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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
Abstract
Background
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
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 higherlevel
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 largescale
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 sistergroup
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 longstanding
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 sistergroup
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 nonmonophyly
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 nonmonophyletic
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 wellsupported
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 nonmonophly
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 nonmonophyletic
(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 (30–44). 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 nonscolecophidian
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 nonmonophyly
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 20–44 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 genericlevel
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 nonmonophyly
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 (

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 270–11153 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+Γ 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 nearestneighbor
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
A
B
C
D
E
F
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H) Serpentes
H
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Cercosaurinae
Acontiinae
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Xenodermatidae
Anniellidae
Crotaphytidae
Hoplocercidae
Sphenodontidae
Leiolepidinae
Polychrotidae
Pseudoxyrhophiinae
Loxocemidae
Dibamidae
Prosymninae
Lygosominae
Natricinae
Xantusiinae
Tropiduridae
Corytophanidae
Ecpleopinae
Anomochilidae
Amphisbaenidae
Leiosaurinae
Xenophiidae
Scincinae
Draconinae
Bipedidae
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Rhineuridae
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Aniliidae
Azemiopinae
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Lanthanotidae
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Tupinambinae
Xenotyphlopidae
Blanidae
Gerrhopilidae
Liolaemidae
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Gallotiinae
Leptotyphlopidae
Platysaurinae
Pythonidae
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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
83
98
100
100
98
99
100
99
100
99
83
54
98
99
84
100
68
100
100
95
100
94
63
84
71
90
100
100
100
100
100
81
100
100
100
100
87
99
69
90
100
100
88
65
97
72
89
100
90
100
100
100
100
96
100
100
96
100
94
100
95
100
97
100
100
100
100
100
100
100
100
58
100
77
100
74
100
95
95
100
99
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54
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95
96
79
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100
99
87
100
100
100
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Sphaerodactylidae
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100
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100
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100
100
Eublepharis turcmenicus
Holodactylus africanus
Hemitheconyx caudicinctus
100
100
100
Hemitheconyx taylori
Goniurosaurus kuroiwae
Goniurosaurus lichtenfelderi
97
100
Goniurosaurus catbaensis
96
Goniurosaurus luii
90 Goniurosaurus araneus
Pristurus celerrimus
100
Pristurus insignis
100
Pristurus sokotranus
Pristurus guichardi
76
92 Pristurus abdelkuri
100
Pristurus flavipunctatus
Pristurus rupestris
60
100
Pristurus minimus
Pristurus carteri
63 98
85
Pristurus crucifer
Pristurus somalicus
100 Quedenfeldtia trachyblepharus
100
Quedenfeldtia moerens
100 Aristelliger lar
Aristelliger praesignis
91 Aristelliger georgeensis
75
Saurodactylus fasciatus
100
Euleptes europaea
78
Teratoscincus microlepis
100
Teratoscincus scincus
97
Teratoscincus przewalskii
98 Teratoscincus roborowskii
Saurodactylus mauritanicus
Chatogekko amazonicus
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Lepidoblepharis xanthostigma
Lepidoblepharis festae
99
97
Gonatodes eladioi
83
Gonatodes caudiscutatus
89
Gonatodes daudini
100
Gonatodes albogularis
100
96 Gonatodes petersi
Gonatodes vittatus
100
98
Gonatodes infernalis
Gonatodes hasemani
70
Gonatodes annularis
60
Gonatodes superciliaris
100 Gonatodes alexandermendesi
60
Gonatodes purpurogularis
100
Gonatodes taniae
Gonatodes falconensis
79
95
Gonatodes humeralis
97
100
Gonatodes antillensis
93
Gonatodes concinnatus
89
Gonatodes seigliei
100
99
Gonatodes ceciliae
Gonatodes ocellatus
Coleodactylus septentrionalis
100
Coleodactylus brachystoma
99
Coleodactylus meridionalis
100
Coleodactylus natalensis
100
Pseudogonatodes manessi
96
Pseudogonatodes lunulatus
82
Pseudogonatodes guianensis
Sphaerodactylus fantasticus
98
Sphaerodactylus sputator
87 Sphaerodactylus elegantulus
87
Sphaerodactylus sabanus
81
Sphaerodactylus parvus
Sphaerodactylus microlepis
Sphaerodactylus vincenti
100 82
100 Sphaerodactylus kirbyi
100
Sphaerodactylus schwartzi
Sphaerodactylus ramsdeni
84 84
Sphaerodactylus cricoderus
83
Sphaerodactylus richardi
Sphaerodactylus oliveri
91
100
Sphaerodactylus molei
84
Sphaerodactylus glaucus
Sphaerodactylus thompsoni
69 81 Sphaerodactylus cinereus
Sphaerodactylus torrei
100
Sphaerodactylus intermedius
100 Sphaerodactylus nigropunctatus
93
Sphaerodactylus copei
83
Sphaerodactylus leucaster
Sphaerodactylus elegans
Sphaerodactylus shrevei
85 99 Sphaerodactylus cryphius
90
Sphaerodactylus darlingtoni
Sphaerodactylus notatus
Sphaerodactylus altavelensis
52
Sphaerodactylus roosevelti
85
Sphaerodactylus argus
93
Sphaerodactylus macrolepis
Sphaerodactylus armstrongi
848366 Sphaerodactylus townsendi
79 Sphaerodactylus goniorhynchus
Sphaerodactylus semasiops
Sphaerodactylus klauberi
Phyllodactylidae
94 Sphaerodactylus gaigeae
Sphaerodactylus ocoae
100
99 Sphaerodactylus nicholsi
Thecadactylus solimoensis
Thecadactylus rapicauda
98
Haemodracon riebeckii
Asaccus platyrhynchus
65 100
Ptyodactylus ragazzii
Ptyodactylus oudrii
100 Ptyodactylus hasselquistii
Ptyodactylus guttatus
Homonota gaudichaudii
93
100
100
85
100
92
100
92
C
73
100
100
65
90
92
100
100
99
99
67
75
96
Phyllopezus periosus
100
100
87
97
99
100
93
76
9162
97
Homonota fasciata
Homonota underwoodi
Homonota borellii
Homonota darwinii
Homonota andicola
Phyllodactylus wirshingi
Phyllodactylus reissii
Phyllodactylus tuberculosus
Phyllodactylus lanei
Phyllodactylus bordai
Phyllodactylus xanti
Phyllodactylus unctus
100 Phyllodactylus bugastrolepis
Phyllodactylus nocticolus
Phyllodactylus paucituberculatus
Phyllodactylus delcampoi
Phyllopezus pollicaris
Phyllopezus lutzae
Phyllopezus maranjonensis
Tarentola americana
Tarentola boehmei
Tarentola deserti
Tarentola mauritanica
Tarentola angustimentalis
Tarentola neglecta
Tarentola mindiae
Tarentola boettgeri
100
86
100 99
Tarentola ephippiata
Tarentola annularis
Tarentola gomerensis
Tarentola delalandii
Tarentola chazaliae
Tarentola darwini
73
57
Phyllodactylus duellmani
Phyllodactylus davisi
Phyllodactylus homolepidurus
Tarentola rudis
Tarentola caboverdiana
Tarentola gigas

100
C
Figure 4
(i)
(ii)
Gekkonidae
(i)
Perochirus ateles
Urocotyledon inexpectata
Ebenavia inunguis
Paroedura masobe
Paroedura gracilis
Paroedura homalorhina
Paroedura oviceps
Paroedura karstophila
Paroedura lohatsara
Paroedura stumpffi
Paroedura sanctijohannis
Paroedura picta
Paroedura androyensis
Paroedura vazimba
Paroedura tanjaka
Paroedura bastardi
Ailuronyx tachyscopaeus
Ailuronyx seychellensis
Ailuronyx trachygaster
Calodactylodes illingworthorum
Calodactylodes aureus
Ptenopus carpi
Narudasia festiva
Cnemaspis uzungwae
Cnemaspis dickersonae
69
Cnemaspis africana
Uroplatus guentheri
Uroplatus malahelo
Uroplatus malama
Uroplatus ebenaui
Uroplatus phantasticus
Uroplatus alluaudi
Uroplatus pietschmanni
Uroplatus lineatus
Uroplatus sikorae
Uroplatus henkeli
Uroplatus giganteus
Uroplatus fimbriatus
Paragehyra gabriellae
Christinus marmoratus
Afrogecko swartbergensis
Cryptactites peringueyi
Matoatoa brevipes
Afrogecko porphyreus
Afroedura pondolia
52
Afroedura karroica
Geckolepis typica
Geckolepis maculata
89
Homopholis fasciata
Homopholis walbergii
Homopholis mulleri
Blaesodactylus boivini
Blaesodactylus antongilensis
98
Blaesodactylus sakalava
Goggia lineata
Rhoptropus afer
Rhoptropus bradfieldi
Rhoptropus boultoni
99
Rhoptropus biporosus
Rhoptropus barnardi
Elasmodactylus tetensis
100
Elasmodactylus tuberculosus
Chondrodactylus angulifer
Pachydactylus laevigatus
96
100
Chondrodactylus turneri
100 Chondrodactylus fitzsimonsi
Chondrodactylus bibronii
Pachydactylus robertsi
100 93
Colopus wahlbergii
Colopus kochii
98
Pachydactylus haackei
Pachydactylus kladaroderma
89
100
Pachydactylus namaquensis
68
Pachydactylus scutatus
74 100 Pachydactylus parascutatus
Pachydactylus reconditus
70
95 Pachydactylus gaiasensis
90
Pachydactylus oreophilus
100 91
Pachydactylus bicolor
Pachydactylus caraculicus
63 Pachydactylus sansteynae
86
Pachydactylus scherzi
96 Pachydactylus punctatus
85 100
Pachydactylus rugosus
99 Pachydactylus formosus
95
Pachydactylus barnardi
84
Pachydactylus labialis
Pachydactylus geitje
52 Pachydactylus maculatus
93
Pachydactylus oculatus
Pachydactylus purcelli
61 100
Pachydactylus waterbergensis
97
Pachydactylus tsodiloensis
Pachydactylus fasciatus
98 Pachydactylus carinatus
85
Pachydactylus griffini
68 Pachydactylus serval
74
Pachydactylus weberi
Pachydactylus monicae
69
Pachydactylus mclachlani
Pachydactylus mariquensis
99
Pachydactylus austeni
Pachydactylus rangei
100
Pachydactylus vanzyli
Pachydactylus montanus
Pachydactylus tigrinus
100
Pachydactylus oshaughnessyi
72
Pachydactylus capensis
100
Pachydactylus vansoni
100 Pachydactylus affinis
Cnemaspis podihuna
Cnemaspis kandiana
100 99 Cnemaspis tropidogaster
Rhoptropella ocellata
Lygodactylus expectatus
Lygodactylus rarus
Lygodactylus madagascariensis
71
98
Lygodactylus miops
92 Lygodactylus guibei
Lygodactylus tolampyae
100 Lygodactylus heterurus
100 100
Lygodactylus verticillatus
81
Lygodactylus blancae
90
91
Lygodactylus arnoulti
85 Lygodactylus pauliani
Lygodactylus gravis
81
99
Lygodactylus montanus
82
Lygodactylus tuberosus
73
Lygodactylus mirabilis
98
Lygodactylus pictus
Lygodactylus lawrencei
Lygodactylus stevensoni
68 89
93 Lygodactylus capensis
84
Lygodactylus bradfieldi
Lygodactylus klugei
Lygodactylus conraui
100
97 Lygodactylus thomensis
78
Lygodactylus angularis
67
Lygodactylus gutturalis
Lygodactylus chobiensis
94
Lygodactylus williamsi
94 Lygodactylus picturatus
68 100 Lygodactylus luteopicturatus
97 Lygodactylus kimhowelli
93 Lygodactylus keniensis
92
Phelsuma vanheygeni
100
Phelsuma astriata
100 Phelsuma sundbergi
Phelsuma guttata
Phelsuma madagascariensis
100 Phelsuma abbotti
10087 Phelsuma parkeri
Phelsuma seippi
Phelsuma barbouri
100
96
100 Phelsuma pronki
Phelsuma breviceps
85
Phelsuma mutabilis
92
Phelsuma andamanense
82
Phelsuma standingi
Phelsuma edwardnewtoni
94 Phelsuma gigas
99 99
Phelsuma guentheri
95
100
100
55 100
100
100
86
Lepidodactylus novaeguineae
Pseudogekko smaragdinus
100 100
Pseudogekko compressicorpus
93
Lepidodactylus orientalis
83
100 Luperosaurus macgregori
100
Luperosaurus cumingii
98
99
79
Luperosaurus joloensis
73
100
Lepidodactylus lugubris
91
100
Lepidodactylus moestus
100 100
100 Gekko smithii
85
Gekko gecko
99
100
Gekko chinensis
100
Gekko japonicus
92
Gekko hokouensis
99
100 95
61
Gekko auriverrucosus
98 100
54
Gekko swinhonis
Gekko athymus
100 Gekko monarchus
100
100
Gekko mindorensis
98
100
99
Gekko romblon
Gekko crombota
80
(ii) 65
100 Gekko porosus
89
Ptychozoon rhacophorus
53
100
Ptychozoon kuhli
64
87
95
Ptychozoon lionotum
92
Luperosaurus iskandari
100
97
Gekko vittatus
100
94
Gekko petricolus
Gekko badenii
85 100
96
Gekko grossmanni
50 100
Dixonius melanostictus
100 Dixonius vietnamensis
100
100
100 Dixonius siamensis
77 100
100 Heteronotia planiceps
100
100
Heteronotia binoei
100
Heteronotia spelea
56
Nactus acutus
97
Nactus eboracensis
100
Nactus vankampeni
100
100
83 100 Nactus galgajuga
52
Nactus cheverti
100
98 100 Nactus multicarinatus
Nactus pelagicus
79
Hemiphyllodactylus typus
100
99
100
Hemiphyllodactylus yunnanensis
93
100
85
Hemiphyllodactylus aurantiacus
100 Gehyra fehlmanni
100
Gehyra mutilata
100
99
97
Gehyra lacerata
100
Gehyra brevipalmata
100 Gehyra baliola
100
Gehyra barea
99
84
59 Gehyra marginata
100
91
Gehyra oceanica
98
98
96
Gehyra membranacruralis
86
100 Gehyra dubia
Gehyra catenata
100
Gehyra pamela
100
55
Gehyra borroloola
97 Gehyra robusta
70 Gehyra koira
100 Gehyra occidentalis
Gehyra australis
Gehyra xenopus
Gehyra nana
98
Gehyra purpurascens
98 100 Gehyra variegata
Gehyra punctata
Gehyra pilbara
98
Gehyra montium
92 Gehyra minuta
Alsophylax pipiens
Tropiocolotes helenae
65 100
Cnemaspis limi
Cnemaspis kendallii
100
Mediodactylus spinicaudum
98
Mediodactylus russowii
Pseudoceramodactylus khobarensis
Tropiocolotes tripolitanus
96
Stenodactylus arabicus
92
Stenodactylus petrii
100
Stenodactylus leptocosymbotus
96
100 Stenodactylus doriae
Stenodactylus yemenensis
100
85
Stenodactylus sthenodactylus
Mediodactylus kotschyi
Mediodactylus sagittiferum
99
69
Mediodactylus heterocercum
99 Mediodactylus heteropholis
75
100
Bunopus tuberculatus
Crossobamon orientalis
86
Bunopus crassicauda
95
Agamura persica
Cyrtopodion sistanensis
99
Cyrtopodion scabrum
Cyrtopodion longipes
79 100 Cyrtopodion caspium
Cyrtopodion agamuroides
99 Cyrtopodion gastrophole
Cyrtodactylus oldhami
100 87
Cyrtodactylus ayeyarwadyensis
100
Cyrtodactylus angularis
Cyrtodactylus jarujini
Cyrtodactylus triedrus
88
Cyrtodactylus marmoratus
92
99
Cyrtodactylus irregularis
100
Cyrtodactylus consobrinus
52
Cyrtodactylus annulatus
Cyrtodactylus philippinicus
92
97
98 Cyrtodactylus agusanensis
Cyrtodactylus intermedius
Cyrtodactylus pulchellus
79
Cyrtodactylus sermowaiensis
94
Cyrtodactylus loriae
77
Cyrtodactylus novaeguineae
96 Cyrtodactylus tuberculatus
98
97
Cyrtodactylus klugei
Cyrtodactylus robustus
98 Cyrtodactylus tripartitus
98 Cyrtodactylus epiroticus
99 Cyrtodactylus louisiadensis
100
Hemidactylus bowringii
100
Hemidactylus garnotii
Hemidactylus karenorum
Hemidactylus platyurus
Hemidactylus fasciatus
100
Hemidactylus aaronbaueri
81 93
Hemidactylus giganteus
Hemidactylus depressus
Hemidactylus triedrus
89
Hemidactylus prashadi
100
8876
93
Hemidactylus maculatus
100
Hemidactylus leschenaultii
Hemidactylus flaviviridis
Hemidactylus frenatus
Hemidactylus brookii
100
Hemidactylus sataraensis
100
Hemidactylus imbricatus
99 Hemidactylus albofasciatus
56
Hemidactylus reticulatus
97
Hemidactylus gracilis
Hemidactylus angulatus
100 Hemidactylus haitianus
57
Hemidactylus mabouia
100 Hemidactylus mercatorius
Hemidactylus longicephalus
100
Hemidactylus platycephalus
97 Hemidactylus greeffii
100
Hemidactylus brasilianus
96
Hemidactylus bouvieri
99
95
Hemidactylus palaichthus
97
Hemidactylus agrius
96
Hemidactylus modestus
98
Hemidactylus citernii
Hemidactylus foudaii
98
97
91
91
82
96
66
99
97
Hemidactylus pumilio
Hemidactylus dracaenacolus
100 Hemidactylus granti
Hemidactylus persicus
Hemidactylus yerburii
Hemidactylus robustus
Hemidactylus turcicus
Hemidactylus lemurinus
Hemidactylus mindiae
Hemidactylus macropholis
Hemidactylus oxyrhinus
Hemidactylus forbesii
98 Hemidactylus homoeolepis
100
98
94
95
99
95
99 96
87
99
1005794
Phelsuma borbonica
Phelsuma cepediana
Phelsuma guimbeaui
Phelsuma ornata
Phelsuma inexpectata
Phelsuma nigristriata
Phelsuma modesta
Phelsuma dubia
Phelsuma ravenala
Phelsuma flavigularis
Phelsuma hielscheri
Phelsuma berghofi
Phelsuma malamakibo
Phelsuma serraticauda
Phelsuma laticauda
Phelsuma robertmertensi
Phelsuma klemmeri
Phelsuma antanosy
Phelsuma quadriocellata
Phelsuma pusilla
Phelsuma comorensis
Phelsuma lineata
Phelsuma kely

D
Figure 5
99
Xantusiidae
Cricosaurinae 100
Cricosaura typica
Xantusia gracilis
100
Xantusiinae 100
100
84 97
92
Xantusia henshawi
Xantusia bolsonae
Xantusia sanchezi
Xantusia riversiana
Xantusia arizonae
Xantusia vigilis
100
100
66
Xantusia bezyi
Xantusia wigginsi
Lepidophyma mayae
100
Lepidophyminae
100
100
100
Lepidophyma tuxtlae
Lepidophyma lipetzi
Lepidophyma flavimaculatum
Lepidophyma reticulatum
Lepidophyma pajapanensis
94
87
95
100
Lepidophyma occulor
Lepidophyma micropholis
Lepidophyma sylvaticum
Lepidophyma gaigeae
Lepidophyma lineri
Lepidophyma smithii
Gerrhosaurinae 100
95
95 Lepidophyma cuicateca
94 Lepidophyma lowei
100100 Lepidophyma radula
Lepidophyma dontomasi
Gerrhosaurus major
Cordylosaurus subtessellatus
Tetradactylus seps
98
69
Tetradactylus africanus
Tetradactylus tetradactylus
Gerrhosaurus validus
79
Gerrhosaurus skoogi
Gerrhosaurus typicus
100 91
100
Gerrhosaurus nigrolineatus
100 Gerrhosaurus multilineatus
76 Gerrhosaurus flavigularis
Tracheloptychus madagascariensis
100
Zonosaurinae
Tracheloptychus petersi
100 Zonosaurus haraldmeieri
Zonosaurus madagascariensis
Zonosaurus ornatus
100 Zonosaurus trilineatus
100
91
96
Zonosaurus quadrilineatus
Zonosaurus karsteni
100 Zonosaurus anelanelany
100 Zonosaurus laticaudatus
Zonosaurus boettgeri
Gerrhosauridae
Platysaurinae
92
100
Cordylidae
100
Cordylinae
55
95
91
96
94
99
100
99
66 73
82
89
87
100
93
100
100
99
86
100
95
99
81 88
82
83
92
100
100
85
86 100
Zonosaurus tsingy
Zonosaurus brygooi
Zonosaurus subunicolor
Zonosaurus bemaraha
Zonosaurus aeneus
Zonosaurus rufipes
Platysaurus pungweensis
100
Platysaurus mitchelli
Platysaurus broadleyi
Platysaurus capensis
Platysaurus intermedius
Platysaurus minor
Platysaurus monotropis
Ouroborus cataphractus
Karusasaurus jordani
Karusasaurus polyzonus
Namazonurus campbelli
Namazonurus pustulatus
Namazonurus namaquensis
Namazonurus lawrenci
Namazonurus peersi
Smaug warreni
Smaug giganteus
Chamaesaura aenea
Chamaesaura anguina
Pseudocordylus langi
Pseudocordylus microlepidotus
83
100
84
Pseudocordylus spinosus
Pseudocordylus melanotus
Ninurta coeruleopunctatus
Hemicordylus nebulosus
Hemicordylus capensis
Cordylus tropidosternum
Cordylus meculae
Cordylus vittifer
Cordylus ukingensis
Cordylus beraduccii
Cordylus jonesii
Cordylus rhodesianus
Cordylus macropholis
Cordylus imkeae
Cordylus aridus
Cordylus minor
Cordylus niger
Cordylus mclachlani
Cordylus oelofseni
Cordylus tasmani
Cordylus cordylus

E
Figure 6
Scincidae
100
Typhlosaurus braini
Typhlosaurus meyeri
Typhlosaurus caecus
Typhlosaurus vermis
Typhlosaurus lomiae
Acontias gariepensis
Acontias lineatus
Acontias litoralis
Acontias kgalagadi
Acontias meleagris
Acontias percivali
Acontias rieppeli
Acontias breviceps
Acontias gracilicauda
Acontias plumbeus
Acontias poecilus
Mesoscincus schwartzei
Mesoscincus managuae
Ophiomorus punctatissimus
Ophiomorus latastii
Brachymeles apus
Brachymeles miriamae
Brachymeles tridactylus
Brachymeles bonitae
Brachymeles minimus
Brachymeles cebuensis
Brachymeles samarensis
Brachymeles talinis
Brachymeles elerae
Brachymeles schadenbergi
Brachymeles boulengeri
Brachymeles bicolor
Brachymeles gracilis
Brachymeles pathfinderi
Plestiodon tamdaoensis
Plestiodon kishinouyei
Plestiodon chinensis
Plestiodon quadrilineatus
Plestiodon tunganus
Plestiodon capito
Plestiodon barbouri
Plestiodon japonicus
Plestiodon latiscutatus
Plestiodon elegans
Plestiodon marginatus
Plestiodon stimpsonii
Plestiodon reynoldsi
Plestiodon egregius
Plestiodon anthracinus
Plestiodon inexpectatus
97
Plestiodon laticeps
Plestiodon tetragrammus
Plestiodon callicephalus
Plestiodon obsoletus
Plestiodon fasciatus
Plestiodon multivirgatus
Plestiodon septentrionalis
Plestiodon longirostris
Plestiodon gilberti
Plestiodon lagunensis
Plestiodon skiltonianus
Plestiodon parviauriculatus
Plestiodon sumichrasti
Plestiodon lynxe
Plestiodon ochoterenae
Plestiodon parvulus
Plestiodon copei
Plestiodon brevirostris
Plestiodon dugesii
Eurylepis taeniolatus
Eumeces schneideri
Scincopus fasciatus
Eumeces algeriensis
Scincus scincus
Scincus mitranus
Pamelaescincus gardineri
Janetaescincus veseyfitzgeraldi
Janetaescincus braueri
Gongylomorphus bojerii
81
Chalcides mauritanicus
Chalcides minutus
Chalcides guentheri
Chalcides chalcides
Chalcides pseudostriatus
Chalcides striatus
Chalcides ocellatus
Chalcides sepsoides
Chalcides colosii
100
Chalcides bedriagai
Chalcides boulengeri
Chalcides parallelus
Chalcides lanzai
Chalcides sexlineatus
Chalcides coeruleopunctatus
Chalcides viridanus
Chalcides sphenopsiformis
Chalcides mionecton
Chalcides manueli
Chalcides polylepis
Chalcides montanus
Sepsina angolensis
97
Typhlacontias brevipes
Typhlacontias punctatissimus
Feylinia grandisquamis
Feylinia polylepis
93
Feylinia currori
Melanoseps occidentalis
Melanoseps ater
Melanoseps loveridgei
Hakaria simonyi
Proscelotes eggeli
Scelotes caffer
100
Scelotes anguineus
Scelotes mirus
99
Scelotes arenicolus
Scelotes bipes
100 Scelotes sexlineatus
Scelotes gronovii
Scelotes montispectus
92
Scelotes kasneri
100
Paracontias holomelas
Paracontias brocchii
Paracontias manify
100 60
69
Paracontias hildebrandti
Paracontias rothschildi
Madascincus melanopleura
89
Pseudoacontias menamainty
52
Madascincus igneocaudatus
97 Madascincus mouroundavae
64 Madascincus nanus
100 Madascincus stumpffi
100
Madascincus polleni
87 Madascincus intermedius
100 Amphiglossus melanurus
90
Amphiglossus ornaticeps
100 Amphiglossus mandokava
Amphiglossus tanysoma
100
Pygomeles braconnieri
100
Androngo trivittatus
93
Amphiglossus tsaratananensis
85
Amphiglossus reticulatus
86 Amphiglossus astrolabi
93
Voeltzkowia fierinensis
100
Voeltzkowia lineata
95 Voeltzkowia rubrocaudata
24
Amphiglossus splendidus
80
Amphiglossus anosyensis
7090
Amphiglossus macrocercus
Amphiglossus punctatus
96 Amphiglossus frontoparietalis
97
89
95
Acontiinae 99
100 100
100
96
94
98
98
92
100
98
91
99
100
99
94 94
95
83
88
85
85
73
85
100
100
98
100
100 86
70
97
93
100
97 100
88
74
56
Scincinae
100
74
7671
100
98 86
92
100
100 91
73 73
76
98
77
100
100 100
99
100
55 92
57
100
8675
94
74
100
91
74
88
87
99
98
99
100
94
95
96
97
100
100
100
96
98
96
100
80
89
87
75
94
F-I

F
Figure 7
Lygosominae
Lygosominae
cont.
H-I G
100
Ateuchosaurus pellopleurus
Asymblepharus alaicus
Ablepharus pannonicus
81
Sphenomorphus praesignis
Sphenomorphus simus
98 60
100
Tropidophorus berdmorei
Tropidophorus matsuii
Tropidophorus latiscutatus
99
90 Tropidophorus noggei
Tropidophorus murphyi
89 100
98
Tropidophorus hainanus
Tropidophorus baviensis
Tropidophorus sinicus
98
Tropidophorus robinsoni
Tropidophorus thai
89
83
Tropidophorus cocincinensis
Tropidophorus microlepis
97
100
95
94
Tropidophorus grayi
Tropidophorus baconi
Tropidophorus beccarii
Tropidophorus brookei
100 Tropidophorus partelloi
95 Tropidophorus misaminius
86
Lipinia vittigera
Isopachys anguinoides
77
98
Sphenomorphus melanopogon
Sphenomorphus jobiensis
Sphenomorphus muelleri
Tytthoscincus aesculeticola
100
Tytthoscincus parvus
94
99
95
100 Tytthoscincus hallieri
92 Tytthoscincus atrigularis
Sphenomorphus concinnatus
100 Sphenomorphus scutatus
Sphenomorphus solomonis
100 Sphenomorphus fasciatus
90
100
87
76
Sphenomorphus leptofasciatus
Sphenomorphus cranei
Sphenomorphus maindroni
93
Otosaurus cumingi
100
Pinoyscincus mindanensis
96
100
80
76
99
91
100
99
89
65
98
100
100
100
99
97
99
68
83
96
93
54
100
94 100
100
100
80
Pinoyscincus jagori
Pinoyscincus coxi
Pinoyscincus abdictus
Pinoyscincus llanosi
Sphenomorphus diwata
Sphenomorphus acutus
Parvoscincus steerei
Parvoscincus decipiens
Parvoscincus leucospilos
Parvoscincus tagapayo
100
Parvoscincus sisoni
Parvoscincus beyeri
100
Parvoscincus laterimaculatus
Parvoscincus luzonense
Parvoscincus kitangladensis
Parvoscincus lawtoni
Larutia seribuatensis
Sphenomorphus maculatus
Sphenomorphus indicus
Sphenomorphus multisquamatus
Sphenomorphus variegatus
Sphenomorphus cyanolaemus
100 Sphenomorphus sabanus
Scincella reevesii
Asymblepharus sikimmensis
Scincella lateralis
Scincella gemmingeri
Scincella cherriei
99
Scincella assatus
Sphenomorphus buenloicus
Prasinohaema virens
Insulasaurus arborens
Insulasaurus wrighti
Insulasaurus victoria
Lipinia pulchella
Lipinia noctua
Papuascincus stanleyanus

G
Figure 8
Lygosominae
cont. 100
97
95
80
70
55
Eulamprus frerei
Nangura spinosa
Calyptotis lepidorostrum
Calyptotis scutirostrum
100
77
Calyptotis ruficauda
98
Gnypetoscincus queenslandiae
Eulamprus amplus
Eulamprus tenuis
78
Eulamprus tigrinus
96
Eulamprus martini
88
100 Eulamprus sokosoma
Eulamprus brachyosoma
Eulamprus luteilateralis
85
Eulamprus tryoni
83
Eulamprus murrayi
77
Coggeria naufragus
91
Coeranoscincus frontalis
Ophioscincus ophioscincus
95
Saiphos equalis
95
Coeranoscincus reticulatus
Ophioscincus truncatus
Anomalopus swansoni
Anomalopus mackayi
100
Anomalopus verreauxi
100
Anomalopus leuckartii
Eremiascincus fasciolatus
Eremiascincus pardalis
100
Eremiascincus richardsonii
97
91
Eremiascincus douglasi
62
88
Eremiascincus isolepis
100
Hemiergis initialis
100 Hemiergis peronii
100
Hemiergis quadrilineatum
Hemiergis gracilipes
82
Hemiergis millewae
60
Hemiergis decresiensis
Glaphyromorphus punctulatus
Glaphyromorphus mjobergi
95
Glaphyromorphus fuscicaudis
93
Glaphyromorphus pumilus
99
Glaphyromorphus cracens
78
Glaphyromorphus darwiniensis
Eulamprus quoyii
93
100
Eulamprus leuraensis
Eulamprus kosciuskoi
82
Eulamprus heatwolei
87
Eulamprus tympanum
Notoscincus ornatus
Ctenotus labillardieri
76
99
Ctenotus brooksi
Ctenotus rubicundus
Ctenotus nasutus
100 Ctenotus pantherinus
95
Ctenotus strauchii
Ctenotus youngsoni
81
Ctenotus schomburgkii
85
Ctenotus calurus
84
Ctenotus rawlinsoni
Ctenotus fallens
Ctenotus saxatilis
67
85
Ctenotus inornatus
Ctenotus spaldingi
99 Ctenotus robustus
76
Ctenotus taeniolatus
89
Ctenotus rutilans
Ctenotus uber
Ctenotus australis
95 88
Ctenotus leae
Ctenotus leonhardii
100 Ctenotus quattuordecimlineatus
Ctenotus serventyi
100 Ctenotus greeri
83
Ctenotus tanamiensis
86
Ctenotus mimetes
88
Ctenotus astarte
7363
Ctenotus septenarius
Ctenotus regius
Ctenotus olympicus
97
Ctenotus maryani
66
Ctenotus atlas
90
Ctenotus grandis
51
Ctenotus angusticeps
79
Ctenotus hanloni
Ctenotus piankai
85
92
Ctenotus essingtonii
78
Ctenotus hebetior
Ctenotus hilli
91 Ctenotus gagudju
65
Ctenotus pulchellus
95
Lerista stylis
Lerista karlschmidti
81
Lerista carpentariae
100
Lerista ameles
99
Lerista cinerea
98
97
Lerista wilkinsi
Lerista kalumburu
91
Lerista apoda
100
Lerista griffini
Lerista ips
88
Lerista bipes
99
Lerista labialis
93
Lerista greeri
98
Lerista robusta
90
100 Lerista vermicularis
Lerista simillima
99
Lerista walkeri
96
Lerista borealis
Lerista frosti
97
89
Lerista fragilis
Lerista chordae
Lerista xanthura
99
90
100
Lerista aericeps
Lerista taeniata
100
100
Lerista orientalis
100
Lerista ingrami
Lerista zonulata
100 87
Lerista neander
Lerista puncticauda
100 Lerista desertorum
99
79 Lerista eupoda
Lerista gerrardii
100 Lerista axillaris
93 Lerista macropisthopus
Lerista microtis
100
Lerista arenicola
Lerista edwardsae
Lerista baynesi
100
Lerista picturata
Lerista flammicauda
85
100
Lerista zietzi
61
Lerista speciosa
100
Lerista elongata
100 Lerista tridactyla
Lerista terdigitata
82
99
90
Lerista dorsalis
Lerista punctatovittata
Lerista emmotti
100
100
Lerista elegans
90
Lerista distinguenda
87
Lerista christinae
Lerista lineata
92
Lerista planiventralis
93
Lerista stictopleura
90
Lerista allochira
89
Lerista haroldi
96
Lerista muelleri
Lerista viduata
93 100
93
89
98
100
84
100
100
56
81 77
100
96
Lerista bougainvillii
Lerista praepedita
Lerista humphriesi
Lerista petersoni
Lerista gascoynensis
Lerista nichollsi
Lerista kendricki
Lerista yuna
100
Lerista lineopunctulata
Lerista varia
Lerista connivens
Lerista uniduo
Lerista onsloviana
Lerista kennedyensis

H
Figure 9
Lygosominae
cont.
100 Tribolonotus novaeguineae
100
Tribolonotus gracilis
Tribolonotus blanchardi
Tribolonotus schmidti
86
9793
Tribolonotus brongersmai
96 Tribolonotus ponceleti
93
Tribolonotus pseudoponceleti
Corucia zebrata
Egernia saxatilis
86 Bellatorias major
77
Egernia depressa
Egernia kingii
Bellatorias frerei
100 74
90 Egernia richardi
Egernia napoleonis
Lissolepis luctuosa
73 Egernia stokesii
Egernia hosmeri
96 66 Cyclodomorphus michaeli
Cyclodomorphus casuarinae
97
Cyclodomorphus branchialis
81
Tiliqua adelaidensis
95
Tiliqua rugosa
84 Tiliqua occipitalis
71
Tiliqua nigrolutea
Tiliqua gigas
91
100 Tiliqua scincoides
88 Liopholis striata
Liopholis inornata
98
Liopholis multiscutata
90 Liopholis kintorei
85
Liopholis pulchra
99 73
Liopholis modesta
Liopholis margaretae
56 Liopholis whitii
52 Liopholis guthega
90
Liopholis montana
94
Ristella rurkii
Lankascincus fallax
Eutropis longicaudata
95 96
Eutropis macularia
Eutropis rudis
88
Eutropis macrophthalma
Eutropis multifasciata
83 90
100 Eutropis cumingi
Eutropis multicarinata
73
Eutropis clivicola
97
Eutropis bibronii
96 100 Eutropis beddomii
Eutropis nagarjuni
97
80 Eutropis trivittata
97
Dasia vittata
Dasia grisea
91
99
87
98
93
92
83
84
90
99
90
54
74
100
99
78
89
95
98
98
100
98
78
97
89
81
100
70
80
Dasia olivacea
Trachylepis aurata
Trachylepis vittata
Trachylepis brevicollis
Trachylepis socotrana
Trachylepis maculilabris
Trachylepis wrightii
Trachylepis sechellensis
Trachylepis affinis
Trachylepis perrotetii
Trachylepis quinquetaeniata
Trachylepis margaritifera
Trachylepis atlantica
Trachylepis varia
Trachylepis capensis
100
100
99
100 95
91
96
95
77 80
97 95
100
Trachylepis occidentalis
Trachylepis spilogaster
100 Trachylepis striata
Trachylepis hoeschi
Trachylepis variegata
Trachylepis sulcata
Trachylepis homalocephala
Trachylepis acutilabris
Trachylepis gravenhorstii
Trachylepis elegans
Trachylepis madagascariensis
Trachylepis boettgeri
Trachylepis vato
Trachylepis aureopunctata
Trachylepis dumasi
Eumecia anchietae
Chioninia vaillantii
Chioninia delalandii
Chioninia coctei
Chioninia spinalis
Chioninia fogoensis
Chioninia stangeri
Mabuya carvalhoi
Mabuya croizati
Mabuya nigropalmata
Mabuya sloanii
Mabuya altamazonica
Mabuya nigropunctata
Mabuya cochabambae
Mabuya dorsivittata
Mabuya meridensis
100
Mabuya mabouya
Mabuya unimarginata
Mabuya falconensis
Mabuya bistriata
Mabuya frenata
Mabuya agmosticha
Mabuya macrorhyncha
Mabuya guaporicola
Mabuya agilis
100 Mabuya caissara
99 Mabuya heathi
100
100

I
Figure 10
Lygosominae
cont.
90
100
63
60
Ablepharus budaki
Ablepharus chernovi
Ablepharus kitaibelii
Sphenomorphus stellatus
Emoia concolor
96 Emoia tongana
Lamprolepis smaragdina
Lygosoma quadrupes
98
Lygosoma koratense
Lygosoma albopunctata
95
Lepidothyris fernandi
93
Lygosoma lineolatum
92
Mochlus afer
100 Lygosoma sundevalli
Lygosoma punctata
Mochlus brevicaudis
76
70
Lygosoma bowringii
Eugongylus rufescens
100
Eugongylus albofasciolatus
Emoia loyaltiensis
Leiolopisma telfairii
75
100 Leiolopisma mauritiana
Panaspis breviceps
100
Panaspis togoensis
Afroablepharus wahlbergi
84
99
99
Afroablepharus annobonensis
85
Afroablepharus africanus
90
Lacertaspis reichenowi
85
Lacertaspis rohdei
93
Lacertaspis chriswildi
91 Lacertaspis gemmiventris
96
Lacertaspis lepesmei
100
Leptosiaphos hackarsi
95 Leptosiaphos graueri
Leptosiaphos amieti
81
95
Leptosiaphos kilimensis
100
99 Leptosiaphos vigintiserierum
Pseudemoia pagenstecheri
80
99
Bassiana duperreyi
Pseudemoia entrecasteauxii
Oligosoma lichenigera
Oligosoma suteri
Oligosoma pikitanga
100 99 95 Oligosoma taumakae
Oligosoma acrinasum
98
Oligosoma infrapunctatum
100 Oligosoma waimatense
86 91
Oligosoma otagense
98 100 Oligosoma chloronoton
61
Oligosoma lineoocellatum
99 Oligosoma longipes
99
Oligosoma nigriplantare
98 Oligosoma grande
Oligosoma stenotis
Oligosoma maccanni
100
90 85
100
98
Oligosoma inconspicuum
Oligosoma notosaurus
Oligosoma zelandicum
100 Oligosoma homalonotum
100 Oligosoma striatum
100 Oligosoma smithi
Oligosoma microlepis
94 93
Oligosoma aeneum
99
99 Oligosoma levidensum
Oligosoma hardyi
57
Oligosoma fallai
Oligosoma alani
98
63
Oligosoma moco
93 Oligosoma macgregori
Oligosoma ornatum
Oligosoma townsi
89 Oligosoma oliveri
9796 Oligosoma whitakeri
98 Nannoscincus garrulus
98
Nannoscincus slevini
89 Nannoscincus gracilis
Nannoscincus mariei
82
Nannoscincus greeri
94 Nannoscincus hanchisteus
93
Nannoscincus humectus
Marmorosphax montana
90 100
Marmorosphax tricolor
96
100
Celatiscincus similis
Celatiscincus euryotis
96
Lioscincus vivae
96 Lioscincus steindachneri
Kanakysaurus viviparus
84
Lioscincus nigrofasciolatum
80
96 80
Lacertoides pardalis
Phoboscincus garnieri
Sigaloseps ruficauda
100
Sigaloseps deplanchei
85
Lioscincus novaecaledoniae
85
Lioscincus maruia
98 92
Tropidoscincus aubrianus
Lioscincus tillieri
100
Tropidoscincus boreus
100 Tropidoscincus variabilis
87
Graciliscincus shonae
Simiscincus aurantiacus
97
Caledoniscincus orestes
100 Caledoniscincus renevieri
95
Caledoniscincus auratus
95 Caledoniscincus festivus
83
Caledoniscincus austrocaledonicus
97
Caledoniscincus haplorhinus
53
Caledoniscincus atropunctatus
Caledoniscincus chazeaui
87 98
95
Caledoniscincus aquilonius
Caledoniscincus terma
100 Cryptoblepharus nigropunctatus
Cryptoblepharus boutonii
93
Cryptoblepharus novocaledonicus
93 79
Menetia greyii
Menetia alanae
Emoia schmidti
100
91
Emoia cyanogaster
Emoia caeruleocauda
98
Emoia atrocostata
100
100
Emoia jakati
Emoia physicae
77
Emoia impar
Emoia cyanura
98 71 98
52
Emoia pseudocyanura
Emoia isolata
Bassiana trilineata
73
Morethia ruficauda
Morethia butleri
Morethia adelaidensis
Bartleia jigurru
Saproscincus basiliscus
96
Saproscincus lewisi
72 96
Saproscincus czechurai
79
98
Saproscincus tetradactylus
Saproscincus hannahae
76
100 Saproscincus oriarus
Saproscincus mustelinus
71
Saproscincus challengeri
Saproscincus rosei
100
100 97
Saproscincus spectabilis
Lampropholis guichenoti
92
Lampropholis delicata
100
Lampropholis coggeri
Lampropholis robertsi
Proablepharus reginae
Niveoscincus greeni
72
Niveoscincus ocellatus
76
Niveoscincus pretiosus
100 Niveoscincus metallicus
87
Cautula zia
96
Liburnascincus coensis
Liburnascincus scirtetis
88
91
Liburnascincus mundivensis
Menetia timlowi
100
98
Carlia triacantha
Carlia johnstonei
Carlia jarnoldae
90
Carlia bicarinata
Carlia gracilis
79
75
Lygisaurus sesbrauna
Lygisaurus parrhasius
88
Lygisaurus macfarlani
98 99 Lygisaurus novaeguineae
Lygisaurus aeratus
85
Lygisaurus laevis
100 100
Lygisaurus foliorum
78
68
Lygisaurus abscondita
89
100 Lygisaurus tanneri
Lygisaurus malleolus
91
Carlia schmeltzii
Carlia storri
98
Carlia fusca
100
Carlia longipes
Carlia mysi
80 93
73
Carlia munda
Carlia pectoralis
Carlia rufilatus
85 100 Carlia rhomboidalis
Carlia rubrigularis
92
Carlia tetradactyla
Carlia amax
76 Carlia rostralis
53 Carlia dogare
62
Carlia vivax

J
Figure 11
Tupinambinae
Teiidae
100
Gymnophthalmidae
98
54
100
Teiinae
100
84
Callopistes flavipunctatus
Callopistes maculatus
Tupinambis rufescens
Tupinambis merianae
Tupinambis duseni
Tupinambis quadrilineatus
Tupinambis longilineus
Tupinambis teguixin
Crocodilurus amazonicus
Dracaena guianensis
Teius teyou
Ameiva ameiva
Ameiva bifrontata
100
Cnemidophorus ocellifer
Kentropyx calcarata
Kentropyx striata
Kentropyx altamazonica
Kentropyx pelviceps
56
Kentropyx paulensis
Kentropyx vanzoi
Kentropyx viridistriga
Ameiva undulata
Ameiva quadrilineata
93
Ameiva festiva
Cnemidophorus vanzoi
Cnemidophorus gramivagus
Cnemidophorus lemniscatus
Cnemidophorus arenivagus
Aspidoscelis inornata
Aspidoscelis sexlineata
99 Aspidoscelis burti
Aspidoscelis communis
98
93 Aspidoscelis costata
99
Aspidoscelis gularis
Aspidoscelis laredoensis
Aspidoscelis velox
98 Aspidoscelis deppei
Aspidoscelis guttata
Aspidoscelis lineattissima
84
100
Aspidoscelis marmorata
92
Aspidoscelis tigris
Aspidoscelis hyperythra
98 Aspidoscelis ceralbensis
Ameiva auberi
100 Ameiva dorsalis
Ameiva polops
86
Ameiva exsul
99
Ameiva wetmorei
97 Ameiva leberi
59 100 Ameiva chrysolaema
96 Ameiva taeniura
95
100 Ameiva lineolata
Ameiva maynardi
100 Ameiva plei
Ameiva corax
98 Ameiva pluvianotata
100 Ameiva griswoldi
93 Ameiva erythrocephala
94 Ameiva fuscata
55
Dicrodon guttulatum
85
Cnemidophorus longicaudus
97
Cnemidophorus lacertoides
Ptychoglossus brevifrontalis
100
Alopoglossus atriventris
99
100
Alopoglossus copii
Alopoglossus angulatus
99
97
100
97
98
8766
91
99
82
71
100
91
96
97
100
99
94
100
81
83
Alopoglossinae
Ecpleopinae
99
99
100 77
100
100
80
97
Cercosaurinae
Bachiinae
Gymnophthalminae
100
98
100
100
100
99
100
88
93
91
72
50
65
100
Rhachisaurinae
100 98 97
93
91
94
97
55
100
96
86
98
61
Ecpleopus gaudichaudii
Leposoma nanodactylus
Leposoma baturitensis
Leposoma puk
Leposoma scincoides
Leposoma annectans
Colobosauroides cearensis
Anotosaura collaris
Riama unicolor
Riama colomaromani
Riama simoterus
Neusticurus rudis
Neusticurus bicarinatus
Placosoma cordylinum
Placosoma glabellum
Pholidobolus montium
Pholidobolus macbrydei
Cercosaura ocellata
Cercosaura schreibersii
Cercosaura eigenmanni
Proctoporus sucullucu
Proctoporus subsolanus
Proctoporus pachyurus
Bachia flavescens
Bachia bresslaui
Bachia dorbignyi
Bachia huallagana
Bachia scolecoides
Bachia trisanale
Bachia panoplia
97 95 100
Potamites ecpleopus
Potamites juruazensis
Cercosaura quadrilineata
100 Cercosaura oshaughnessyi
Cercosaura argulus
Proctoporus guentheri
Proctoporus unsaacae
Proctoporus bolivianus
Petracola ventrimaculatus
Bachia peruana
Bachia bicolor
Bachia barbouri
Bachia intermedia
Bachia heteropa
Rhachisaurus brachylepis
Heterodactylus imbricatus
Colobodactylus dalcyanus
Colobodactylus taunayi
Iphisa elegans
98
100
92
98
98
88
100
99
94 99
100
100
100
82
100
78
74
98
100
100
95
96
Colobosaura modesta
Stenolepis ridleyi
Acratosaura mentalis
Tretioscincus agilis
Tretioscincus oriximinensis
Micrablepharus atticolus
Micrablepharus maximiliani
Vanzosaura rubricauda
Procellosaurinus erythrocercus
Procellosaurinus tetradactylus
Nothobachia ablephara
Calyptommatus sinebrachiatus
Calyptommatus confusionibus
93 Calyptommatus leiolepis
86 Calyptommatus nicterus
Arthrosaura reticulata
Arthrosaura kockii
Leposoma percarinatum
Leposoma osvaldoi
Leposoma parietale
Leposoma southi
Leposoma guianense
Psilophthalmus paeminosus
Gymnophthalmus pleei
Gymnophthalmus leucomystax
Gymnophthalmus vanzoi
100
Gymnophthalmus speciosus
87
100
Gymnophthalmus underwoodi
Gymnophthalmus cryptus

K
Figure 12
99
100
84
100
Rhineura floridana
100
91
Amphisbaenidae
86
100
73
100
100
97
89
95
90
92
87
Bipes biporus
Bipes canaliculatus
Blanus strauchi
Blanus cinereus
Blanus mettetali
Blanus tingitanus
Cadea blanoides
55
81
Bipes tridactylus
Diplometopon zarudnyi
Trogonophis wiegmanni
Geocalamus acutus
Monopeltis capensis
Amphisbaena brasiliana
Amphisbaena fuliginosa
Amphisbaena cunhai
Amphisbaena mertensii
Amphisbaena hyporissor
Amphisbaena innocens
Amphisbaena leali
91 Amphisbaena ignatiana
Amphisbaena saxosa
100
Amphisbaena kraoh
100
100 Amphisbaena roberti
Amphisbaena vermicularis
98 Amphisbaena alba
Amphisbaena camura
Amphisbaena bolivica
Amphisbaena anomala
Amphisbaena polystegum
100
Amphisbaena microcephalum
100 Amphisbaena infraorbitale
90
Amphisbaena hastata
100
Amphisbaena cuiabana
78 Amphisbaena kingii
100
Amphisbaena munoai
99
Amphisbaena darwini
93 Amphisbaena angustifrons
100
89
95
100
100
Amphisbaena leeseri
Amphisbaena silvestrii
Amphisbaena anaemariae
Amphisbaena barbouri
100
Amphisbaena cubana
97
100
95
96
67
Rhineuridae
100
Amphisbaena carlgansi
Amphisbaena schmidti
Amphisbaena manni
Amphisbaena fenestrata
Amphisbaena caeca
Amphisbaena bakeri
Amphisbaena xera
Bipedidae
Blanidae
Cadeidae
Trogonophiidae
Cynisca leucura
Chirindia swynnertoni

L
Figure 13
Lacertidae
Gallotiinae
100
Lacertinae
Psammodromus hispanicus
Psammodromus algirus
99
95
Psammodromus blanci
100
Gallotia stehlini
Gallotia atlantica
99
Gallotia galloti
95
Gallotia caesaris
Gallotia intermedia
68
Gallotia simonyi
100
97 Gallotia bravoana
Atlantolacerta andreanskyi
73
Poromera fordii
Nucras lalandii
Latastia longicaudata
96
99
Philochortus spinalis
Pseuderemias smithii
8890
100
Heliobolus lugubris
Heliobolus spekii
99 84
Australolacerta australis
54
Tropidosaura gularis
Ichnotropis capensis
Meroles reticulatus
Meroles knoxii
92
100
Meroles suborbitalis
Ichnotropis squamulosa
76
80
Meroles anchietae
97
100
Meroles ctenodactylus
97
Meroles micropholidotus
Meroles cuneirostris
Pedioplanis lineoocellata
Nucras tessellata
100
Pedioplanis laticeps
100
Pedioplanis burchelli
Pedioplanis breviceps
Pedioplanis namaquensis
96
Pedioplanis husabensis
100 69
Pedioplanis undata
76
Pedioplanis rubens
96
96 Pedioplanis inornata
Pedioplanis gaerdesi
100
56
Holaspis laevis
100
Holaspis guentheri
100
Gastropholis vittata
Gastropholis prasina
72
Adolfus africanus
96
89
99
Adolfus alleni
Adolfus jacksoni
Eremias brenchleyi
97
Eremias argus
Eremias vermiculata
76
Eremias velox
100
99
Eremias montanus
Eremias persica
Eremias nigrolateralis
95
Eremias arguta
Eremias przewalskii
93
93 100 Eremias multiocellata
56 Eremias pleskei
86
Eremias grammica
Congolacerta vauereselli
Omanosaura cyanura
98
Omanosaura jayakari
100
97
Mesalina simoni
Mesalina olivieri
Mesalina bahaeldini
100
91 Mesalina guttulata
Mesalina balfouri
89 93 Mesalina adramitana
63
Mesalina brevirostris
Mesalina rubropunctata
Ophisops occidentalis
100
Ophisops elegans
Acanthodactylus orientalis
100 Acanthodactylus tristrami
Acanthodactylus blanci
73
95
99 Acanthodactylus erythrurus
94
Acanthodactylus busacki
Acanthodactylus beershebensis
100
76
Acanthodactylus pardalis
100
86 Acanthodactylus maculatus
Acanthodactylus aureus
95
Acanthodactylus scutellatus
93 Acanthodactylus longipes
80
Acanthodactylus schmidti
99
Acanthodactylus cantoris
96
Acanthodactylus masirae
100
Acanthodactylus gongrorhynchatus
Acanthodactylus opheodurus
85
75
Acanthodactylus boskianus
99 Acanthodactylus schreiberi
100
Phoenicolacerta kulzeri
98
Phoenicolacerta laevis
Phoenicolacerta cyanisparsa
95
Zootoca vivipara
Takydromus kuehnei
100
Takydromus sexlineatus
Takydromus tachydromoides
100
Takydromus smaragdinus
95
Takydromus sauteri
85
Takydromus intermedius
100
100
Takydromus dorsalis
Takydromus sylvaticus
79
Takydromus amurensis
100
99 Takydromus hsuehshanensis
100
Takydromus formosanus
97 Takydromus wolteri
100
Takydromus toyamai
99 Takydromus septentrionalis
75 Takydromus stejnegeri
Timon princeps
94
Timon pater
99 98
Timon lepidus
69
Timon tangitanus
Lacerta viridis
58
100 100 Lacerta bilineata
80
Lacerta strigata
Lacerta schreiberi
Lacerta agilis
92
98
Lacerta media
99
Lacerta trilineata
Lacerta pamphylica
100
98
Teira dugesii
94
86
62
64
73
97
92
53
99
96
100
97
100
100
94 98
100
85
78
74
55
99 85
88
92
91 86
97
93
92 100
96
79
100
Scelarcis perspicillata
Podarcis melisellensis
Podarcis tauricus
Podarcis milensis
Podarcis gaigeae
Podarcis filfolensis
Podarcis tiliguerta
Podarcis muralis
Podarcis siculus
Podarcis pityusensis
Podarcis lilfordi
Podarcis raffoneae
Podarcis erhardii
Podarcis peloponnesiacus
Podarcis liolepis
Podarcis vaucheri
Podarcis hispanicus
Podarcis bocagei
Podarcis carbonelli
Dalmatolacerta oxycephala
Hellenolacerta graeca
Archaeolacerta bedriagae
100
99
95
Apathya cappadocica
Iberolacerta galani
Iberolacerta cyreni
Iberolacerta monticola
Iberolacerta horvathi
Iberolacerta aurelioi
Iberolacerta bonnali
Iberolacerta aranica
93
100
100 94
100
100
89
Parvilacerta fraasii
Parvilacerta parva
Anatololacerta anatolica
Anatololacerta oertzeni
Anatololacerta danfordi
Algyroides moreoticus
Algyroides nigropunctatus
Dinarolacerta mosorensis
Dinarolacerta montenegrina
Algyroides marchi
Algyroides fitzingeri
Iranolacerta brandtii
Iranolacerta zagrosica
Darevskia parvula
Darevskia rudis
Darevskia portschinskii
Darevskia valentini
Darevskia praticola
Darevskia chlorogaster
100
87
100
Darevskia alpina
Darevskia lindholmi
Darevskia brauneri
Darevskia saxicola
Darevskia rostombekovi
Darevskia raddei
97
Darevskia uzzelli
Darevskia sapphirina
93
Darevskia bendimahiensis
94
100
Darevskia armeniaca
Darevskia clarkorum
98 Darevskia mixta
7099 Darevskia daghestanica
Darevskia caucasica
90 Darevskia derjugini

M
Figure 14
Xenosauridae 100 Xenosaurus platyceps
Xenosaurus grandis
Helodermatidae Heloderma suspectum
100
100 Heloderma horridum
Anniellidae Anniella pulchra
100 Anniella geronimensis
95
Celestus enneagrammus
98
Diploglossus bilobatus
Diploglossus pleii
Ophiodes striatus
Diploglossinae
100
100
93
100 Celestus agasepsoides
Celestus haetianus
Ophisaurus ventralis
90 100 83 Ophisaurus koellikeri
Anguidae
Pseudopus apodus
99 Anguis fragilis
Anguinae
87 Ophisaurus attenuatus
Dopasia gracilis
100 Dopasia harti
100 100 Elgaria coerulea
Elgaria kingii
99 Elgaria paucicarinata
8584 Elgaria panamintina
100 Elgaria multicarinata
Gerrhonotus parvus
Gerrhonotinae 88
Coloptychon rhombifer
Gerrhonotus liocephalus
100
92
Gerrhonotus infernalis
97 Abronia mixteca
100 Barisia levicollis
Barisia imbricata
89 95 Barisia herrerae
94 Barisia rudicollis
Mesaspis moreletii
79
72
Mesaspis gadovii
Abronia chiszari
66 Abronia oaxacae
99 Abronia graminea
Abronia frosti
Abronia ornelasi
96 84 Abronia lythrochila
89 Abronia fimbriata
96 Abronia matudai
97
Abronia anzuetoi
95 Abronia campbelli
Shinisauridae Abronia aurita
Shinisaurus crocodilurus
Lanthanotidae
Lanthanotus borneensis
Varanus griseus
Varanus niloticus
94
95 Varanus exanthematicus
97 Varanus albigularis
99 Varanus yemenensis
100
Varanus olivaceus
98 Varanus keithhornei
95 100 Varanus beccarii
Varanidae
95 Varanus boehmei
Varanus macraei
100
75 Varanus prasinus
86
86 Varanus rainerguentheri
78
Varanus indicus
Varanus melinus
88 Varanus cerambonensis
100 Varanus caerulivirens
100
84
100 69
100
85
72
100
100
86
99
88
76
7974
92 9694
97
100
99
100
87
96
76 86100
100
99 10099
Varanus jobiensis
Varanus yuwonoi
Varanus doreanus
Varanus finschi
Varanus marmoratus
Varanus salvator
Varanus rudicollis
Varanus dumerilii
Varanus flavescens
Varanus bengalensis
Varanus mertensi
Varanus spenceri
Varanus giganteus
Varanus rosenbergi
Varanus panoptes
Varanus gouldii
Varanus salvadorii
Varanus varius
Varanus komodoensis
Varanus glebopalma
Varanus pilbarensis
Varanus tristis
Varanus glauerti
Varanus scalaris
Varanus timorensis
Varanus mitchelli
100
100
99
Varanus semiremex
Varanus brevicauda
Varanus eremius
Varanus caudolineatus
Varanus gilleni
Varanus bushi
Varanus kingorum
Varanus primordius
Varanus storri
Varanus acanthurus
Varanus baritji

N
Figure 15
Chamaeleonidae
100
Brookesia lolontany
79
Brookesia nasus
100
Brookesia dentata
100
Brookesia exarmata
63
Brookesia minima
Brookesia tuberculata
83 100
Brookesia karchei
100
Brookesia peyrierasi
100
Brookesia perarmata
Brookesia decaryi
100
98 Brookesia brygooi
Brookesia bonsi
100
Brookesia therezieni
Brookesiinae
99
Brookesia superciliaris
93 Brookesia valerieae
100
Brookesia griveaudi
Brookesia stumpffi
100 Brookesia ambreensis
Brookesia antakarana
Brookesia ebenaui
Brookesia vadoni
100 Brookesia thieli
Brookesia betschi
51 Brookesia lineata
Furcifer balteatus
99
Furcifer bifidus
99 62
Furcifer minor
Furcifer willsii
86
Furcifer petteri
Furcifer campani
93 96 Furcifer cephalolepis
91
Furcifer polleni
94 100 Furcifer pardalis
Furcifer angeli
99 93 Furcifer oustaleti
Furcifer verrucosus
98 Furcifer belalandaensis
98
Furcifer lateralis
94
100 Furcifer labordi
Furcifer antimena
100 Kinyongia oxyrhina
Kinyongia tenue
95
100 Kinyongia adolfifriderici
Kinyongia excubitor
67 Kinyongia xenorhina
98 Kinyongia carpenteri
82
Kinyongia uthmoelleri
Kinyongia tavetana
100 92
100 Kinyongia boehmei
55 100
Kinyongia matschiei
100 Kinyongia multituberculata
59 Kinyongia vosseleri
100 Kinyongia fischeri
96 Bradypodion pumilum
Bradypodion damaranum
Bradypodion caffer
100 100 Bradypodion melanocephalum
94 Bradypodion thamnobates
98 Bradypodion transvaalense
72 Bradypodion dracomontanum
87 Bradypodion nemorale
Bradypodion setaroi
Bradypodion occidentale
85 Bradypodion atromontanum
98
Bradypodion gutturale
749595
Bradypodion taeniabronchum
Bradypodion karrooicum
Bradypodion ventrale
100
Calumma furcifer
99
Calumma gastrotaenia
Rieppeleon kerstenii
100
Rieppeleon brachyurus
58
Rieppeleon brevicaudatus
Calumma cucullatum
82 100 88 Calumma crypticum
Calumma brevicorne
98 Calumma tsaratananense
100 75 Calumma hilleniusi
Calumma guibei
91
Calumma malthe
78
93 Calumma gallus
85 Calumma fallax
97 Calumma boettgeri
94 Calumma nasutum
Nadzikambia mlanjensis
73
Rhampholeon spectrum
88
Rhampholeon temporalis
98
Rhampholeon spinosus
98
Rhampholeon viridis
99
Rhampholeon marshalli
Chamaeleoninae
85
95
90
100
66
86
100
97
100
100
93
98
92
92
97 91
70
98
100
73
99
100
85
100
96
50
Calumma capuroni
Calumma oshaughnessyi
Calumma parsonii
Calumma globifer
100
61
Chamaeleo namaquensis
100
90
85 879766
100
99
95
81
91
90 100
100
98 100
Rhampholeon moyeri
Rhampholeon uluguruensis
Rhampholeon acuminatus
Rhampholeon boulengeri
Rhampholeon beraduccii
Rhampholeon nchisiensis
Rhampholeon platyceps
Rhampholeon chapmanorum
Chamaeleo laevigatus
Chamaeleo necasi
Chamaeleo gracilis
Chamaeleo quilensis
Chamaeleo dilepis
Chamaeleo roperi
Chamaeleo senegalensis
Chamaeleo monachus
Chamaeleo africanus
Chamaeleo calcaricarens
Chamaeleo chamaeleon
Chamaeleo zeylanicus
Chamaeleo calyptratus
Chamaeleo arabicus
Trioceros affinis
Trioceros harennae
Trioceros balebicornutus
Trioceros feae
Trioceros montium
Trioceros cristatus
Trioceros wiedersheimi
Trioceros quadricornis
Trioceros pfefferi
Trioceros oweni
Trioceros johnstoni
Trioceros melleri
Trioceros deremensis
Trioceros werneri
Trioceros tempeli
Trioceros goetzei
Trioceros fuelleborni
Trioceros bitaeniatus
Trioceros jacksonii
Trioceros narraioca
Trioceros schubotzi
Trioceros hoehnelii
Trioceros ellioti
Trioceros rudis
Trioceros sternfeldi

O
Figure 16
Uromasticinae
(i)
100
Agamidae
(i)
(ii)
96
100
100
94
86
Leiolepidinae
95
Uromastyx hardwickii
Uromastyx loricata
Uromastyx asmussi
Uromastyx princeps
Uromastyx macfadyeni
100
74
94
Uromastyx geyri
Uromastyx acanthinura
Uromastyx dispar
Uromastyx thomasi
100 Uromastyx aegyptia
91 Uromastyx leptieni
70
99 Uromastyx ornata
Uromastyx ocellata
100 Uromastyx benti
100 Uromastyx yemenensis
100 Leiolepis belliana
Leiolepis reevesii
100 100 Leiolepis guttata
Leiolepis guentherpetersi
Hydrosaurus amboinensis
Physignathus cocincinus
100
92
85
Hypsilurus spinipes
Hypsilurus boydii
97
Hypsilurus dilophus
Moloch horridus
98
Chelosania brunnea
Hypsilurus modestus
100
Hypsilurus papuensis
100 Hypsilurus nigrigularis
51
Hypsilurus bruijnii
100 75
Intellagama lesueurii
Ctenophorus maculosus
Ctenophorus adelaidensis
Ctenophorus clayi
100
96
Ctenophorus gibba
Ctenophorus salinarum
Ctenophorus cristatus
71
100
Ctenophorus nuchalis
98
Ctenophorus reticulatus
Ctenophorus rufescens
99
Ctenophorus tjantjalka
Ctenophorus vadnappa
99 Ctenophorus decresii
79 90 Ctenophorus fionni
Ctenophorus caudicinctus
100
Ctenophorus ornatus
Ctenophorus isolepis
100 53 92
Ctenophorus scutulatus
100
Ctenophorus mckenziei
76 Ctenophorus pictus
90
Ctenophorus maculatus
100
94
Ctenophorus fordi
Ctenophorus femoralis
71
Lophognathus temporalis
Lophognathus longirostris
100
Chlamydosaurus kingii
Lophognathus gilberti
94
Amphibolurus muricatus
100
97 Amphibolurus norrisi
Tympanocryptis uniformis
100
Tympanocryptis intima
99
Tympanocryptis tetraporophora
Hydrosaurinae Agaminae
Amphibolurinae
71
99
Tympanocryptis cephalus
Tympanocryptis pinguicolla
Tympanocryptis lineata
Rankinia diemensis
Pogona barbata
Pogona nullarbor
99
Pogona henrylawsoni
Pogona minima
99 Pogona minor
94 Pogona vitticeps
Diporiphora superba
Diporiphora linga
99
Diporiphora winneckei
81
Diporiphora reginae
Diporiphora magna
76
Diporiphora bilineata
95 100
95
100
53
63
67
56
100
95
100
Diporiphora pindan
Diporiphora valens
Diporiphora amphiboluroides
Diporiphora australis
Diporiphora nobbi
Diporiphora bennettii
Diporiphora albilabris
Diporiphora arnhemica
Diporiphora lalliae
(ii)
Draconinae
Laudakia stellio
94 99 Laudakia sacra
Laudakia tuberculata
Laudakia nupta
Laudakia lehmanni
85 Laudakia himalayana
84 99 Laudakia stoliczkana
84
Laudakia microlepis
88100
Laudakia caucasia
Laudakia erythrogaster
Phrynocephalus scutellatus
Phrynocephalus interscapularis
Phrynocephalus forsythii
100 100 Phrynocephalus theobaldi
64 90
Phrynocephalus putjatai
7573 Phrynocephalus vlangalii
Phrynocephalus lidskii
Phrynocephalus axillaris
Phrynocephalus helioscopus
91 Phrynocephalus mystaceus
100
Phrynocephalus raddei
89
100 Phrynocephalus versicolor
94 Phrynocephalus przewalskii
100 Phrynocephalus melanurus
9690 Phrynocephalus albolineatus
Phrynocephalus guttatus
100
Pseudotrapelus sinaitus
Acanthocercus atricollis
66
95 Xenagama taylori
Bufoniceps laungwalaensis
Trapelus sanguinolentus
100 Trapelus mutabilis
99 Trapelus agilis
Trapelus ruderatus
99
93 Trapelus pallidus
89 Trapelus flavimaculatus
100
100 Trapelus savignii
Agama spinosa
Agama boueti
100
100
Agama impalearis
96 Agama castroviejoi
76
Agama boulengeri
Agama insularis
100
84 Agama gracilimembris
69 Agama weidholzi
Agama anchietae
100 100 Agama atra
91
Agama hispida
100
50
Agama armata
100 Agama aculeata
Agama caudospinosa
100 Agama rueppelli
Agama lionotus
91 Agama kaimosae
65 Agama mwanzae
98 Agama sankaranica
99 Agama doriae
100 Agama agama
100 Agama finchi
6868 Agama planiceps
Agama paragama
Mantheyus phuwuanensis
Japalura variegata
70 Japalura tricarinata
100
Ptyctolaemus gularis
Ptyctolaemus collicristatus
100
Draco dussumieri
Draco lineatus
95 Draco maculatus
Draco fimbriatus
86 99 97 Draco cristatellus
53 Draco maximus
100
Draco mindanensis
92
Draco quinquefasciatus
100
65
Draco melanopogon
59 95
Draco haematopogon
Draco indochinensis
96 Draco blanfordii
Draco taeniopterus
86 61
100 Draco obscurus
100 Draco spilonotus
Draco caerulhians
100 97 Draco biaro
Draco beccarii
Draco bourouniensis
100
99 Draco rhytisma
95 Draco bimaculatus
100 Draco volans
Draco timorensis
99 Draco boschmai
100
100 Draco reticulatus
Draco cyanopterus
Draco quadrasi
91 Draco guentheri
Draco cornutus
85 Draco spilopterus
Draco palawanensis
87 Draco ornatus
Phoxophrys nigrilabris
Japalura polygonata
100
Gonocephalus robinsonii
Aphaniotis fusca
97 98
Coryphophylax subcristatus
Bronchocela cristatella
85 Gonocephalus grandis
87 Gonocephalus chamaeleontinus
86 100 Gonocephalus kuhlii
52 97 Lyriocephalus scutatus
Cophotis dumbara
100 Cophotis ceylanica
100
Ceratophora aspera
Ceratophora karu
90 Ceratophora stoddartii
100 Ceratophora erdeleni
Calotes mystaceus
81
72 Calotes chincollium
100 Calotes emma
55 Calotes liocephalus
100 90 Calotes ceylonensis
99Calotes
nigrilabris
Calotes liolepis
99 Calotes versicolor
100 Calotes irawadi
50
Calotes calotes
91 Calotes htunwini
Salea horsfieldii
96
69
100
100
100
99
10095
Acanthosaura crucigera
Acanthosaura armata
Acanthosaura capra
Acanthosaura lepidogaster
Sitana ponticeriana
Otocryptis wiegmanni
Japalura flaviceps
Japalura splendida
Pseudocalotes kakhienensis
Pseudocalotes brevipes
Pseudocalotes flavigula

P
Figure 17
94 Stenocercus scapularis
86
Stenocercus apurimacus
Stenocercus formosus
94 Stenocercus ochoai
Stenocercus roseiventris
64 Stenocercus azureus
100 100 Stenocercus doellojuradoi
69 Stenocercus limitaris
Stenocercus caducus
88 Stenocercus ornatus
78
100 Stenocercus percultus
Stenocercus puyango
100 Stenocercus iridescens
96 89 Stenocercus angulifer
Stenocercus rhodomelas
Stenocercus chota
84 82
9996100 Stenocercus festae
Stenocercus guentheri
Stenocercus angel
Stenocercus humeralis
Stenocercus marmoratus
71
100
Stenocercus crassicaudatus
100 Stenocercus torquatus
73 Stenocercus varius
89
Stenocercus imitator
94
Stenocercus eunetopsis
Stenocercus empetrus
Stenocercus boettgeri
100
88 100
Stenocercus cupreus
78 Stenocercus chrysopygus
79 Stenocercus ornatissimus
100
Stenocercus orientalis
Stenocercus latebrosus
85 Stenocercus melanopygus
88 Stenocercus stigmosus
100
Microlophus thoracicus
Microlophus theresiae
100 Microlophus heterolepis
99 96Microlophus
tigris
Microlophus peruvianus
100 Microlophus quadrivittatus
100 100 Microlophus atacamensis
Microlophus theresioides
98 Microlophus yanezi
Microlophus koepckeorum
100 Microlophus occipitalis
100 Microlophus bivittatus
100 Microlophus habelii
Microlophus stolzmanni
100
Microlophus delanonis
100
Microlophus grayii
1006495 Microlophus pacificus
Microlophus albemarlensis
Microlophus duncanensis
Uranoscodon superciliosus
74
Uracentron flaviceps
98 Tropidurus bogerti
Strobilurus torquatus
78
Plica umbra
Plica lumaria
99
100
Plica plica
Tropidurus callathelys
100
100 Tropidurus spinulosus
100 Eurolophosaurus divaricatus
100 Eurolophosaurus amathites
Eurolophosaurus nanuzae
Tropidurus hygomi
Tropidurus montanus
100 100 Tropidurus psammonastes
73 Tropidurus itambere
98 Tropidurus cocorobensis
97 83 Tropidurus etheridgei
Tropidurus mucujensis
Tropidurus erythrocephalus
Tropidurus insulanus
100 Tropidurus oreadicus
Iguanidae
9889 Tropidurus hispidus
Tropidurus torquatus
Dipsosaurus dorsalis
Brachylophus fasciatus
100 Brachylophus vitiensis
99 Iguana iguana
92 Iguana delicatissima
Sauromalus ater
100 100 Sauromalus klauberi
Sauromalus hispidus
61 Sauromalus varius
Cyclura pinguis
100 94 Cyclura cornuta
100
Cyclura ricordi
97 Cyclura carinata
95 Cyclura collei
57 Cyclura rileyi
8586 Cyclura nubila
56
Cyclura cychlura
Amblyrhynchus cristatus
100 Conolophus subcristatus
72
Conolophus pallidus
62 Ctenosaura similis
100 Ctenosaura hemilopha
96 Ctenosaura acanthura
99 Ctenosaura pectinata
99 98 Ctenosaura melanosterna
Ctenosaura oedirhina
Ctenosaura bakeri
100 74 Ctenosaura palearis
Ctenosaura flavidorsalis
99 Ctenosaura quinquecarinata
72 Ctenosaura oaxacana
Tropiduridae
Q-R

Q
Figure 18
(i)
(ii)
Leiocephalidae
(i)
54
81
87
100
100
100
100 100
100 99
86
90
75
100
100
100
100
96
100
100
100
83
93 100
100
100
99 100100
96
92
99
99
95
89
94
93
Crotaphytidae
Phrynosomatidae
100
100
100
96
100 76100
100
100
99
Leiocephalus carinatus
Leiocephalus raviceps
Leiocephalus psammodromus
Leiocephalus personatus
Leiocephalus schreibersii
Leiocephalus barahonensis
Gambelia wislizenii
Gambelia sila
Gambelia copeii
Crotaphytus antiquus
Crotaphytus reticulatus
82
100 97 10099
95
96
82
Crotaphytus vestigium
Crotaphytus insularis
Crotaphytus grismeri
100
Crotaphytus bicinctores
Crotaphytus nebrius
Crotaphytus collaris
Uma exsul
100 Uma paraphygas
Uma scoparia
100 100
99 100
100
88
92
100
100
100
100
82
100
99
96
Uma inornata
Uma notata
Callisaurus draconoides
Cophosaurus texanus
Holbrookia lacerata
Holbrookia propinqua
Holbrookia maculata
Phrynosoma cornutum
Phrynosoma solare
Phrynosoma mcallii
Phrynosoma platyrhinos
Phrynosoma coronatum
Phrynosoma blainvillii
Phrynosoma cerroense
Phrynosoma wigginsi
Phrynosoma asio
Phrynosoma braconnieri
Phrynosoma taurus
Phrynosoma modestum
Phrynosoma orbiculare
Phrynosoma ditmarsi
Phrynosoma douglassii
Phrynosoma hernandesi
Petrosaurus mearnsi
Petrosaurus repens
Petrosaurus thalassinus
Uta squamata
Uta palmeri
Uta stansburiana
Uta stejnegeri
Urosaurus gadovi
Urosaurus bicarinatus
Urosaurus lahtelai
Urosaurus nigricaudus
Urosaurus graciosus
Urosaurus ornatus
Urosaurus clarionensis
Urosaurus auriculatus
Sceloporus parvus
Sceloporus couchii
Sceloporus chrysostictus
Sceloporus teapensis
Sceloporus variabilis
Sceloporus smithi
Sceloporus cozumelae
100
92
96
100
91 97
Sceloporus grandaevus
Sceloporus angustus
Sceloporus utiformis
Sceloporus carinatus
Sceloporus squamosus
100 Sceloporus siniferus
Sceloporus merriami
100 99
99
100 99
100 99
97
89 99
100
99
98
98
100
89 97
100
100
98
98 98100
100 91
65
100
100
98 100
74
100
Sceloporus pyrocephalus
Sceloporus nelsoni
Sceloporus gadoviae
Sceloporus maculosus
Sceloporus jalapae
Sceloporus ochoterenae
Sceloporus vandenburgianus
Sceloporus graciosus
Sceloporus arenicolus
Sceloporus magister
Sceloporus zosteromus
Sceloporus lineatulus
Sceloporus licki
Sceloporus orcutti
Sceloporus hunsakeri
Sceloporus melanorhinus
Sceloporus grammicus
Sceloporus palaciosi
Sceloporus heterolepis
Sceloporus aeneus
Sceloporus bicanthalis
Sceloporus scalaris
Sceloporus slevini
Sceloporus chaneyi
Sceloporus samcolemani
Sceloporus goldmani
Sceloporus megalepidurus
Sceloporus insignis
Sceloporus jarrovii
Sceloporus torquatus
Sceloporus bulleri
Sceloporus mucronatus
Sceloporus macdougalli
Sceloporus poinsettii
Sceloporus dugesii
Sceloporus minor
Sceloporus ornatus
Sceloporus serrifer
61
100 97
Sceloporus cyanogenys
Sceloporus clarkii
Sceloporus olivaceus
Sceloporus occidentalis
Sceloporus virgatus
Sceloporus woodi
Sceloporus consobrinus
Sceloporus undulatus
Sceloporus cautus
Sceloporus horridus
Sceloporus edwardtaylori
Sceloporus spinosus
Sceloporus taeniocnemis
Sceloporus smaragdinus
Sceloporus malachiticus
Sceloporus lundelli
Sceloporus cryptus
Sceloporus subpictus
Sceloporus formosus
Sceloporus stejnegeri
Sceloporus adleri
100
Polychrotidae
Hoplocercidae
(ii)
63
99
99
95
96
69 Polychrus gutturosus
100
Polychrus acutirostris
Polychrus femoralis
92
Polychrus marmoratus
100
Hoplocercus spinosus
Morunasaurus annularis
100
Enyalioides laticeps
88
Enyalioides heterolepis
Enyalioides oshaughnessyi
Enyalioides palpebralis
96 Enyalioides microlepis
96
96 Enyalioides praestabilis
Chalarodon madagascariensis
90 Oplurus cyclurus
99 Oplurus cuvieri
100
Oplurus quadrimaculatus
Oplurus saxicola
73
96
Oplurus grandidieri
88 Oplurus fierinensis
Enyalius bilineatus
Enyalius leechii
97
Urostrophus gallardoi
99
Anisolepis longicauda
Urostrophus vautieri
100 98 Pristidactylus scapulatus
100
Diplolaemus darwinii
Pristidactylus torquatus
Leiosaurus bellii
78
7770 Leiosaurus paronae
Leiosaurus catamarcensis
Ctenoblepharys adspersa
100 Phymaturus indistinctus
Phymaturus somuncurensis
100 98 Phymaturus patagonicus
100 Phymaturus dorsimaculatus
Phymaturus palluma
96
Phymaturus punae
89
Phymaturus mallimaccii
88 Phymaturus antofagastensis
Liolaemus tenuis
Liolaemus lemniscatus
95 99
Liolaemus monticola
100 Liolaemus nitidus
68 Liolaemus nigroviridis
93 Liolaemus fuscus
100 Liolaemus atacamensis
Liolaemus zapallarensis
91
Liolaemus pseudolemniscatus
Liolaemus nigromaculatus
67 Liolaemus platei
66 97
99
Liolaemus paulinae
99 Liolaemus austromendocinus
100
Liolaemus thermarum
100 Liolaemus dicktracyi
Liolaemus heliodermis
95
98 Liolaemus capillitas
83 Liolaemus umbrifer
Liolaemus petrophilus
100 Liolaemus buergeri
59 Liolaemus ceii
100 Liolaemus leopardinus
100 6698 Liolaemus kriegi
Liolaemus elongatus
Liolaemus coeruleus
98 Liolaemus bellii
Liolaemus gravenhorstii
97
100
Liolaemus schroederi
99 Liolaemus chiliensis
Liolaemus cyanogaster
98 Liolaemus pictus
Liolaemus hernani
86 99
Liolaemus bibronii
56
Liolaemus pagaburoi
Liolaemus bitaeniatus
100 53 Liolaemus chaltin
100
100 Liolaemus puna
97 68 Liolaemus walkeri
91 Liolaemus yanalcu
Liolaemus ramirezae
74 Liolaemus robertmertensi
84 Liolaemus gracilis
100 Liolaemus saxatilis
94 Liolaemus hatcheri
Liolaemus lineomaculatus
70 Liolaemus silvanae
100 Liolaemus kolengh
100 Liolaemus magellanicus
Liolaemus uptoni
99 Liolaemus somuncurae
100
100 Liolaemus baguali
100 95
Liolaemus tari
Liolaemus escarchadosi
Liolaemus kingii
100
83
Liolaemus gallardoi
Liolaemus sarmientoi
99 Liolaemus scolaroi
98 Liolaemus zullyae
78 Liolaemus tristis
Liolaemus archeforus
100
Liolaemus stolzmanni
100 Liolaemus orientalis
98
Liolaemus famatinae
Liolaemus vallecurensis
82 82 Liolaemus ruibali
Liolaemus audituvelatus
72
78 99
Liolaemus fabiani
Liolaemus huacahuasicus
84
Liolaemus dorbignyi
87 Liolaemus molinai
Liolaemus multicolor
100 Liolaemus andinus
100
Liolaemus pseudoanomalus
97 99
Liolaemus occipitalis
Liolaemus lutzae
Liolaemus salinicola
85 65 Liolaemus riojanus
100 Liolaemus multimaculatus
99 Liolaemus scapularis
98 Liolaemus azarai
100 Liolaemus wiegmannii
100 Liolaemus rothi
99
Liolaemus boulengeri
Liolaemus inacayali
85 Liolaemus telsen
99
Liolaemus cuyanus
Liolaemus donosobarrosi
100
Liolaemus melanops
Liolaemus canqueli
98 93 Liolaemus morenoi
64 Liolaemus chehuachekenk
95
79
Opluridae
Leiosaurinae
Liolaemidae
R
Enyaliinae
94
100
78
95
99100
100
94
100
66
99
67 86
Liolaemus fitzingerii
Liolaemus xanthoviridis
Liolaemus hermannunezi
Liolaemus uspallatensis
Liolaemus chacoensis
Liolaemus olongasta
Liolaemus grosseorum
Liolaemus darwinii
Liolaemus laurenti
Liolaemus koslowskyi
Liolaemus quilmes
Liolaemus espinozai
Liolaemus abaucan
Liolaemus crepuscularis
Liolaemus irregularis
100
Liolaemus albiceps
Liolaemus calchaqui
Liolaemus ornatus
Liolaemus lavillai
Enyaliidae

R
Figure 19
(i)
(ii)
(i)
99
100
Dactyloidae
100
Laemanctus longipes
Corytophanes percarinatus
Corytophanes cristatus
Basiliscus galeritus
Basiliscus vittatus
98
92
Basiliscus plumifrons
Basiliscus basiliscus
67
Anolis boettgeri
Anolis luciae
64
Anolis bonairensis
Anolis griseus
100
100
62
96
100
100
89
Anolis trinitatis
Anolis richardii
Anolis aeneus
Anolis roquet
Anolis extremus
Anolis fitchi
Anolis huilae
96 Anolis peraccae
Anolis festae
Anolis chloris
95
Anolis ventrimaculatus
90
99
96
Anolis aequatorialis
Anolis gemmosus
Anolis euskalerriari
100
100
9965
Anolis nicefori
Anolis heterodermus
Anolis vanzolinii
Anolis inderenae
83
100
100
Anolis punctatus
Anolis transversalis
Anolis tigrinus
99
Anolis jacare
100 Anolis anatoloros
71 98
Anolis calimae
Anolis neblininus
100
Anolis agassizi
Anolis microtus
100
100
80
98
Anolis insignis
Anolis danieli
Anolis fraseri
Anolis chocorum
87
100
100
Anolis princeps
Anolis frenatus
Anolis casildae
Anolis maculigula
100
Anolis bartschi
75
Anolis vermiculatus
79
82
Anolis occultus
Anolis monticola
Anolis darlingtoni
99
56
100
100
Anolis bahorucoensis
Anolis dolichocephalus
Anolis hendersoni
94
Anolis coelestinus
Anolis chlorocyanus
100
59 99
90
Anolis singularis
Anolis aliniger
Anolis smallwoodi
100 Anolis noblei
Anolis baracoae
59 Anolis luteogularis
89 Anolis equestris
98
98
Anolis etheridgei
Anolis fowleri
100 97
86
97
99
Anolis insolitus
Anolis barbouri
Anolis olssoni
Anolis semilineatus
Anolis alumina
Anolis argenteolus
95 100 Anolis barbatus
Anolis porcus
86
86 Anolis chamaeleonides
66 Anolis guamuhaya
Anolis cuvieri
Anolis christophei
93 90
90
Anolis eugenegrahami
Anolis ricordi
10095 Anolis baleatus
Anolis barahonae
100
99
Anolis marcanoi
Anolis strahmi
Anolis longitibialis
96
99
95
Anolis haetianus
Anolis shrevei
Anolis armouri
Anolis cybotes
60
99 Anolis whitemani
Anolis lucius
97 Anolis clivicola
Anolis rejectus
100 100
Anolis cyanopleurus
Anolis cupeyalensis
99
Anolis macilentus
Anolis alfaroi
65
Anolis vanidicus
76
100
Anolis inexpectatus
Anolis alutaceus
86
85
100
Anolis placidus
Anolis sheplani
Anolis alayoni
100 Anolis paternus
100
Anolis angusticeps
80
Anolis garridoi
98 89
97
100 Anolis guazuma
Anolis loysiana
Anolis pumilus
95
100
100
Anolis centralis
Anolis argillaceus
Anolis oporinus
Anolis isolepis
99
100
Anolis carolinensis
Anolis porcatus
Anolis longiceps
Anolis brunneus
100 Anolis maynardi
74
97
Anolis allisoni
Anolis smaragdinus
Corytophanidae
100
100
56
99
100
99
100
90
77
100
95
57
96
94 100
Anolis wattsi
Anolis pogus
Anolis leachii
Anolis bimaculatus
Anolis gingivinus
Anolis oculatus
Anolis terraealtae
Anolis ferreus
Anolis lividus
Anolis nubilus
Anolis sabanus
Anolis marmoratus
Anolis distichus
Anolis websteri
Anolis brevirostris
Anolis marron
Anolis caudalis
95 100 Anolis acutus
Anolis stratulus
Anolis evermanni
100
Anolis poncensis
88
Anolis gundlachi
91
Anolis pulchellus
100
Anolis krugi
98 100 Anolis monensis
Anolis cooki
100 Anolis scriptus
96 Anolis ernestwilliamsi
75
100 Anolis desechensis
100 Anolis cristatellus
98
Anolis imias
Anolis rubribarbaris
90
100
98
100
Anolis allogus
Anolis ahli
Anolis guafe
Anolis confusus
100
72
94
Anolis jubar
Anolis homolechis
Anolis mestrei
100
99
Anolis ophiolepis
Anolis sagrei
89
99
Anolis quadriocellifer
Anolis bremeri
58
100
Anolis lineatopus
Anolis reconditus
Anolis valencienni
100
95
100
90
Anolis opalinus
Anolis garmani
Anolis conspersus
100 Anolis grahami
Anolis auratus
99
Anolis annectens
100
Anolis onca
Anolis lineatus
52
Anolis meridionalis
84
Anolis nitens
59
Anolis bombiceps
99
90
99 Anolis chrysolepis
Anolis loveridgei
100
Anolis purpurgularis
Anolis utilensis
96
Anolis crassulus
Anolis sminthus
72
94
Anolis polyrhachis
Anolis uniformis
Anolis bitectus
Anolis biporcatus
95
100
Anolis woodi
Anolis aquaticus
92 93
Anolis quercorum
Anolis ortonii
Anolis laeviventris
100
Anolis intermedius
Anolis isthmicus
100
Anolis sericeus
100
86
69
Anolis pachypus
Anolis humilis
Anolis altae
100
86
Anolis kemptoni
Anolis fuscoauratus
93
98
Anolis cupreus
Anolis polylepis
90 99
Anolis capito
Anolis tropidonotus
Anolis ocelloscapularis
Anolis carpenteri
100 100 Anolis bicaorum
56
Anolis lemurinus
91
Anolis limifrons
100
Anolis zeus
94 Anolis oxylophus
86
Anolis lionotus
97 Anolis tropidogaster
96 Anolis poecilopus
92 Anolis trachyderma
(ii)

S
Figure 20
100
90
100
100
T-AA
97
83
97
100
91
93
100
100
100
100
100
Liotyphlops albirostris
Typhlophis squamosus
Tricheilostoma bicolor
Siagonodon septemstriatus
Epictia albifrons
Epictia goudotii
Epictia columbi
Trilepida macrolepis
Rena dulcis
Rena humilis
100 Tetracheilostoma carlae
Tetracheilostoma breuili
Mitophis asbolepis
Mitophis pyrites
Mitophis leptipileptus
Myriopholis longicauda
Myriopholis algeriensis
Myriopholis rouxestevae
100 Myriopholis boueti
Myriopholis blanfordi
100 Myriopholis macrorhyncha
Myriopholis adleri
Namibiana occidentalis
Leptotyphlops nigroterminus
Leptotyphlops nigricans
Leptotyphlops sylvicolus
Leptotyphlops conjunctus
Leptotyphlops distanti
Leptotyphlops scutifrons
Gerrhopilus hedraeus
Gerrhopilus mirus
Xenotyphlops grandidieri
90
96
71
95
100
Typhlops brongersmianus
Typhlops reticulatus
Typhlops biminiensis
Typhlops pusillus
Typhlops hectus
Typhlops syntherus
Typhlops eperopeus
92
87
Typhlops lumbricalis
84
Typhlops schwartzi
56
100
Typhlops titanops
Typhlops sulcatus
77
Typhlops rostellatus
Typhlops capitulatus
77
Typhlops jamaicensis
92 Typhlops sylleptor
92 99 Typhlops agoralionis
100
Typhlops caymanensis
Typhlops arator
100
Typhlops contorhinus
74
Typhlops anchaurus
Typhlops anousius
Typhlops notorachius
Typhlops monastus
100
Typhlops dominicanus
86 Typhlops granti
87
Typhlops hypomethes
84
99
Typhlops platycephalus
95 Typhlops richardi
75 Typhlops catapontus
Rhinotyphlops lalandei
Letheobia feae
100 Letheobia newtoni
Letheobia obtusa
Typhlops elegans
100 100 Afrotyphlops angolensis
87
77
99
87
Megatyphlops schlegelii
Afrotyphlops fornasinii
89
Afrotyphlops bibronii
Afrotyphlops lineolatus
99 Afrotyphlops congestus
72 Afrotyphlops punctatus
100
Typhlops vermicularis
Typhlops arenarius
Typhlops luzonensis
Typhlops ruber
76
Ramphotyphlops albiceps
99
84
100
97
Typhlops pammeces
Ramphotyphlops braminus
Typhlopidae sp. (Sri Lanka)
72
65
100
Ramphotyphlops lineatus
Ramphotyphlops acuticaudus
Acutotyphlops subocularis
Acutotyphlops kunuaensis
Ramphotyphlops polygrammicus
91 74
Austrotyphlops diversus
75
Austrotyphlops howi
87
Typhlopidae
100 Anomalepididae
100
100
100 100
56
100
98
79
69
99
100
51 100
98
76
99
100 52
59
92
87
98
81
93
74 91
Austrotyphlops guentheri
Austrotyphlops bituberculatus
Austrotyphlops grypus
Austrotyphlops longissimus
Austrotyphlops leptosomus
Austrotyphlops unguirostris
Austrotyphlops ammodytes
Austrotyphlops kimberleyensis
96
Austrotyphlops troglodytes
Austrotyphlops ganei
Austrotyphlops ligatus
Ramphotyphlops bicolor
Austrotyphlops pinguis
90 Austrotyphlops splendidus
Austrotyphlops waitii
Austrotyphlops australis
Austrotyphlops endoterus
Austrotyphlops hamatus
Austrotyphlops pilbarensis
96
Leptotyphlopidae
Gerrhopilidae
Xenotyphlopidae

T
Figure 21
U-AA
98 100
Anilius scytale
Trachyboa gularis
Trachyboa boulengeri
Aniliidae
100
100 Tropidophis pardalis
Tropidophis wrighti
100
53
Tropidophis greenwayi
100 Tropidophis haetianus
Tropidophis feicki
98 Tropidophis melanurus
Xenophidion schaeferi
100
Casarea dussumieri
Sanzinia madagascariensis
Acrantophis madagascariensis
Bolyeriidae
Sanziniinae
100 100 Acrantophis dumerili
Calabaria reinhardtii
100
Exiliboa placata
100
Ungaliophis continentalis
99
Charina bottae
100
Lichanura trivirgata
Ungaliophiinae
99
100
81
Candoia aspera
Candoia carinata
Candoia bibroni
Candoiinae
69
100
87
95
Eryx jayakari
Eryx colubrinus
53
Eryx conicus
Eryx johnii
87
Eryx jaculus
Erycinae
83
96 Eryx elegans
93 Eryx miliaris
100 Eryx tataricus
Boa constrictor
Boidae
97
98
99 Corallus hortulanus
Corallus caninus
Corallus annulatus
Epicrates cenchria
88 100
96
100
Eunectes murinus
Eunectes notaeus
94
Epicrates angulifer
Epicrates inornatus
85
Epicrates monensis
Boinae
90 Epicrates fordi
Epicrates subflavus
95 Epicrates chrysogaster
100
92
Epicrates exsul
Epicrates striatus
65
100
Anomochilus leonardi
Cylindrophis maculatus
Cylindrophis ruffus
Melanophidium punctatum
98
86
90
73
Brachyophidium rhodogaster
Uropeltis liura
Uropeltis ceylanicus
Rhinophis travancoricus
100 Uropeltis melanogaster
89
80
69
Uropeltis phillipsi
Rhinophis drummondhayi
82
Rhinophis dorsimaculatus
77
Rhinophis philippinus
Rhinophis oxyrhynchus
84
8580
Pseudotyphlops philippinus
Rhinophis homolepis
Rhinophis blythii
98
100
99
Xenopeltis unicolor
Loxocemus bicolor
Python brongersmai
Python regius
99
Python curtus
86
96
Python sebae
Python molurus
100
98
Broghammerus reticulatus
Broghammerus timoriensis
Morelia oenpelliensis
76
97
Morelia boeleni
Morelia amethistina
100 100
Aspidites ramsayi
Aspidites melanocephalus
75
Liasis olivaceus
Apodora papuana
98
96 Liasis mackloti
100 Liasis fuscus
Leiopython albertisii
100
Bothrochilus boa
71
96
85
Morelia viridis
84 Morelia carinata
100
Morelia spilota
Morelia bredli
51
83100
Antaresia maculosa
Antaresia perthensis
Antaresia stimsoni
Antaresia childreni
Tropidophiidae
Xenophidiidae
Calabariidae
Anomochilidae
Cylindrophiidae
Uropeltidae
Xenopeltidae
Loxocemidae
Pythonidae

U
Figure 22
Acrochordidae
(i)
(ii)
(i)
100
95
Xenodermatidae
100
V-AA
95
Pareatidae
100
95
100
99
Viperinae
100
Viperidae
96
100
98
95
100
94
100
100
Acrochordus javanicus
Acrochordus granulatus
Acrochordus arafurae
Stoliczkia borneensis
Xenodermus javanicus
Achalinus meiguensis
Achalinus rufescens
Aplopeltura boa
Pareas monticola
Pareas boulengeri
Pareas formosensis
Pareas macularius
Pareas hamptoni
Eristicophis macmahoni
Pseudocerastes persicus
Pseudocerastes fieldi
Macrovipera lebetina
Macrovipera schweizeri
100
Montivipera xanthina
Montivipera raddei
Montivipera bornmuelleri
94 Montivipera albizona
83
88
Montivipera wagneri
Daboia palaestinae
96
Daboia russelii
59 Macrovipera deserti
100 Macrovipera mauritanica
95
Vipera ammodytes
Vipera latastei
100
100 Vipera aspis
Vipera seoanei
93
77 Vipera nikolskii
100
Vipera berus
97
100
97
91
99
86
100
51
96
100
99
97
99
85
59
80
89
93
77
53
Vipera barani
Vipera kaznakovi
Vipera eriwanensis
Vipera ursinii
Vipera dinniki
Vipera renardi
Vipera lotievi
Asthenodipsas vertebralis
Pareas margaritophorus
100 Pareas carinatus
100 Pareas nuchalis
Proatheris superciliaris
Cerastes vipera
Cerastes cerastes
Cerastes gasperettii
Causus resimus
Causus rhombeatus
Causus defilippii
Echis omanensis
100
Echis coloratus
Atheris ceratophora
Atheris barbouri
Atheris chlorechis
Atheris hispida
100
Atheris squamigera
Atheris nitschei
Echis carinatus
Atheris desaixi
Bitis worthingtoni
63
Bitis arietans
Bitis nasicornis
100
Bitis gabonica
98
99
100
99
100
100
62
100
100
91
98
100
100
100
Bitis peringueyi
Bitis caudalis
Bitis xeropaga
Bitis atropos
Bitis cornuta
Bitis rubida
Echis ocellatus
Echis jogeri
Echis leucogaster
Echis pyramidum
(ii)
100
100
Crotalinae
Azemiops feae
91
Garthius chaseni
Tropidolaemus wagleri
50
Deinagkistrodon acutus
Calloselasma rhodostoma
Hypnale nepa
100
Hypnale hypnale
100
Hypnale zara
99
95
Trimeresurus puniceus
98
Trimeresurus borneensis
Trimeresurus malabaricus
100
96 Trimeresurus gramineus
Trimeresurus trigonocephalus
100
99
Trimeresurus hageni
Trimeresurus malcolmi
Trimeresurus flavomaculatus
99
89
Trimeresurus schultzei
97
Trimeresurus sumatranus
98 89
Trimeresurus popeiorum
Trimeresurus tibetanus
94 Trimeresurus medoensis
Trimeresurus yunnanensis
Trimeresurus gumprechti
81 Trimeresurus stejnegeri
72
96 Trimeresurus vogeli
93
100 Trimeresurus kanburiensis
Trimeresurus venustus
Trimeresurus macrops
96 Trimeresurus fasciatus
64
Trimeresurus insularis
85 Trimeresurus septentrionalis
100
Trimeresurus andersonii
93 Trimeresurus albolabris
Trimeresurus cantori
77
100
Trimeresurus erythrurus
97
99 Trimeresurus purpureomaculatus
100
Ovophis monticola
Ovophis zayuensis
98
Ovophis tonkinensis
97
Protobothrops kaulbacki
Protobothrops sieversorum
Protobothrops mangshanensis
99 92
Protobothrops cornutus
100 Protobothrops xiangchengensis
90
Protobothrops jerdonii
100 100
Protobothrops elegans
Protobothrops mucrosquamatus
63 100 Protobothrops flavoviridis
Protobothrops tokarensis
100
Ovophis okinavensis
Trimeresurus gracilis
85
100
Gloydius tsushimaensis
100 Gloydius brevicaudus
99 Gloydius ussuriensis
Gloydius blomhoffii
100
Gloydius strauchi
97
Gloydius halys
96
100
Gloydius shedaoensis
Gloydius intermedius
9995 Gloydius saxatilis
100 Atropoides occiduus
100 Atropoides nummifer
99
Atropoides olmec
Atropoides picadoi
Cerrophidion godmani
94
Cerrophidion tzotzilorum
90
99 Cerrophidion petlalcalensis
78
Porthidium ophryomegas
96
Porthidium dunni
100
Porthidium yucatanicum
Porthidium nasutum
100
8690
Porthidium porrasi
Porthidium lansbergii
Bothrocophias campbelli
99 Bothrocophias microphthalmus
Bothrocophias hyoprora
Bothrops pictus
100
Rhinocerophis ammodytoides
96 100 Rhinocerophis cotiara
Rhinocerophis fonsecai
90 94 Rhinocerophis alternatus
99
Rhinocerophis itapetiningae
100 Bothropoides erythromelas
Bothropoides diporus
91 100
94 Bothropoides neuwiedi
100 Bothropoides jararaca
Bothropoides insularis
90 Bothropoides alcatraz
99 100
Bothriopsis pulchra
Bothriopsis chloromelas
98 Bothriopsis taeniata
95 Bothriopsis bilineata
100
Bothrops brazili
100 Bothrops jararacussu
Bothrops punctatus
100 97 Bothrops caribbaeus
Bothrops lanceolatus
100
Bothrops asper
87 Bothrops marajoensis
90 Bothrops colombiensis
99 Bothrops atrox
72 Bothrops moojeni
Bothrops leucurus
100
Ophryacus undulatus
Mixcoatlus barbouri
85
100
Mixcoatlus melanurus
100
Lachesis stenophrys
Lachesis muta
Bothriechis schlegelii
53
51
Bothriechis nigroviridis
98
Bothriechis lateralis
98 Bothriechis marchi
100 100 Bothriechis thalassinus
Bothriechis bicolor
91
Bothriechis aurifer
84 Bothriechis rowleyi
100
Agkistrodon contortrix
96
99 99
100
87
74
97
97
99
100
Agkistrodon piscivorus
Agkistrodon taylori
Agkistrodon bilineatus
Sistrurus catenatus
Sistrurus miliarius
Crotalus pricei
100
99
63
82
100
100 91
100
95
56
98
52
98
77
89 90
100
58
100
Crotalus intermedius
Crotalus transversus
Crotalus tancitarensis
Crotalus triseriatus
Crotalus pusillus
Crotalus lepidus
Crotalus aquilus
Crotalus enyo
Crotalus polystictus
Crotalus cerastes
Crotalus ravus
Crotalus willardi
Crotalus horridus
Crotalus durissus
Crotalus simus
Crotalus basiliscus
Crotalus molossus
Crotalus totonacus
Crotalus ruber
Crotalus catalinensis
Crotalus atrox
Crotalus tortugensis
Crotalus scutulatus
100
100
Azemiopinae
Crotalus oreganus
Crotalus viridis
Crotalus mitchellii
Crotalus tigris
Crotalus adamanteus

V
Figure 23
X-AA
100
Homalopsidae
58
98
95
95
100
100
96 95
90
W
100
100
Enhydris chinensis
53
Enhydris plumbea
97
100 Enhydris matannensis
Enhydris enhydris
Enhydris jagorii
100
Enhydris longicauda
100
100 Enhydris innominata
100
Myron richardsonii
100
Pseudoferania polylepis
71
Erpeton tentaculatum
89
Enhydris bocourti
96
Bitia hydroides
85
Cantoria violacea
Gerarda prevostiana
70
Fordonia leucobalia
88 98
Enhydris punctata
Homalopsis buccata
88 Cerberus australis
97 Cerberus microlepis
100 100
Cerberus rynchops
Micrelaps bicoloratus
Oxyrhabdium leporinum
100
Prosymna ruspolii
86
Prosymna visseri
Prosymna janii
100
Prosymna greigerti
Prosymna meleagris
99
Rhamphiophis oxyrhynchus
99
Rhamphiophis rubropunctatus
96
Malpolon monspessulanus
Rhagerhis moilensis
54
Mimophis mahfalensis
Dipsina multimaculata
97
100
Hemirhagerrhis viperina
100
Hemirhagerrhis kelleri
Hemirhagerrhis hildebrandtii
65
Psammophylax acutus
Psammophylax rhombeatus
97
100
Psammophylax variabilis
90
95 Psammophylax tritaeniatus
70
Psammophis crucifer
Psammophis lineolatus
100
Psammophis condanarus
Psammophis trigrammus
100
Psammophis jallae
100 Psammophis leightoni
8550
Psammophis notostictus
100
Psammophis angolensis
76
Psammophis schokari
Psammophis punctulatus
80
Psammophis praeornatus
100 Psammophis tanganicus
69
Psammophis biseriatus
Psammophis lineatus
96 97 Psammophis subtaeniatus
73
Psammophis sudanensis
60 Psammophis orientalis
100 Psammophis rukwae
Psammophis sibilans
80 Psammophis leopardinus
71 100 Psammophis mossambicus
100 Psammophis phillipsi
Homoroselaps lacteus
Atractaspis irregularis
98
Lamprophiidae
97
54
96
64
92
82
95
92
76
96
98
95
99
98
99
100 94
93
95
90
97
98 58
100
100 92
69
92
97
97
100
100 94
94
98
95
94
99
98
100
99
100
99
93
100
98
100
100
100
100
89 99
100
73
100
Atractaspis microlepidota
Atractaspis boulengeri
Atractaspis bibronii
Atractaspis micropholis
Atractaspis corpulenta
Macrelaps microlepidotus
Amblyodipsas polylepis
Xenocalamus transvaalensis
Amblyodipsas dimidiata
100 100
Polemon notatus
Polemon collaris
Polemon acanthias
Aparallactus modestus
Aparallactus werneri
Aparallactus capensis
Aparallactus guentheri
Pythonodipsas carinata
Pseudaspis cana
Psammodynastes pulverulentus
Psammodynastes pictus
Buhoma procterae
Buhoma depressiceps
Lycophidion nigromaculatum
Lycophidion laterale
Lycophidion capense
Lycophidion ornatum
Hormonotus modestus
Inyoka swazicus
Gonionotophis stenophthalmus
Gonionotophis nyassae
Gonionotophis brussauxi
Gonionotophis poensis
Gonionotophis capensis
Pseudoboodon lemniscatus
Bothrolycus ater
Bothrophthalmus brunneus
100 Bothrophthalmus lineatus
Boaedon virgatus
Boaedon lineatus
Boaedon fuliginosus
Boaedon olivaceus
Lamprophis guttatus
Lamprophis fuscus
Lamprophis aurora
Lamprophis fiskii
Lycodonomorphus inornatus
Lycodonomorphus rufulus
Lycodonomorphus laevissimus
Lycodonomorphus whytii
Amplorhinus multimaculatus
Duberria variegata
Duberria lutrix
Ditypophis vivax
Compsophis boulengeri
Compsophis albiventris
Compsophis laphystius
Compsophis infralineatus
Alluaudina bellyi
100
100
100
100
Parastenophis betsileanus
Leioheterodon geayi
Leioheterodon madagascariensis
Leioheterodon modestus
Langaha madagascariensis
Micropisthodon ochraceus
Ithycyphus miniatus
Ithycyphus oursi
Madagascarophis colubrinus
Dromicodryas quadrilineatus
Dromicodryas bernieri
Thamnosophis infrasignatus
Thamnosophis martae
Thamnosophis epistibes
Thamnosophis stumpffi
Thamnosophis lateralis
Pseudoxyrhopus ambreensis
Heteroliodon occipitalis
Liopholidophis dimorphus
Liopholidophis dolicocercus
Liopholidophis sexlineatus
Liophidium rhodogaster
Liophidium vaillanti
Liophidium therezieni
Liophidium torquatum
99
100
93
100
98
100
95
98
54
Liophidium mayottensis
Liophidium chabaudi
Madagascarophis meridionalis
Lycodryas inornatus
Lycodryas citrinus
Lycodryas sanctijohannis
Lycodryas inopinae
100 Lycodryas pseudogranuliceps
Lycodryas granuliceps
Atractaspidinae
Aparallactinae
Prosymninae
Psammophiinae
Pseudaspidinae
Lamprophiinae
Pseudoxyrhophiinae

W
Figure 24
100
Elapidae
Calliophis melanurus
Maticora bivirgata
61
Micruroides euryxanthus
Sinomicrurus japonicus
100
Sinomicrurus kelloggi
85
95
Sinomicrurus macclellandi
Micrurus corallinus
100 Micrurus albicinctus
90 Micrurus psyches
Micrurus fulvius
99 Micrurus diastema
100
Micrurus narduccii
98
Micrurus mipartitus
Micrurus dissoleucus
91
Micrurus surinamensis
97
Micrurus hemprichii
Micrurus lemniscatus
Micrurus decoratus
Micrurus baliocoryphus
94
97 Micrurus pyrrhocryptus
98 Micrurus altirostris
Micrurus ibiboboca
88 Micrurus spixii
98
89 Micrurus frontalis
59 Micrurus brasiliensis
84
Hemibungarus calligaster
Ophiophagus hannah
84
100
Dendroaspis angusticeps
87
Dendroaspis polylepis
63
Walterinnesia aegyptia
Aspidelaps scutatus
Hemachatus haemachatus
Naja kaouthia
100
100
Naja atra
Naja naja
91
Naja mandalayensis
99 Naja siamensis
87 Naja sumatrana
90 69
Naja multifasciata
Naja melanoleuca
58
Naja annulata
100 Naja nivea
83
Naja annulifera
95
88 Naja haje
92
78
Naja nubiae
Naja pallida
99 Naja katiensis
96 Naja mossambica
9676 Naja nigricollis
Naja ashei
100
Elapsoidea nigra
99 Elapsoidea semiannulata
Elapsoidea sundevallii
Bungarus flaviceps
98
Bungarus bungaroides
Bungarus fasciatus
90
Bungarus sindanus
100
97
Bungarus ceylonicus
97
Bungarus caeruleus
100
Bungarus niger
99
100 Bungarus multicinctus
Bungarus candidus
Laticauda laticaudata
100
Laticauda saintgironsi
98
Laticauda guineai
100 Laticauda colubrina
Micropechis ikaheka
Toxicocalamus preussi
100
100
Demansia vestigiata
100
Demansia papuensis
91
Demansia psammophis
Toxicocalamus loriae
82 100
92
85
67
89
68
75
99
88
98
71
99
94
78
91
100 100
100
97
100
88
95
100 97
98
100
100
100
90
100
99 98
98
98
72
100
100
100
Furina ornata
Furina diadema
Simoselaps semifasciatus
Simoselaps anomalus
Simoselaps bertholdi
Aspidomorphus schlegeli
Aspidomorphus lineaticollis
Aspidomorphus muelleri
Acanthophis praelongus
Acanthophis antarcticus
Pseudechis porphyriacus
Pseudechis butleri
Pseudechis australis
Pseudechis colletti
Pseudechis papuanus
Pseudechis guttatus
Cacophis squamulosus
Elapognathus coronata
Cryptophis nigrescens
Rhinoplocephalus bicolor
Suta fasciata
Suta monachus
Suta suta
Suta spectabilis
Vermicella intermedia
Simoselaps calonotus
Denisonia devisi
Oxyuranus microlepidotus
Oxyuranus scutellatus
Pseudonaja modesta
Pseudonaja textilis
Echiopsis curta
Drysdalia mastersii
Drysdalia coronoides
Austrelaps labialis
Austrelaps superbus
Hoplocephalus bitorquatus
Echiopsis atriceps
Notechis scutatus
Tropidechis carinatus
Hemiaspis signata
Hemiaspis damelii
100
96
100
100
94
90 100
97
Emydocephalus annulatus
Aipysurus eydouxii
Aipysurus duboisii
Aipysurus apraefrontalis
Aipysurus fuscus
Aipysurus laevis
Parahydrophis mertoni
Ephalophis greyae
Hydrelaps darwiniensis
Hydrophis elegans
Hydrophis lapemoides
94 Hydrophis spiralis
95
67
83
100
94
100
97
98
54
83
77
93
88
74100
100 75
Hydrophis semperi
Hydrophis pacifica
Hydrophis cyanocincta
Hydrophis melanocephala
Hydrophis parviceps
Hydrophis curtus
Hydrophis platura
Hydrophis stokesii
Hydrophis atriceps
Hydrophis brooki
Hydrophis caerulescens
Hydrophis czeblukovi
Hydrophis major
Hydrophis schistosa
Hydrophis macdowelli
Hydrophis kingii
Hydrophis peronii
Hydrophis ornata

X
Figure 25
Calamariinae
100
Colubridae
68
74
97
71
96
100
57
100
100
68
73
99
100
86
71
79
60
68
100
100
89 96
100
94
100
60
100
Pseudoxenodontinae
Sibynophiinae
Colubrinae
Grayiinae
100
74
100
90
99
94
100
69
99
96 68
85
69
92 86 100
99
100
100
97 91
94
87
68
100
100
Y
Z-AA Colubrinae cont.
98
100
52
92
99
83
100
70
100
98
100
Pseudorabdion oxycephalum
Calamaria pavimentata
Calamaria yunnanensis
Plagiopholis styani
Pseudoxenodon bambusicola
Pseudoxenodon macrops
Pseudoxenodon karlschmidti
Scaphiodontophis annulatus
Sibynophis bistrigatus
Sibynophis subpunctatus
Sibynophis triangularis
Sibynophis collaris
100 Sibynophis chinensis
Grayia tholloni
Grayia ornata
Grayia smithii
Ahaetulla fronticincta
Ahaetulla pulverulenta
Ahaetulla nasuta
Chrysopelea taprobanica
Chrysopelea ornata
Chrysopelea paradisi
Dendrelaphis bifrenalis
Dendrelaphis caudolineolatus
Dendrelaphis caudolineatus
Dendrelaphis schokari
Dendrelaphis tristis
Boiga kraepelini
Crotaphopeltis tornieri
Dipsadoboa unicolor
Telescopus fallax
Boiga irregularis
Boiga dendrophila
Boiga forsteni
Boiga cynodon
Boiga barnesii
Boiga trigonata
Boiga ceylonensis
Boiga beddomei
Boiga multomaculata
Toxicodryas pulverulenta
Dasypeltis confusa
83
90
100
100
95
100
100
98
99
98
52
100
100
100
83
100
99
86
100
97 85
93
88
61
100
97
100
99
86
92 77
98
91
56
Dasypeltis atra
Dasypeltis scabra
Dasypeltis sahelensis
Dasypeltis gansi
Dasypeltis fasciata
Scaphiophis albopunctatus
Oligodon arnensis
Oligodon sublineatus
Oligodon taeniolatus
Oligodon octolineatus
Oligodon cyclurus
Oligodon barroni
Oligodon taeniatus
Oligodon chinensis
Oligodon ocellatus
Oligodon formosanus
Oligodon cinereus
Oligodon maculatus
Oligodon splendidus
Oligodon cruentatus
Oligodon theobaldi
Oligodon torquatus
Oligodon planiceps
Coelognathus radiatus
Coelognathus helena
Coelognathus erythrurus
Coelognathus subradiatus
Coelognathus flavolineatus
Thrasops jacksonii
Dispholidus typus
Thelotornis capensis
Philothamnus carinatus
Philothamnus heterodermus
Philothamnus nitidus
Philothamnus semivariegatus
Philothamnus angolensis
Philothamnus girardi
Philothamnus thomensis
Philothamnus natalensis
Philothamnus hoplogaster
Hapsidophrys lineatus
Hapsidophrys smaragdina
Hapsidophrys principis
Lytorhynchus diadema
82
89
85
99 90
97
90
99
100
Coluber zebrinus
Bamanophis dorri
Macroprotodon cucullatus
Macroprotodon abubakeri
Hemerophis socotrae
Hemorrhois hippocrepis
Hemorrhois algirus
Hemorrhois nummifer
Hemorrhois ravergieri
Spalerosophis microlepis
Spalerosophis diadema
Platyceps rhodorachis
Platyceps rogersi
Platyceps karelini
Platyceps ventromaculatus
Platyceps najadum
Platyceps collaris
Platyceps florulentus
Dolichophis jugularis
Dolichophis schmidti
Dolichophis caspius
Hierophis viridiflavus
Hierophis gemonensis
Hierophis spinalis
Eirenis modestus
Eirenis aurolineatus
Eirenis persicus
Eirenis decemlineatus
Eirenis levantinus
Eirenis medus
Eirenis thospitis
86
Eirenis lineomaculatus
59
Eirenis rothii
Eirenis coronelloides
Eirenis eiselti
100 Eirenis collaris
Eirenis barani
Eirenis punctatolineatus

Y
Figure 26
Colubrinae cont.
64
83
93
53
100
100
93
98
83
93
100
99
81
87
90
82
96 100
86
75
97
98
100
94
100
99
99
84
88
92
64
92
91
87
92
88
98
71
100
98
83
100
93 60
100
61
100
87
89
100
82
86
100
100
98
83
96
Cyclophiops major
Ptyas korros
Ptyas mucosa
Oxybelis fulgidus
Oxybelis aeneus
Opheodrys vernalis
Opheodrys aestivus
Salvadora mexicana
Tantilla melanocephala
Coluber taeniatus
Coluber constrictor
Coluber flagellum
Chironius quadricarinatus
Trimorphodon biscutatus
Phyllorhynchus decurtatus
Spilotes pullatus
Pseustes sulphureus
Drymarchon corais
Chironius fuscus
Chironius scurrulus
Chironius laevicollis
Chironius grandisquamis
Chironius flavolineatus
Chironius bicarinatus
Chironius monticola
Ficimia streckeri
Gyalopion canum
100
100
100
75
Chironius carinatus
Leptophis ahaetulla
Dendrophidion dendrophis
Dendrophidion percarinatum
Drymobius rhombifer
Rhadinophis prasinus
Rhynchophis boulengeri
Rhadinophis frenatus
Lycodon ruhstrati
Lycodon laoensis
Lycodon fasciatus
Lycodon paucifasciatus
Lycodon rufozonatum
Lycodon semicarinatum
Dryocalamus nympha
Lycodon carinatus
Lycodon capucinus
Lycodon osmanhilli
Lycodon zawi
98 94 76
100
93
100
99 66
55
98
81
74
100
92
92
Archelaphe bella
Euprepiophis conspicillata
Euprepiophis mandarinus
Oreocryptophis porphyraceus
Orthriophis taeniurus
Orthriophis hodgsoni
Orthriophis moellendorffi
Orthriophis cantoris
Zamenis hohenackeri
Zamenis persicus
Zamenis longissimus
Zamenis lineatus
Rhinechis scalaris
Zamenis situla
Elaphe davidi
91
100 98
82
83
99
Coronella girondica
94 99
100
100
100
54
100
100
100
87
Drymoluber brazili
Mastigodryas melanolomus
Mastigodryas boddaerti
Mastigodryas bifossatus
Rhinobothryum lentiginosum
Stenorrhina freminvillei
Chionactis occipitalis
Chilomeniscus stramineus
Sonora semiannulata
Conopsis biserialis
Conopsis nasus
Pseudoficimia frontalis
Sympholis lippiens
Gonyosoma oxycephalum
Gonyosoma jansenii
Elaphe carinata
Elaphe bimaculata
Elaphe dione
Elaphe climacophora
Elaphe schrenckii
Elaphe quadrivirgata
Elaphe quatuorlineata
Elaphe sauromates
Chironius exoletus
Chironius laurenti
Chironius multiventris
Drymoluber dichrous
Coronella austriaca
Oocatochus rufodorsatus
Senticolis triaspis
Pituophis deppei
Pituophis vertebralis
Pituophis lineaticollis
Pituophis melanoleucus
Pituophis ruthveni
Pituophis catenifer
Pantherophis vulpinus
Pantherophis guttatus
Pantherophis emoryi
99 Pantherophis slowinskii
Pantherophis spiloides
100 Pantherophis alleghaniensis
Pantherophis obsoletus
Pantherophis bairdi
Bogertophis subocularis
Bogertophis rosaliae
Rhinocheilus lecontei
Arizona elegans
Pseudelaphe flavirufa
Cemophora coccinea
Lampropeltis calligaster
Lampropeltis webbi
72
79 94
96 98
74
96
60
98
99
Lampropeltis pyromelana
Lampropeltis zonata
Lampropeltis elapsoides
Lampropeltis mexicana
Lampropeltis ruthveni
Lampropeltis triangulum
Lampropeltis extenuatum
Lampropeltis alterna
Lampropeltis nigra
Lampropeltis getula
Lampropeltis holbrooki
Lampropeltis splendida
Lampropeltis californiae
Lycodon aulicus

Z
Figure 27
Natricinae
100
99
68
98
69
99
100
98
100
98
100
86
100
Trachischium monticola
Amphiesma sauteri
Amphiesma craspedogaster
Natriciteres olivacea
Afronatrix anoscopus
Lycognathophis seychellensis
Macropisthodon rudis
100
Balanophis ceylonensis
Rhabdophis subminiatus
62 Rhabdophis tigrinus
96 Rhabdophis nuchalis
Amphiesma stolatum
Xenochrophis vittatus
Xenochrophis flavipunctatus
Xenochrophis piscator
100
Atretium schistosum
Xenochrophis punctulatus
Xenochrophis asperrimus
88 Atretium yunnanensis
100
Aspidura drummondhayi
Aspidura trachyprocta
Aspidura ceylonensis
99
Aspidura guentheri
Opisthotropis guangxiensis
Opisthotropis lateralis
Opisthotropis latouchii
100 Opisthotropis cheni
100 Sinonatrix aequifasciata
88
100
82
88
100
72
97
76
96
100
100
80
100
99
Sinonatrix percarinata
Sinonatrix annularis
Natrix maura
Natrix natrix
Natrix tessellata
Clonophis kirtlandii
Virginia striatula
Storeria occipitomaculata
Storeria dekayi
Seminatrix pygaea
98
50
100
100
100
100
69
100
93
100
Regina rigida
Regina alleni
Regina septemvittata
Regina grahami
Tropidoclonion lineatum
Nerodia cyclopion
Nerodia floridana
Nerodia taxispilota
Nerodia rhombifer
Nerodia erythrogaster
Nerodia harteri
Nerodia fasciata
Nerodia sipedon
Thamnophis sirtalis
Thamnophis sauritus
Thamnophis proximus
Thamnophis rufipunctatus
Adelophis foxi
Thamnophis valida
Thamnophis melanogaster
Thamnophis exsul
72
Thamnophis godmani
96
85
100
Thamnophis scaliger
Thamnophis sumichrasti
98
Thamnophis mendax
86
99
Thamnophis fulvus
100
Thamnophis chrysocephalus
Thamnophis cyrtopsis
Thamnophis eques
99
Thamnophis marcianus
100 Thamnophis hammondii
92
63
73
Thamnophis ordinoides
99
Thamnophis couchii
69
Thamnophis atratus
Thamnophis gigas
Thamnophis elegans
94 Thamnophis brachystoma
100 Thamnophis radix
89 Thamnophis butleri

AA
Figure 28
(i)
100
Dipsadinae
Conophis lineatus
Thermophis zhaoermii
95
Crisantophis nevermanni
100
Psomophis obtusus
Thermophis baileyi
Psomophis genimaculatus
100
94
Psomophis joberti
Contia tenuis
100 Pseudalsophis biserialis
72
Pseudalsophis elegans
Heterodon platirhinos
100
100
Arrhyton taeniatum
Arrhyton supernum
Heterodon simus
Arrhyton vittatum
58
99
Arrhyton landoi
Heterodon nasicus
73 Arrhyton procerum
91
Diadophis punctatus
75 100 Arrhyton tanyplectum
98 Arrhyton dolichura
Magliophis exiguum
Carphophis amoenus
(ii) 81
87
100 Cubophis cantherigerus
100
Cubophis vudii
80
Farancia abacura
99
Caraiba andreae
98
93 Haitiophis anomalus
Farancia erytrogramma
Borikenophis portoricensis
80
100 Alsophis antillensis
Nothopsis rugosus
Alsophis rijgersmaei
97 97 Alsophis antiguae
68
Amastridium veliferum
100 Alsophis rufiventris
99
Ialtris dorsalis
Tantalophis discolor
89
Darlingtonia haetiana
99
Hypsirhynchus ferox
Coniophanes fissidens
83
Antillophis parvifrons
98 Schwartzophis callilaemum
Rhadinaea flavilata
93 96
100 Schwartzophis polylepis
100 Schwartzophis funereum
86
Rhadinaea fulvivittis
100
Uromacer catesbyi
Uromacer oxyrhynchus
Pseudoleptodeira latifasciata
99 Uromacer frenatus
Lygophis anomalus
80
Trimetopon gracile
100 Lygophis elegantissimus
99
99
Lygophis lineatus
Hypsiglena slevini
Lygophis paucidens
78
76
73
Lygophis flavifrenatus
Hypsiglena jani
70
Lygophis meridionalis
Xenodon severus
63
100
Hypsiglena affinis
Xenodon merremi
100
98
Xenodon werneri
100
52
Xenodon neuwiedii
99 Hypsiglena ochrorhyncha
98 Xenodon dorbignyi
75
Xenodon histricus
84 Hypsiglena torquata
99 Xenodon nattereri
85
Xenodon guentheri
Hypsiglena chlorophaea
71
Xenodon semicinctus
90
94
61 98
Xenodon matogrossensis
Tretanorhinus variabilis
62 Xenodon pulcher
92 Eryrthrolamprus atraventer
64
Leptodeira nigrofasciata
Eryrthrolamprus jaegeri
73
Eryrthrolamprus almadensis
Imantodes inornatus
Eryrthrolamprus ceii
89 71
99 100 Eryrthrolamprus poecilogyrus
Imantodes lentiferus
Eryrthrolamprus epinephelus
67
87 94 Eryrthrolamprus juliae
100
Imantodes gemmistratus
Eryrthrolamprus miliaris
86
96 Eryrthrolamprus reginae
Imantodes cenchoa
Eryrthrolamprus breviceps
88
Eryrthrolamprus pygmaea
Leptodeira uribei
97 Eryrthrolamprus typhlus
Erythrolamprus mimus
100
87
Leptodeira frenata
100 Erythrolamprus aesculapii
51
Philodryas baroni
Leptodeira splendida
Philodryas nattereri
100
100 88
Philodryas viridissima
Leptodeira punctata
Philodryas olfersii
Philodryas argentea
91
Leptodeira septentrionalis
68 100 Philodryas georgeboulengeri
90
Philodryas mattogrossensis
98 Leptodeira annulata
68 96 Philodryas psammophidea
97
Philodryas aestiva
Leptodeira bakeri
62
Philodryas agassizii
94
Philodryas patagoniensis
88
Leptodeira maculata
Sordellina punctata
95
Taeniophallus brevirostris
100 Leptodeira rubricata
100
Taeniophallus nicagus
66 Echinanthera melanostigma
Adelphicos quadrivirgatum
67 Echinanthera undulata
79 75 Taeniophallus affinis
90
Hydromorphus concolor
95 Phalotris lemniscatus
100
Phalotris nasutus
Tretanorhinus nigroluteus
100
Phalotris lativittatus
100
Phalotris mertensi
100
100
Cryophis hallbergi
Elapomorphus quinquelineatus
Apostolepis assimilis
56
Geophis carinosus
Apostolepis dimidiata
95
91
Apostolepis albicollaris
97
Apostolepis flavotorquata
94
Geophis godmani
94
69
Apostolepis sanctaeritae
Apostolepis cearensis
Atractus zidoki
99
Manolepis putnami
55
Hydrops triangularis
Atractus wagleri
Pseudoeryx plicatilis
83 86
Helicops infrataeniatus
Atractus schach
100
68
Helicops hagmanni
91 98
Helicops carinicaudus
96
Atractus albuquerquei
91 99 Helicops gomesi
68
Helicops angulatus
Atractus elaps
Gomesophis brasiliensis
(i)
(ii)
70
100
82
73
70
75
73
90
84
75
89
79
88
97
79
Atractus flammigerus
Atractus trihedrurus
Ninia atrata
Sibon nebulatus
96
Atractus reticulatus
Tropidodipsas sartorii
100
Dipsas indica
Dipsas variegata
Dipsas pratti
Atractus badius
Atractus zebrinus
Dipsas catesbyi
Dipsas neivai
Sibynomorphus turgidus
Dipsas articulata
Sibynomorphus mikanii
Dipsas albifrons
Sibynomorphus ventrimaculatus
Sibynomorphus neuwiedi
91
68
87
56
100
87
86
94 90
90
93 99
100
100
100
97
98
95
95
87
Calamodontophis paucidens
Pseudotomodon trigonatus
Tachymenis peruviana
Ptychophis flavovirgatus
Tomodon dorsatus
Thamnodynastes pallidus
Thamnodynastes lanei
Thamnodynastes hypoconia
Thamnodynastes strigatus
Thamnodynastes rutilus
Tropidodryas serra
Tropidodryas striaticeps
Xenopholis undulatus
Xenopholis scalaris
Caaeteboia amarali
Hydrodynastes bicinctus
100 Hydrodynastes gigas
Siphlophis cervinus
91 Siphlophis compressus
Siphlophis pulcher
100 Siphlophis longicaudatus
67
63 95 67
96
96
87
74
92
90
Oxyrhopus petolarius
Oxyrhopus formosus
Oxyrhopus trigeminus
Oxyrhopus clathratus
Oxyrhopus rhombifer
Oxyrhopus melanogenys
Oxyrhopus guibei
Rodriguesophis iglesiasi
Paraphimophis rusticus
Phimophis guerini
Clelia clelia
Mussurana bicolor
Drepanoides anomalus
Boiruna maculata
Rhachidelus brazili
Pseudoboa neuwiedii
Pseudoboa nigra
Pseudoboa coronata
100

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