficimia frontalis
Gyalopion canum
Ficimia streckeri
Conopsis nasus
Conopsis biserialis
Sonora semiannulata
Chilomeniscus stramineus
Chionactis occipitalis
Stenorrhina freminvillei
Rhinobothryum lentiginosum
Mastigodryas bifossatus
Mastigodryas boddaerti
Mastigodryas melanolomus
Drymoluber brazili
Drymoluber dichrous
Chironius multiventris
Chironius laurenti
Chironius exoletus
Chironius monticola
Chironius bicarinatus
Chironius flavolineatus
Chironius grandisquamis
Chironius laevicollis
Chironius scurrulus
Chironius fuscus
Drymarchon corais
Pseustes sulphureus
Spilotes pullatus
Phyllorhynchus decurtatus
Trimorphodon biscutatus
Drymobius rhombifer
Dendrophidion percarinatum
Dendrophidion dendrophis
Leptophis ahaetulla
Chironius carinatus
Chironius quadricarinatus
Coluber flagellum
Coluber constrictor
Coluber taeniatus
Tantilla melanocephala
Salvadora mexicana
Opheodrys aestivus
Opheodrys vernalis
Oxybelis aeneus
Oxybelis fulgidus
Ptyas mucosa
Ptyas korros
Cyclophiops major
64
83
100
99
90
75
84
98
100
87
100
75
92
82
100
96
74
96
60
98
98
100
72
79
94
98
100
100
96
100
98
100
100
99
100
91
94
99
98
83
100
61
83 100
55
93
100
99
64
100
100
100
99
88
98
100
53
83
98 94
76
86
92
93
60
98
100
100
100
93
93
100
87
94
100
99
71
89
100
92
87
100
98
87
86
81
83
54
99
74
91
82
97
92
99
66
92
93
88
96
100
82
100
81
Colubrinae cont.
Y
Figure 26
Thamnophis butleri
Thamnophis radix
Thamnophis brachystoma
Thamnophis elegans
Thamnophis gigas
Thamnophis atratus
Thamnophis couchii
Thamnophis ordinoides
Thamnophis hammondii
Thamnophis marcianus
Thamnophis eques
Thamnophis cyrtopsis
Thamnophis chrysocephalus
Thamnophis fulvus
Thamnophis mendax
Thamnophis sumichrasti
Thamnophis scaliger
Thamnophis godmani
Thamnophis exsul
Thamnophis melanogaster
Thamnophis valida
Adelophis foxi
Thamnophis rufipunctatus
Thamnophis proximus
Thamnophis sauritus
Thamnophis sirtalis
Nerodia sipedon
Nerodia fasciata
Nerodia harteri
Nerodia erythrogaster
Nerodia rhombifer
Nerodia taxispilota
Nerodia floridana
Nerodia cyclopion
Tropidoclonion lineatum
Regina grahami
Regina septemvittata
Regina alleni
Regina rigida
Seminatrix pygaea
Storeria dekayi
Storeria occipitomaculata
Virginia striatula
Clonophis kirtlandii
Natrix tessellata
Natrix natrix
Natrix maura
Sinonatrix annularis
Sinonatrix percarinata
Sinonatrix aequifasciata
Opisthotropis cheni
Opisthotropis latouchii
Opisthotropis lateralis
Opisthotropis guangxiensis
Aspidura guentheri
Aspidura ceylonensis
Aspidura trachyprocta
Aspidura drummondhayi
Atretium yunnanensis
Xenochrophis asperrimus
Xenochrophis punctulatus
Atretium schistosum
Xenochrophis piscator
Xenochrophis flavipunctatus
Xenochrophis vittatus
Amphiesma stolatum
Rhabdophis nuchalis
Rhabdophis tigrinus
Rhabdophis subminiatus
Balanophis ceylonensis
Macropisthodon rudis
Lycognathophis seychellensis
Afronatrix anoscopus
Natriciteres olivacea
Amphiesma craspedogaster
Amphiesma sauteri
Trachischium monticola
100
98
100
100
100
100
96
86
99
100
92
63
73
94
100
89
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99
100
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100
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69
100
96
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99
100
100
100
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50
97
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82
100
86
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100
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100
99
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69
98
100
88
88
100
62
96
98
99
100
Natricinae
Z
Figure 27
Sibynomorphus neuwiedi
Sibynomorphus ventrimaculatus
Dipsas albifrons
Dipsas articulata
Sibynomorphus turgidus
Sibynomorphus mikanii
Dipsas pratti
Dipsas variegata
Dipsas neivai
Dipsas catesbyi
Dipsas indica
Tropidodipsas sartorii
Sibon nebulatus
Ninia atrata
Atractus zebrinus
Atractus trihedrurus
Atractus reticulatus
Atractus badius
Atractus flammigerus
Atractus elaps
Atractus albuquerquei
Atractus schach
Atractus wagleri
Atractus zidoki
Geophis godmani
Geophis carinosus
Cryophis hallbergi
Tretanorhinus nigroluteus
Hydromorphus concolor
Adelphicos quadrivirgatum
Leptodeira rubricata
Leptodeira maculata
Leptodeira bakeri
Leptodeira annulata
Leptodeira septentrionalis
Leptodeira punctata
Leptodeira splendida
Leptodeira frenata
Leptodeira uribei
Imantodes cenchoa
Imantodes gemmistratus
Imantodes lentiferus
Imantodes inornatus
Leptodeira nigrofasciata
Tretanorhinus variabilis
Hypsiglena chlorophaea
Hypsiglena torquata
Hypsiglena ochrorhyncha
Hypsiglena affinis
Hypsiglena jani
Hypsiglena slevini
Trimetopon gracile
Pseudoleptodeira latifasciata
Rhadinaea fulvivittis
Rhadinaea flavilata
Coniophanes fissidens
Tantalophis discolor
Amastridium veliferum
Nothopsis rugosus
Farancia erytrogramma
Farancia abacura
Carphophis amoenus
Diadophis punctatus
Heterodon nasicus
Heterodon simus
Heterodon platirhinos
Contia tenuis
Thermophis baileyi
Thermophis zhaoermii
100
100
93
63
89
90
91
83
70
100
82
70
75
79
88
79
96
84
100
90
86
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73
75
73
97
89
68
68
94
100
64
67
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91
97
88
100
98
100
71
100
86
99
100
99
84
85
80
96
86
68
58
87
80
98
72
100
99
100
Pseudoboa coronata
Pseudoboa nigra
Pseudoboa neuwiedii
Rhachidelus brazili
Boiruna maculata
Drepanoides anomalus
Mussurana bicolor
Clelia clelia
Phimophis guerini
Paraphimophis rusticus
Rodriguesophis iglesiasi
Oxyrhopus guibei
Oxyrhopus melanogenys
Oxyrhopus rhombifer
Oxyrhopus clathratus
Oxyrhopus trigeminus
Oxyrhopus formosus
Oxyrhopus petolarius
Siphlophis longicaudatus
Siphlophis pulcher
Siphlophis compressus
Siphlophis cervinus
Hydrodynastes gigas
Hydrodynastes bicinctus
Caaeteboia amarali
Xenopholis scalaris
Xenopholis undulatus
Tropidodryas striaticeps
Tropidodryas serra
Thamnodynastes rutilus
Thamnodynastes strigatus
Thamnodynastes hypoconia
Thamnodynastes lanei
Thamnodynastes pallidus
Tomodon dorsatus
Ptychophis flavovirgatus
Tachymenis peruviana
Pseudotomodon trigonatus
Calamodontophis paucidens
Gomesophis brasiliensis
Helicops angulatus
Helicops gomesi
Helicops carinicaudus
Helicops hagmanni
Helicops infrataeniatus
Pseudoeryx plicatilis
Hydrops triangularis
Manolepis putnami
Apostolepis cearensis
Apostolepis sanctaeritae
Apostolepis flavotorquata
Apostolepis albicollaris
Apostolepis dimidiata
Apostolepis assimilis
Elapomorphus quinquelineatus
Phalotris mertensi
Phalotris lativittatus
Phalotris nasutus
Phalotris lemniscatus
Taeniophallus affinis
Echinanthera undulata
Echinanthera melanostigma
Taeniophallus nicagus
Taeniophallus brevirostris
Sordellina punctata
Philodryas patagoniensis
Philodryas agassizii
Philodryas aestiva
Philodryas psammophidea
Philodryas mattogrossensis
Philodryas georgeboulengeri
Philodryas argentea
Philodryas olfersii
Philodryas viridissima
Philodryas nattereri
Philodryas baroni
Erythrolamprus aesculapii
Erythrolamprus mimus
Eryrthrolamprus typhlus
Eryrthrolamprus pygmaea
Eryrthrolamprus breviceps
Eryrthrolamprus reginae
Eryrthrolamprus miliaris
Eryrthrolamprus juliae
Eryrthrolamprus epinephelus
Eryrthrolamprus poecilogyrus
Eryrthrolamprus ceii
Eryrthrolamprus almadensis
Eryrthrolamprus jaegeri
Eryrthrolamprus atraventer
Xenodon pulcher
Xenodon matogrossensis
Xenodon semicinctus
Xenodon guentheri
Xenodon nattereri
Xenodon histricus
Xenodon dorbignyi
Xenodon neuwiedii
Xenodon werneri
Xenodon merremi
Xenodon severus
Lygophis meridionalis
Lygophis flavifrenatus
Lygophis paucidens
Lygophis lineatus
Lygophis elegantissimus
Lygophis anomalus
Uromacer frenatus
Uromacer oxyrhynchus
Uromacer catesbyi
Schwartzophis funereum
Schwartzophis polylepis
Schwartzophis callilaemum
Antillophis parvifrons
Hypsirhynchus ferox
Darlingtonia haetiana
Ialtris dorsalis
Alsophis rufiventris
Alsophis antiguae
Alsophis rijgersmaei
Alsophis antillensis
Borikenophis portoricensis
Haitiophis anomalus
Caraiba andreae
Cubophis vudii
Cubophis cantherigerus
Magliophis exiguum
Arrhyton dolichura
Arrhyton tanyplectum
Arrhyton procerum
Arrhyton landoi
Arrhyton vittatum
Arrhyton supernum
Arrhyton taeniatum
Pseudalsophis elegans
Pseudalsophis biserialis
Psomophis joberti
Psomophis genimaculatus
Psomophis obtusus
Crisantophis nevermanni
Conophis lineatus
91
90
90
91
68
100
95
87
96
74
92
100
87
90
96
95
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63
95
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100
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100
100
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100
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93 99
90
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98
91
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100
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100
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95
AA
D
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(i)
(ii)
(ii)
(i)
Figure 28
Additional files provided with this submission:
Additional file 1: 2046042875907394_add1.txt, 264K
http://www.biomedcentral.com/imedia/1032288879981940/supp1.txt
Additional file 2: 2046042875907394_add2.docx, 681K
http://www.biomedcentral.com/imedia/7057154239819418/supp2.docx

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