A phylogeny and revised classification of Squamata, including 4161

Transcription

A phylogeny and revised classification of
Squamata, including 4161 species of lizards
and snakes
Pyron et al.
Pyron et al. BMC Evolutionary Biology 2013, 13:93
http://www.biomedcentral.com/1471-2148/13/93
RESEARCH ARTICLE
Open Access
A phylogeny and revised classification of
and snakes
R Alexander Pyron1*, Frank T Burbrink2,3 and John J Wiens4
Abstract
Background: The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and
conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the
group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to
address their classification. Here, we present the first large-scale phylogenetic estimate for Squamata.
Results: The estimated phylogeny contains 4161 species, representing all currently recognized families and
subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from
12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial
genes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates of
higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that
are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ
from previous molecular estimates and many that differ from traditional taxonomy.
Conclusions: We present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for
future comparative studies. We also present a revised classification of squamates at the family and subfamily level
to bring the taxonomy more in line with the new phylogenetic hypothesis. This classification includes new,
resurrected, and modified subfamilies within gymnophthalmid and scincid lizards, and boid, colubrid, and
lamprophiid snakes.
Keywords: Amphisbaenia, Lacertilia, Likelihood support measures, Missing data, Serpentes, Squamata,
Phylogenetics, Reptilia, 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,
* Correspondence: [email protected]
1
Department of Biological Sciences, The George Washington University,
2023 G St. NW, Washington, DC 20052, USA
Full list of author information is available at the end of the article
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.
© 2013 Pyron et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative
Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and
reproduction in any medium, provided the original work is properly cited.
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 broadscale 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], higherlevel 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
Page 2 of 53
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 genes (7 nuclear, 5 mitochondrial). We include species
from all currently described families and subfamilies.
In terms of species sampled, this is 5 times larger than any
previous phylogeny for any one squamate group [30,41],
3 times larger than the largest supertree estimate [11],
and 25 times larger than the largest molecular study of
higher-level squamate relationships [20]. While we did
not sequence any new taxa specifically for this project,
much of the data in the combined matrix were generated in our labs or from our previous collaborative projects [16,19,20,34,36,37,41,44,78-82], including thousands
of gene sequences from hundreds of species (>550 species; ~13% of the total).
The supermatrix approach can provide a relatively
comprehensive phylogeny, and uncover novel relationships not seen in any of the separate analyses in which
the data were generated. Such novel relationships can be
revealed via three primary mechanisms. First, different
studies may have each sampled different species from a
given group for the same genes, and combining these
data may reveal novel relationships not apparent in the
separate analyses. Second, different studies may have
used different genetic markers for the same taxa, and
combining these markers can dramatically increase character sampling, potentially revealing new relationships
and providing stronger support for previous hypotheses.
Third, even for clades that were previously studied using
complete taxon sampling and multiple loci, novel relationships may be revealed by including these lineages
with other related groups in a large-scale phylogeny.
The estimated tree and branch-lengths should be useful for comparative studies of squamate biology. However, this phylogeny is based on a supermatrix with
extensive missing data (mean = 81% per species). Some
authors have suggested that matrices with missing cells
may yield misleading estimates of topology, support, and
branch lengths [83]. Nevertheless, most empirical and
simulation studies have not found this to be the case, at
least for topology and support [41,73,84,85]. Though
fewer studies have examined the effects of missing data
on branch lengths [44,86,87], these also suggest that
missing data do not strongly impact estimates. Here, we
test whether branch lengths for terminal taxa are related
to their completeness.
In general, our results corroborate those of many recent
molecular studies with regard to higher-level relationships,
species-level relationships, and the monophyly, composition, and relationships of most families, subfamilies, and
genera. However, our results differ from previous estimates
for some groups, and reveal (or corroborate) numerous
problems in the existing classification of squamates. We
therefore provide a conservative, updated classification of
extant squamates at the family and subfamily level based
on the new phylogeny, while highlighting problematic taxonomy at the genus level, without making changes. The
generic composition of all families and subfamilies under
our revised taxonomy are provided in Appendix I.
We note dozens of problems in the genus-level taxonomy suggested by our tree, but we acknowledge in advance that we do not provide a comprehensive review of
the previous literature dealing with all these taxonomic issues (this would require a monographic treatment). Similarly, we do not attempt to fix these genus-level problems
here, as most will require more extensive taxon (and potentially character) sampling to adequately resolve.
Throughout the paper, we address only extant squamates. Squamata also includes numerous extinct species classified in both extant and extinct families,
subfamilies, and genera. Relationships and classification
of extinct squamates based on morphological data
from fossils have been addressed by numerous authors
(e.g. [14,15,19,22,88-93]). A classification based only on
living taxa may create some problems for classifying
fossil taxa, but these can be addressed in future studies
that integrate molecular and fossil data [19,86].
Results
Supermatrix phylogeny
We generated the final tree (lnL = −2609551.07) using
Maximum Likelihood (ML) in RAxMLv7.2.8. Support
was assessed using the non-parametric ShimodairaHasegawa-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.
Page 3 of 53
Higher-level relationships
Our tree (Figure 1) is broadly congruent with most previous molecular studies of higher-level squamate phylogeny
using both nuclear data and combined nuclear and mitochondrial data (e.g. [16-20]), providing important confirmation of previous molecular studies based on more limited
taxon sampling. Specifically we support (Figure 1): (i) the
placement of dibamids and gekkotans near the base of the
tree (Figure 1A); (ii) a sister-group relationship between
Scincoidea (scincids, cordylids, gerrhosaurids, and xantusiids; Figure 1B) and a clade (Episquamata; Figure 1C)
containing the rest of the squamates excluding dibamids
and gekkotans; (iii) Lacertoidea (lacertids, amphisbaenians,
teiids, and gymnophthalmids; Figure 1D), and (iv) a clade
(Toxicofera; Figure 1E) containing anguimorphs (Figure 1F),
iguanians (Figure 1G), and snakes (Figure 1H) as the sister
taxon to Lacertoidea.
These relationships are strongly supported in general
(Figure 1), but differ sharply from most trees based on
morphological data [13-15,19,22,95]. Nevertheless, many
clades found in previous morphological taxonomies and
phylogenies are also present in this tree in some
form, including Amphisbaenia, Anguimorpha, Gekkota,
Iguania, Lacertoidea (but including amphisbaenians),
Scincoidea, Serpentes, and many families and subfamilies.
In contrast, the relationships among these groups differ
strongly between molecular analyses [17-20] and morphological analyses [14,15]. Our results demonstrate that this
incongruence is not explained by limited taxon sampling in
the molecular data sets. In fact, our species-level sampling
is far more extensive than in any morphological analyses
(e.g. [14,15]), by an order of magnitude.
We find that the basal squamate relationships are strongly supported in our tree. The family Dibamidae is the sister
group to all other squamates, and Gekkota is the sister
group to all squamates excluding Dibamidae (Figure 1), as
in some previous studies (e.g. [16,18]). Other recent molecular analyses have also placed Dibamidae near the squamate root, but differed in placing it as either the sister
taxon to all squamates excluding Gekkota [17], or the
sister- group of Gekkota [19,20]. Our results also corroborate that the New World genus Anelytropsis is nested within
the Old World genus Dibamus [96], but the associated
branches are weakly supported (Figure 2).
Gekkota
Within Gekkota, we corroborate both earlier morphological [97] and recent molecular estimates [55,56,59,98]
in supporting a clade containing the Australian radiation of
"diplodactylid" geckos (Carphodactylidae and Diplodactylidae) and the snakelike pygopodids (Figures 1, 2).
As in previous studies [55], Carphodactylidae is the
weakly supported sister group to Pygopodidae, and
this clade is the sister group of Diplodactylidae
Page 4 of 53
Sphenodontidae
Dibamidae
77
Carphodactylidae
Pygopodidae
Diplodactylidae
Eublepharidae
100
Sphaerodactylidae
100
Phyllodactylidae
Gekkonidae
100
Cricosaurinae
Xantusiidae
Xantusiinae
100
Lepidophyminae
99
100
Gerrhosaurinae
Gerrhosauridae
Zonosaurinae
B 100 100 100
Platysaurinae
Cordylidae
Cordylinae
100
Acontiinae
95
Scincinae
Scincidae
100
Lygosominae
94
Tupinambinae
54
Teiidae
Teiinae
Alopoglossinae
100
Bachiinae
84
Rhachisaurinae
98
Gymnophthalmidae
Gymnophthalminae
99
100
Ecpleopinae
100
Cercosaurinae
D
Rhineuridae
99
Bipedidae
100
Blanidae
100
Cadeidae
84
100
Trogonophiidae
Amphisbaenidae
100
100
Gallotiinae
Lacertidae
Lacertinae
Xenosauridae
100
Helodermatidae
Anniellidae
Diploglossinae
F 95
100
Anguinae
Anguidae
90
100
Gerrhonotinae
100
C
Shinisauridae
100
Lanthanotidae
94
Varanidae
100
100
Brookesiinae
79
Chamaeleonidae
Chamaeleoninae
Uromastycinae
100
Leiolepidinae
100
Hydrosaurinae
Agamidae
96
Amphibolurinae
100
Agaminae
100
G
Draconinae
100
Tropiduridae
100
Iguanidae
Leiocephalidae
Crotaphytidae
72
87
Phrynosomatidae
54
96 E
Polychrotidae
99
Hoplocercidae
81
Opluridae
99
Enyaliinae
63
Leiosauridae
Leiosaurinae
95
100
Liolaemidae
Corytophanidae
Dactyloidae
99
Anomalepididae
Leptotyphlopidae
90
Gerrhopilidae
H
100
Xenotyphlopidae
100
Typhlopidae
83
Aniliidae
98
Tropidophiidae
Xenophiidae
Bolyeriidae
Sanziniinae
100
100
Calabariidae
Ungaliophiinae
Boidae
69
Candoiinae
99
87
97
Erycinae
88 83
Boinae
Anomochilidae
65
Cylindrophiidae
100
Uropeltidae
89
Xenopeltidae
Loxocemidae
98
100
Pythonidae
Acrochordidae
95
Xenodermatidae
Pareatidae
Viperinae
100
100
Azemiopinae
Viperidae
Crotalinae
100
100
Homalopsidae
Prosymninae
95
Psammophiinae
58 95
95
Atractaspidinae
100
Aparallactinae
96
Lamprophiidae
Pseudaspidinae
Lamprophiinae
90
Pseudoxyrhophiinae
100
Elapidae
Calamariinae
97
Pseudoxenodontinae
Sibynophiinae
Colubridae
100 74
Grayiinae
71
Colubrinae
68
Natricinae
0.2 subst./site
Dipsadinae
A
Squamata
A) Gekkota
B) Scincoidea
C) Episquamata
D) Lacertoidea
E) Toxicofera
F) Anguimorpha
G) Iguania
H) Serpentes
100
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.
A
Figure 2 (See legend on next page.)
Page 5 of 53
Page 6 of 53
(See figure on previous page.)
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-AA). Within panels, branch lengths are proportional to expected substitutions per site, but the relative scale differs between panels.
(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 re-
cognized 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 reclassification based on multiple nuclear and mitochondrial
genes [108]. This classification broke up the nonmonophyletic 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 support the distinctiveness of
Platysaurus (Figure 5) and recognition of the subfamily
Platysaurinae [108].
We strong support (SHL = 100) for the monophyly of
Scincidae (Figure 6) as in previous studies (e.g.
[20,50,51]). We strongly support 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 approxi
\mate 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
Page 7 of 53
79
Eublepharidae
100
100
100
97
60
100
75
100
78
99
83
100
Sphaerodactylidae
Aeluroscalabotes felinus
Coleonyx brevis
Coleonyx variegatus
Coleonyx mitratus
Coleonyx elegans
100
100 Eublepharis macularius
Eublepharis turcmenicus
Holodactylus africanus
Hemitheconyx caudicinctus
100
Hemitheconyx taylori
100
Goniurosaurus kuroiwae
Goniurosaurus lichtenfelderi
Goniurosaurus catbaensis
100
Goniurosaurus luii
96
Goniurosaurus araneus
90
Pristurus celerrimus
100
Pristurus insignis
100
Pristurus sokotranus
Pristurus guichardi
76
Pristurus abdelkuri
92
100
Pristurus flavipunctatus
Pristurus rupestris
Pristurus minimus
100
Pristurus carteri
63
98
Pristurus crucifer
85
Pristurus somalicus
100
Quedenfeldtia trachyblepharus
Quedenfeldtia moerens
Aristelliger lar
100
Aristelliger praesignis
Aristelliger georgeensis
91
Saurodactylus fasciatus
Euleptes europaea
Teratoscincus microlepis
Teratoscincus scincus
100
Teratoscincus
przewalskii
97
Teratoscincus roborowskii
98
Saurodactylus mauritanicus
Chatogekko amazonicus
100
Lepidoblepharis xanthostigma
Lepidoblepharis festae
97
Gonatodes eladioi
Gonatodes caudiscutatus
89
Gonatodes daudini
100
Gonatodes albogularis
96
Gonatodes petersi
100
Gonatodes vittatus
Gonatodes infernalis
98
Gonatodes hasemani
Gonatodes annularis
70
Gonatodes superciliaris
60
Gonatodes alexandermendesi
100
Gonatodes purpurogularis
60
Gonatodes taniae
100
Gonatodes falconensis
95
Gonatodes humeralis
97
Gonatodes antillensis
100
Gonatodes concinnatus
93
89
Gonatodes seigliei
100
Gonatodes ceciliae
99
Gonatodes ocellatus
Coleodactylus septentrionalis
Coleodactylus brachystoma
100
Coleodactylus meridionalis
99
Coleodactylus natalensis
100
100
Pseudogonatodes manessi
96
Pseudogonatodes lunulatus
Pseudogonatodes guianensis
Sphaerodactylus fantasticus
Sphaerodactylus sputator
98
87
Sphaerodactylus elegantulus
Sphaerodactylus sabanus
Sphaerodactylus parvus
81
Sphaerodactylus microlepis
Sphaerodactylus vincenti
82
100
100 Sphaerodactylus kirbyi
Sphaerodactylus schwartzi
Sphaerodactylus ramsdeni
84 84
Sphaerodactylus cricoderus
Sphaerodactylus richardi
83
Sphaerodactylus oliveri
100
91
Sphaerodactylus molei
84
Sphaerodactylus glaucus
Sphaerodactylus thompsoni
81
69
Sphaerodactylus cinereus
Sphaerodactylus torrei
Sphaerodactylus intermedius
100
100 Sphaerodactylus nigropunctatus
93
Sphaerodactylus copei
83
Sphaerodactylus leucaster
Sphaerodactylus elegans
Sphaerodactylus shrevei
99
85
Sphaerodactylus cryphius
Sphaerodactylus darlingtoni
90
Sphaerodactylus notatus
Sphaerodactylus altavelensis
52
Sphaerodactylus roosevelti
85
Sphaerodactylus argus
Sphaerodactylus macrolepis
93
Sphaerodactylus armstrongi
84
Sphaerodactylus townsendi
83
Sphaerodactylus goniorhynchus
66 79
Sphaerodactylus semasiops
Sphaerodactylus klauberi
Sphaerodactylus gaigeae
94
Sphaerodactylus ocoae
99 Sphaerodactylus nicholsi
100
Thecadactylus solimoensis
Thecadactylus rapicauda
Haemodracon riebeckii
Asaccus platyrhynchus
Ptyodactylus ragazzii
100
Ptyodactylus oudrii
100
Ptyodactylus hasselquistii
Ptyodactylus guttatus
Homonota gaudichaudii
Homonota fasciata
Homonota underwoodi
100
Homonota borellii
85
Homonota darwinii
Homonota andicola
92
Phyllodactylus wirshingi
Phyllodactylus reissii
100
Phyllodactylus tuberculosus
86
Phyllodactylus lanei
65
Phyllodactylus bordai
100
97
Phyllodactylus xanti
Phyllodactylus
unctus
99
100
Phyllodactylus bugastrolepis
97
Phyllodactylus nocticolus
100
Phyllodactylus paucituberculatus
Phyllodactylus delcampoi
67
Phyllodactylus duellmani
75
Phyllodactylus davisi
96
57 Phyllodactylus homolepidurus
Phyllopezus periosus
Phyllopezus pollicaris
100
Phyllopezus lutzae
90
92
Phyllopezus maranjonensis
Tarentola americana
Tarentola boehmei
100
Tarentola deserti
100
Tarentola mauritanica
99
Tarentola angustimentalis
Tarentola neglecta
87
100
Tarentola mindiae
99
Tarentola boettgeri
100
Tarentola ephippiata
93
Tarentola annularis
Tarentola gomerensis
76
Tarentola delalandii
91
Tarentola chazaliae
62
Tarentola darwini
Tarentola rudis
100 99
Tarentola caboverdiana
73 Tarentola gigas
100
100
79
82
87
100
Phyllodactylidae
98
65
93
100
100
100
92
73
B
Figure 3 Species-level squamate phylogeny continued (B).
C
Lepidodactylus novaeguineae
Perochirus ateles
Pseudogekko smaragdinus
Urocotyledon inexpectata
Ebenavia inunguis
93
Pseudogekko compressicorpus
Paroedura masobe
83
Lepidodactylus orientalis
Paroedura gracilis
Luperosaurus macgregori
100
100
Paroedura homalorhina
99
98
Luperosaurus cumingii
Paroedura oviceps
Luperosaurus joloensis
79
Paroedura karstophila
73
100 Lepidodactylus lugubris
Paroedura lohatsara
100
100
100
91
Lepidodactylus moestus
Paroedura stumpffi
Gekko smithii
100
Paroedura sanctijohannis
85
Gekko gecko
Paroedura picta
99
Gekko chinensis
Paroedura androyensis
100
100
Paroedura vazimba
Gekko japonicus
92
99
Paroedura tanjaka
Gekko hokouensis
61
Paroedura bastardi
100
95
Gekko auriverrucosus
98
100
Ailuronyx tachyscopaeus
Gekko swinhonis
54
Ailuronyx seychellensis
Gekko athymus
100 Ailuronyx trachygaster
Gekko monarchus
100
Calodactylodes illingworthorum
Gekko mindorensis
Calodactylodes aureus
100
100
98
Gekko romblon
Ptenopus carpi
99
Gekko crombota
Narudasia festiva
65
80
Cnemaspis uzungwae
Gekko porosus
100
Cnemaspis dickersonae
Ptychozoon rhacophorus
53
100
89
69
Cnemaspis africana
Ptychozoon kuhli
87
Uroplatus guentheri
64
Ptychozoon lionotum
92
95
Uroplatus malahelo
Luperosaurus iskandari
Uroplatus malama
100
Gekko vittatus
100
Uroplatus ebenaui
97
Gekko petricolus
Uroplatus phantasticus
94
100
85
Gekko badenii
Uroplatus alluaudi
96
Gekko grossmanni
50
Uroplatus pietschmanni
100
Dixonius melanostictus
Uroplatus lineatus
100
Uroplatus sikorae
100 Dixonius vietnamensis
100
100
Uroplatus henkeli
77
Dixonius siamensis
100
Uroplatus giganteus
100
Heteronotia planiceps
100
Uroplatus fimbriatus
100
Heteronotia binoei
100
Paragehyra gabriellae
Heteronotia spelea
56
Christinus marmoratus
97
Nactus acutus
Afrogecko swartbergensis
Nactus eboracensis
Cryptactites peringueyi
100
100
Nactus vankampeni
Matoatoa brevipes
100
Nactus galgajuga
100
Afrogecko porphyreus
83
52
Nactus cheverti
Afroedura pondolia
100
52
Afroedura karroica
Nactus multicarinatus
100
98
79
Geckolepis typica
Nactus pelagicus
Geckolepis
maculata
100
Hemiphyllodactylus typus
Homopholis
fasciata
99
89
Hemiphyllodactylus yunnanensis
100
100
Homopholis walbergii
93
Hemiphyllodactylus aurantiacus
85
Homopho lis mulleri
Gehyra fehlmanni
100
100
Blaesodactylus boivini
Gehyra mutilata
Blaesodactylus antongilensis
99
100
98
Gehyra
lacerata
100
Blaesodactylus
sakalava
97
Gehyra brevipalmata
Goggia lineata
100
Rhoptropus afer
Gehyra baliola
100
Rhoptropus bradfieldi
Gehyra barea
84
99
Rhoptropus boultoni
Gehyra marginata
100
59
99
Rhoptropus biporosus
Gehyra oceanica
98
91
Rhoptropus barnardi
98
Gehyra membranacruralis
96
86
Elasmodactylus tetensis
Gehyra dubia
100
Elasmodactylus tuberculosus
100
Gehyra catenata
Chondrodactylus angulifer
100
Gehyra
pamela
Pachydactylus laevigatus
100
Gehyra borroloola
Chondrodactylus turneri
55
100
96
97
Gehyra robusta
Chondrodactylus fitzsimonsi
100 86
70
Chondrodactylus bibronii
Gehyra koira
Pachydactylus robertsi
100
Gehyra occidentalis
93
100
Colopus wahlbergii
Gehyra australis
Colopus kochii
Gehyra xenopus
98
Pachydactylus haackei
Gehyra nana
Pachydactylus kladaroderma
Gehyra purpurascens
98
89
Pachydactylus namaquensis
100
Pachydactylus scutatus
98
68
100 Gehyra variegata
Gehyra punctata
74 100
Pachydactylus parascutatus
Gehyra pilbara
Pachydactylus reconditus
98
70
Gehyra montium
Pachydactylus gaiasensis
95
92
Pachydactylus oreophilus
90
Gehyra minuta
100 91
Pachydactylus bicolor
Alsophylax pipiens
Pachydactylus caraculicus
Tropiocolotes helenae
Pachydactylus sansteynae
65
100
63
Cnemaspis limi
Pachydactylus scherzi
86
Cnemaspis kendallii
Pachydactylus punctatus
96
100
Mediodactylus spinicaudum
85
Pachydactylus rugosus
100
Mediodactylus russowii
99
98
Pachydactylus formosus
Pseudoceramodactylus khobarensis
Pachydactylus barnardi
95
Tropiocolotes tripolitanus
Pachydactylus labialis
84
96
Pachydactylus geitje
Stenodactylus arabicus
Pachydactylus maculatus
92
Stenodactylus petrii
52
Pachydactylus oculatus
93
100
Stenodactylus leptocosymbotus
Pachydactylus purcelli
Stenodactylus doriae
96
100
Pachydactylus waterbergensis
61 100
Stenodactylus yemenensis
Pachydactylus tsodiloensis
100
97
Stenodactylus sthenodactylus
85
Pachydactylus fasciatus
Mediodactylus kotschyi
98
Pachydactylus carinatus
85
Mediodactylus sagittiferum
Pachydactylus griffini
99
Mediodactylus heterocercum
Pachydactylus serval
68
69
Mediodactylus heteropholis
Pachydactylus weberi
99
74
Pachydactylus monicae
Bunopus tuberculatus
100
75
Pachydactylus mclachlani
69
Crossobamon orientalis
Pachydactylus mariquensis
Bunopus crassicauda
86
99
Pachydactylus austeni
Agamura
persica
95
Pachydactylus rangei
Cyrtopodion sistanensis
100
Pachydactylus vanzyli
Cyrtopodion scabrum
99
Pachydactylus montanus
Cyrtopodion longipes
Pachydactylus tigrinus
79
Cyrtopodion caspium
100
100
Pachydactylus oshaughnessyi
Cyrtopodion agamuroides
Pachydactylus capensis
72
Pachydactylus vansoni
Cyrtopodion gastrophole
99
100
100
Pachydactylus affinis
Cyrtodactylus oldhami
Cnemaspis podihuna
87
100
Cyrtodactylus ayeyarwadyensis
Cnemaspis kandiana
100
Cyrtodactylus angularis
100
99
Cnemaspis
tropidogaster
Cyrtodactylus jarujini
Rhoptropella ocellata
Cyrtodactylus triedrus
Lygodactylus expectatus
88
Cyrtodactylus marmoratus
Lygodactylus rarus
92
Cyrtodactylus irregularis
Lygodactylus madagascariensis
99
71
Cyrtodactylus consobrinus
100
Lygodactylus miops
98
Cyrtodactylus annulatus
92
Lygodactylus guibei
52
Lygodactylus tolampyae
Cyrtodactylus philippinicus
97
100
92
Lygodactylus heterurus
Cyrtodactylus agusanensis
98
100
100
Lygodactylus verticillatus
Cyrtodactylus intermedius
Lygodactylus blancae
81
Cyrtodactylus pulchellus
Lygodactylus arnoulti
79
91
90
Cyrtodactylus sermowaiensis
85
Lygodactylus pauliani
94
Cyrtodactylus loriae
Lygodactylus gravis
77
Cyrtodactylus novaeguineae
81
Lygodactylus montanus
99
82
Cyrtodactylus tuberculatus
Lygodactylus tuberosus
96
98
Cyrtodactylus klugei
Lygodactylus mirabilis
73
97
Cyrtodactylus robustus
98
Lygodactylus pictus
Lygodactylus lawrencei
Cyrtodactylus tripartitus
98
Lygodactylus stevensoni
Cyrtodactylus epiroticus
89
98
68
Lygodactylus capensis
Cyrtodactylus louisiadensis
93
99
84
Lygodactylus bradfieldi
Hemidactylus bowringii
100
Lygodactylus klugei
Hemidactylus garnotii
100
Lygodactylus conraui
Hemidactylus karenorum
100
97
Lygodactylus thomensis
Hemidactylus platyurus
Lygodactylus angularis
78
Hemidactylus fasciatus
Lygodactylus gutturalis
67
100
Hemidactylus aaronbaueri
Lygodactylus chobiensis
94
93
Lygodactylus williamsi
Hemidactylus giganteus
81
94
Lygodactylus picturatus
Hemidactylus depressus
68
100 Lygodactylus luteopicturatus
Hemidactylus triedrus
89
97
Lygodactylus kimhowelli
Hemidac
tylus
prashadi
93
88
Lygodactylus keniensis
Hemidactylus maculatu s
100
76
92
93
Phelsuma vanheygeni
100
Hemidactylus leschenaultii
Phelsuma astriata
100
Hemidactylus flaviviridis
100
Phelsuma sundbergi
Hemidactylus frenatus
Phelsuma guttata
Hemidactylus brookii
Phelsuma madagascariensis
100
Hemidactylus sataraensis
Phelsuma abbotti
100
100
Phelsuma parkeri
Hemidactylus imbricatus
100
99
87
Phelsuma seippi
Hemidactylus albofasciatus
56
Phelsuma barbouri
Hemidactylus reticulatus
100
100 Phelsuma pronki
Hemidactylus gracilis
96
97
Phelsuma breviceps
Hemidactylus angulatus
Phelsuma mutabilis
85
Hemidactylus haitianus
100
Phelsuma andamanense
92
57
Hemidactylus mabouia
Phelsuma standingi
82
Phelsuma edwardnewtoni
100 Hemidactylus mercatorius
94
Hemidactylus longicephalus
Phelsuma gigas
Hemidactylus platycephalus
guentheri
100
99
99 Phelsuma
97
Phelsuma borbonica
Hemidac tylus greeffii
95
100
Phelsuma cepediana
Hemidactylus bra silianus
100
Phelsuma guimbeaui
Hemidactylus bouvieri
96
Phelsuma ornata
100
99
Hemidactylus
palaichthus
95
100
Phelsuma inexpectata
55
97
Hemidactylus agrius
Phelsuma nigristriata
Hemidactylus modestus
96
Phelsuma modesta
100
98
Hemidactylus citernii
Phelsuma dubia
Hemidactylus foudaii
100
Phelsuma ravenala
Hemidactylus pumilio
98
Phelsuma flavigularis
98
Phelsuma hielscheri
Hemidactylus dracaenacolus
94
Phelsuma berghofi
Hemidactylus granti
100
99
100
Phelsuma malamakibo
Hemidactylus persicus
97
Phelsuma serraticauda
82
Hemidactylus yerburii
95
Phelsuma laticauda
Hemidactylus
robustus
95
91
Phelsuma robertmertensi
Hemidactylus turcicus
99
Phelsuma klemmeri
99 96
Hemidactylus lemurinus
91
Phelsuma antanosy
Hemidactylus mindiae
87
Phelsuma quadriocellata
96
Hemidactylus macropholis
Phelsuma pusilla
99
Hemidactylus oxyrhinus
Phelsuma comorensis
100
66
Phelsuma lineata
Hemidactylus forbesii
57
97
94
Phelsuma kely
98 Hemidactylus homoeolepis
100
(i)
Page 8 of 53
100
(ii)
100
Gekkonidae
(ii)
(i)
C
Figure 4 Species-level squamate phylogeny continued (C).
Page 9 of 53
Cricosaura typica
Xantusia gracilis
Xantusia henshawi
Xantusia bolsonae
100
Xantusia sanchezi
100
Xantusia riversiana
84
97
Xantusia arizonae
92
Xantusia vigilis
Xantusia bezyi
100
100
Xantusia wigginsi
66
Lepidophyma mayae
Lepidophyma tuxtlae
100 100
Lepidophyma lipetzi
Lepidophyma flavimaculatum
Lepidophyminae
100
Lepidophyma reticulatum
100
Lepidophyma pajapanensis
Lepidophyma occulor
94
Lepidophyma
micropholis
87
Lepidophyma sylvaticum
100
Lepidophyma gaigeae
95
Lepidophyma lineri
Lepidophyma smithii
Lepidophyma cuicateca
95
Lepidophyma lowei
94
Lepidophyma radula
100
Lepidophyma dontomasi
100
Gerrhosaurus major
100
Cordylosaurus
subtessellatus
Gerrhosaurinae
95
Tetradactylus seps
Tetradactylus africanus
98
69
Tetradactylus tetradactylus
Gerrhosaurus validus
Gerrhosaurus skoogi
79
Gerrhosaurus typicus
Gerrhosauridae
Gerrhosaurus nigrolineatus
91
100
Gerrhosaurus multilineatus
100
Gerrhosaurus flavigularis
76
100
Tracheloptychus madagascariensis
Tracheloptychus petersi
100
Zonosaurus haraldmeieri
100
Zonosaurus madagascariensis
Zonosaurinae
Zonosaurus ornatus
100 Zonosaurus trilineatus
Zonosaurus quadrilineatus
91
Zonosaurus karsteni
100
Zonosaurus anelanelany
100
Zonosaurus laticaudatus
96
Zonosaurus boettgeri
100
Zonosaurus tsingy
Zonosaurus brygooi
66 73
Zonosaurus subunicolor
82
Zonosaurus bemaraha
89
Zonosaurus aeneus
87
Zonosaurus rufipes
Platysaurus
pungweensis
Platysaurinae
Platysaurus mitchelli
92
Platysaurus broadleyi
100 Platysaurus capensis
Platysaurus intermedius
91
Platysaurus minor
Platysaurus monotropis
100
Ouroborus cataphractus
100
Cordylidae
Karusasaurus jordani
Karusasaurus polyzonus
99
Namazonurus campbelli
Namazonurus pustulatus
100
100
Namazonurus namaquensis
Namazonurus lawrenci
Cordylinae
100
Namazonurus peersi
94
Smaug warreni
Smaug giganteus
100
Chamaesaura aenea
55
Chamaesaura anguina
Pseudocordylus langi
93
Pseudocordylus microlepidotus
Pseudocordylus spinosus
100
Pseudocordylus melanotus
99
95
Ninurta coeruleopunctatus
86
Hemicordylus nebulosus
100
Hemicordylus capensis
95
Cordylus tropidosternum
Cordylus meculae
99
Cordylus vittifer
96
81 88 Cordylus ukingensis
Cordylus beraduccii
82
Cordylus jonesii
83
Cordylus rhodesianus
99
Cordylus macropholis
92
Cordylus imkeae
83
Cordylus aridus
100
Cordylus minor
100
84 Cordylus niger
Cordylus mclachlani
85
Cordylus oelofseni
Cordylus tasmani
86
100 Cordylus cordylus
100
Cricosaurinae
Xantusiinae
100
Xantusiidae
99
D
Figure 5 Species-level squamate phylogeny continued (D).
Page 10 of 53
89
Acontiinae
95
99
100
Typhlosaurus braini
Typhlosaurus meyeri
Typhlosaurus caecus
Typhlosaurus vermis
100 Typhlosaurus lomiae
Acontias gariepensis
Acontias lineatus
Acontias litoralis
100
Acontias kgalagadi
Acontias meleagris
Acontias percivali
Acontias rieppeli
Acontias breviceps
98
Acontias gracilicauda
92
Acontias plumbeus
Acontias poecilus
100
Mesoscincus schwartzei
98
91
Mesoscincus managuae
Ophiomorus punctatissimus
Ophiomorus latastii
99
Brachymeles apus
Brachymeles miriamae
99
Brachymeles tridactylus
100
Brachymeles bonitae
94
Brachymeles minimus
94
Brachymeles cebuensis
95
Brachymeles samarensis
Brachymeles talinis
83
Brachymeles elerae
88
Brachymeles schadenbergi
Brachymeles boulengeri
85
Brachymeles bicolor
85 73
Brachymeles gracilis
85 Brachymeles pathfinderi
Plestiodon tamdaoensis
100 Plestiodon kishinouyei
100
Plestiodon chinensis
Plestiodon quadrilineatus
98
Plestiodon tunganus
Plestiodon capito
100
100 86
Plestiodon barbouri
Plestiodon japonicus
Plestiodon latiscutatus
97
70
Plestiodon elegans
93
Plestiodon marginatus
100
Plestiodon stimpsonii
Plestiodon reynoldsi
Plestiodon egregius
100
97
88
Plestiodon anthracinus
74
Plestiodon inexpectatus
Plestiodon laticeps
56
97
Plestiodon tetragrammus
100
Plestiodon callicephalus
74
Plestiodon obsoletus
76
Plestiodon fasciatus
71
100
Plestiodon multivirgatus
98 86 Plestiodon
septentrionalis
Plestiodon longirostris
92
Plestiodon gilberti
Plestiodon
lagunensis
100
Plestiodon skiltonianus
Plestiodon parviauriculatus
Plestiodon sumichrasti
100 91
Plestiodon lynxe
Plestiodon ochoterenae
73
73
Plestiodon parvulus
76
Plestiodon copei
Plestiodon brevirostris
Plestiodon dugesii
98
Eurylepis taeniolatus
Eumeces schneideri
77
Scincopus fasciatus
100
Eumeces algeriensis
100
Scincus scincus
100
Scincus mitranus
Pamelaescincus gardineri
99
Janetaescincus veseyfitzgeraldi
Janetaescincus braueri
100
Gongylomorphus bojerii
Chalcides mauritanicus
55
81
92
Chalcides minutus
57
Chalcides guentheri
Chalcides chalcides
100
Chalcides pseudostriatus
86
Chalcides striatus
75
Chalcides ocellatus
74
100
Chalcides sepsoides
Chalcides colosii
91
Chalcides bedriagai
100
74
Chalcides boulengeri
Chalcides parallelus
87
88
Chalcides lanzai
99
Chalcides sexlineatus
98
99
Chalcides coeruleopunctatus
Chalcides viridanus
Chalcides sphenopsiformis
100
Chalcides mionecton
Chalcides manueli
94
Chalcides polylepis
95
96 Chalcides montanus
Sepsina angolensis
97
100
97
Typhlacontias brevipes
Typhlacontias punctatissimus
100
Feylinia grandisquamis
100
Feylinia polylepis
96
Feylinia currori
98
93
Melanoseps occidentalis
96
100
Melanoseps ater
Melanoseps loveridgei
Hakaria simonyi
Proscelotes eggeli
Scelotes caffer
80
Scelotes anguineus
89
100
Scelotes mirus
Scelotes arenicolus
87
99
Scelotes bipes
Scelotes sexlineatus
100 97
Scelotes gronovii
Scelotes montispectus
75
92
Scelotes kasneri
94
Paracontias holomelas
100
Paracontias brocchii
Paracontias
manify
60
100
Paracontias hildebrandti
69
Paracontias rothschildi
Madascincus melanopleura
89
Pseudoacontias menamainty
52
Madascincus igneocaudatus
Madascincus mouroundavae
97
Madascincus nanus
64
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
Amphiglossus tsaratananensis
93
Amphiglossus reticulatus
85
86
Amphiglossus astrolabi
Voeltzkowia fierinensis
93
Voeltzkowia lineata
100
95 Voeltzkowia rubrocaudata
24
Amphiglossus splendidus
Amphiglossus anosyensis
80
Amphiglossus macrocercus
70
Amphiglossus punctatus
90
96
Amphiglossus frontoparietalis
96
94
Scincidae
100
Scincinae
94
F-I
E
Figure 6 Species-level squamate phylogeny continued (E).
98
Page 11 of 53
Ateuchosaurus pellopleurus
Asymblepharus alaicus
Ablepharus pannonicus
Sphenomorphus praesignis
81
Sphenomorphus si mus
Tropidophorus berdmorei
98
60
Tropidophorus matsuii
100
Tropidophorus latiscutatus
Tropidophorus noggei
90
99
Tropidophorus murphyi
Tropidophorus hainanus
100
89
98
Tropidophorus baviensis
Tropidophorus sinicus
Tropidophorus robinsoni
98
Tropidophorus thai
Tropidophorus cocincinensis
83
89
Tropidophorus microlepis
Tropidophorus grayi
97
95
Tropidophorus baconi
100
94
Tropidophorus beccarii
Tropidophorus brookei
100
Tropidophorus partelloi
95
Tropidophorus misaminius
Lipinia vittigera
86
Isopachys anguinoides
Sphenomorphus
melanopogon
77
98
Sphenomorphus jobiensis
Sphenomorphus muelleri
Tytthoscincus aesculeticola
100
Tytthoscincus parvus
Tytthoscincus hallieri
100
92
Tytthoscincus atrigularis
94
Sphenomorphus concinnatus
99 95
Sphenomorphus scutatus
100
Sphenomorphus solomonis
100
Sphenomorphus fasciatus
Sphenomorphus leptofasciatus
100
87 Sphenomorphus cranei
90
76
Sphenomorphus maindroni
93
Otosaurus cumingi
Pinoyscincus mindanen sis
100
Pinoyscincus jagori
96
Pinoyscincus coxi
100
80
Pinoyscincus abdictus
100
100
Pinoyscincus llanosi
Sphenomorphus diwata
Sphenomorphus acutus
89
Parvoscincus steerei
Parvoscincus decipiens
100
Parvoscincus leucospilos
Parvoscincus tagapayo
100
Parvoscincus sisoni
76
Parvoscincus beyeri
97
100
Parvoscincus laterimaculatus
Parvoscincus luzonense
99
Parvoscincus kitangladensis
68
83
Parvoscincus lawtoni
Larutia seribuatensis
Sphenomorphus maculatus
Sphenomorphus indicus
100
100
Sphenomorphus multisquamatus
91
Sphenomorphus variegatus
100
Sphenomorphus cyanolaemus
100 Sphenomorphus sabanus
Scincella reevesii
65
Asymblepharus sikimmensis
Scincella lateralis
96
Scincella gemmingeri
93
Scincella cherriei
54
99
Scincella assatus
99
99
Sphenomorphus buenloicus
Prasinohaema virens
Insulasaurus arborens
100
98
Insulasaurus wrighti
80
Insulasaurus victoria
99
Lipinia pulchella
Lipinia noctua
94
100
Papuascincus stanleyanus
G
100
Lygosominae
F
Lygosominae
cont.
H-I
Figure 7 Species-level squamate phylogeny continued (F).
Page 12 of 53
Eulamprus frerei
Nangura spinosa
Calyptotis lepidorostrum
Calyptotis scutirostrum
Calyptotis ruficauda
77
97
Gnypetoscincus queenslandiae
98
Eulamprus amplus
Eulamprus tenuis
78
Eulamprus tigrinus
96
Eulamprus martini
Eulamprus sokosoma
100
88
Eulamprus brachyosoma
80
Eulamprus luteilateralis
85
Eulamprus tryoni
Eulamprus murrayi
83
77
Coggeria naufragus
91
Coeranoscincus frontalis
Ophioscincus ophioscincus
95
Saiphos equalis
Coeranoscincus reticulatus
95
Ophioscincus truncatus
Anomalopus swansoni
Anomalopus mackayi
100
Anomalopus verreauxi
100
Anomalopus leuckartii
Eremiascincus fasciolatus
Eremiascincus pardal is
100
Eremiascincus richardsonii
97
Eremiascincus douglasi
91
62 88
Eremiascincus isolepis
Hemiergis
initialis
100
100
Hemiergis peronii
100
Hemiergis quadrilineatum
70
Hemiergis gracilipes
Hemiergis millewae
82
Hemiergis decresiensis
60
Glaphyromorphus punctulatus
Glaphyromorphus mjobergi
95
Glaphyromorphus fuscicaudis
93
Glaphyromorphus pumilus
Glaphyromorphus cracens
99
Glaphyromorphus darwiniensis
78
Eulamprus quoyii
100
Eulamprus leuraensis
93
Eulamprus kosciusk oi
Eulamprus heatwolei
82
Eulamprus tympanum
87
Notoscincus ornatus
Ctenotus labillardieri
76
Ctenotus brooksi
99
95
Ctenotus rubicundus
Ctenotus nasutus
Ctenotus pantherinus
100
Ctenotus strauchii
95
Ctenotus youngsoni
81
Ctenotus schomburgkii
Ctenotus calurus
85
Ctenotus rawlinsoni
84
Ctenotus fallens
Ctenotus saxatilis
67
Ctenotus inornatus
85
Ctenotus spaldingi
Ctenotus robustus
99
Ctenotus taeniolatus
76
Ctenotus
rutilans
89
55
Ctenotus uber
Ctenotus australis
Ctenotus leae
88
95
Ctenotus leonhardii
Ctenotus quattuordecimlineatus
100
Ctenotus serventyi
100
Ctenotus greeri
83
Ctenotus tanamiensis
86
Ctenotus mimetes
Ctenotus astarte
88
Ctenotus
septenarius
73
Ctenotus regius
63
Ctenotus olympicus
97
Ctenotus maryani
Ctenotus atlas
66
Ctenotus grandis
90
Ctenotus angusticeps
51
Ctenotus hanloni
79
Ctenotus piankai
92
85
Ctenotus essingtonii
Ctenotus
hebetior
78
Ctenotus hilli
Ctenotus gagudju
91
Ctenotus pulchellus
65
95
Lerista stylis
Lerista karlschmidti
Lerista carpentariae
81
100
Lerista ameles
Lerista cinerea
99
Lerista wilkinsi
97
98
Lerista kalumburu
Lerista apoda
91
Lerista griffini
100
Lerista ips
88
Lerista bipes
99
Lerista labialis
Lerista greeri
93
Lerista robusta
98
100
Lerista vermicularis
90
Lerista simillima
99
Lerista walkeri
96
Lerista borealis
Lerista frosti
97
Lerista fragilis
89
Lerista chordae
Lerista xanthura
99
100
Lerista aericeps
90
Lerista taeniata
100
100
Lerista orientalis
100
Lerista ingrami
Lerista zonulata
100
87
Lerista neander
Lerista puncticauda
100
Lerista desertorum
79
Lerista eupoda
99
Lerista gerrardii
Lerista axillaris
100
Lerista macropisthopus
93
Lerista microtis
100
Lerista arenicola
Lerista edwardsae
Lerista baynesi
100
Lerista picturata
Lerista flammicauda
85
Lerista zietzi
100
Lerista speciosa
61
Lerista
elongata
100
Lerista tridactyla
100
Lerista terdigitata
99
82
90
Lerista dorsalis
Lerista punctatovittata
Lerista emmotti
100
100
Lerista elegans
90
Lerista distinguenda
Lerista christinae
87
Lerista lineata
Lerista planiventralis
92
93
Lerista stictopleura
90
Lerista allochira
Lerista haroldi
89
Lerista muelleri
96
Lerista viduata
93
Lerista bougainvillii
100
Lerista praepedita
100
Lerista humphriesi
93
Lerista petersoni
56
Lerista gascoynensis
100
Lerista nichollsi
89
81
Lerista kendricki
77
Lerista yuna
98
Lerista lineopunctulata
Lerista varia
100
100 Lerista connivens
84
Lerista uniduo
Lerista onsloviana
100
96
Lerista kennedyensis
100
Lygosominae
100
cont.
G
Figure 8 Species-level squamate phylogeny continued (G).
Page 13 of 53
Tribolonotus novaeguineae
Tribolonotus gracilis
Tribolonotus blanchardi
Tribolonotus schmidti
86
Tribolonotus brongersmai
97
Tribolonotus ponceleti
93 96
Tribolonotus pseudoponceleti
Corucia zebrata
Egernia saxatilis
86
Bellatorias major
Egernia depressa
77
Egernia kingii
Bellatorias frerei
90
Egernia richardi
100
74
Egernia napoleonis
Lissolepis luctuosa
73
Egernia stokesii
Egernia hosmeri
66 Cyclodomorphus michaeli
96
Cyclodomorphus casuarinae
97
Cyclodomorphus branchialis
81
Tiliqua adelaidensis
Tiliqua rugosa
95
Tiliqua occipitalis
84
Tiliqua nigrolutea
71
Tiliqua gigas
Tiliqua scincoides
100
91
88
Liopholis striata
Liopholis inornata
Liopholis multiscutata
98
Liopholis kintorei
90
Liopholis pulchra
85
99 73
Liopholis modesta
Liopholis margaretae
Liopholis whitii
56
Liopholis guthega
52
Liopholis montana
90
94
Ristella rurkii
Lankascincus fallax
Eutropis longicaudata
Eutropis macularia
96
95
Eutropis rudis
Eutropis macrophthalma
88
Eutropis multifasciata
100
Eutropis cumingi
90
Eutropis multicarinata
73
Eutropis clivicola
97
Eutropis bibronii
Eutropis
beddomii
100
96
Eutropis nagarjuni
Eutropis trivittata
80
97
97
Dasia vittata
Dasia grisea
Dasia olivacea
93
Trachylepis aurata
Trachylepis vittata
99
Trachylepis brevicollis
Trachylepis socotrana
Trachylepis maculilabris
83
98
91
100 Trachylepis wrightii
Trachylepis sechellensis
99
Trachylepis affinis
Trachylepis perrotetii
92
100
Trachylepis quinquetaeniata
Trachylepis margaritifera
99
Trachylepis atlantica
84 54
Trachylepis varia
Trachylepis capensis
Trachylepis occidentalis
100
78
Trachylepis spilogaster
89
Trachylepis striata
100
Trachylepis hoeschi
99
100
90
Trachylepis variegata
Trachylepis sulcata
95
Trachylepis homalocephala
Trachylepis acutilabris
Trachylepis gravenhorstii
Trachylepis elegans
74
100
Trachylepis madagascariensis
95
98
Trachylepis boettgeri
Trachylepis vato
100
Trachylepis aureopunctata
97
Trachylepis dumasi
95
Eumecia anchietae
90
91
Chioninia vaillantii
98
Chioninia delalandii
Chioninia coctei
Chioninia spinalis
80
Chioninia fogoensis
Chioninia stangeri
87
100
Mabuya carvalhoi
Mabuya croizati
Mabuya nigropalmata
Mabuya sloanii
100
78
Mabuya altamazonica
Mabuya nigropunctata
98
Mabuya cochabambae
97
Mabuya dorsivittata
100
89
Mabuya meridensis
Mabuya mabouya
96
Mabuya unimarginata
95
Mabuya falconensis
81
Mabuya bistriata
Mabuya frenata
70
100
Mabuya agmosticha
Mabuya macrorhyncha
Mabuya guaporicola
77
Mabuya agilis
80
Mabuya caissara
100
99
Mabuya heathi
100
93
Lygosominae
cont.
83
H
Figure 9 Species-level squamate phylogeny continued (H).
100
Page 14 of 53
Ablepharus budaki
Ablepharus chernovi
Ablepharus kitaibelii
100
Sphenomorphus stellatus
Emoia concolor
Emoia tongana
96
63
98
60
95
93
92
76
Lygosominae
90
cont.
70
100
75
Lamprolepis smaragdina
Lygosoma quadrupes
Lygosoma koratense
Lygosoma albopunctata
Lepidothyris fernandi
Lygosoma lineolatum
Mochlus afer
100 Lygosoma sundevalli
Lygosoma punctata
Mochlus brevicaudis
Lygosoma bowringii
Eugongylus rufescens
Eugongylus albofasciolatus
Emoia loyaltiensis
Leiolopis ma telfairii
Leiolopisma mauriti ana
100
Panaspis breviceps
Panaspis togoensis
Afroablepharus wahlbergi
Afroablepharus annobonensis
Afroablepharus africanus
90
Lacertaspis reichenowi
Lacertaspis rohdei
85
Lacertaspis chriswildi
93
91
Lacertaspis gemmiventris
96
Lacertaspis lepesmei
Leptosiaphos hackarsi
100
Leptosiaphos graueri
95
Leptosiaphos amieti
81
Leptosiaphos kilimensis
95
Leptosiaphos vigintiserierum
99
Pseudemoia pagenstecheri
80
Bassiana duperreyi
99
Pseudemoia entrecasteauxii
Oligosoma lichenigera
Oligosoma suteri
Oligosoma pikitanga
99 95
100
Oligosoma taumakae
Oligosoma acrinasum
Oligosoma infrapunctatum
98
100
Oligosoma waimatense
91
86
Oligosoma otagense
100
Oligosoma chloronoton
98
Oligosoma
lineoocellatum
61
Oligosoma longipes
99
Oligosoma nigriplantare
99
Oligosoma grande
98
Oligosoma stenotis
Oligosoma maccanni
90 85
100
100
Oligosoma inconspicuum
98
Oligosoma notosaurus
Oligosoma zelandicum
100
Oligosoma homalonotum
Oligosoma striatum
100
Oligosoma smithi
100
Oligosoma microlepis
94 93
Oligosoma aeneum
Oligosoma levidensum
99
99
Oligosoma hardyi
57
Oligosoma fallai
Oligosoma alani
Oligosoma moco
98 63
Oligosoma
macgregori
93
Oligosoma ornatum
Oligosoma townsi
89
Oligosoma oliveri
9796
Oligosoma whitakeri
Nannoscincus garrulus
98
Nannoscincus slevini
98
Nannoscincus gracilis
89
Nannoscincus mariei
Nannoscincus greeri
82
94
Nannoscincus hanchisteus
93
Nannoscincus humectus
Marmorosphax montana
Marmorosphax tricolor
90
100
100
Celatiscincus similis
96
Celatiscincus euryotis
Lioscincus vivae
96
Lioscincus steindachneri
96
Kanakysaurus viviparus
Lioscincus nigrofasciolatum
84
80
Lacertoides pardalis
96 80
Phoboscincus garnieri
Sigaloseps ruficauda
Sigaloseps deplanchei
100
Lioscincus novaecaledoniae
85
Lioscincus maruia
85
Tropidoscincus aubrianus
98
92
Lioscincus tillieri
Tropidoscincus boreus
100
100 Tropidoscincus variabilis
Graciliscincus shonae
87
Simiscincus aurantiacus
Caledoniscincus orestes
97
100
Caledoniscincus renevieri
Caledoniscincus auratus
95 95
Caledoniscincus festivus
Caledoniscincus austrocaledonicus
83
Caledoniscincus haplorhinus
97
Caledoniscincus atropunctatus
53
Caledoniscincus chazeaui
87
98 Caledoniscincus aquilonius
95
Caledoniscincus terma
Cryptoblepharus nigropunctatus
100
Cryptoblepharus boutonii
Cryptoblepharus novocaledonicus
79
93
93
Menetia greyii
Menetia alanae
Emoia schmidti
100
Emoia cyanogaster
91
Emoia caeruleocauda
Emoia atrocostata
98
100
100
Emoia jakati
Emoia physicae
Emoia impar
77
Emoia cyanura
98
71 98
Emoia pseudocyanura
52
Emoia isolata
Bassiana trilineata
73
Morethia ruficauda
Morethia butleri
Morethia adelaidensis
Bartleia jigurru
Saproscincus basiliscus
96
Saproscincus lewisi
96
72
Saproscincus czechurai
79
Saproscincus tetradactylus
98
Saproscincus hannahae
100
Saproscincus oriarus
76
Saproscincus mustelinus
Saproscincus challengeri
71
Saproscincus rosei
100
100
Saproscincus spectabilis
97
Lampropholis guichenoti
92
Lampropholis delicata
100
Lampropholis coggeri
Lampropholis robertsi
Proablepharus reginae
Niveoscincus greeni
72
Niveoscincus ocellatus
76
Niveoscincus pretiosus
Niveoscincus metallicus
100
Cautula zia
87
Liburnascincus coensis
96
Liburnascincus scirtetis
Liburnascincus mundivensis
91
88
Menetia timlowi
100
Carlia triacantha
98
Carlia johnstonei
Carlia jarnoldae
Carlia bicarinata
90
Carlia gracilis
79
Lygisaurus sesbrauna
75
Lygisaurus parrhasius
88
Lygisaurus macfarlani
Lygisaurus novaeguineae
98
99
Lygisaurus aeratus
Lygisaurus laevis
85
100 100Lygisaurus foliorum
78
Lygisaurus abscondita
68
100
Lygisaurus tanneri
89
Lygisaurus malleolus
91
Carlia schmeltzii
Carlia storri
Carlia fusca
98
Carlia longipes
100
Carlia mysi
73
93
Carlia munda
80
Carlia pectoralis
Carlia rufilatus
85
100
Carlia rhomboidalis
Carlia rubrigularis
92
Carlia tetradactyla
Carlia amax
Carlia rostralis
76
Carlia dogare
53
Carlia vivax
62
100
84
100
I
Figure 10 Species-level squamate phylogeny continued (I).
99
99
85
Page 15 of 53
Callopistes flavipunctatus
Callopistes maculatus
Tupinambis rufescens
Tupinambis merianae
100 Tupinambis
duseni
Tupinambis quadrilineatus
97
Tupinambis longilineus
98
Tupinambis teguixin
87
Crocodilurus amazonicus
54
66
Dracaena guianensis
91
Teius teyou
99
Ameiva ameiva
Ameiva bifrontata
100
Cnemidophorus ocellifer
82
Kentropyx calcarata
Kentropyx striata
71
Kentropyx altamazonica
100
Kentropyx pelviceps
Kentropyx paulensis
91
56
Kentropyx vanzoi
96
Kentropyx viridistriga
Ameiva undulata
100 Ameiva quadrilineata
97
Ameiva festiva
93
Cnemidophorus vanzoi
Cnemidophorus gramivagus
99
Cnemidophorus lemniscatus
Cnemidophorus arenivagus
94
Aspidoscelis inornata
Aspidoscelis sexlineata
100
Aspidoscelis burti
99
Aspidoscelis communis
99
93
Aspidoscelis costata
98
99
Aspidoscelis gularis
81
83 Aspidoscelis laredoensis
Aspidoscelis velox
Aspidoscelis deppei
98
Aspidoscelis guttata
Aspidoscelis lineattissima
100
Aspidoscelis marmorata
84
Aspidoscelis
tigris
92
Aspidoscelis hyperythra
Aspidoscelis ceralbensis
98
Ameiva auberi
Ameiva dorsalis
100
Ameiva polops
86
Ameiva exsul
99
Ameiva wetmorei
97
Ameiva leberi
Ameiva chrysolaema
59
100
Ameiva
taeniura
96
Ameiva lineolata
95 100
Ameiva maynardi
100
Ameiva plei
Ameiva corax
Ameiva pluvianotata
98
Ameiva griswoldi
100
Ameiva erythrocephala
93
Ameiva fuscata
94
Dicrodon guttulatum
55
Cnemidophorus longicaudus
85
Cnemidophorus lacertoides
97
Ptychoglossus brevifrontalis
Alopoglossus atriventris
100
99
Alopoglossus copii
100
Alopoglossus angulatus
Ecpleopus gaudichaudii
Leposoma nanodactylus
Leposoma baturitensis
Leposoma puk
100
100
Leposoma scincoides
98
Leposoma annectans
97
Colobosauroides cearensis
97
Anotosaura collaris
100
Arthrosaura reticulata
99
Arthrosaura kockii
86
Leposoma percarinatum
65
96
Leposoma osvaldoi
100
Leposoma parietale
98
Leposoma southi
95
Leposoma guianense
Riama
unicolor
100
Riama colomaromani
Riama simoterus
91
Neusticurus rudis
Neusticurus bicarinatus
94
99
Placosoma cordylinum
98
Placosoma glabellum
100
Pholidobolus montium
Pholidobolus macbrydei
100
80
Potamites ecpleopus
Potamites juruazensis
92
100
Cercosaura quadrilineata
98
100
Cercosaura oshaughnessyi
Cercosaura argulus
97
Cercosaura ocellata
99
100
Cercosaura schreibersii
Cercosaura eigenmanni
82
55
Proctoporus sucullucu
Proctoporus subsolanus
Proctoporus pachyurus
98
100
Proctoporus guentheri
Proctoporus unsaacae
Proctoporus bolivianus
94 99
Petracola ventrimaculatus
Bachia flavescens
Bachia bresslaui
100
Bachia dorbignyi
77
100 Bachia huallagana
Bachia scolecoides
100
Bachia trisanale
88
Bachia panoplia
97
Bachia peruana
95 100 Bachia bicolor
84
78 Bachia barbouri
74 Bachia intermedia
98 Bachia heteropa
Rhachisaurus brachylepis
Heterodactylus imbricatus
100
Colobodactylus dalcyanus
93
Colobodactylus
taunayi
99
Iphisa elegans
100
100
Colobosaura modesta
Stenolepis ridleyi
91
96
Acratosaura mentalis
Tretioscincus agilis
Tretioscincus oriximinensis
98
72
Micrablepharus atticolus
100
Micrablepharus maximiliani
Vanzosaura rubricauda
98
Procellosaurinus erythrocercus
61
100
Procellosaurinus tetradactylus
100 93
Nothobachia ablephara
Calyptommatus sinebrachiatus
Calyptommatus confusionibus
88
Calyptommatus leiolepis
93
50
86
Calyptommatus nicterus
Psilophthalmus paeminosus
Gymnophthalmus pleei
Gymnophthalmus leucomystax
100
Gymnophthalmus vanzoi
Gymnophthalmus speciosus
100
Gymnophthalmus underwoodi
87
100
Gymnophthalmus cryptus
Tupinambinae
97
100
Teiidae
Teiinae
100
Alopoglossinae
Ecpleopinae
Gymnophthalmidae
Cercosaurinae
Bachiinae
Rhachisaurinae
Gymnophthalminae
J
Figure 11 Species-level squamate phylogeny continued (J).
Page 16 of 53
Rhineuridae
Rhineura floridana
Bipes tridactylus
Bipedidae
Bipes biporus
100
99
73
Bipes canaliculatus
Blanus strauchi
100
100
Blanus cinereus
Blanus mettetali
100
97
Blanidae
Blanus tingitanus
84
Cadea blanoides
Cadeidae
Diplometopon zarudnyi
100
Trogonophiidae
Trogonophis wiegmanni
Cynisca leucura
100
100
Chirindia swynnertoni
Geocalamus acutus
Monopeltis capensis
91
Amphisbaenidae
Amphisbaena brasiliana
89
Amphisbaena fuliginosa
55
Amphisbaena cunhai
95
86
Amphisbaena mertensii
Amphisbaena hyporissor
96
67
81
Amphisbaena innocens
Amphisbaena leali
Amphisbaena ignatiana
91
Amphisbaena saxosa
100
Amphisbaena kraoh
100
100 Amphisbaena roberti
Amphisbaena vermicularis
98
Amphisbaena alba
Amphisbaena camura
95
100
Amphisbaena bolivica
Amphisbaena anomala
89
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
95
Amphisbaena leeseri
Amphisbaena silvestrii
100
Amphisbaena anaemariae
100
Amphisbaena barbouri
Amphisbaena cubana
Amphisbaena carlgansi
90
Amphisbaena schmidti
92
Amphisbaena manni
97
87
K
Figure 12 Species-level squamate phylogeny continued (K).
100
100
Amphisbaena fenestrata
Amphisbaena caeca
Amphisbaena bakeri
Amphisbaena xera
Page 17 of 53
Gallotiinae
99
100
95
99
95
68
Psammodromus hispanicus
Psammodromus algirus
Psammodromus blanci
Gallotia stehlini
Gallotia atlantica
Gallotia galloti
Gallotia caesaris
Gallotia intermedia
Gallotia simonyi
100 97
Gallotia bravoana
Atlantolacerta andreanskyi
Poromera fordii
Nucras lalandii
Latastia longicaudata
Philochortus spinalis
Pseuderemias smithii
Heliobolus lugubris
90
Heliobolus spekii
84
99
Australolacerta australis
Tropidosaura gularis
54
Ichnotropis capensis
Meroles reticulatus
Meroles knoxii
92
Meroles suborbitalis
100
Ichnotropis squamulosa
80
Meroles anchietae
76
Meroles ctenodactylus
97
100
97
Meroles micropholidotus
Meroles cuneirostris
Pedioplanis lineoocellata
Nucras tessellata
100
Pedioplanis laticeps
100
Pedioplanis burchelli
Pedioplanis breviceps
Pedioplanis namaquensis
96
Pedioplanis husabensis
69
100
Pedioplanis undata
Pedioplanis rubens
76
96
Pedioplanis inornata
96
Pedioplanis gaerdesi
56
100
Holaspis laevis
Holaspis guentheri
100
100
Gastropholis vittata
Gastropholis prasina
Adolfus africanus
72
89
Adolfus alleni
96
99
Adolfus jacksoni
Eremias brenchleyi
Eremias argus
97
Eremias vermiculata
Eremias velox
76
99
Eremias montanus
100
Eremias persica
Eremias nigrolateralis
95
Eremias arguta
Eremias przewalskii
93
Eremias multiocellata
100
93
Eremias pleskei
56
Eremias grammica
86
Congolacerta vauereselli
Omanosaura cyanura
Omanosaura jayakari
98
97
Mesalina simoni
100
Mesalina olivieri
Mesalina bahaeldini
Mesalina guttulata
100
91
Mesalina balfouri
89
Mesalina adramitana
93
Mesalina brevirostris
63
Mesalina rubropunctata
Ophisops occidentalis
Ophisops elegans
100
Acanthodactylus orientalis
Acanthodactylus tristrami
100
Acanthodactylus blanci
95
Acanthodactylus erythrurus
99
73
Acanthodactylus busacki
94
Acanthodactylus beershebensis
100
Acanthodactylus pardalis
76
Acanthodactylus maculatus
86
100
Acanthodactylus aureus
Acanthodactylus scutellatus
95
Acanthodactylus longipes
93
80
Acanthodactylus schmidti
99
Acanthodactylus cantoris
Acanthodactylus masirae
96
Acanthodactylus gongrorhynchatus
100
Acanthodactylus opheodurus
85
Acanthodactylus boskianus
75
Acanthodactylus schreiberi
99
100
Phoenicolacerta kulzeri
98
Phoenicolacerta laevis
Phoenicolacerta cyanisparsa
Zootoca vivipara
95
Takydromus kuehnei
100
Takydromus sexlineatus
Takydromus tachydromoides
100
Takydromus smaragdinus
Takydromus sauteri
95
85
Takydromus intermedius
100
Takydromus dorsalis
100
Takydromus sylvaticus
Takydromus amurensis
79
100
99
Takydromus hsuehshanensis
Takydromus formosanus
100
Takydromus wolteri
97
100
Takydromus toyamai
Takydromus septentrionalis
99
Takydromus stejnegeri
75
Timon princeps
94
Timon pater
Timon lepidus
99
98 69
Timon tangitanus
Lacerta viridis
58
100
Lacerta bilineata
100
Lacerta strigata
80
Lacerta schreiberi
Lacerta agilis
92
Lacerta media
98
Lacerta trilineata
99
Lacerta pamphylica
98
100
Teira dugesii
Scelarcis perspicillata
Podarcis
melisellensis
85
Podarcis tauricus
Podarcis milensis
62
74
Podarcis gaigeae
55
Podarcis filfolensis
99 85
Podarcis tiliguerta
100
Podarcis muralis
Podarcis siculus
92 95
Podarcis pityusensis
Podarcis lilfordi
94
78
Podarcis raffoneae
Podarcis erhardii
Podarcis peloponnesiacus
88 79
Podarcis liolepis
Podarcis vaucheri
93
Podarcis hispanicus
97
100
92
Podarcis bocagei
Podarcis carbonelli
97
Dalmatolacerta oxycephala
Hellenolacerta graeca
92
Archaeolacerta bedriagae
Apathya cappadocica
91
Iberolacerta galani
86
86
Iberolacerta cyreni
Iberolacerta monticola
100
Iberolacerta horvathi
100
Iberolacerta aurelioi
Iberolacerta bonnali
93
Iberolacerta aranica
100
Parvilacerta fraasii
99
Parvilacerta parva
64
Anatololacerta anatolica
100
Anatololacerta oertzeni
89
Anatololacerta danfordi
96
Algyroides moreoticus
Algyroides nigropunctatus
100
73
100
Dinarolacerta mosorensis
Dinarolacerta montenegrina
94
Algyroides marchi
98
Algyroides fitzingeri
53
Iranolacerta brandtii
99
Iranolacerta zagrosica
Darevskia parvula
97
Darevskia rudis
Darevskia portschinskii
100
100
94 Darevskia valentini
Darevskia praticola
Darevskia chlorogaster
100
Darevskia alpina
96
Darevskia lindholmi
Darevskia brauneri
100
Darevskia saxicola
87
rostombekovi
100 Darevskia
97 Darevskia raddei
Darevskia uzzelli
Darevskia sapphirina
100 Darevskia bendimahiensis
93 94 Darevskia
armeniaca
Darevskia clarkorum
Darevskia mixta
98
Darevskia daghestanica
70
Darevskia caucasica
99
Darevskia derjugini
90
73
96
Lacertidae
100
Lacertinae
L
Figure 13 Species-level squamate phylogeny continued (L).
99
88
100
Page 18 of 53
Xenosauridae 100
Xenosaurus platyceps
Xenosaurus grandis
Helodermatidae 100 Heloderma suspectum
100
Heloderma horridum
Anniellidae
Anniella pulchra
Anniella geronimensis
Celestus enneagrammus
Diploglossus bilobatus
98
Diploglossus pleii
Diploglossinae
Ophiodes striatus
100
100
Celestus agasepsoides
100
93
Celestus haetianus
Ophisaurus ventralis
Ophisaurus koellikeri
100 83
Pseudopus apodus
Anguidae 90
Anguis fragilis
Anguinae
99
87
Ophisaurus attenuatus
Dopasia gracilis
Dopasia harti
100
Elgaria coerulea
100
100
Elgaria kingii
Elgaria paucicarinata
99
85 Elgaria panamintina
84 Elgaria multicarinata
100
Gerrhonotus parvus
Gerrhonotinae 88
Coloptychon rhombifer
Gerrhonotus liocephalus
92
100
Gerrhonotus infernalis
Abronia mixteca
97
Barisia levicollis
100
Barisia imbricata
Barisia herrerae
89
95
94 Barisia rudicollis
Mesaspis moreletii
79
Mesaspis gadovii
72
Abronia chiszari
66
Abronia oaxacae
Abronia graminea
99
Abronia frosti
Abronia ornelasi
96
84 Abronia lythrochila
89
Abronia fimbriata
Abronia matudai
96
Abronia anzuetoi
97
95 Abronia campbelli
Abronia aurita
Shinisauridae Shinisaurus crocodilurus
Lanthanotidae
Lanthanotus borneensis
Varanus griseus
Varanus niloticus
94
Varanus exanthematicus
95
Varanus
albigularis
97
99
Varanus yemenensis
100
Varanus olivaceus
98
Varanus keithhornei
100
Varanus beccarii
95
95 Varanus boehmei
Varanidae
Varanus macraei
100
75 Varanus prasinus
86
Varanus
rainerguentheri
86
78Varanus indicus
Varanus melinus
88 Varanus cerambonensis
100 Varanus caerulivirens
Varanus jobiensis
Varanus yuwonoi
76
Varanus doreanus
100
79
74 Varanus finschi
86
Varanus marmoratus
Varanus salvator
100 69
Varanus rudicollis
Varanus dumerilii
Varanus flavescens
85
72
Varanus bengalensis
Varanus
mertensi
100
Varanus spenceri
84
Varanus giganteus
Varanus rosenbergi
92
Varanus panoptes
96
94
Varanus gouldii
Varanus
salvadorii
100 100
Varanus varius
99
Varanus komodoensis
Varanus glebopalma
99
Varanus pilbarensis
100
Varanus tristis
87
Varanus glauerti
Varanus scalaris
96
Varanus
timorensis
76
Varanus mitchelli
86
100
100
Varanus semiremex
Varanus brevicauda
100
Varanus eremius
Varanus caudolineatus
88 100
Varanus gilleni
100 Varanus bushi
Varanus kingorum
97 99
Varanus primordius
Varanus storri
99
Varanus acanthurus
100
Varanus baritji
99
100
95
M
Figure 14 Species-level squamate phylogeny continued (M).
Page 19 of 53
79
Brookesia lolontany
Brookesia nasus
Brookesia dentata
100
Brookesia exarmata
Brookesia minima
63
Brookesia tuberculata
100
Brookesia karchei
83
Brookesia
peyrierasi
100
Brookesia perarmata
100
Brookesia decaryi
98
Brookesia
brygooi
100
Brookesia bonsi
Brookesia therezieni
100
99
Brookesia superciliaris
93
Brookesia valerieae
Brookesia griveaudi
100
Brookesia stumpffi
100 Brookesia ambreensis
Brookesia antakarana
Brookesia ebenaui
Brookesia vadoni
100
Brookesia thieli
Brookesia betschi
51
Brookesia lineata
Furcifer balteatus
99
Furcifer bifidus
Furcifer minor
62
99
Furcifer willsii
Furcifer petteri
86
Furcifer campani
93
96
Furcifer cephalolepis
91
Furcifer polleni
100
Furcifer pardalis
94
Furcifer angeli
Furcifer oustaleti
99 93
Furcifer verrucosus
Furcifer belalandaensis
98
Furcifer lateralis
98
94
Furcifer labordi
100
Furcifer antimena
100
Kinyongia oxyrhina
Kinyongia tenue
Kinyongia adolfifriderici
95
100
Kinyongia excubitor
Kinyongia xenorhina
67
Kinyongia carpenteri
98
82
Kinyongia uthmoelleri
Kinyongia tavetana
100
100
Kinyongia boehmei
92
Kinyongia matschiei
55
100
Kinyongia multituberculata
100
Kinyongia vosseleri
59
100 Kinyongia fischeri
96
Bradypodion pumilum
Bradypodion damaranum
Bradypodion caffer
100 Bradypodion melanocephalum
100
Bradypodion thamnobates
94
98
Bradypodion transvaalense
Bradypodion dracomontanum
72
87 Bradypodion nemorale
Bradypodion setaroi
Bradypodion occidentale
Bradypodion atromontanum
85
Bradypodion
gutturale
98
Bradypodion taeniabronchum
74
95 Bradypodion karrooicum
Bradypodion
ventrale
95
100
Calumma furcifer
99
Calumma gastrotaenia
Rieppeleon kerstenii
Rieppeleon brachyurus
100
Rieppeleon brevicaudatus
58
Calumma cucullatum
Calumma crypticum
88
100
82
Calumma brevicorne
98
Calumma tsaratananense
Calumma hilleniusi
100 75
Calumma guibei
Calumma malthe
91
Calumma gallus
93
78
Calumma fallax
85
Calumma boettgeri
97
94
Calumma nasutum
Nadzikambia mlanjensis
Rhampholeon spectrum
73
Rhampholeon temporalis
88
Rhampholeon spinosus
98
98
Rhampholeon viridis
99
Rhampholeon marshalli
Rhampholeon moyeri
86
Rhampholeon uluguruensis
Rhampholeon acuminatus
100
81
Rhampholeon boulengeri
73
Rhampholeon beraduccii
Rhampholeon nchisiensis
91
Rhampholeon platyceps
90
100
Rhampholeon chapmanorum
100
Calumma capuroni
Calumma oshaughnessyi
Calumma parsonii
100
Calumma globifer
95
61
Chamaeleo namaquensis
Chamaeleo laevigatus
Chamaeleo necasi
99 100
Chamaeleo gracilis
90
Chamaeleo quilensis
100
Chamaeleo dilepis
99
Chamaeleo roperi
Chamaeleo senegalensis
Chamaeleo monachus
95
Chamaeleo africanus
Chamaeleo calcaricarens
Chamaeleo chamaeleon
85
100
Chamaeleo zeylanicus
Chamaeleo calyptratus
98
100
Chamaeleo arabicus
100
Trioceros affinis
Trioceros harennae
100 Trioceros balebicornutus
66
Trioceros feae
Trioceros montium
100
85
Trioceros cristatus
100
Trioceros wiedersheimi
Trioceros quadricornis
96
100
50
Trioceros pfefferi
97
Trioceros oweni
Trioceros johnstoni
93
Trioceros melleri
Trioceros deremensis
98
92
Trioceros werneri
Trioceros tempeli
92
Trioceros goetzei
97 91
Trioceros fuelleborni
Trioceros bitaeniatus
70
Trioceros
jacksonii
98
90 Trioceros narraioca
Trioceros schubotzi
Trioceros hoehnelii
85
Trioceros ellioti
87
Trioceros rudis
97
66
Trioceros sternfeldi
100
Chamaeleonidae
100
Chamaeleoninae
N
Figure 15 Species-level squamate phylogeny continued (N).
Brookesiinae
Page 20 of 53
Uromastyx hardwickii
Uromastyx loricata
Uromastyx asmussi
95
Uromastyx princeps
100
Uromastyx macfadyeni
Uromastyx geyri
86
100
Uromastyx acanthinura
74
Uromastyx dispar
94
Uromastyx thomasi
Uromastyx aegyptia
100
Uromastyx leptieni
91
Uromastyx ornata
99
70
Uromastyx ocellata
Uromastyx benti
100
100 Uromastyx yemenensis
100 Leiolepis belliana
Leiolepis reevesii
100 100 Leiolepis guttata
Leiolepis guentherpetersi
Hydrosaurus amboinensis
Physignathus cocincinus
Hypsilurus spinipes
92
Hypsilurus boydii
97
Hypsilurus dilophus
85
Moloch horridus
98
Chelosania brunnea
100
Hypsilurus modestus
100
Hypsilurus papuensis
Hypsilurus nigrigularis
100
51
Hypsilurus bruijnii
Intellagama lesueurii
Ctenophorus maculosus
100
75
Ctenophorus adelaidensis
Ctenophorus clayi
100
Ctenophorus gibba
96
Ctenophorus salinarum
Ctenophorus cristatus
100
Ctenophorus nuchalis
98
Ctenophorus reticulatus
71
Ctenophorus rufescens
99
Ctenophorus tjantjalka
Ctenophorus vadnappa
99
Ctenophorus decresii
Ctenophorus fionni
79 90
Ctenophorus caudicinctus
100 Ctenophorus ornatus
Ctenophorus isolepis
100 53 92
Ctenophorus scutulatus
100
Ctenophorus mckenziei
76
Ctenophorus pictus
Ctenophorus maculatus
90
Ctenophorus fordi
100
94
Ctenophorus femoralis
Lophognathus temporalis
71
Lophognathus longirostris
Chlamydosaurus kingii
100
Lophognathus gilberti
94
Amphibolurus muricatus
Amphibolurus norrisi
97
100
Tympanocryptis uniformis
100
Tympanocryptis intima
99
Tympanocryptis tetraporophora
Tympanocryptis cephalus
Tympanocryptis pinguicolla
71
100
53
Tympanocryptis lineata
Rankinia diemensis
63
Pogona barbata
100
Pogona nullarbor
99
Pogona henrylawsoni
Pogona minima
99 99 Pogona minor
94 Pogona vitticeps
Diporiphora superba
Diporiphora linga
99
Diporiphora winneckei
81
Diporiphora reginae
Diporiphora magna
76
Diporiphora bilineata
67
Diporiphora pindan
95 100 Diporiphora valens
Diporiphora amphiboluroides
Diporiphora australis
Diporiphora nobbi
95
Diporiphora bennettii
56
Diporiphora albilabris
100
Diporiphora arnhemica
95
Diporiphora lalliae
Agaminae
Uromastycinae
Leiolepidinae
100
Hydrosaurinae
Amphibolurinae
Agamidae
(i)
96
(i)
(ii)
100
100
Draconinae
(ii)
100
O
Figure 16 Species-level squamate phylogeny continued (O).
Laudakia stellio
Laudakia sacra
Laudakia tuberculata
Laudakia nupta
Laudakia lehmanni
85
Laudakia himalayana
Laudakia stoliczkana
84 99
Laudakia microlepis
84
Laudakia caucasia
88
100 Laudakia erythrogaster
Phrynocephalus scutellatus
Phrynocephalus interscapularis
Phrynocephalus forsythii
100 100
Phrynocephalus theobaldi
Phrynocephalus putjatai
64 90
75 Phrynocephalus vlangalii
73 Phrynocephalus lidskii
Phrynocephalus axillaris
Phrynocephalus helioscopus
Phrynocephalus mystaceus
91
Phrynocephalus raddei
100
89 100 Phrynocephalus versicolor
Phrynocephalus przewalskii
94
melanurus
Phrynocephalus
100
Phrynocephalus albolineatus
96
90 Phrynocephalus guttatus
Pseudotrapelus sinaitus
100
Acanthocercus atricollis
66
Xenagama taylori
95
Bufoniceps laungwalaensis
Trapelus sanguinolentus
100
Trapelus mutabilis
99
Trapelus agilis
Trapelus ruderatus
Trapelus pallidus
99 93
Trapelus flavimaculatus
89
100
Trapelus
savignii
100
Agama spinosa
Agama boueti
100
Agama impalearis
100
96 Agama castroviejoi
Agama boulengeri
76
Agama insularis
100
Agama gracilimembris
84
Agama weidholzi
69
Agama anchietae
Agama
atra
100
100
91
Agama hispida
Agama armata
50
Agama aculeata
100
Agama caudospinosa
Agama rueppelli
100
Agama lionotus
Agama kaimosae
91
Agama mwanzae
65
98
Agama sankaranica
Agama doriae
99
Agama
agama
100
Agama finchi
100
Agama planiceps
68
Agama paragama
68
Mantheyus phuwuanensis
Japalura variegata
70
Japalura tricarinata
100
Ptyctolaemus gularis
Ptyctolaemus collicristatus
100
Draco dussumieri
Draco lineatus
Draco maculatus
95
Draco fimbriatus
86
Draco cristatellus
99 97
53
Draco maximus
Draco mindanensis
Draco quinquefasciatus
92
100
melanopogon
65 Draco
haematopogon
59
95 Draco
Draco indochinensis
96
Draco blanfordii
Draco taeniopterus
61
86
Draco obscurus
100
100 Draco spilonotus
Draco caerulhians
100 97 Draco biaro
Draco beccarii
Draco bourouniensis
100
Draco rhytisma
99
95
Draco bimaculatus
Draco volans
100
Draco timorensis
99 Draco boschmai
100
Draco reticulatus
100
Draco cyanopterus
Draco quadrasi
Draco guentheri
91
Draco cornutus
Draco spilopterus
85
Draco palawanensis
Draco ornatus
87
Phoxophrys nigrilabris
Japalura polygonata
Gonocephalus robinsonii
100
Aphaniotis fusca
97 98
Coryphophylax subcristatus
Bronchocela cristatella
Gonocephalus grandis
85
Gonocephalus chamaeleontinus
87
100 Gonocephalus kuhlii
86
Lyriocephalus scutatus
97
52
Cophotis dumbara
100 Cophotis ceylanica
100
Ceratophora aspera
Ceratophora karu
Ceratophora stoddartii
90
100 Ceratophora erdeleni
Calotes mystaceus
72
81
Calotes chincollium
100 Calotes emma
55
Calotes liocephalus
Calotes ceylonensis
100 90
99 Calotes nigrilabris
Calotes liolepis
99
Calotes versicolor
100 Calotes irawadi
50
Calotes calotes
Calotes htunwini
91
Salea horsfieldii
Acanthosaura crucigera
Acanthosaura armata
100
96
Acanthosaura capra
Acanthosaura lepidogaster
69
Sitana ponticeriana
100
Otocryptis wiegmanni
Japalura flaviceps
100
Japalura splendida
Pseudocalotes kakhienensis
99
Pseudocalotes brevipes
100
Pseudocalotes flavigula
95
94
94
99
Page 21 of 53
P
94
Stenocercus scapularis
Stenocercus apurimacus
Stenocercus formosus
Stenocercus ochoai
94
Stenocercus roseiventris
64
Stenocercus azureus
Stenocercus doellojuradoi
100
100
69
Stenocercus limitaris
Stenocercus caducus
88
Stenocercus ornatus
Stenocercus percultus
100
78
Stenocercus puyango
100
Stenocercus iridescens
Stenocercus angulifer
96 89
Stenocercus rhodomelas
Stenocercus chota
84 82
Stenocercus festae
99
Stenocercus guentheri
96
100 Stenocercus angel
Stenocercus humeralis
Stenocercus marmoratus
71
Stenocercus crassicaudatus
100 100
Stenocercus torquatus
Stenocercus varius
73
Stenocercus imitator
89
Stenocercus eunetopsis
94 Stenocercus
empetrus
Tropiduridae
100 Stenocercus boettgeri
88
100
Stenocercus cupreus
78
Stenocercus chrysopygus
79
Stenocercus ornatissimus
Stenocercus orientalis
100
Stenocercus latebrosus
85
Stenocercus melanopygus
88
Stenocercus stigmosus
Microlophus thoracicus
100
Microlophus theresiae
Microlophus
heterolepis
100
99
96 Microlophus tigris
Microlophus peruvianus
100 Microlophus quadrivittatus
100 Microlophus atacamensis
100
Microlophus theresioides
98 Microlophus yanezi
Microlophus koepckeorum
Microlophus occipitalis
100
Microlophus bivittatus
100
100
Microlophus habelii
Microlophus stolzmanni
Microlophus
delanonis
100
Microlophus grayii
100
Microlophus pacificus
100
64 Microlophus albemarlensis
95 Microlophus duncanensis
Uranoscodon superciliosus
74
Uracentron flaviceps
Tropidurus bogerti
98
Strobilurus torquatus
Plica umbra
78
Plica lumaria
99
Plica plica
100
Tropidurus callathelys
100
Tropidurus spinulosus
100
100
Eurolophosaurus divaricatus
100
Eurolophosaurus amathites
Eurolophosaurus nanuzae
Tropidurus hygomi
Tropidurus montanus
100
100
Tropidurus psammonastes
Tropidurus itambere
73 98
Tropidurus cocorobensis
97 83 Tropidurus etheridgei
Tropidurus mucujensis
Tropidurus erythrocephalus
Tropidurus insulanus
Tropidurus oreadicus
100
Tropidurus
hispidus
98
Iguanidae
89 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
Cyclura rileyi
57
Cyclura nubila
85
86 Cyclura cychlura
56
Amblyrhynchus cristatus
100 Conolophus subcristatus
72
Conolophus pallidus
Ctenosaura similis
62
Ctenosaura hemilopha
100
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
86
Q-R
Figure 17 Species-level squamate phylogeny continued (P).
Page 22 of 53
69
100
(i)
81
Q
Figure 18 Species-level squamate phylogeny continued (Q).
Opluridae
99
Enyaliinae
Leiosaurinae
95
96
(ii)
63
Liolaemidae
54
Phrynosomatidae
(i)
Polychrus gutturosus
Polychrus acutirostris
Polychrus femoralis
Polychrus marmoratus
Hoplocercus spinosus
100
Morunasaurus annularis
100
Enyalioides laticeps
Enyalioides heterolepis
88
Enyalioides oshaughnessyi
Enyalioides palpebralis
96
Enyalioides microlepis
96
Enyalioides praestabilis
96
Chalarodon madagascariensis
90
Oplurus cyclurus
Oplurus cuvieri
99
Oplurus quadrimaculatus
100
Oplurus saxicola
73
Oplurus grandidieri
96
Oplurus fierinensis
88
Enyalius bilineatus
Enyalius leechii
97
Urostrophus gallardoi
Anisolepis longicauda
99
Urostrophus vautieri
100
Pristidactylus scapulatus
98
Diplolaemus darwinii
100
Pristidactylus torquatus
Leiosaurus bellii
78
Leiosaurus paronae
77
Leiosaurus catamarcensis
70
Ctenoblepharys adspersa
Phymaturus indistinctus
100
Phymaturus somuncurensis
100
98
Phymaturus patagonicus
100 Phymaturus dorsimaculatus
Phymaturus palluma
punae
96 Phymaturus
mallimaccii
89 Phymaturus
Phymaturus
antofagastensis
88
Liolaemus tenuis
Liolaemus lemniscatus
95 99
Liolaemus monticola
100
Liolaemus nitidus
Liolaemus nigroviridis
68
93
Liolaemus fuscus
Liolaemus atacamensis
100
Liolaemus zapallarensis
Liolaemus pseudolemniscatus
91
Liolaemus nigromaculatus
67
Liolaemus platei
66
97 Liolaemus paulinae
99
99 Liolaemus austromendocinus
thermarum
100 Liolaemus
Liolaemus dicktracyi
100
Liolaemus heliodermis
95
Liolaemus
capillitas
98
83 Liolaemus umbrifer
Liolaemus petrophilus
100 Liolaemus buergeri
Liolaemus ceii
59
Liolaemus leopardinus
100
100
Liolaemus kriegi
66
Liolaemus elongatus
98
Liolaemus coeruleus
Liolaemus bellii
98
Liolaemus gravenhorstii
97 Liolaemus schroederi
100 Liolaemus chiliensis
99
Liolaemus cyanogaster
98
Liolaemus pictus
99 Liolaemus hernani
86
Liolaemus bibronii
Liolaemus pagaburoi
56
Liolaemus bitaeniatus
53
Liolaemus chaltin
100
100
100 Liolaemus puna
68 Liolaemus walkeri
97
yanalcu
91 Liolaemus
Liolaemus ramirezae
Liolaemus robertmertensi
74
Liolaemus gracilis
84
100 Liolaemus saxatilis
Liolaemus hatcheri
94
Liolaemus lineomaculatus
70 Liolaemus silvanae
100 Liolaemus kolengh
Liolaemus magellanicus
100
Liolaemus uptoni
99 Liolaemus somuncurae
100
100 Liolaemus baguali
tari
100
95 Liolaemus
Liolaemus escarchadosi
Liolaemus kingii
100
gallardoi
83 Liolaemus
Liolaemus sarmientoi
99 Liolaemus scolaroi
zullyae
98 Liolaemus
78 Liolaemus tristis
Liolaemus archeforus
100
Liolaemus stolzmanni
Liolaemus orientalis
100
famatinae
98 Liolaemus
Liolaemus vallecurensis
82 82 Liolaemus ruibali
Liolaemus
78
99 Liolaemus audituvelatus
72
fabiani
Liolaemus huacahuasicus
Liolaemus dorbignyi
84
Liolaemus
molinai
87
Liolaemus multicolor
Liolaemus andinus
100
Liolaemus pseudoanomalus
100
Liolaemus
occipitalis
97
99
Liolaemus lutzae
Liolaemus salinicola
65
85
Liolaemus riojanus
100 Liolaemus multimaculatus
99
Liolaemus scapularis
Liolaemus azarai
98
Liolaemus wiegmannii
100
Liolaemus
rothi
100
Liolaemus
boulengeri
99
Liolaemus inacayali
Liolaemus telsen
85
Liolaemus
cuyanus
99 Liolaemus donosobarrosi
Liolaemus melanops
100
Liolaemus canqueli
98 93 Liolaemus morenoi
Liolaemus chehuachekenk
64
95 Liolaemus fitzingerii
79 Liolaemus xanthoviridis
Liolaemus hermannunezi
Liolaemus uspallatensis
94
Liolaemus chacoensis
100 Liolaemus
olongasta
78
Liolaemus grosseorum
95
Liolaemus darwinii
99
100 Liolaemus laurenti
100
Liolaemus koslowskyi
94
Liolaemus quilmes
100 Liolaemus espinozai
66
Liolaemus abaucan
Liolaemus crepuscularis
Liolaemus irregularis
99 100Liolaemus albiceps
Liolaemus calchaqui
67
Liolaemus ornatus
86
Liolaemus lavillai
92
99
Polychrotidae
Hoplocercidae
Leiocephalidae
Crotaphytidae
87
(ii)
93
R
Leiosauridae
Leiocephalus carinatus
Leiocephalus raviceps
Leiocephalus psammodromus
Leiocephalus personatus
Leiocephalus
schreibersii
92
Leiocephalus barahonensis
Gambelia wislizenii
Gambelia sila
100
Gambelia copeii
Crotaphytus antiquus
99
100
Crotaphytus reticulatus
Crotaphytus
vestigium
100
Crotaphytus insularis
100
82 Crotaphytus grismeri
83
Crotaphytus bicinctores
Crotaphytus nebrius
93
100 Crotaphytus collaris
Uma exsul
Uma paraphygas
100
100
Uma scoparia
Uma inornata
100
100
100 Uma notata
Callisaurus draconoides
Cophosaurus texanus
99
Holbrookia lacerata
Holbrookia propinqua
100
99
Holbrookia maculata
100
Phrynosoma cornutum
Phrynosoma solare
96
Phrynosoma mcallii
100 Phrynosoma platyrhinos
100
Phrynosoma coronatum
Phrynosoma blainvillii
100
Phrynosoma cerroense
96 Phrynosoma wigginsi
95
Phrynosoma asio
88
Phrynosoma braconnieri
92
Phrynosoma taurus
Phrynosoma modestum
100
Phrynosoma orbiculare
100
Phrynosoma ditmarsi
97
Phrynosoma douglassii
100
Phrynosoma
hernandesi
99
Petrosaurus mearnsi
100
Petrosaurus repens
100 Petrosaurus thalassinus
Uta squamata
Uta palmeri
100
Uta stansburiana
76
100 Uta stejnegeri
Urosaurus gadovi
Urosaurus bicarinatus
100
100
Urosaurus lahtelai
100 99
Urosaurus nigricaudus
Urosaurus
graciosus
100
Urosaurus ornatus
99
Urosaurus clarionensis
100
100 Urosaurus auriculatus
96
Sceloporus parvus
Sceloporus couchii
86 100
Sceloporus chrysostictus
Sceloporus teapensis
100
Sceloporus variabilis
Sceloporus smithi
91
Sceloporus cozumelae
97
Sceloporus grandaevus
90
Sceloporus angustus
100 100
Sceloporus utiformis
Sceloporus carinatus
Sceloporus squamosus
100
Sceloporus siniferus
100
75
Sceloporus merriami
95
Sceloporus pyrocephalus
Sceloporus nelsoni
100
Sceloporus gadoviae
100
Sceloporus maculosus
82
Sceloporus jalapae
96
Sceloporus ochoterenae
100
Sceloporus vandenburgianus
Sceloporus
graciosus
100
99 Sceloporus arenicolus
89
Sceloporus magister
99
Sceloporus zosteromus
Sceloporus lineatulus
100 99
Sceloporus licki
100
Sceloporus orcutti
100
99
Sceloporus hunsakeri
Sceloporus melanorhinus
Sceloporus grammicus
100
99
Sceloporus palaciosi
Sceloporus heterolepis
97
Sceloporus aeneus
89 99
Sceloporus bicanthalis
Sceloporus scalaris
100
99
Sceloporus slevini
Sceloporus chaneyi
98
Sceloporus samcolemani
98
100 Sceloporus goldmani
Sceloporus megalepidurus
96
Sceloporus insignis
Sceloporus jarrovii
96 92
Sceloporus torquatus
89 97
Sceloporus bulleri
100
Sceloporus mucronatus
Sceloporus macdougalli
Sceloporus poinsettii
100
Sceloporus dugesii
Sceloporus minor
98
Sceloporus ornatus
98
82
Sceloporus serrifer
98
100 Sceloporus cyanogenys
Sceloporus clarkii
Sceloporus olivaceus
Sceloporus occidentalis
Sceloporus virgatus
100
91 Sceloporus woodi
65
Sceloporus consobrinus
100
Sceloporus undulatus
Sceloporus cautus
99
Sceloporus horridus
100
Sceloporus edwardtaylori
74
Sceloporus spinosus
100 Sceloporus taeniocnemis
Sceloporus smaragdinus
100 98
Sceloporus malachiticus
Sceloporus lundelli
100
Sceloporus cryptus
100
Sceloporus subpictus
61
Sceloporus formosus
Sceloporus stejnegeri
100
Sceloporus adleri
97
94
100
Page 23 of 53
Laemanctus longipes
Corytophanes percarinatus
Corytophanes cristatus
Basiliscus galeritus
Basiliscus vittatus
Basiliscus plumifrons
98
Basiliscus basiliscus
92
Anolis boettgeri
67
Anolis luciae
Anolis bonairensis
64
Anolis griseus
Anolis trinitatis
100
Anolis richardii
62
Anolis aeneus
96
Anolis roquet
100
Anolis extremus
100
100
Anolis fitchi
89
Anolis huilae
Anolis peraccae
96
Anolis festae
Anolis chloris
95
Anolis ventrimaculatus
Anolis aequatorialis
99
96
Anolis gemmosus
90
Anolis euskalerriari
Anolis nicefori
100
Anolis heterodermus
100
Anolis vanzolinii
99
Anolis inderenae
65
100
Anolis punctatus
83
Anolis transversalis
100
Anolis tigrinus
Anolis jacare
99
Anolis anatoloros
100
71 98
Anolis calimae
Anolis neblininus
Anolis agassizi
100
Anolis microtus
Anolis insignis
100
Anolis danieli
100
80
Anolis fraseri
98
Anolis chocorum
Anolis princeps
87
100
Anolis frenatus
100
Anolis casildae
Anolis maculigula
100
Anolis bartschi
Anolis vermiculatus
75
Anolis occultus
79
Anolis monticola
82
Anolis darlingtoni
Anolis bahorucoensis
99 56 100
Anolis dolichocephalus
100
Anolis hendersoni
Anolis coelestinus
94
Anolis chlorocyanus
Anolis singularis
100
99
Anolis aliniger
59
90 Anolis smallwoodi
100 Anolis noblei
Anolis baracoae
59 Anolis luteogularis
89 Anolis equestris
Anolis etheridgei
98
98
Anolis fowleri
100
Anolis insolitus
97
Anolis barbouri
86
Anolis olssoni
97
Anolis semilineatus
99
Anolis alumina
Anolis argenteolus
Anolis barbatus
95
100
Anolis porcus
Anolis chamaeleonides
86
66 Anolis guamuhaya
86
Anolis cuvieri
Anolis christophei
Anolis eugenegrahami
93
90
Anolis ricordi
90
Anolis baleatus
100
95 Anolis barahonae
Anolis marcanoi
100
Anolis strahmi
99
Anolis longitibialis
Anolis haetianus
96
Anolis shrevei
99
Anolis armouri
95
Anolis cybotes
99
Anolis whitemani
60
Anolis lucius
Anolis clivicola
97
Anolis rejectus
Anolis cyanopleurus
100
100 Anolis cupeyalensis
Anolis macilentus
99
Anolis alfaroi
Anolis vanidicus
65
Anolis inexpectatus
76
100 Anolis alutaceus
Anolis placidus
86
100
Anolis sheplani
85
Anolis alayoni
Anolis paternus
100
100
Anolis angusticeps
Anolis garridoi
80
100 Anolis guazuma
98
89
Anolis loysiana
97
Anolis pumilus
Anolis centralis
100
Anolis argillaceus
95
Anolis oporinus
100
Anolis isolepis
100 Anolis carolinensis
Anolis porcatus
Anolis longiceps
99
Anolis brunneus
Anolis maynardi
100
Anolis allisoni
74
97
Anolis smaragdinus
100
100
(i)
99
Dactyloidae
(i)
(ii)
R
Figure 19 Species-level squamate phylogeny continued (R).
Corytophanidae
Anolis wattsi
Anolis pogus
Anolis leachii
Anolis bimaculatus
90
Anolis gingivinus
Anolis oculatus
99
77
Anolis terraealtae
Anolis ferreus
99
Anolis lividus
100
Anolis nubilus
95
100
Anolis sabanus
57
Anolis marmoratus
Anolis distichus
100
Anolis websteri
Anolis brevirostris
96
Anolis marron
94
100
Anolis caudalis
Anolis
acutus
95 100
Anolis stratulus
Anolis evermanni
Anolis poncensis
88
Anolis gundlachi
100
91
Anolis pulchellus
100
Anolis krugi
98 100
Anolis monensis
Anolis cooki
Anolis scriptus
100
Anolis ernestwilliamsi
96
Anolis desechensis
100
75
100
Anolis cristatellus
Anolis imias
98
Anolis rubribarbaris
Anolis allogus
100
98
Anolis ahli
90
Anolis guafe
100
Anolis confusus
Anolis jubar
72
94 Anolis homolechis
100
Anolis mestrei
Anolis ophiolepis
100
Anolis sagrei
99
Anolis quadriocellifer
89
99
Anolis bremeri
Anolis lineatopus
100
Anolis reconditus
58
Anolis valencienni
100
Anolis opalinus
100
Anolis garmani
90
95
Anolis conspersus
100 Anolis grahami
Anolis auratus
99
Anolis annectens
100
Anolis onca
Anolis lineatus
Anolis meridionalis
52
Anolis nitens
84
Anolis bombiceps
59
99
Anolis
chrysolepis
99
Anolis loveridgei
100
Anolis purpurgularis
90
Anolis utilensis
Anolis crassulus
96
Anolis sminthus
72
Anolis polyrhachis
94
Anolis uniformis
Anolis bitectus
Anolis biporcatus
95
Anolis woodi
100
Anolis aquaticus
Anolis quercorum
Anolis ortonii
Anolis laeviventris
100
Anolis intermedius
93
92
Anolis isthmicus
100
Anolis sericeus
Anolis pachypus
86
100
Anolis humilis
69
Anolis altae
100 86 Anolis kemptoni
Anolis fuscoauratus
93
Anolis cupreus
98
Anolis polylepis
Anolis capito
99
90
Anolis tropidonotus
Anolis ocelloscapularis
Anolis carpenteri
100 Anolis bicaorum
100
Anolis lemurinus
91
56
Anolis limifrons
100
Anolis zeus
94
Anolis oxylophus
86
Anolis lionotus
97
Anolis tropidogaster
Anolis poecilopus
96
92
Anolis trachyderma
100
100 56
(ii)
Page 24 of 53
Liotyphlops albirostris
Typhlophis squamosus
Tricheilostoma bicolor
Siagonodon septemstriatus
93
97
Epictia albifrons
100
Epictia goudotii
100
Epictia columbi
Trilepida macrolepis
97 100
Rena dulcis
100
Rena humilis
100 Tetracheilostoma carlae
Tetracheilostoma breuili
Mitophis asbolepis
100
100
100
Mitophis pyrites
Mitophis leptipileptus
98
Myriopholis longicauda
100
Myriopholis algeriensis
Myriopholis rouxestevae
56
100 Myriopholis boueti
Myriopholis blanfordi
79
Myriopholis macrorhyncha
100
100
69
Myriopholis adleri
Namibiana occidentalis
Leptotyphlops nigroterminus
100
Leptotyphlops nigricans
99
100
Leptotyphlops sylvicolus
Leptotyphlops conjunctus
100
Leptotyphlops distanti
51
Leptotyphlops scutifrons
100
91
Gerrhopilus hedraeus
Gerrhopilus mirus
Xenotyphlops grandidieri
Typhlops brongersmianus
96
Typhlops reticulatus
Typhlops biminiensis
100
Typhlops pusillus
95
Typhlops hectus
100
Typhlops syntherus
71
90
Typhlops eperopeus
87
Typhlops lumbricalis
84
Typhlops schwartzi
56
Typhlops titanops
100
92
83
Typhlops sulcatus
77
Typhlops rostellatus
Typhlops capitulatus
Typhlops jamaicensis
77
92 Typhlops sylleptor
92
99 Typhlops agoralionis
Typhlops caymanensis
100
Typhlops arator
Typhlops contorhinus
74
Typhlops anchaurus
100
Typhlops anousius
Typhlops notorachius
Typhlops monastus
100
Typhlops dominicanus
Typhlops granti
86
Typhlops hypomethes
84
99 Typhlops platycephalus
95 Typhlops richardi
75 Typhlops catapontus
Rhinotyphlops lalandei
Letheobia feae
100 Letheobia newtoni
87
Letheobia obtusa
Typhlops elegans
100 Afrotyphlops angolensis
100
Megatyphlops schlegelii
77
Afrotyphlops fornasinii
89
99
Afrotyphlops bibronii
87
Afrotyphlops lineolatus
87
Afrotyphlops congestus
99
72 Afrotyphlops punctatus
Typhlops vermicularis
Typhlops arenarius
Typhlops luzonensis
100
Typhlops ruber
76
Ramphotyphlops albiceps
84
Typhlops pammeces
100
Ramphotyphlops braminus
99
97
Typhlopidae sp. (Sri Lanka)
Ramphotyphlops lineatus
65
Ramphotyphlops acuticaudus
72
Acutotyphlops subocularis
100
Acutotyphlops kunuaensis
Ramphotyphlops polygrammicus
Austrotyphlops diversus
74
91
Austrotyphlops howi
75 87
Austrotyphlops guentheri
Austrotyphlops bituberculatus
100
Austrotyphlops grypus
Austrotyphlops longissimus
100 52
Austrotyphlops leptosomus
Austrotyphlops unguirostris
59
98
Austrotyphlops ammodytes
92
Austrotyphlops kimberleyensis
96
Austrotyphlops troglodytes
93
Austrotyphlops ganei
87 Austrotyphlops ligatus
76
Ramphotyphlops bicolor
96
Austrotyphlops pinguis
90 Austrotyphlops splendidus
99
Austrotyphlops waitii
Austrotyphlops australis
98
81 Austrotyphlops endoterus
Austrotyphlops hamatus
74
91
Austrotyphlops pilbarensis
100
90
S
Leptotyphlopidae
Gerrhopilidae
Xenotyphlopidae
Typhlopidae
100
Anomalepididae
T-AA
Figure 20 Species-level squamate phylogeny continued (S).
Page 25 of 53
98
100
97
T
U-AA
Figure 21 Species-level squamate phylogeny continued (T).
Anilius scytale
Aniliidae
Trachyboa gularis
Trachyboa boulengeri
100 Tropidophis pardalis
100
Tropidophis wrighti
Tropidophiidae
Tropidophis greenwayi
100
100 Tropidophis haetianus
53
Tropidophis feicki
98 Tropidophis melanurus
Xenophidiidae
Xenophidion schaeferi
Casarea dussumieri
Bolyeriidae
Sanzinia madagascariensis
100
Sanziniinae
Acrantophis madagascariensis
100 100 Acrantophis dumerili
Calabariidae
Calabaria reinhardtii
Exiliboa placata
100
Ungaliophis continentalis
Ungaliophiinae
99
Charina bottae
100
Lichanura trivirgata
Candoia aspera
100
Candoia carinata
Candoiinae
99
81
Candoia bibroni
Eryx jayakari
69
Eryx colubrinus
100 53
Eryx
conicus
87
Eryx johnii
Erycinae
95 87 Eryx jaculus
Eryx elegans
96
Boidae
Eryx miliaris
93
83
100 Eryx tataricus
Boa constrictor
Corallus hortulanus
99
Corallus caninus
98
Corallus annulatus
Epicrates cenchria
88 100
100 Eunectes murinus
Eunectes notaeus
Epicrates angulifer
Boinae
96 94 Epicrates inornatus
85
Epicrates monensis
Epicrates fordi
90
Epicrates subflavus
Epicrates chrysogaster
95
100 Epicrates exsul
92 Epicrates striatus
Anomochilidae
Anomochilus leonardi
65
Cylindrophis maculatus
Cylindrophiidae
100
Cylindrophis ruffus
Melanophidium punctatum
Brachyophidium rhodogaster
98
Uropeltis liura
86
Uropeltis ceylanicus
90
Rhinophis travancoricus
73 100 Uropeltis melanogaster
Uropeltis
phillipsi
80
Uropeltidae
Rhinophis drummondhayi
82
89
69
Rhinophis dorsimaculatus
Rhinophis philippinus
77
Rhinophis oxyrhynchus
Pseudotyphlops philippinus
84
Rhinophis homolepis
85
80
Rhinophis blythii
Xenopeltis unicolor
Xenopeltidae
Loxocemus bicolor
Loxocemidae
Python brongersmai
98
99
Python regius
99
Python curtus
86
100
96 Python sebae
Python molurus
98 Broghammerus reticulatus
100
Broghammerus timoriensis
Morelia oenpelliensis
76
Morelia
boeleni
97
Morelia amethistina
100
100 Aspidites ramsayi
Aspidites melanocephalus
75
Liasis olivaceus
Pythonidae
Apodora papuana
98
Liasis mackloti
96
100
Liasis fuscus
Leiopython albertisii
100
Bothrochilus boa
Morelia viridis
71
Morelia
carinata
84
96 100 Morelia spilota
Morelia bredli
85
Antaresia maculosa
Antaresia perthensis
51
Antaresia stimsoni
83
100 Antaresia childreni
100
Acrochordidae
Acrochordus javanicus
95
100
Xenodermus javanicus
100
Achalinus meiguensis
98
Achalinus rufescens
Asthenodipsas vertebralis
99
Aplopeltura boa
Pareatidae
Pareas monticola
Pareas boulengeri
100
96
Pareas formosensis
Pareas margaritophorus
95
91
Pareas macularius
Pareas hamptoni
Pareas carinatus
100 Pareas nuchalis
100
Eristicophis macmahoni
100
Pseudocerastes persicus
99
(i)
Pseudocerastes fieldi
Macrovipera lebetina
100
100
Macrovipera schweizeri
100
100
Montivipera xanthina
Montivipera raddei
99
Montivipera bornmuelleri
94 Montivipera albizona
83 Montivipera wagneri
88
Daboia palaestinae
96
Daboia russelii
59
Macrovipera deserti
100 Macrovipera mauritanica
95
Vipera ammodytes
100
100
Vipera seoanei
93
Vipera nikolskii
100
Vipera berus
77
100
Vipera latastei
Vipera aspis
Vipera barani
99
Vipera kaznakovi
Viperinae
100
Vipera eriwanensis
97
99
Vipera ursinii
Vipera dinniki
85
59 Vipera renardi
80
Vipera lotievi
Proatheris superciliaris
Cerastes vipera
100
Cerastes cerastes
100
86
Cerastes gasperettii
Causus resimus
Causus rhombeatus
100
Causus defilippii
89
Echis carinatus
100
100
Echis omanensis
100
Echis coloratus
62
(i)
97
91
Viperidae
100
(ii)
Echis ocellatus
Echis jogeri
Echis leucogaster
100 Echis pyramidum
Atheris ceratophora
93
Atheris barbouri
100
Atheris chlorechis
51
Atheris hispida
100
Atheris squamigera
77
Atheris nitschei
53
94
Atheris desaixi
Bitis worthingtoni
63
Bitis arietans
Bitis nasicornis
100
Bitis gabonica
95
100
100
96
Bitis peringueyi
Bitis caudalis
98
U
Bitis xeropaga
99
V-AA
98
100
Bitis atropos
Bitis cornuta
Bitis rubida
Figure 22 Species-level squamate phylogeny continued (U).
100
99
100
Azemiopinae
Calloselasma rhodostoma
Hypnale nepa
Hypnale hypnale
Hypnale zara
Trimeresurus puniceus
Trimeresurus borneensis
98
Trimeresurus malabaricus
Trimeresurus gramineus
96
100
Trimeresurus trigonocephalus
100
Trimeresurus
hageni
99
Trimeresurus malcolmi
Trimeresurus flavomaculatus
99
Trimeresurus schultzei
89
Trimeresurus sumatranus
97
Trimeresurus
popeiorum
89
98
Trimeresurus tibetanus
Trimeresurus
medoensis
94
Trimeresurus yunnanensis
Trimeresurus gumprechti
81
Trimeresurus stejnegeri
72 96
Trimeresurus vogeli
Trimeresurus kanburiensis
100
93
Trimeresurus venustus
Trimeresurus macrops
Trimeresurus fasciatus
96
64
Trimeresurus insularis
85
Trimeresurus septentrionalis
100
Trimeresurus andersonii
Trimeresurus albolabris
93
Trimeresurus cantori
77
Trimeresurus erythrurus
100
Trimeresurus purpureomaculatus
99
97
Ovophis
monticola
100
Ovophis zayuensis
Ovophis tonkinensis
98
97
Protobothrops kaulbacki
Protobothrops sieversorum
Protobothrops mangshanensis
Protobothrops cornutus
99
92
Protobothrops xiangchengensis
100
90
Protobothrops jerdonii
Protobothrops elegans
100
100
Protobothrops mucrosquamatus
Protobothrops flavoviridis
100
63
Protobothrops tokarensis
100
Ovophis okinavensis
Trimeresurus gracilis
Gloydius tsushimaensis
85
100
Gloydius brevicaudus
100
99 Gloydius ussuriensis
Gloydius blomhoffii
100
Gloydius strauchi
Gloydius halys
97
96
Gloydius
shedaoensis
100
Gloydius intermedius
99
95 Gloydius saxatilis
Atropoides occiduus
100
Atropoides nummifer
100
Atropoides olmec
99
Atropoides picadoi
Cerrophidion godmani
Cerrophidion tzotzilorum
94
90
Cerrophidion petlalcalensis
99
Porthidium ophryomegas
78
Porthidium dunni
96
Porthidium yucatanicum
100
Porthidium nasutum
100
Porthidium
porrasi
86
Porthidium
lansbergii
90
Bothrocophias campbelli
Bothrocophias microphthalmus
99
Bothrocophias hyoprora
Bothrops pictus
Rhinocerophis ammodytoides
100
96
100
Rhinocerophis cotiara
Rhinocerophis fonsecai
Rhinocerophis alternatus
90
94
Rhinocerophis itapetiningae
99
Bothropoides erythromelas
100
Bothropoides diporus
100
Bothropoides neuwiedi
91
94
Bothropoides jararaca
100
Bothropoides insularis
90 Bothropoides alcatraz
Bothriopsis pulchra
100
99
Bothriopsis chloromelas
Bothriopsis taeniata
98
Bothriopsis bilineata
95
Bothrops brazili
100
Bothrops jararacussu
100
Bothrops punctatus
100
97
Bothrops caribbaeus
Bothrops lanceolatus
Bothrops asper
100
87
Bothrops marajoensis
90
Bothrops colombiensis
Bothrops atrox
99
Bothrops moojeni
72
Bothrops leucurus
Ophryacus undulatus
100
Mixcoatlus barbouri
Mixcoatlus melanurus
85
100
100
Lachesis stenophrys
Lachesis muta
Bothriechis schlegelii
53
51
Bothriechis nigroviridis
Bothriechis lateralis
98
Bothriechis marchi
98
100
100
Bothriechis thalassinus
Bothriechis bicolor
Bothriechis aurifer
91
Bothriechis rowleyi
84
Agkistrodon contortrix
100
Agkistrodon piscivorus
Agkistrodon
taylori
99
Agkistrodon bilineatus
99
Sistrurus catenatus
Sistrurus miliarius
97
96
Crotalus pricei
Crotalus intermedius
100
100 Crotalus transversus
98
Crotalus tancitarensis
100
52
Crotalus triseriatus
100
Crotalus pusillus
Crotalus lepidus
87
Crotalus aquilus
95
74
Crotalus enyo
56
Crotalus polystictus
Crotalus cerastes
99
Crotalus ravus
63
Crotalus willardi
Crotalus horridus
97
100
Crotalus durissus
82
Crotalus simus
Crotalus basiliscus
100
Crotalus molossus
100
Crotalus totonacus
91
Crotalus ruber
99
Crotalus catalinensis
Crotalus atrox
100
100 Crotalus tortugensis
Crotalus scutulatus
98
100
Crotalus oreganus
Crotalus viridis
58
77
Crotalus mitchellii
Crotalus tigris
89
Crotalus adamanteus
90
100
(ii)
Crotalinae
Stoliczkia borneensis
Xenodermatidae
50
Acrochordus arafurae
97
Azemiops feae
Garthius chaseni
Tropidolaemus wagleri
Deinagkistrodon acutus
91
Acrochordus granulatus
100
95
Page 26 of 53
95
Page 27 of 53
Enhydris chinensis
Enhydris plumbea
Enhydris matannensis
100
Enhydris enhydris
Enhydris jagorii
100
Enhydris longicauda
100
100 Enhydris innominata
100
Myron richardsonii
100
Pseudoferania polylepis
71
Erpeton tentaculatum
Enhydris
bocourti
89
Bitia hydroides
96
Cantoria violacea
85
Gerarda prevostiana
70
Fordonia leucobalia
98
88
Enhydris punctata
Homalopsis buccata
88
Cerberus australis
97
Cerberus microlepis
100 100
Cerberus rynchops
Micrelaps bicoloratus
Oxyrhabdium leporinum
Prosymna ruspolii
100
Prosymna visseri
86
Prosymna janii
Prosymna greigerti
100
Prosymna meleagris
99
Rhamphiophis oxyrhynchus
95
99
Rhamphiophis rubropunctatus
Malpolon monspessulanus
96
Rhagerhis moilensis
54
Mimophis mahfalensis
Dipsina multimaculata
97
Hemirhagerrhis viperina
100
Hemirhagerrhis kelleri
100
Hemirhagerrhis hildebrandtii
Psammophylax acutus
65
Psammophylax rhombeatus
97
Psammophylax variabilis
100
Psammophylax tritaeniatus
90
95
Psammophis crucifer
70
Psammophis lineolatus
Psammophis condanarus
100
Psammophis trigrammus
Psammophis jallae
100
100
Psammophis leightoni
85 50
Psammophis notostictus
Psammophis angolensis
100
Psammophis schokari
76
Psammophis punctulatus
80
Psammophis praeornatus
100
Psammophis tanganicus
69
Psammophis biseriatus
Psammophis lineatus
96
95
Psammophis subtaeniatus
97
Psammophis sudanensis
73
Psammophis orientalis
60
Psammophis rukwae
100
Psammophis sibilans
80
Psammophis leopardinus
71
100 Psammophis mossambicus
100
Psammophis phillipsi
Homoroselaps lacteus
Atractaspis irregularis
98
Atractaspis microlepidota
Atractaspis boulengeri
96
Atractaspis bibronii
98
Atractaspis micropholis
58
100
Atractaspis corpulenta
99
Macrelaps microlepidotus
96
Amblyodipsas polylepis
Xenocalamus transvaalensis
100
Amblyodipsas dimidiata
94
Polemon notatus
97
Polemon collaris
100
Polemon acanthias
93
Aparallactus modestus
54
Aparallactus werneri
100
100
Aparallactus capensis
92
Aparallactus guentheri
100
Pythonodipsas carinata
Pseudaspis
cana
96 95
Psammodynastes pulverulentus
Psammodynastes pictus
100
64
Buhoma procterae
Buhoma depressiceps
92
Lycophidion nigromaculatum
100
Lycophidion laterale
Lycophidion capense
69
Lycophidion ornatum
92
97
Hormonotus modestus
Inyoka swazicus
Gonionotophis stenophthalmus
93
Gonionotophis nyassae
100
Gonionotophis brussauxi
100
Gonionotophis poensis
Gonionotophis capensis
100
Pseudoboodon lemniscatus
Bothrolycus ater
97
Bothrophthalmus brunneus
92
Bothrophthalmus lineatus
100
Boaedon virgatus
Boaedon lineatus
98
100
Boaedon fuliginosus
100
Boaedon olivaceus
Lamprophis guttatus
95
Lamprophis fuscus
99
Lamprophis aurora
95
Lamprophis fiskii
Lycodonomorphus inornatus
Lycodonomorphus rufulus
90
Lycodonomorphus laevissimus
100
Lycodonomorphus whytii
98
99
Amplorhinus multimaculatus
100
Duberria variegata
82
Duberria lutrix
Ditypophis vivax
99
Compsophis boulengeri
98
Compsophis albiventris
Compsophis laphystius
100
Compsophis infralineatus
94
Alluaudina bellyi
Parastenophis betsileanus
Leioheterodon geayi
100
100
Leioheterodon madagascariensis
Leioheterodon modestus
100
Langaha madagascariensis
90
100
Micropisthodon ochraceus
Ithycyphus miniatus
Ithycyphus oursi
100
100
Madagascarophis colubrinus
97
Madagascarophis meridionalis
Lycodryas inornatus
94
Lycodryas citrinus
100
Lycodryas sanctijohannis
98
95
Lycodryas inopinae
100 Lycodryas pseudogranuliceps
54
Lycodryas granuliceps
100
Dromicodryas quadrilineatus
Dromicodryas bernieri
98
Thamnosophis infrasignatus
95
Thamnosophis martae
93
Thamnosophis epistibes
100
98
Thamnosophis stumpffi
Thamnosophis lateralis
95
Pseudoxyrhopus ambreensis
76
94
Heteroliodon occipitalis
Liopholidophis dimorphus
Liopholidophis dolicocercus
98
Liopholidophis
sexlineatus
100
99
Liophidium rhodogaster
Liophidium vaillanti
100
Liophidium therezieni
99
Liophidium torquatum
99
89
Liophidium mayottensis
Liophidium chabaudi
73
97
53
Homalopsidae
58
Prosymninae
Psammophiinae
Lamprophiidae
98
Atractaspidinae
Aparallactinae
Pseudaspidinae
100
Lamprophiinae
Pseudoxyrhophiinae
V
X-AA
W
Figure 23 Species-level squamate phylogeny continued (V).
Page 28 of 53
Calliophis melanurus
Maticora bivirgata
Micruroides euryxanthus
Sinomicrurus japonicus
Sinomicrurus kelloggi
100
Sinomicrurus macclellandi
95
85
Micrurus corallinus
Micrurus albicinctus
100
Micrurus
psyches
90
Micrurus fulvius
Micrurus diastema
99
100
Micrurus narduccii
98
Micrurus mipartitus
Micrurus dissoleucus
Micrurus surinamensis
91
Micrurus hemprichii
97
Micrurus lemniscatus
Micrurus decoratus
Micrurus baliocoryphus
94
Micrurus pyrrhocryptus
97
Micrurus altirostris
98
Micrurus ibiboboca
88
Micrurus spixii
Micrurus frontalis
98
89
59 Micrurus brasiliensis
Hemibungarus calligaster
84
Ophiophagus hannah
100
Dendroaspis angusticeps
84
Dendroaspis polylepis
87
63
Walterinnesia aegyptia
Aspidelaps scutatus
Hemachatus haemachatus
Naja kaouthia
100
Naja atra
100
Naja naja
Naja mandalayensis
91
Naja siamensis
99
Naja sumatrana
87
Naja multifasciata
69
90
Naja melanoleuca
Naja annulata
58
100
Naja nivea
83
Naja annulifera
88 Naja haje
95
78
Naja nubiae
92
Naja pallida
Naja katiensis
99
Naja mossambica
96
Naja nigricollis
96
Naja ashei
76
100
Elapsoidea nigra
99
Elapsoidea semiannulata
Elapsoidea sundevallii
Bungarus flaviceps
Bungarus bungaroides
98
Bungarus fasciatus
Bungarus sindanus
90
Bungarus ceylonicus
100
97
Bungarus caeruleus
97
100
Bungarus niger
100
Bungarus multicinctus
99
Bungarus candidus
Laticauda laticaudata
Laticauda saintgironsi
100
Laticauda guineai
98
100 Laticauda colubrina
Micropechis ikaheka
Toxicocalamus preussi
100
Demansia vestigiata
100
Demansia papuensis
100
Demansia psammophis
91
Toxicocalamus loriae
100
82
Furina ornata
92
Furina diadema
Simoselaps semifasciatus
99
100
Simoselaps anomalus
Simoselaps bertholdi
100
Aspidomorphus schlegeli
85
Aspidomorphus lineaticollis
68
Aspidomorphus muelleri
100
Acanthophis praelongus
Acanthophis antarcticus
Pseudechis porphyriacus
67
Pseudechis butleri
100
Pseudechis australis
100
100
100 Pseudechis colletti
Pseudechis papuanus
Pseudechis guttatus
Cacophis squamulosus
89
Elapognathus
coronata
88
88
Cryptophis nigrescens
Rhinoplocephalus bicolor
95
98
Suta fasciata
Suta monachus
100
Suta suta
90
Suta spectabilis
94
Vermicella intermedia
Simoselaps calonotus
75
71
Denisonia devisi
100
Oxyuranus microlepidotus
Oxyuranus scutellatus
100 97
Pseudonaja modesta
Pseudonaja textilis
Echiopsis curta
100
78
Drysdalia mastersii
Drysdalia coronoides
100
Austrelaps labialis
97
Austrelaps superbus
98
Hoplocephalus bitorquatus
98
Echiopsis atriceps
99
Notechis scutatus
99
98
Tropidechis carinatus
100
Hemiaspis signata
Hemiaspis damelii
Emydocephalus annulatus
100
Aipysurus eydouxii
97
Aipysurus duboisii
91
94
Aipysurus apraefrontalis
Aipysurus fuscus
90 100
Aipysurus laevis
100
96
Parahydrophis mertoni
Ephalophis greyae
Hydrelaps darwiniensis
98
Hydrophis elegans
Hydrophis lapemoides
72
Hydrophis spiralis
94
94 Hydrophis semperi
100
100
Hydrophis pacifica
97 Hydrophis cyanocincta
Hydrophis melanocephala
95
100
75 Hydrophis parviceps
Hydrophis curtus
Hydrophis platura
Hydrophis stokesii
Hydrophis atriceps
98
Hydrophis brooki
67
54
Hydrophis caerulescens
Hydrophis czeblukovi
83 83 Hydrophis
major
77
Hydrophis schistosa
93
Hydrophis macdowelli
Hydrophis kingii
88
Hydrophis peronii
74
100
Hydrophis ornata
61
100
Elapidae
W
Figure 24 Species-level squamate phylogeny continued (W).
Page 29 of 53
Calamariinae
Pseudorabdion oxycephalum
Calamaria pavimentata
Calamaria yunnanensis
Plagiopholis styani
100
Pseudoxenodon bambusicola
97
Pseudoxenodon macrops
85
Pseudoxenodon karlschmidti
Scaphiodontophis annulatus
96
Sibynophis bistrigatus
100
Sibynophis subpunctatus
68
Sibynophis triangularis
Sibynophis collaris
100
Sibynophis chinensis
100
Grayia tholloni
100
Grayia ornata
Grayia smithii
Ahaetulla fronticincta
Ahaetulla pulverulenta
100
Ahaetulla nasuta
100
Chrysopelea taprobanica
100
Chrysopelea ornata
100
Chrysopelea paradisi
69
Dendrelaphis bifrenalis
Dendrelaphis caudolineolatus
Dendrelaphis caudolineatus
100
Dendrelaphis schokari
97
Dendrelaphis tristis
91
Boiga kraepelini
71
Crotaphopeltis tornieri
99
73
Dipsadoboa unicolor
Telescopus fallax
89
Boiga irregularis
96
Boiga dendrophila
Boiga forsteni
96
100
Boiga cynodon
68
Boiga barnesii
100 85
Boiga trigonata
Boiga ceylonensis
Boiga beddomei
74
Boiga
multomaculata
79
Toxicodryas pulverulenta
Dasypeltis confusa
Dasypeltis atra
98
Dasypeltis scabra
70
Dasypeltis sahelensis
92
Dasypeltis gansi
77
Dasypeltis fasciata
90
Scaphiophis albopunctatus
Oligodon arnensis
100
Oligodon sublineatus
86
Oligodon taeniolatus
83
Oligodon octolineatus
Oligodon cyclurus
85
Oligodon barroni
100
100
Oligodon taeniatus
99
89
Oligodon chinensis
100
Oligodon ocellatus
99
Oligodon formosanus
90
99
Oligodon cinereus
93
Oligodon maculatus
Oligodon splendidus
56
97
Oligodon cruentatus
98
Oligodon theobaldi
100
Oligodon torquatus
98
Oligodon planiceps
Coelognathus radiatus
100
Coelognathus helena
Coelognathus erythrurus
100
99
Coelognathus subradiatus
Coelognathus flavolineatus
Thrasops jacksonii
90
Dispholidus typus
98
Thelotornis capensis
52
Philothamnus carinatus
Philothamnus heterodermus
60
Philothamnus nitidus
94
Philothamnus semivariegatus
90
57
88
Philothamnus angolensis
99
Philothamnus girardi
Philothamnus thomensis
68
99
Philothamnus natalensis
69
Philothamnus hoplogaster
Hapsidophrys lineatus
87
99
Hapsidophrys smaragdina
68
Hapsidophrys principis
Lytorhynchus diadema
Coluber zebrinus
92
Bamanophis dorri
86
100
Macroprotodon cucullatus
100
Macroprotodon abubakeri
Hemerophis socotrae
100
Hemorrhois hippocrepis
94
100
Hemorrhois algirus
Hemorrhois nummifer
100
Hemorrhois ravergieri
99
Spalerosophis microlepis
60
Spalerosophis diadema
95
86
Platyceps rhodorachis
100
Platyceps rogersi
Platyceps karelini
100
61
Platyceps ventromaculatus
Platyceps najadum
94
100
98
Platyceps collaris
Platyceps florulentus
52
Dolichophis jugularis
100
Dolichophis schmidti
100
Dolichophis caspius
100
Hierophis viridiflavus
100
Hierophis gemonensis
Hierophis spinalis
92
100
Eirenis modestus
83
Eirenis aurolineatus
Eirenis persicus
100
Eirenis decemlineatus
Eirenis levantinus
86
Eirenis medus
83
82
Eirenis thospitis
Eirenis lineomaculatus
97 86
Eirenis rothii
59
Eirenis coronelloides
Eirenis eiselti
100
Eirenis collaris
Eirenis barani
91
Eirenis punctatolineatus
100
99
97
Pseudoxenodontinae
Sibynophiinae
Grayiinae
74
71
68
X
Z-AA
Figure 25 Species-level squamate phylogeny continued (X).
Colubrinae
Colubridae
100
Y
Colubrinae cont.
Page 30 of 53
Cyclophiops major
Ptyas korros
Ptyas mucosa
Oxybelis fulgidus
82
Oxybelis aeneus
96
100
Opheodrys vernalis
Opheodrys aestivus
Salvadora mexicana
93
Tantilla melanocephala
93
Coluber taeniatus
Coluber constrictor
88
Coluber flagellum
92
Chironius quadricarinatus
Chironius carinatus
Leptophis ahaetulla
97
Dendrophidion dendrophis
92
93
Dendrophidion percarinatum
99
66
Drymobius rhombifer
Trimorphodon biscutatus
91
Phyllorhynchus decurtatus
82
Spilotes pullatus
98
Pseustes sulphureus
Drymarchon
corais
100
Chironius fuscus
Chironius scurrulus
Chironius laevicollis
87
Chironius grandisquamis
74
Chironius flavolineatus
86
Chironius bicarinatus
Chironius monticola
81
Chironius exoletus
83
Chironius laurenti
54
99
Chironius multiventris
100
Drymoluber dichrous
100
Drymoluber brazili
92
Mastigodryas melanolomus
64
87
Mastigodryas boddaerti
Mastigodryas bifossatus
Rhinobothryum lentiginosum
71
87
Stenorrhina freminvillei
Chionactis occipitalis
Chilomeniscus stramineus
89
Sonora semiannulata
94
99
Conopsis biserialis
Conopsis nasus
Ficimia streckeri
100
Gyalopion canum
Pseudoficimia frontalis
Sympholis lippiens
100
Gonyosoma oxycephalum
98
Gonyosoma jansenii
Rhadinophis prasinus
100
100
Rhynchophis boulengeri
53
Rhadinophis frenatus
Lycodon ruhstrati
Lycodon laoensis
86
Lycodon fasciatus
83
Lycodon
paucifasciatus
92
Lycodon rufozonatum
93
60
Lycodon semicarinatum
Dryocalamus nympha
Lycodon carinatus
83
Lycodon capucinus
94
98
76
Lycodon osmanhilli
Lycodon zawi
Lycodon aulicus
Archelaphe bella
100
Euprepiophis conspicillata
Euprepiophis mandarinus
100
Oreocryptophis porphyraceus
Orthriophis taeniurus
99
Orthriophis hodgsoni
Orthriophis moellendorffi
88
98
Orthriophis cantoris
Zamenis hohenackeri
99
Zamenis persicus
100
Zamenis longissimus
99
64
Zamenis lineatus
Rhinechis scalaris
100
100
Zamenis situla
Elaphe davidi
Elaphe carinata
93
Elaphe bimaculata
90
100
100
Elaphe dione
61
Elaphe climacophora
55
Elaphe schrenckii
Elaphe quadrivirgata
100
83
Elaphe quatuorlineata
Elaphe sauromates
75
Coronella girondica
98
Coronella austriaca
83
Oocatochus rufodorsatus
Senticolis triaspis
Pituophis deppei
100
Pituophis vertebralis
84
Pituophis
lineaticollis
91
Pituophis melanoleucus
Pituophis ruthveni
94
100
99
Pituophis catenifer
98
Pantherophis vulpinus
Pantherophis guttatus
100
Pantherophis emoryi
99
Pantherophis slowinskii
96
Pantherophis spiloides
100
Pantherophis
alleghaniensis
100
100 98
Pantherophis obsoletus
Pantherophis bairdi
100
Bogertophis subocularis
Bogertophis rosaliae
Rhinocheilus lecontei
98
87
Arizona elegans
Pseudelaphe flavirufa
Cemophora coccinea
Lampropeltis calligaster
100
Lampropeltis webbi
Lampropeltis pyromelana
100
75
Lampropeltis zonata
92
Lampropeltis elapsoides
72
Lampropeltis mexicana
79
94
82
Lampropeltis ruthveni
Lampropeltis triangulum
Lampropeltis extenuatum
100
Lampropeltis alterna
96
98
Lampropeltis nigra
74
Lampropeltis getula
96
Lampropeltis holbrooki
Lampropeltis splendida
60
98
Lampropeltis californiae
100
81
Colubrinae cont.
Y
Figure 26 Species-level squamate phylogeny continued (Y).
Page 31 of 53
Trachischium monticola
Amphiesma sauteri
100
Amphiesma craspedogaster
99
Natriciteres olivacea
98
Afronatrix anoscopus
Lycognathophis seychellensis
Macropisthodon rudis
68
Balanophis ceylonensis
100
Rhabdophis subminiatus
69
Rhabdophis tigrinus
62
96
Rhabdophis nuchalis
98
88
Amphiesma stolatum
Xenochrophis vittatus
Xenochrophis flavipunctatus
Natricinae
Xenochrophis piscator
100
Atretium schistosum
100
Xenochrophis punctulatus
Xenochrophis asperrimus
88
Atretium yunnanensis
100
Aspidura drummondhayi
100
Aspidura trachyprocta
Aspidura ceylonensis
99
Aspidura guentheri
Opisthotropis guangxiensis
100
Opisthotropis lateralis
Opisthotropis latouchii
86
100
Opisthotropis cheni
Sinonatrix aequifasciata
100
98
Sinonatrix percarinata
82
Sinonatrix annularis
Natrix maura
100
Natrix natrix
88
Natrix tessellata
Clonophis kirtlandii
Virginia striatula
72
100
Storeria occipitomaculata
98
97
Storeria dekayi
Seminatrix pygaea
80
Regina rigida
100
100
Regina alleni
Regina septemvittata
76
Regina grahami
50
Tropidoclonion lineatum
96
100
Nerodia cyclopion
Nerodia floridana
100
100 Nerodia taxispilota
Nerodia rhombifer
Nerodia erythrogaster
99
Nerodia harteri
Nerodia fasciata
100
100
Nerodia sipedon
Thamnophis sirtalis
69
Thamnophis sauritus
100
Thamnophis proximus
Thamnophis rufipunctatus
93
Adelophis foxi
Thamnophis valida
100
Thamnophis melanogaster
100
Thamnophis exsul
72
Thamnophis godmani
85
Thamnophis scaliger
96 100
Thamnophis sumichrasti
98
Thamnophis mendax
Thamnophis fulvus
100
Thamnophis chrysocephalus
Thamnophis cyrtopsis
86
Thamnophis eques
99
99
Thamnophis marcianus
Thamnophis hammondii
100
Thamnophis ordinoides
92
99Thamnophis couchii
63
69 Thamnophis atratus
Thamnophis gigas
73
Thamnophis elegans
Thamnophis brachystoma
94
100 Thamnophis radix
89 Thamnophis butleri
99
Z
Figure 27 Species-level squamate phylogeny continued (Z).
Page 32 of 53
Conophis lineatus
Crisantophis nevermanni
Psomophis obtusus
94 Psomophis genimaculatus
Psomophis joberti
Contia tenuis
100
Pseudalsophis biserialis
72
Pseudalsophis elegans
Heterodon platirhinos
Arrhyton taeniatum
100
100
Arrhyton supernum
Heterodon simus
Arrhyton vittatum
58
Arrhyton landoi
99 Heterodon nasicus
73
Arrhyton procerum
Arrhyton tanyplectum
91
75
100
Diadophis punctatus
98 Arrhyton dolichura
Magliophis exiguum
81
100
Carphophis amoenus
Cubophis cantherigerus
87
100
Cubophis vudii
Farancia abacura
Caraiba andreae
99
80
Haitiophis anomalus
93
98
Borikenophis portoricensis
Farancia erytrogramma
80
Alsophis antillensis
100
Alsophis rijgersmaei
Nothopsis rugosus
97
Alsophis antiguae
97
Amastridium
veliferum
100 Alsophis rufiventris
68
99
Ialtris dorsalis
Darlingtonia haetiana
Tantalophis discolor
89
100
99
Hypsirhynchus ferox
83
Antillophis parvifrons
Coniophanes fissidens
Schwartzophis callilaemum
98
Schwartzophis polylepis
Rhadinaea flavilata
100
96
93
100 Schwartzophis funereum
86
Uromacer catesbyi
100
Rhadinaea fulvivittis
Uromacer oxyrhynchus
Uromacer frenatus
99
Pseudoleptodeira latifasciata
Lygophis anomalus
Lygophis elegantissimus
100
80
Trimetopon gracile
Lygophis lineatus
99
99
Lygophis paucidens
Hypsiglena slevini
76
78
Lygophis flavifrenatus
73
Lygophis meridionalis
70
Hypsiglena jani
Xenodon severus
Xenodon merremi
63
98
Hypsiglena affinis
100
100
Xenodon werneri
52
100
Xenodon neuwiedii
Hypsiglena
ochrorhyncha
98
99
Xenodon dorbignyi
Xenodon histricus
75
Hypsiglena torquata
84
Xenodon nattereri
99
Xenodon guentheri
85
71
Hypsiglena chlorophaea
Xenodon semicinctus
61 98
90
Xenodon matogrossensis
94
Tretanorhinus variabilis
62 Xenodon pulcher
Eryrthrolamprus atraventer
92
nigrofasciata
Leptodeira
Eryrthrolamprus jaegeri
64
Eryrthrolamprus almadensis
73
Imantodes inornatus
Eryrthrolamprus ceii
71
99
89
100 Eryrthrolamprus poecilogyrus
Imantodes lentiferus
Eryrthrolamprus epinephelus
Eryrthrolamprus juliae
67
87
94
Imantodes gemmistratus
Eryrthrolamprus miliaris
100
Eryrthrolamprus
reginae
96
86
Imantodes cenchoa
Eryrthrolamprus breviceps
88
Eryrthrolamprus pygmaea
Leptodeira uribei
Eryrthrolamprus
typhlus
97
Erythrolamprus mimus
87
100 Leptodeira frenata
Erythrolamprus aesculapii
100
51
Philodryas baroni
Philodryas nattereri
Leptodeira splendida
100 88
Philodryas viridissima
100
Philodryas olfersii
Leptodeira punctata
Philodryas argentea
68
Philodryas
georgeboulengeri
Leptodeira
septentrionalis
100
91
Philodryas mattogrossensis
90
68
Philodryas psammophidea
96
Leptodeira annulata
98
Philodryas
aestiva
97
Philodryas agassizii
62
Leptodeira bakeri
Philodryas patagoniensis
94
88
Sordellina punctata
Leptodeira maculata
95
Taeniophallus brevirostris
100
Taeniophallus nicagus
100
Leptodeira rubricata
Echinanthera melanostigma
66
Echinanthera undulata
Adelphicos quadrivirgatum
67
Taeniophallus affinis
75
79
90
Phalotris lemniscatus
95
Hydromorphus concolor
Phalotris nasutus
100
Phalotris lativittatus
100
Tretanorhinus nigroluteus
Phalotris mertensi
100
100
Elapomorphus
quinquelineatus
Cryophis hallbergi
100
Apostolepis assimilis
56
Apostolepis
dimidiata
Geophis carinosus
95
Apostolepis albicollaris
91
97
Apostolepis flavotorquata
94
Geophis godmani
94
Apostolepis sanctaeritae
69
Apostolepis cearensis
99
Atractus zidoki
Manolepis putnami
55
Hydrops triangularis
Atractus wagleri
Pseudoeryx plicatilis
86
83
Helicops infrataeniatus
100
Atractus schach
Helicops hagmanni
68
91
98
Helicops carinicaudus
Atractus albuquerquei
99
Helicops gomesi
96
91
68
Helicops angulatus
Atractus elaps
Gomesophis brasiliensis
Calamodontophis paucidens
97
73
Atractus flammigerus
89
Pseudotomodon trigonatus
100
Tachymenis peruviana
70
Atractus badius
Ptychophis flavovirgatus
87
Tomodon dorsatus
86
75
Atractus reticulatus
Thamnodynastes pallidus
94
90 Thamnodynastes lanei
90
Atractus trihedrurus
73
Thamnodynastes hypoconia
91
99
Thamnodynastes strigatus
93
97
Thamnodynastes rutilus
Atractus zebrinus
100
Tropidodryas serra
Tropidodryas
striaticeps
Ninia atrata
87
100
Xenopholis undulatus
Xenopholis scalaris
Sibon nebulatus
90
Caaeteboia amarali
Hydrodynastes bicinctus
100
Tropidodipsas sartorii
56
Hydrodynastes gigas
100
Siphlophis cervinus
Dipsas indica
68
98 91
Siphlophis compressus
Siphlophis pulcher
Dipsas catesbyi
84
100 Siphlophis longicaudatus
Oxyrhopus petolarius
Dipsas neivai
95
82
Oxyrhopus formosus
100 Dipsas variegata
100
Oxyrhopus trigeminus
Oxyrhopus clathratus
67
Oxyrhopus rhombifer
Dipsas pratti
63
70
Oxyrhopus melanogenys
95
95
Oxyrhopus guibei
67
Sibynomorphus mikanii
Rodriguesophis iglesiasi
96
96
Paraphimophis rusticus
Sibynomorphus turgidus
Phimophis guerini
87
75
Clelia clelia
87
(i)
Dipsas articulata
Mussurana bicolor
96
Drepanoides anomalus
90
Dipsas albifrons
79
74
Boiruna maculata
(ii)
Rhachidelus
brazili
92
Sibynomorphus ventrimaculatus
88
Pseudoboa neuwiedii
Pseudoboa nigra
79
100
Sibynomorphus neuwiedi
Pseudoboa coronata
Thermophis zhaoermii
100
95
Thermophis baileyi
100
(ii)
Dipsadinae
(i)
AA
Figure 28 Species-level squamate phylogeny continued (AA).
need for considering these clades as families, since the
family Scincidae is clearly monophyletic, based on our results and others (see above). Thus, their new taxonomy
changes the long-standing definition of Scincidae unnecessarily (see [113]). Furthermore, these changes were
done without defining the full content (beyond a type
genus) of any of these families other than Scincidae (the
former Scincinae + Feylininae) and Acontiidae (the former
Acontiinae).
Most importantly, the new taxonomy proposed by these
authors [112] is at odds with the phylogeny estimated
here, with respect to the familial and subfamilial classification of >1000 skink species (Figures 6, 7, 8, 9, 10). For instance, Sphenomorphus stellatus is found in a strongly
supported clade containing Lygosoma (presumably
Lygosomidae; Figure 10), which is separate from the other
clade (presumably Sphenomorphidae) containing the
other sampled Sphenomorphus species (Figure 7; note that
these Sphenomorphus species are divided among several
subclades within this latter clade). An additional problem
is that Egernia, Lygosoma, and Sphenomorphus are the
type genera of Egerniidae, Lygosomidae, and Sphenomorphidae, but are paraphyletic as currently defined (Figures 7,
8, 9, 10), leading to further uncertainty in the content and
definition of these putative families.
Furthermore, Mabuyidae apparently refers to the
clade (Figure 9) containing Chioninia, Dasia, Mabuya,
Trachylepis, with each of these genera placed in its own
subfamily (Chioniniinae, Dasiinae, Mabuyinae, and
Trachylepidinae). However, several other genera are
strongly placed in this group, such as Eumecia, Eutropis,
Lankaskincus, and Ristella (Figure 9). These other genera cannot be readily fit into these subfamilial groups
(i.e. they are not the sister group of any genera in those
subfamilies), and Trachylepis is paraphyletic with respect
to Eumecia, Chioninia, and Mabuya (Figure 9). Also, we
find that Emoia is divided between clades containing
Lygosoma (Lygosomidae) and Eugongylus (Eugongylidae),
and many of these relationships have strong support
(Figure 10). Finally, Ateuchosaurus is apparently not
accounted for in their classification, and here is weakly
placed as the sister-group to a clade comprising their
Sphenomorphidae, Egerniidae, Mabuyidae, and Lygosomidae (i.e. Lygosominae as recognized here; Figures 7,
8, 9, 10).
These authors [112] argued that a more heavily
subdivided classification for skinks may be desirable for
facilitating future taxonomic revisions and species descriptions. However, this classification seems likely to
only exacerbate existing taxonomic problems (e.g. placing congeneric species in different families without revising the genus-level taxonomy). Here, we retain the
previous definition of Mabuya (restricted to the New
World clade; sensu [114]), and we support the traditional
Page 33 of 53
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 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 within
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) placed in 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 nonmonophyletic [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 morphologybased 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 [1]). Those authors erected several new genera and subfamilies in an attempt to deal with the apparent non-monophyly of currently recognized taxa in their
Page 34 of 53
tree. However, in our tree, some of these new taxa conflict
strongly with the phylogeny or are rendered unnecessary.
First, they recognize Callopistinae as a distinct subfamily
for Callopistes, arguing that failure to do so would
produce a taxonomy inconsistent with teiid phylogeny.
However, we find strong support for Callopistes in its
traditional placement as part of Tupinambinae (Figure 11),
and this change is thus not needed based on our results.
The genus Ameiva is paraphyletic under traditional definitions [62]. In our tree, their conception of Ameiva is also
non-monophyletic, with species found in three distinct
clades (Figure 11). We also find non-monophyly of many
of their species groups within Ameiva, including the
ameiva, bifrontata, dorsalis, and erythrocephala groups
(Figure 11). Their genera Aurivela (Cnemidophorus longicaudus) and Contomastyx (Cnemidophorus lacertoides)
are strongly supported as sister taxa in our tree, and are
nested within Ameiva in their erythrocephala species
group, along with Dicrodon (Figure 11).
On the positive side, many of the genera they recognize
are monophyletic and are not nested in other genera in our
tree, including their Ameivula (Cnemidophorus ocellifer),
Aspidoscelis (unchanged from previous definitions),
Cnemidophorus (excluding C. ocellifer, C. lacertoides, and
C. longicaudus), Holcosus (Ameiva undulata, A. festiva, and
A. quadrilineatus), Kentropyx (unchanged from previous
definitions), Salvator (Tupinambis rufescens, T. duseni, and
T. merianae), and Teius (unchanged from previous definitions). We did not sample Ameiva edracantha (their
Medopheos).
Given our results, major taxonomic rearrangements
within Teiidae seem problematic at present, especially
with the extensive paraphyly of many traditional and redefined teiid genera, the lack of strong resolution of many
of these relationships based on molecular and morphological data, and incomplete taxon sampling in all studies
so far. Thus, we provisionally retain the traditional taxonomy of Teiidae, pending additional data and analyses.
However, we note that Ameiva, Cnemidophorus, and
Tupinambis are clearly non-monophyletic based on both
our results and those of recent authors [123], and will require taxonomic changes in the future. We anticipate that
many of these newly proposed genera [123] will be useful
in such revisions.
We find strong support (SHL = 98) 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 sistergroup 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 (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 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
Page 35 of 53
anguimorphs with snakes as the sister group to
iguanians [127,128].
Anguimorpha
Our hypothesis for family-level anguimorphan relationships (Figures 1, 14) is generally similar to that of other
recent studies [17,19,20,129], and is strongly supported.
Our results differ from some analyses based only on
morphology, which place Anguidae near the base of
Anguimorpha [130]. Here, Shinisauridae is strongly
supported as the sister taxon to a well-supported
clade of Varanidae + Lanthanotidae (Figures 1, 14).
Varanid relationships are similar to previous estimates
(e.g. [131]). Xenosauridae is here strongly supported
as the sister-group to a strongly supported clade
containing Helodermatidae and the strongly supported
Anniellidae + Anguidae clade (Figures 1, 14). However,
previous molecular analyses have placed Helodermatidae
as the sister to Xenosauridae + (Anniellidae + Anguidae),
typically with strong support [16,17,19,20].
Within Anguidae (Figure 14), our phylogeny indicates
non-monophyly of genera within every subfamily, including Diploglossinae (Diploglossus and Celestus are strongly
supported as paraphyletic with respect to each other and
to Ophiodes), Anguinae (Ophisaurus is strongly supported
as paraphyletic with respect to Anguis, Dopasia, and
Pseudopus), and Gerrhonotinae (Abronia and Mesaspis
are non-monophyletic, and Coloptychon is nested inside
Gerrhonotus). Some of these problems were not reported
previously (e.g. Coloptychon, Abronia, and Mesaspis), due
to incomplete taxon sampling in previous studies
[129,132,133], but relationships within Gerrhonotinae are
under detailed investigation by other researchers, so these
issues are likely to be resolved in the near future.
Iguania
We find strong support (SHL = 100) for the monophyly
of Iguania (Figure 1). This clade is strongly supported by
nuclear data [16,17,19,20], but an apparent episode of
convergent molecular evolution in several mitochondrial
genes has seemingly misled some analyses of mtDNA,
leading to weak support for Iguania [134], or even separation of the acrodonts and pleurodonts [17,135] in previous studies. Within Iguania (Figure 1), we find strong
support (SHL = 100) for a sister-group relationship between Chamaeleonidae and Agamidae (Acrodonta), and
for a clade of mostly New World families (Pleurodonta;
SHL = 100).
We find strong support for the monophyly of Chamaeleonidae and the subfamily Chamaeleoninae, and
weak support for the paraphyly of Brookesiinae (Figures 1,
15). The sampled species of the Brookesia nasus group appear as the sister group to all other chamaeleonids (the
latter clade weakly supported) as found by some previous
authors [136], though other studies have recovered
a monophyletic Brookesia [137,138]. Within Chamaeleoninae (Figure 15), we find strong support for the monophyly of most genera and species-level relationships.
However, we find strong support for the non-monophyly
of Calumma, with some species strongly placed with
Chamaeleo, others strongly placed with Rieppeleon, and a
third set weakly placed with Nadzikambia + Rhampoleon.
While non-monophly of Calumma has also been found in
previous studies [138], a recent study strongly supports
monophyly of Brookesia and weakly supports monophyly
of Calumma [139].
Monophyly of Agamidae is strongly supported
(Figure 16; SHL = 100), contrary to some previous estimates [15,31]. Most relationships among agamid subfamilies and genera are strongly supported (Figure 16), and
largely congruent with earlier studies [17,29,34,140].
There are some differences with earlier studies. For example, previous studies based on 29–44 loci [20,29,34]
placed Hydrosaurinae as sister to Amphibolurinae +
(Agaminae + Draconinae) with strong support, whereas
we place Hydrosaurinae as the sister-group to Amphibolurinae with weak support. Other authors [140] placed
Leiolepiedinae with Uromastycinae, but we (and most
other studies) place Uromastycinae as the sister group to
all other agamids.
Our phylogeny indicates several taxonomic problems
within amphibolurine agamids (Figure 16). The genera
Moloch and Chelosania render Hypsilurus paraphyletic,
although the support for the relevant clades is weak.
The species Lophognathus gilberti is placed in a strongly
supported clade with Chlamydosaurus and Amphibolurus,
a clade that is not closely related to the other
Lophognathus. Many of these taxonomic problems were
also noted by previous authors [141].
Within agamine agamids (Figure 16), most relationships are well supported and monophyly of all sampled genera is strongly supported. In contrast, within
draconine agamids (Figure 16), many intergeneric relationships are weakly supported, and some genera are
non-monophyletic (Figure 16; see also [142]), including
Gonocephalus (G. robinsonii is only distantly related to
other Gonocephalus) and Japalura (with species distributed among three distantly related clades, including
one allied with Ptyctolaemus, another with G. robinsonii,
and a third with Pseudocalotes).
Recent authors suggested dividing Laudakia into
three genera (Stellagama, Paralaudakia, and Laudakia)
based on a non-phylogenetic analysis of morphology
[143]. Here, Laudakia (as previously defined) is
strongly supported as monophyletic (Figure 16), and
this change is not necessitated by the phylogeny. Similarly, based on genetic and morphological data, recent
authors [144] suggested resurrecting the genus Saara for
Page 36 of 53
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
analyses [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 + Phrynoso-
matidae, 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 traditionally 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
Page 37 of 53
previous studies [44,159], our data weakly place Anomalepididae as the sister taxon to all snakes, and the
scolecophidian families Gerrhopilidae, Leptotyphlopidae,
Typhlopidae, and Xenotyphlopidae as the sister-group to
all other snakes excluding Anomalepididae (Figures 1, 20).
Previous studies have also placed Anomalepididae
as the sister-group to all non-scolecophidian snakes
[19,20,35,36,158,160], in some cases with strong support [20]. Although it might appear that recent analyses of scolecophidian relationships [38] support
monophyly of Scolecophidia (e.g. Figure 1 of [38]), the
tree including non-snake outgroups from that study
shows weak support for placing anomalepidids with
alethinophidians, as in other studies [19,20,36,160].
We follow recent authors [38] in recognizing Xenotyphlopidae (strongly placed as the sister taxon of
Typhlopidae) and Gerrhopilidae (strongly placed as the
sister group of Xenotyphlopidae + Typhlopidae) as distinct families (Figure 20). Leptotyphlopidae is strongly
supported as the sister group of a clade comprising Gerrhopilidae, Xenotyphlopidae, and Typhlopidae
(Figure 20). As in previous studies [38,44], we find strong
support for non-monophyly of several typhlopid genera
(Afrotyphlops, Austrotyphlops, Ramphotyphlops, Letheobia, and Typhlops; Figure 20). There are also undescribed
taxa (e.g. Typhlopidae sp. from Sri Lanka; [44]) of uncertain placement within this group (Figure 20). The systematics of typhlopoid snakes will thus require extensive
revision in the future, with additional taxon and character
sampling.
Within Alethinophidia (SHL = 100), Aniliidae is
strongly supported (SHL = 98) as the sister taxon of
Tropidophiidae (together comprising Anilioidea), and all
other alethinophidians form a strongly supported sister
group to this clade (SHL = 97; Figures 1, 21). The enigmatic family Xenophidiidae is weakly placed as the sistergroup 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 in Boidae.
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
Page 38 of 53
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 Cro-
talinae (SHL = 100). Our results generally support
the existing generic-level taxonomy within Viperinae
(Figure 22). However, we recover a strongly supported
clade within Viperinae consisting of Daboia russelii, D.
palaestinae, Macrovipera mauritanica, and M. deserti
(Figure 22), as in previous studies [173]. We corroborate
previous suggestions that these taxa be included in Daboia
[174], though this has not been widely adopted [1]. The
other Macrovipera species (including the type species) remain in that genus (Figure 22).
Within Crotalinae (Figure 22), a number of genera appear to be non-monophyletic. The species Trimeresurus
gracilis is strongly supported as the sister taxon to Ovophis
okinavensis and distantly related to other Trimeresurus,
whereas the other Ovophis are strongly placed as the sister
group to Protobothrops. A well-supported clade (SHL = 90)
containing Atropoides picadoi, Cerrophidion, and Porthidium renders Atropoides paraphyletic (see also [175]).
The species Bothrops pictus, considered incertae sedis in
previous studies [176], is here strongly supported as the
sister taxon to a clade containing Rhinocerophis, Bothropoides, Bothriopsis, and Bothrops (Figure 22). Most of these
relationships are strongly supported.
Viperidae is strongly placed (SHL = 95) as the sister
taxon to a well-supported clade (SHL = 100) containing
Colubridae, Elapidae, Homalopsidae, and Lamprophiidae
(Figure 1). Monophyly of Homalopsidae is also strongly
supported (Figure 23). Within Homalopsidae, nonmonophyly of the genus Enhydris is strongly supported
(Figure 23), and it 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
Page 39 of 53
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 [46] 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. [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 merit
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 nonflight 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,
Page 40 of 53
as in many earlier studies (e.g. [41-43,190]). These problems of non-monophyly include Leptodeira (with respect
to Imantodes), Geophis (with respect to Atractus),
Atractus (with respect to Geophis), Sibynomorphus (with
respect to Dipsas), Dipsas (with respect to Sibynomorphus), Taeniophallus (with respect to Echinanthera), and
Echinanthera (with respect to Taeniophallus). Recent revisions have begun to tackle these problems [42,43,190], but
additional taxon and character sampling will be crucial to
resolve relationships and taxonomy.
Discussion
In this study, we provide a phylogenetic estimate for
4161 species of squamates based on molecular data from
up to 12 genes per species, combining much of the relevant data used in previous molecular phylogenetic
analyses. This tree provides a framework for future evolutionary studies, spanning from the species level to relationships among families, utilizing a common set of
branch lengths. These estimated branch lengths are critically important for most phylogenetic comparative
methods. To further facilitate use of this phylogeny in
comparative studies, we provide the Newick version of
this tree (with estimated branch lengths) in DataDryad
repository 10.5061/dryad.82h0m and Additional file 1:
Data File S1. Our results also suggest that the branch
lengths in this tree should not generally be compromised
by missing data for some genes in some taxa.
Our results also reveal many problems in squamate
classification at nearly all phylogenetic levels. We make
several changes to higher-level taxonomy based on this
phylogeny, including changes to the traditionally recognized subfamilies of boid snakes (i.e. resurrecting
Sanziniinae for the boine genera Acrantophis and
Sanzinia, erecting Candoiinae for the boine genus
Candoia, and moving Lichanura and Charina from
Erycinae to Ungaliophiinae), lamprophiid snakes (expansion of Pseudaspidinae to include the formerly incertae
sedis genera Buhoma and Psammodynastes), colubrid
snakes (expansion of Dipsadinae to include the Asian
pseudoxenodontine genus Thermophis), and gymnophthalmid lizards (recognition of Bachiinae for the tribe
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.
Some 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
Page 41 of 53
on morphology, Iguania and Scleroglossa (e.g. [13,21]).
Despite considerable disagreement among morphologybased hypotheses, this basic division is supported by
nearly all phylogenetic analyses based on morphological
data [13-15,19,22,95,191]. In contrast, our results and
those of most previous molecular analyses strongly support placement of iguanians with anguimorphs and snakes
[16-20,23,24]. The causes of this conflict remain unclear,
but may be related to morphological traits associated with
different feeding strategies of iguanian and (traditional)
scleroglossan squamates [3,17].
Additionally, analyses of morphology often place
dibamids, amphisbaenians, snakes, and (in some cases)
some scincids and anguids in a single clade [13-15]. Our
analyses do not support such a clade (Figure 1), nor do
other analyses of molecular data alone [17-20], or analyses of combined molecular and morphological data
[19]. Instead, these morphological results seem to be
explained by convergence associated with burrowing
(e.g. [19]). Overall, molecular datasets have shown overwhelmingly strong support for placement of dibamids
and gekkonids at the base of the tree, amphisbaenians
with lacertoids, and iguanians with snakes and anguimorphs [17-20,23]. These results have now been corroborated with up to 22 genes (15794 bp) for 45 taxa [19],
25 genes (19020 bp) for 64 taxa [16], and 44 genes
(33717 bp) for 161 taxa [20]. We now support this basic
topology with 4161 species sampled for up to 12 genes
each (up to 12896 bp).
Nevertheless, despite the overall strong support for most
of the tree (i.e. 70% of all nodes have SHL > 85), certain
clades remain poorly supported (e.g. relationships among
many pleurodont iguanian families; Figures 1, 17, 18, 19).
A potential criticism of the supermatrix approach used
here is that this weak support may occur due to missing
data. However, previous studies of 8 datasets have shown
explicitly that there is typically little relationship between
branch support for terminal taxa and the amount of missing data [85]. Instead, these patterns of weak support are
more likely to reflect short underlying branch lengths
[20,36,41], and may be difficult to resolve even with more
complete taxonomic and genomic sampling. Indeed, as
noted above, many of the weakly supported nodes in our
phylogeny are also weakly supported in analyses with little
missing data (<20%) and large numbers of genes (e.g. 44
genes as in [20]), such as the relationships of many
pleurodont lizard families and colubroid snake families
and subfamilies.
We acknowledge that the differences between our results and previous studies (noted above) do not necessarily
mean that our results are right and those of previous studies are wrong. In some cases, we provide strong support
for novel relationships when previous, conflicting studies
showed only weak support (as in scincids, see above). In
other cases, our results disagree with other studies for
clades that were strongly supported (e.g. placement of
xenodermatids). In the best-case scenario, these conflicts
may be resolved because our results are correct, possibly
reflecting the beneficial effects of adding taxa and the
associated subdivision of long branches [25,26,28,87,
192-194]. Furthermore, in many cases, we are including
more genes than used in previous studies of particular
clades, increasing sampling of characters and loci. This
should generally reduce spurious results caused by sampling few characters and by incongruence between gene
and species trees.
However, other explanations for incongruence between
our results and previous studies are also possible.
Adding taxa can potentially lead to incorrect results in
some cases (e.g. [195]), such as when a long terminal
branch is added that further subdivides a short internal
branch. In other cases, conflicts with our results might
reflect the impact of our sampling fewer nuclear genes
and a correspondingly increased influence of mitochondrial data. Mitochondrial genes have relatively fast evolutionary rates (potentially exacerbating the impacts of
long branches), and their phylogenetic resolution for a
particular node may also reflect introgression or incomplete lineage sorting rather than the species phylogeny
(review in [196]). Many taxa in the matrix are represented only by mitochondrial data, and highly variable
mitochondrial genes might also overcome the influence
of less variable nuclear genes in combined analyses
(although this scenario does not seem to be common
[196]). Such cases might explain some strongly supported conflicts between our results and those based on
multiple nuclear loci. Another possibility is that some
cases may represent failure to find the optimal tree
(although we assume that these cases will likely show
only weak support). We acknowledge that there are
many reasons why our results may differ from previous
studies, and the ultimate test of these novel findings will
be corroboration in future studies that include more
taxa and characters.
This analysis also corroborates several recent studies
suggesting that the supermatrix approach is a powerful
strategy for large-scale phylogenetic inference [41,72,
73,75,76,197]. For example, even though each species
had 81% missing data on average, we found that most
species were placed in the families and genera expected
based on previous taxonomy, often with very strong support. Furthermore, we found that incompleteness of terminal taxa is not related to branch lengths (at least not
terminal branch lengths), suggesting that missing data
are not significantly biasing branch-length estimates (see
also [84,86,87]). Also, the ML models we used have been
shown to be robust to missing data in large, sparse
supermatrices [84].
Page 42 of 53
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 [1] (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 [1], incorporating major, wellaccepted 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 recombinationactivating 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
Page 43 of 53
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 [1], 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 nonsquamate 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 twostep 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 nonsquamates, 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
Page 44 of 53
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 wellsupported 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 nearest-neighbor
interchange (NNI)-optimized estimate of the ML tree.
This optimization is needed to calculate the SHL version
of the aLRT for estimating support values [94]. The SHLaLRT 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.
Page 45 of 53
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).
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).
Page 46 of 53
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); Sphaerodactylidae (Aristelliger, Chatogekko, Coleodactylus, Euleptes, Gonatodes, Lepidoblepharis,
Pristurus, Pseudogonatodes, Quedenfeldtia, Saurodactylus,
Sphaerodactylus, Teratoscincus)
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 [1], 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 them 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.
Squamata
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,
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);
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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,
Page 48 of 53
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: Data File S1. The 4162-species ML phylogeny in
Newick format; taxonomic changes are given in Additional file 2: Table S1.
Additional file 2: Table S1. GenBank accession numbers for all taxa
included in this analysis.
Competing interests
The authors declare that they have no competing interests.
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).
Author details
1
Department of Biological Sciences, The George Washington University,
2023 G St. NW, Washington, DC 20052, USA. 2Department of Biology, The
Graduate School and University Center, The City University of New York, 365
5th Ave., New York, NY 10016, USA. 3Department of Biology, The College of
Staten Island, The City University of New York, 2800 Victory Blvd., Staten
Island, NY 10314, USA. 4Department of Ecology and Evolutionary Biology,
University of Arizona, Tucson, AZ 85721-0088, USA.
Received: 30 January 2013 Accepted: 19 March 2013
Published: 29 April 2013
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doi:10.1186/1471-2148-13-93
Cite this article as: Pyron et al.: A phylogeny and revised classification of
and snakes. BMC Evolutionary Biology 2013 13:93.
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A phylogeny and revised classification of Squamata, including 4161

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