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A phylogeny and revised classification of Squamata, including 4161 species oflizards and snakes

BMC Evolutionary Biology 2013, 13:93 doi:10.1186/1471-2148-13-93

Robert Alexander Pyron (rpyron@colubroid.org)Frank T Burbrink (frank.burbrink@csi.cuny.edu)

John J Wiens (wiensj@email.arizona.edu)

ISSN 1471-2148

Article type Research article

Submission date 30 January 2013

Acceptance date 19 March 2013

Publication date 29 April 2013

Article URL http://www.biomedcentral.com/1471-2148/13/93

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A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

Robert Alexander Pyron1* * Corresponding author Email: rpyron@colubroid.org

Frank T Burbrink2,3 Email: frank.burbrink@csi.cuny.edu

John J Wiens4 Email: wiensj@email.arizona.edu

1 Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, USA

2 Department of Biology, The Graduate School and University Center, The City University of New York, 365 5th Ave., New York, NY 10016, USA

3 Department of Biology, The College of Staten Island, The City University of New York, 2800 Victory Blvd., Staten Island, NY 10314, USA

4 Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0088, USA

Abstract

Background

The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to address their classification. Here, we present the first large-scale phylogenetic estimate for Squamata.

Results

The estimated phylogeny contains 4161 species, representing all currently recognized families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy.

Conclusions

We present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for future comparative studies. We also present a revised classification of squamates at the family and subfamily level to bring the taxonomy more in line with the new phylogenetic hypothesis. This classification includes new, resurrected, and modified subfamilies within gymnophthalmid and scincid lizards and boid, colubrid, and lamprophiid snakes.

Keywords

Amphisbaenia, Lacertilia, Likelihood support measures, Missing data, Serpentes, Squamata, Phylogenetics, Reptiles, Supermatrices, Systematics

Background

Squamate reptiles (lizards, snakes, and amphisbaenians ["worm lizards"]) are among the most diverse radiations of terrestrial vertebrates. Squamata includes more than 9400 species as of December 2012 [1]. The rate of new species descriptions shows no signs of slowing, with a record 168 new species described in 2012 [1], greater than the highest yearly rates of the 18th and 19th centuries (e.g. 1758, 118 species; 1854, 144 species [1]). Squamates are presently found on every continent except Antarctica, and in the Indian and Pacific Oceans, and span many diverse ecologies and body forms, from limbless burrowers to arboreal gliders (summarized in [2-4]).

Squamates are key study organisms in numerous fields, from evolution, ecology, and behavior [3] to medicine [5,6] and applied physics [7]. They have also been the focus of many pioneering studies using phylogenies to address questions about trait evolution (e.g. [8,9]). Phylogenies are now recognized as being integral to all comparative studies of squamate biology (e.g. [10,11]). However, hypotheses about squamate phylogeny have changed radically in recent years [12], especially when comparing trees generated from morphological [13-15] and molecular data [16-20]. Furthermore, despite extensive work on squamate phylogeny at all taxonomic levels, a large-scale phylogeny (i.e. including thousands of species and multiple genes) has never been attempted using morphological or molecular data.

Squamate phylogenetics has changed radically in the last 10 years, revealing major conflicts between the results of morphological and molecular analyses [12]. Early estimates of squamate phylogeny [21] and recent studies based on morphological data [13-15,22] consistently supported a basal division between Iguania (including chameleons, agamids, and iguanids, sensu lato), and Scleroglossa, which comprises all other squamates (including skinks, geckos, snakes, and amphisbaenians). Within Scleroglossa, many phylogenetic analyses of morphological data have also supported a clade containing limb-reduced taxa, including various combinations of snakes, dibamids, amphisbaenians, and (in some analyses) limb-reduced skinks and anguids [13-15,19,22], though some of these authors also acknowledged that this clade was likely erroneous.

In contrast, recent molecular analyses have estimated very different relationships. Novel arrangements include placement of dibamids and gekkotans near the root of the squamate tree, a sister-group relationship between amphisbaenians and lacertids, and a clade (Toxicofera) uniting Iguania with snakes and anguimorphs within Scleroglossa [16-20,23,24]. These molecular results (and the results of combined morphological and molecular analyses) suggest that some estimates of squamate phylogeny based on morphology may have been misled, especially by convergence associated with adaptations to burrowing [19]. However, there have also been disagreements among molecular studies, such as placement of dibamids relative to gekkotans and other squamates and relationships among snakes, iguanians, and anguimorphs (e.g. [17,20]).

Analyses of higher-level squamate relationships based on molecular data have so far included relatively few (less than 200) species, and none have included representatives from all described families and subfamilies [17-20,23,24]. This limited taxon sampling makes existing molecular phylogenies difficult to use for broad-scale comparative studies, with some exceptions based on supertrees [10,11]. In addition, limited taxon sampling is potentially a serious issue for phylogenetic accuracy [25-28]. Thus, an analysis with extensive taxon sampling is critically important to test hypotheses based on molecular datasets with more limited sampling and to provide a framework for comparative analyses.

Despite the lack of a large-scale phylogeny across squamates, recent molecular studies have produced phylogenetic estimates for many of the major groups of squamates, including iguanian lizards [29-34], higher-level snake groups [35-37], typhlopoid snakes [38,39], colubroid snakes [40-46], booid snakes [47,48], scincid lizards [49-52], gekkotan lizards [53-60], teiioid lizards [61-64], lacertid lizards [65-69], and amphisbaenians [70,71]. These studies have done an outstanding job of clarifying the phylogeny and taxonomy of these groups, but many were limited in some ways by the number of characters and taxa that they sampled (and which were available at the time for sequencing).

Here, we present a phylogenetic estimate for Squamata based on combining much of the existing sequence data for squamate reptiles, using the increasingly well-established supermatrix approach [41,72-77]. We present a new phylogenetic estimate including 4161 squamate species. The dataset includes up to 12896 bp per species from 12 loci (7 nuclear, 5 mitochondrial). We include species from all currently described families and subfamilies. In terms of species sampled, this is 5 times larger than any previous phylogeny for any one squamate group [30,41], 3 times larger than the largest supertree estimate [11], and 25 times larger than the largest molecular study of higher-level squamate relationships [20]. While we did not sequence any new taxa specifically for this project, much of the data in the combined matrix were generated in our labs or from our previous collaborative projects [16,19,20,34,36,37,41,44,78-82], including thousands of gene sequences from hundreds of species (>550 species; ~13% of the total).

The supermatrix approach can provide a relatively comprehensive phylogeny, and uncover novel relationships not seen in any of the separate analyses in which the data were generated. Such novel relationships can be revealed via three primary mechanisms. First, different studies may have each sampled different species from a given group for the same genes, and combining these data may reveal novel relationships not apparent in the separate analyses. Second, different studies may have used different genetic markers for the same taxa, and combining these markers can dramatically increase character sampling, potentially revealing new relationships and providing stronger support for previous hypotheses. Third, even for

clades that were previously studied using complete taxon sampling and multiple loci, novel relationships may be revealed by including these lineages with other related groups in a large-scale phylogeny.

The estimated tree and branch-lengths should be useful for comparative studies of squamate biology. However, this phylogeny is based on a supermatrix with extensive missing data (mean = 81% per species). Some authors have suggested that matrices with missing cells may yield misleading estimates of topology, support, and branch lengths [83]. Nevertheless, most empirical and simulation studies have not found this to be the case, at least for topology and support [41,73,84,85]. Though fewer studies have examined the effects of missing data on branch lengths [44,86,87], these also suggest that missing data do not strongly impact estimates. Here, we test whether branch lengths for terminal taxa are related to their completeness.

In general, our results corroborate those of many recent molecular studies with regard to higher-level relationships, species-level relationships, and the monophyly, composition, and relationships of most families, subfamilies, and genera. However, our results differ from previous estimates for some groups, and reveal (or corroborate) numerous problems in the existing classification of squamates. We therefore provide a conservative, updated classification of extant squamates at the family and subfamily level based on the new phylogeny, while highlighting problematic taxonomy at the genus level, without making changes. The generic composition of all families and subfamilies under our revised taxonomy are provided in Appendix I.

We note dozens of problems in the genus-level taxonomy suggested by our tree, but we acknowledge in advance that we do not provide a comprehensive review of the previous literature dealing with all these taxonomic issues (this would require a monographic treatment). Similarly, we do not attempt to fix these genus-level problems here, as most will require more extensive taxon (and potentially character) sampling to adequately resolve.

Throughout the paper, we address only extant squamates. Squamata also includes numerous extinct species classified in both extant and extinct families, subfamilies, and genera. Relationships and classification of extinct squamates based on morphological data from fossils have been addressed by numerous authors (e.g. [14,15,19,22,88-93]). A classification based only on living taxa may create some problems for classifying fossil taxa, but these can be addressed in future studies that integrate molecular and fossil data [19,86].

Results

Supermatrix phylogeny

We generated the final tree (lnL = −2609551.07) using Maximum Likelihood (ML) in RAxMLv7.2.8. Support was assessed using the non-parametric Shimodaira-Hasegawa-Like (SHL) implementation of the approximate likelihood-ratio test (aLRT; see [94]). The tree and data matrix are available in NEXUS format in DataDryad repository 10.5061/dryad.82h0m and as Additional file 1: Data File S1. A skeletal representation of the tree (excluding several species which are incertae sedis) is shown in Figure 1. The full species-level phylogeny (minus the outgroup Sphenodon) is shown in Figures 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28. The analysis yields a generally well-

supported phylogenetic estimate for squamates (i.e. 70% of nodes have SHL values >85, indicating they are strongly supported). There is no relationship between proportional completeness (bp of non-missing data in species / 12896 bp of complete data) and branch length (r = −0.29, P = 0.14) for terminal taxa, strongly suggesting that the estimated branch lengths are not consistently biased by missing data.

Figure 1 Higher-level squamate phylogeny. Skeletal representation of the 4161-species tree from maximum-likelihood analysis of 12 genes, with tips representing families and subfamilies (following our taxonomic revision; species considered incertae sedis are not shown). Numbers at nodes are SHL values greater than 50%. The full tree is presented in Figures 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, with panels indicated by bold italic letters.

Figure 2 Species-level squamate phylogeny. Large-scale maximum likelihood estimate of squamate phylogeny, containing 4161 species. Numbers at nodes are SHL values greater than 50%. A skeletal version of this tree is presented in Figure 1. Bold italic letters indicate figure panels (A). Within panels, branch lengths are proportional to expected substitutions per site, but the relative scale differs between panels.

Figure 3 Species-level squamate phylogeny continued (B).

Figure 4 Figure 5 Species-level squamate phylogeny continued (D) Species-level squamate phylogeny continued (D).

Figure 6 Species-level squamate phylogeny continued (E).

Figure 7 Species-level squamate phylogeny continued (F).

Figure 8 Species-level squamate phylogeny continued (G).

Figure 9 Species-level squamate phylogeny continued (H).

Figure 10 Species-level squamate phylogeny continued (I).

Figure 11 Species-level squamate phylogeny continued (J).

Figure 12 Species-level squamate phylogeny continued (K) Species-level squamate phylogeny continued (K).

Figure 13 Species-level squamate phylogeny continued (L).

Figure 14 Species-level squamate phylogeny continued (M).

Figure 15 Species-level squamate phylogeny continued (N).

Figure 16 Species-level squamate phylogeny continued (O).

Figure 17 Species-level squamate phylogeny continued (P).

Figure 18 Species-level squamate phylogeny continued (Q).

Figure 19 Species-level squamate phylogeny continued (R).

Figure 20 Species-level squamate phylogeny continued (S).

Figure 21 Species-level squamate phylogeny continued (T).

Figure 22 Species-level squamate phylogeny continued (U).

Figure 23 Species-level squamate phylogeny continued (V).

Figure 24 Species-level squamate phylogeny continued (W).

Figure 25 Species-level squamate phylogeny continued (X).

Figure 26 Species-level squamate phylogeny continued (Y).

Figure 27 Species-level squamate phylogeny continued (Z).

Figure 28 Species-level squamate phylogeny continued (AA).

Higher-level relationships

Our tree (Figure 1) is broadly congruent with most previous molecular studies of higher-level squamate phylogeny using both nuclear data and combined nuclear and mitochondrial data (e.g. [16-20]), providing important confirmation of previous molecular studies based on more limited taxon sampling. Specifically we support (Figure 1): (i) the placement of dibamids and gekkotans near the base of the tree (Figure 1A); (ii) a sister-group relationship between Scincoidea (scincids, cordylids, gerrhosaurids, and xantusiids; Figure 1B) and a clade (Episquamata; Figure 1C) containing the rest of the squamates excluding dibamids and gekkotans; (iii) Lacertoidea (lacertids, amphisbaenians, teiids, and gymnophthalmids; Figure 1D), and (iv) a clade (Toxicofera; Figure 1E) containing anguimorphs (Figure 1F), iguanians (Figure 1G), and snakes (Figure 1H) as the sister taxon to Lacertoidea.

These relationships are strongly supported in general (Figure 1), but differ sharply from most trees based on morphological data [13-15,19,22,95]. Nevertheless, many clades found in previous morphological taxonomies and phylogenies are also present in this tree in some form, including Amphisbaenia, Anguimorpha, Gekkota, Iguania, Lacertoidea (but including amphisbaenians), Scincoidea, Serpentes, and many families and subfamilies. In contrast, the relationships among these groups differ strongly between molecular analyses [17-20] and morphological analyses [14,15]. Our results demonstrate that this incongruence is not explained by limited taxon sampling in the molecular data sets. In fact, our species-level sampling is far more extensive than in any morphological analyses (e.g. [14,15]), by an order of magnitude.

We find that the basal squamate relationships are strongly supported in our tree. The family Dibamidae is the sister group to all other squamates, and Gekkota is the sister group to all squamates excluding Dibamidae (Figure 1), as in some previous studies (e.g. [16,18]). Other recent molecular analyses have also placed Dibamidae near the squamate root, but differed in placing it as either the sister taxon to all squamates excluding Gekkota [17], or the sister-group of Gekkota [19,20]. Our results also corroborate that the New World genus

Anelytropsis is nested within the Old World genus Dibamus [96], but the associated branches are weakly supported (Figure 2).

Gekkota

Within Gekkota, we corroborate both earlier morphological [97] and recent molecular estimates [55,56,59,98] in supporting a clade containing the Australian radiation of "diplodactylid" geckos (Carphodactylidae and Diplodactylidae) and the snakelike pygopodids (Figures 1, 2). As in previous studies [55], Carphodactylidae is the weakly supported sister group to Pygopodidae, and this strongly supported clade is the sister group to Diplodactylidae (Figures 1, 2). We recover clades within the former Gekkonidae that correspond to the strongly supported families Eublepharidae, Sphaerodactylidae, Phyllodactylidae, and Gekkonidae as in previous studies, and similar relationships among these groups [55-57,59,60,98-100].

Within Gekkota, we find evidence for non-monophyly of many genera. Many relationships among the New Caledonian diplodactylids are weakly supported (Figure 2), and there is apparent non-monophyly of the genera Rhacodactylus, Bavayia, and Eurydactylodes with respect to each other and Oedodera, Dierogekko, Paniegekko, Correlophus, and Mniarogekko [101]. In the Australian diplodactylids, Strophurus taenicauda is strongly supported as belonging to a clade that is only distantly related to the other sampled Strophurus species (Figure 2). The two species of the North African sphaerodactylid genus Saurodactylus are divided between the two major sphaerodactylid clades (Figure 3), but the associated branches are weakly supported. The South American phyllodactylid genus Homonota is strongly supported as being paraphyletic with respect to Phyllodactylus (Figure 3).

A number of gekkonid genera (Figure 4) also appear to be non-monophyletic, including the Asian genera Cnemaspis (sampled species divided into two non-sister clades), Lepidodactylus (with respect to Pseudogekko and some Luperosaurus), Gekko (with respect to Ptychozoon and Lu. iskandari), Luperosaurus (with respect to Lepidodactylus and Gekko), Mediodactylus (with respect to Pseudoceramodactylus, Tropiocolotes, Stenodactylus, Cyrtopodion, Bunopus, Crossobamon, and Agamura), and Bunopus (with respect to Crossobamon), and the African Afrogecko (with respect to Afroedura, Christinus, Cryptactites, and Matoatoa), Afroedura (with respect to Afrogecko, Blaesodactylus, Christinus, Geckolepis, Pachydactylus, Rhoptropus, and numerous other genera), Chondrodactylus (with respect to Pachydactylus laevigatus), and Pachydactylus (with respect to Chondrodactylus and Colopus). Many of these taxonomic problems in gekkotan families have been identified in previous studies (e.g. [59,99,102]), and extensive changes will likely be required to fix them.

Scincoidea

We strongly support (SHL = 100; Figures 1, 5, 6, 7, 8, 9, 10) the monophyly of Scincoidea (Scincidae, Xantusiidae, Gerrhosauridae, and Cordylidae), as in other recent studies [16-20]. All four families are strongly supported (Figures 5, 6, 7, 8, 9, 10). A similar clade is also recognized in morphological phylogenies [14], though without Xantusiidae in some [13].

Within the New World family Xantusiidae, we corroborate previous analyses [103,104] that found strong support for a sister-group relationship between Xantusia and Lepidophyma, excluding Cricosaura (Figure 5). These relationships support the subfamily Cricosaurinae for

Cricosaura [105]. We also recognize Xantusiinae for the North American genus Xantusia and Lepidophyminae for the Central American genus Lepidophyma [106,107].

Within the African and Madagascan family Gerrhosauridae (Figure 5), the genus Gerrhosaurus is weakly supported as being paraphyletic with respect to the clade comprising Tetradactylus + Cordylosaurus, with G. major placed as the sister group to all other gerrhosaurids. Within Cordylidae (Figure 5), we use the generic taxonomy from a recent phylogenetic analysis and re-classification based on multiple nuclear and mitochondrial genes [108]. This classification broke up the non-monophyletic Cordylus [109] into several smaller genera, and we corroborate the non-monophyly of the former Cordylus and support the monophyly of the newly recognized genera (Figure 5). We find support the distinctiveness of Platysaurus (Figure 5) and recognition of the subfamily Platysaurinae [108].

We find strong support (SHL = 100) for the monophyly of Scincidae (Figure 6) as in previous studies (e.g. [20,50,51]). We find strong support for the basal placement of the monophyletic subfamily Acontiinae (Figure 6), as found in some previous studies (e.g. [20,51]) but not others (e.g. [50]). Similar to earlier studies, we find that the subfamily Scincinae sensu [110] is non-monophyletic, as Feylininae is nested within Scincinae (also found in [20,50,51,111]). Based on these results, synonymizing Feylininae with Scincinae produces a monophyletic Scincinae (SHL = 97), which is then sister to a monophyletic Lygosominae (SHL = 100 excluding Ateuchosaurus; see below) with 94% SHL support (Figures 6, 7, 8, 9, 10). This yields a new classification in which all three subfamilies (Acontiinae, Lygosominae, Scincinae) are strongly supported. Importantly, these definitions approximate the traditional content of the three subfamilies [50,110], except for recognition of Feylininae.

We note that a recent revision of the New World genus Mabuya introduced a nontraditional family-level classification for Scincidae [112]. These authors divided Scincidae into seven families: Acontiidae, Egerniidae, Eugongylidae, Lygosomidae, Mabuyidae, Scincidae and Sphenomorphidae. However, there was no phylogenetic need for considering these clades as families (or another rank below family), since the family Scincidae is clearly monophyletic, based on our results and others (see above). Thus, their new taxonomy changes the long-standing definition of Scincidae unnecessarily (see [113]). Furthermore, these changes were done without defining the full content (beyond a type genus) of any of these families other than Scincidae (the former Scincinae + Feylininae), and Acontiidae (the former Acontiinae).

Most importantly, the new taxonomy proposed by these authors [112] is at odds with the phylogeny estimated here, with respect to the familial and subfamilial classification of >1000 skink species (Figures 6, 7, 8, 9, 10). For instance, Sphenomorphus stellatus is found in a strongly supported clade containing Lygosoma (presumably Lygosomidae; Figure 10), which is separate from the other clade (presumably Sphenomorphidae) containing the other sampled Sphenomorphus species (Figure 7; but note that these Sphenomorphus species are divided among several subclades within this latter clade). An additional problem is that Egernia, Lygosoma, and Sphenomorphus are the type genera of Egerniidae, Lygosomidae, and Sphenomorphidae, but are paraphyletic as currently defined (Figures 7, 8, 9, 10), leading to further uncertainty in the content and definition of these putative families.

Furthermore, Mabuyidae apparently refers to the clade (Figure 9) containing Chioninia, Dasia, Mabuya, Trachylepis, with each of these genera placed in its own subfamily (Chioniniinae, Dasiinae, Mabuyinae, and Trachylepidinae). However, several other genera are strongly placed in this group, such as Eumecia, Eutropis, Lankaskincus, and Ristella

(Figure 9). These other genera cannot be readily fit into these subfamilial groups (i.e. they are not the sister group of any genera in those subfamilies), and Trachylepis is paraphyletic with respect to Eumecia, Chioninia, and Mabuya (Figure 9). Also, we find that Emoia is divided between clades containing Lygosoma (Lygosomidae) and Eugongylus (Eugongylidae), and many of these relationships have strong support (Figure 10). Finally, Ateuchosaurus is apparently not accounted for in their classification, and here is weakly placed as the sister-group to a clade comprising their Sphenomorphidae, Egerniidae, Mabuyidae, and Lygosomidae (i.e. Lygosominae as recognized here; Figures 7, 8, 9, 10).

These authors [112] argued that a more heavily subdivided classification for skinks may be desirable for facilitating future taxonomic revisions and species descriptions. However, this classification seems likely to only exacerbate existing taxonomic problems (e.g. placing congeneric species in different families without revising the genus-level taxonomy). Here, we retain the previous definition of Mabuya (restricted to the New World clade; sensu [114]), and we support the traditional definitions of Scincidae, Acontiinae, Scincinae (but including Feylininae), and Lygosominae (Figures 6, 7, 8, 9, 10; note that we leave Ateuchosaurus as incertae sedis). The other taxonomic issues in Scincidae identified here and elsewhere should be resolved in future studies. Our phylogeny provides a framework in which these analyses can take place (i.e. identifying major subclades within skinks), which we think may be more useful than a classification lacking clear taxon definitions.

Of the 133 scincid genera [1], we can assign the 113 sampled in our tree to one of the three subfamilies in our classification (Acontiinae, Lygosominae, and Scincinae; Appendix I). We place 19 of the remaining genera into one of the three subfamilies based on previous classifications (e.g. [110]), with Ateuchosaurus as incertae sedis in Scincidae. Below, we review the non-monophyletic genera in our tree. Many of these problems have been reported by previous authors [51,111,115-118], and for brevity we do not distinguish between cases reported in previous studies, and potentially new instances found here.

Within Acontiinae, we find that the two genera are both strongly supported as monophyletic (Figure 6). Within Scincinae, many genera are now strongly monophyletic (thanks in part to the dismantling of Eumeces; [49,50,119]), but some problems remain (Figure 6). The genera Scincus and Scincopus are strongly supported as being nested inside of the remaining Eumeces. Among Malagasy scincines (see [49,120]), Pseudacontias is nested inside Madascincus, and the genera Androngo, Pygomeles, and Voeltzkowia are all nested in Amphiglossus (Figure 6).

We also find numerous taxonomic problems with lygosomines (Figures 7, 8, 9, 10). Species of Sphenomorphus are widely dispersed among other lygosomine genera. The genus Tropidophorus is paraphyletic with respect to a clade containing many other genera (Figure 7). The sampled species of Asymblepharus are only distantly related to each other, including one species (A. sikimmensis) nested inside of Scincella (Figure 7). The genus Lipinia is polyphyletic, with one species (L. vittigera) strongly placed as the sister taxon to Isopachys, and with two other species (L. pulchella and L. noctua) forming a well-supported clade that also includes Papuascincus (Figure 7).

Among Australian skinks, the genus Eulamprus is polyphyletic with respect to Nangura, Calyptotis, Gnypetoscincus, Coggeria, Coeranoscincus, Ophioscincus, Saiphos, Anomalopus, Eremiascincus, Hemiergis, Glaphyromorphus, Notoscincus, Ctenotus, and Lerista, and most of the relevant nodes are strongly supported (Figure 8). The genera Coeranoscincus and

Ophioscincus are polyphyletic with respect to each other and to Saiphos and Coggeria (Figure 8). The genus Glaphyromorphus is paraphyletic with respect to a clade of Eulamprus (Figure 8). The genus Egernia is paraphyletic with respect to Bellatorias (which is paraphyletic with respect to Egernia and Lissolepis) and Lissolepis, although many of the relevant nodes are not strongly supported (Figure 9). The genera Cyclodomorphus and Tiliqua are paraphyletic with respect to each other (Figure 9).

Among other lygosomines, Trachylepis is non-monophyletic [121], with two species (T. aurata and T. vittata) that fall outside the strongly supported clade containing the other species (Figure 9). The latter clade is weakly supported as the sister group to a clade containing Chioninia, Eumecia, and Mabuya. In Mabuya, a few species (M. altamazonica, M. bistriata, and M. nigropuncata) have unorthodox placements within a monophyletic Mabuya, potentially due to uncertain taxonomic assignment of specimens by previous authors [51,122]. The genus Lygosoma is paraphyletic with respect to Lepidothyris and Mochlus, and many of the relevant nodes are strongly supported (Figure 10). Among New Caledonian skinks, the genus Lioscincus is polyphyletic with respect to Marmorosphax, Celatiscincus, and Tropidoscincus, and both Lioscincus and Tropidoscincus are paraphyletic with respect to, Kanakysaurus, Lacertoides, Phoboscincus, Sigaloseps, Tropidoscincus, Graciliscincus, Simiscincus, and Caledoniscincus, with strong support for most relevant nodes (Figure 10). The genera Emoia and Bassiana are massively polyphyletic and divided across multiple lygosomine clades (Figure 10). The genus Lygisaurus appears to be nested inside of Carlia, although many of the relevant branches are only weakly supported (Figure 10).

Lacertoidea

Within Lacertoidea (Figure 1), we corroborate recent molecular analyses (e.g. [16,17,19,20]) and morphology-based phylogenies and classifications (e.g. [13,15]) in supporting the clade including the New World families Gymnophthalmidae and Teiidae (Figure 11). Within a weakly supported Teiidae (Figure 11), the subfamilies Tupinambinae and Teiinae are each strongly supported as monophyletic, as in previous studies [61]. In Tupinambinae, Callopistes is the sister group to a clade containing Tupinambis, Dracaena, and Crocodilurus. The clade Dracaena + Crocodilurus is nested within Tupinambis, and the associated clades have strong support (Figure 11). We find that the teiine genera Ameiva and Cnemidophorus are non-monophyletic (Figure 11), interdigitating with each other and the monophyletic genera Aspidoscelis, Dicrodon (monotypic), and Kentropyx, as in previous phylogenies [62].

A recent study [123] proposed a re-classification of the family Teiidae based on analysis of 137 morphological characters for 101 terminal species (with ~150 species in the family). Those authors erected several new genera and subfamilies in an attempt to deal with the apparent non-monophyly of currently recognized taxa in their tree. However, in our tree, some of these new taxa conflict strongly with the phylogeny or are rendered unnecessary. First, they recognize Callopistinae as a distinct subfamily for Callopistes, arguing that failure to do so would produce a taxonomy inconsistent with teiid phylogeny. However, we find strong support for Callopistes in its traditional placement as part of Tupinambinae (Figure 11), and this change is thus not needed based on our results. The genus Ameiva is paraphyletic under traditional definitions [62]. In our tree, their conception of Ameiva is also non-monophyletic, with species found in three distinct clades (Figure 11). We also find non-monophyly of many of their species groups within Ameiva, including the ameiva, bifrontata, dorsalis, and erythrocephala groups (Figure 11). Their genera Aurivela (Cnemidophorus

longicaudus) and Contomastyx (Cnemidophorus lacertoides) are strongly supported as sister taxa in our tree, and are nested within Ameiva in their erythrocephala species group, along with Dicrodon (Figure 11).

On the positive side, many of the genera they recognize are monophyletic and are not nested in other genera in our tree, including their Ameivula (Cnemidophorus ocellifer), Aspidoscelis (unchanged from previous definitions), Cnemidophorus (excluding C. ocellifer, C. lacertoides, and C. longicaudus), Holcosus (Ameiva undulata, A. festiva, and A. quadrilineatus), Kentropyx (unchanged from previous definitions), Salvator (Tupinambis rufescens, T. duseni, and T. merianae), and Teius (unchanged from previous definitions). We did not sample Ameiva edracantha (their Medopheos).

Given our results, major taxonomic rearrangements within Teiidae seem problematic at present, especially with the extensive paraphyly of many traditional and re-defined teiid genera, the lack of strong resolution of many of these relationships based on molecular and morphological data, and incomplete taxon sampling in all studies so far. Thus, we provisionally retain the traditional taxonomy of Teiidae, pending additional data and analyses. However, we note that Ameiva, Cnemidophorus, and Tupinambis are clearly non-monophyletic based on both our results and those of recent authors [123], and will require taxonomic changes in the future. We anticipate that many of these newly proposed genera [123] will be useful in such revisions.

We find strong support (SHL = 100) for monophyly of Gymnophthalmidae (Figure 11). Within Gymnophthalmidae, we find strong support for the monophyly of the previously recognized subfamilies [63,64,124], with the exception of Cercosaurinae (Figure 11). Previous researchers considered the genus Bachia a distinct tribe (Bachiini) within Cercosaurinae, based on a poorly supported sister-group relationship with the tribe Cercosaurini [63,64]. Here, we find a moderately well supported relationship (SHL = 84) between Bachia and Gymnophthalminae + Rhachisaurinae, and we find that this clade is only distantly related to other Cercosaurinae. Therefore, we restrict Cercosaurinae to the tribe Cercosaurini, and elevate the tribe Bachiini [64] to the subfamily level. The subfamily Bachiinae contains only the genus Bachia (Figure 11), identical in content to the previously recognized tribe [64]. Within Cercosaurinae, we find that the genus Petracola is nested within Proctoporus (Figure 11). In Ecpleopinae, Leposoma is divided into two clades, separated by Anotosaura, Colobosauroides, and Arthrosaura (Figure 11), and many of the relevant nodes are very strongly supported. These issues should be addressed in future studies.

Our results show strong support for a clade uniting Lacertidae and Amphisbaenia (Lacertoidea; Figure 1), as in many previous studies [16-20,23]. We also find strong support for monophyly of amphisbaenians (SHL = 99), in contrast to some molecular analyses [19,20]. Relationships among amphisbaenian families (Figure 12) are generally strongly supported and similar to those in earlier molecular studies (Figure 12), including the placement of the New World family Rhineuridae as sister group to all other amphisbaenians [70,71,125]. The family Cadeidae is placed as the sister-group to Amphisbaenidae + Trogonophiidae (Figures 1 and Figure 12) with weak support, but has been placed with Blanidae in previous studies, with strong support but less extensive taxon sampling [125,126].

We find strong support for monophyly of the Old World family Lacertidae (Figure 13). Within Lacertidae, branch support for the monophyly of most genera and for the subfamilies Gallotiinae and Lacertinae is very high (Figure 13). However, we find that relationships among many genera are poorly supported, as in previous studies [65,67,68]. Our results (Figure 13) also indicate that several lacertid genera are non-monophyletic with strong support for the associated nodes, including Algyroides (paraphyletic with respect to Dinarolacerta), Ichnotropis (paraphyletic with respect to Meroles), Meroles (paraphyletic with respect to Ichnotropis), Nucras (polyphyletic with respect to several genera, including Pedioplanis, Poromera, Latastia, Philocortus, Pseuderemias, and Heliobolus), and Pedioplanis (paraphyletic with respect to Nucras).

Higher-level phylogeny of Toxicofera

We find strong support (SHL = 96) for monophyly of Toxicofera (Anguimorpha, Iguania, and Serpentes; Figure 1), and moderate support for a sister-group relationship between Iguania and Anguimorpha (SHL = 79). Relationships among Anguimorpha, Iguania, and Serpentes were weakly supported in some Bayesian and likelihood analyses [16-19], but strongly supported in others [20]. We further corroborate previous studies in also placing Anguimorpha with Iguania [16-20]. In contrast, some other studies have placed anguimorphs with snakes as the sister group to iguanians [127,128].

Anguimorpha

Our hypothesis for family-level anguimorphan relationships (Figures 1, 14) is generally similar to that of other recent studies [17,19,20,129], and is strongly supported. Our results differ from some analyses based only on morphology, which place Anguidae near the base of Anguimorpha [130]. Here, Shinisauridae is strongly supported as the sister taxon to a well-supported clade of Varanidae + Lanthanotidae (Figures 1, 14). Varanid relationships are similar to previous estimates (e.g. [131]). Xenosauridae is here strongly supported as the sister-group to a strongly supported clade containing Helodermatidae and the strongly supported Anniellidae + Anguidae clade (Figures 1, 14). However, previous molecular analyses have placed Helodermatidae as the sister to Xenosauridae (Anniellidae + Anguidae), typically with strong support [16,17,19,20].

Within Anguidae (Figure 14), our phylogeny indicates non-monophyly of genera within every subfamily, including Diploglossinae (Diploglossus and Celestus are strongly supported as paraphyletic with respect to each other and to Ophiodes), Anguinae (Ophisaurus is strongly supported as paraphyletic with respect to Anguis, Dopasia, and Pseudopus), and Gerrhonotinae (Abronia and Mesaspis are non-monophyletic, and Coloptychon is nested inside Gerrhonotus). Some of these problems were not reported previously (e.g. Coloptychon, Abronia, and Mesaspis), due to incomplete taxon sampling in previous studies [129,132,133], but relationships within Gerrhonotinae are under detailed investigation by other researchers, so these issues are likely to be resolved in the near future.

Iguania

We find strong support (SHL = 100) for the monophyly of Iguania (Figure 1). This clade is strongly supported by nuclear data [16,17,19,20], but an apparent episode of convergent molecular evolution in several mitochondrial genes has seemingly misled some analyses of mtDNA, leading to weak support for Iguania [134], or even separation of the acrodonts and

pleurodonts [17,135] in previous studies. Within Iguania (Figure 1), we find strong support (SHL = 100) for a sister-group relationship between Chamaeleonidae and Agamidae (Acrodonta), and for a clade of mostly New World families (Pleurodonta; SHL = 100).

We find strong support for the monophyly of Chamaeleonidae and the subfamily Chamaeleoninae, and weak support for the paraphyly of Brookesiinae (Figures 1, 15). The sampled species of the Brookesia nasus group appear as the sister group to all other chamaeleonids (the latter clade weakly supported) as found by some previous authors [136], though other studies have recovered a monophyletic Brookesia [137,138]. Within Chamaeleoninae (Figure 15), we find strong support for the monophyly of most genera and species-level relationships. However, we find strong support for the non-monophyly of Calumma, with some species strongly placed with Chamaeleo, others strongly placed with Rieppeleon, and a third set weakly placed with Nadzikambia + Rhampoleon. While non-monophly of Calumma has also been found in previous studies [138], a recent study strongly supports monophyly of Brookesia and weakly supports monophyly of Calumma [139].

Monophyly of Agamidae is strongly supported (Figure 16; SHL = 100), contrary to some previous estimates [15,31]. Most relationships among agamid subfamilies and genera are strongly supported (Figure 16), and largely congruent with earlier studies [17,29,34,140]. There are some differences with earlier studies. For example, previous studies based on 29–44 loci [20,29,34] placed Hydrosaurinae as sister to Amphibolurinae + (Agaminae + Draconinae) with strong support, whereas we place Hydrosaurinae as the sister-group to Amphibolurinae with weak support. Other authors [140] placed Leiolepiedinae with Uromastycinae, but we (and most other studies) place Uromastycinae as the sister group to all other agamids.

Our phylogeny indicates several taxonomic problems within amphibolurine agamids (Figure 16). The genera Moloch and Chelosania render Hypsilurus paraphyletic, although the support for the relevant clades is weak. The species Lophognathus gilberti is placed in a strongly supported clade with Chlamydosaurus and some Amphibolurus (including the type species, A. muricatus), a clade that is not closely related to the other Lophognathus. Many of these taxonomic problems were also noted by previous authors [141].

Within agamine agamids (Figure 16), most relationships are well supported and monophyly of all sampled genera is strongly supported. In contrast, within draconine agamids (Figure 16), many intergeneric relationships are weakly supported, and some genera are non-monophyletic (Figure 16; see also [142]), including Gonocephalus (G. robinsonii is only distantly related to other Gonocephalus) and Japalura (with species distributed among three distantly related clades, including one allied with Ptyctolaemus, another with G. robinsonii, and a third with Pseudocalotes).

Recent authors suggested dividing Laudakia into three genera (Stellagama, Paralaudakia, and Laudakia) based on a non-phylogenetic analysis of morphology [143]. Here, Laudakia (as previously defined) is strongly supported as monophyletic (Figure 16), and this change is not necessitated by the phylogeny. Similarly, based on genetic and morphological data, recent authors [144] suggested resurrecting the genus Saara for the basal clade of Uromastyx (U. asmussi, U. hardwickii, and U. loricata). However, Uromastyx (as previously defined) is strongly supported as monophyletic in our results (Figure 16) and in those of the recent revision [144], and this change is not needed. We therefore retain Laudakia and Uromastyx as previously defined, to preserve taxonomic stability in these groups [113]. We note that recent

studies have also begun to revise species limits in other groups such as Trapelus [145], and taxa such as T. pallidus (Figure 16) may represent populations within other species.

Within Pleurodonta we generally confirm the monophyly and composition of the clades that were ranked as families (or subfamilies) within the group (e.g. Phrynosomatidae, Opluridae, Leiosauridae, Leiocephalidae, and Corytophanidae; Figures 1, 17, 18, 19) based on previous molecular studies [31,33,34] and earlier morphological studies [146,147].

One important exception is the previously recognized Polychrotidae. Our results confirm that Anolis and Polychrus are not sister taxa (Figures 1, 18, 19), as also found in some previous molecular studies [31,33,34], but not others [20,29]. Our results provide strong support for non-monophyly of Polychrotidae, placing Polychrus with Hoplocercidae (SHL = 99) and Anolis with Corytophanidae (SHL = 99; the latter also found by [34]). Recent analyses placing Anolis with Polychrus showed only weak support for this relationship [20,29], despite many loci (30–44). We support continued recognition of Dactyloidae for Anolis and Polychrotidae for Polychrus [34], based on a limited number of loci but extensive taxon sampling. We note that these families are still monophlyetic, even if they prove to be sister taxa.

Interestingly, our results for relationships among pleurodont families differ from most previous studies, and are surprisingly well-supported in some cases by SHL values (but see below). In previous studies, many relationships among pleurodont families were poorly supported by Bayesian posterior probabilities and by parsimony and likelihood bootstrap values, though typically sampling fewer taxa or characters [17,31,33,148-151]. Studies including 29 nuclear loci found strong concatenated Bayesian support for many relationships but weak support from ML bootstrap analyses for many of the same relationships [34]. The latter pattern (typically weak ML support) was also found in an analysis including those same 29 loci and mitochondrial data for >150 species [29]. We also find a mixture of strongly and weakly supported clades, but with many relationships that are incongruent with these previous studies. First, we find that Tropiduridae is weakly supported as the sister group to all other pleurodonts (also found by [29]), followed successively (Figures 1, 17, 18, 19) by Iguanidae, Leiocephalidae, Crotaphytidae + Phrynosomatidae, Polychrotidae + Hoplocercidae, and Corytophanidae + Dactyloidae.

The relatively strong support for the clades Crotaphytidae + Phrynosomatidae (SHL = 87), Polychrotidae + Hoplocercidae (SHL = 99), and Corytophanidae + Dactyloidae (SHL = 99) is largely unprecedented in previous studies (although Corytophanidae + Dactyloidae is strongly supported in some Bayesian analyses [34]). As in many previous analyses, deeper relationships among the families remain weakly supported. We also find a strongly supported clade containing Liolaemidae, Opluridae, and Leiosauridae (SHL = 95), with Opluridae + Leiosauridae also strongly supported (SHL = 99). Both clades have also been found in previous studies [149,151], including studies based on 29 or more nuclear loci [20,29,34].

We note that previous studies have shown strong support for some pleurodont relationships (e.g. basal placement of phrynosomatids; see [34]), only to be strongly overturned with additional data [20,29]. Therefore, the relationships found here should be taken with some caution (even if strongly supported), with the possible exception of the recurring clade of Liolaemidae + (Opluridae + Leiosauridae).

All pleurodont families are strongly supported as monophyletic (SHL > 85). Within the pleurodont families, our results generally support the current generic-level taxonomy (Figures 17, 18, 19). However, there are some exceptions. Within Tropiduridae (Figure 17), Tropidurus is paraphyletic with respect to Eurolophosaurus, Strobilurus, Uracentron, and Plica. Within Opluridae (Figure 18), the monotypic genus Chalarodon renders Oplurus paraphyletic. Two leiosaurid genera are also problematic (Figure 18). In Enyaliinae, Anisolepis is paraphyletic with respect to Urostrophus, and this clade is nested within Enyalius. In Leiosaurinae, Pristidactylus is rendered paraphyletic by Leiosaurus and Diplolaemus (Figure 18).

Within Dactyloidae, a recent study re-introduced a more subdivided classification of anoles [152], an issue that has been debated extensively in the past [153-156]. Our results support the monophyly of all the genera recognized by recent authors [152], including Anolis, Audantia, Chamaelinorops, Dactyloa, Deiroptyx, Norops, and Xiphosurus (see Figure 19). However, since Anolis is monophyletic as previously defined, we retain that definition here (including the seven listed genera) for continuity with the recent literature [113,157].

Serpentes

Relationships among the major serpent groups (Figure 1) are generally similar to other recent studies [20,35,36,38,41,44,47,158-160]. We find that the blindsnakes, Scolecophidia (Figures 1, 20) are not monophyletic, as in previous studies [19,20,36,44,159,160]. Similar to some previous studies [44,159], our data weakly place Anomalepididae as the sister taxon to all snakes, and the scolecophidian families Gerrhopilidae, Leptotyphlopidae, Typhlopidae, and Xenotyphlopidae as the sister-group to all other snakes excluding Anomalepididae (Figures 1, 20). Previous studies have also placed Anomalepididae as the sister-group to all non-scolecophidian snakes [19,20,35,36,158,160], in some cases with strong support [20]. Although it might appear that recent analyses of scolecophidian relationships [38] support monophyly of Scolecophidia (e.g. Figure 1 of [38]), the tree including non-snake outgroups from that study shows weak support for placing anomalepidids with alethinophidians, as in other studies [19,20,36,160].

We follow recent authors [38] in recognizing Xenotyphlopidae (strongly placed as the sister taxon of Typhlopidae) and Gerrhopilidae (strongly placed as the sister group of Xenotyphlopidae + Typhlopidae) as distinct families (Figure 20). Leptotyphlopidae is strongly supported as the sister group of a clade comprising Gerrhopilidae, Xenotyphlopidae, and Typhlopidae (Figure 20). As in previous studies [38,44], we find strong support for non-monophyly of several typhlopid genera (Afrotyphlops, Austrotyphlops, Ramphotyphlops, Letheobia, and Typhlops; Figure 20). There are also undescribed taxa (e.g. Typhlopidae sp. from Sri Lanka; [44]) of uncertain placement within this group (Figure 20). The systematics of typhlopoid snakes will thus require extensive revision in the future, with additional taxon and character sampling.

Within Alethinophidia (SHL = 100), Aniliidae is strongly supported (SHL = 98) as the sister taxon of Tropidophiidae (together comprising Anilioidea), and all other alethinophidians form a strongly supported sister group to this clade (SHL = 97; Figures 1, 21). The enigmatic family Xenophidiidae is weakly placed as the sister-group to all alethinophidians exclusive of Anilioidea (Figures 1, 21). The family Bolyeriidae is weakly placed as the sister-group to pythons, boas, and relatives (Booidea), which are strongly supported (SHL = 88).

Relationships in this group are generally consistent with other recent molecular studies [20,35-37,47,159].

Relationships among other alethinophidians are a mixture of strongly and weakly supported nodes (Figures 1, 21). We find strong support (SHL = 100) for a clade containing Anomochilidae + Cylindrophiidae + Uropeltidae. This clade of three families is strongly supported (SHL = 89) as the sister taxon to Xenopeltidae + (Loxocemidae + Pythonidae). Together, these six families form a strongly supported clade (SHL = 89; Figures 1, 21) that is weakly supported as the sister group to the strongly supported clade of Boidae + Calabariidae. Within the clade of Anomochilidae, Cylindrophiidae, and Uropeltidae (Figure 21), we weakly place Anomochilus as the sister group to Cylindrophiidae [44], in contrast to previous studies which placed Anomochilus within Cylindrophis [161]. However, support for monophyly of Cylindrophis excluding Anomochilus is weak (Figure 21). As in previous studies [44,162], we find several taxonomic problems within Uropeltidae (Figure 21). Specifically, Rhinophis and Uropeltis are paraphyletic with respect to each other and to Pseudotyphlops. The problematic taxa are primarily Sri Lankan [44], and forthcoming analyses will address these issues.

Within Pythonidae (Figure 21), the genus Python is the sister group to all other genera. Some species that were traditionally referred to as Python (P. reticulatus and P. timoriensis) are instead sister to an Australasian clade consisting of Antaresia, Apodora, Aspidites, Bothrochilus, Leiopython, Liasis, and Morelia (Figure 21). These taxa (P. reticulatus and P. timoriensis) have been referred to as Broghammerus, a name originating from an act of "taxonomic vandalism" (i.e. an apparently intentional attempt to disrupt stable taxonomy) in a non-peer reviewed organ without data or analyses [163,164]. However, this name was, perhaps inadvertently, subsequently used by researchers in peer-reviewed work [165] and has entered into somewhat widespread usage [1]. This name should be ignored and replaced with a suitable substitute. Within the Australasian clade (Figure 21), Morelia is paraphyletic with respect to all other genera, and Liasis is non-monophyletic with respect to Apodora, although many of the relevant relationships are weakly supported.

Within Boidae (Figure 21), our results and those of other recent studies [20,36,47,48,150,166] have converged on estimated relationships that are generally similar to each other but which differ from traditional taxonomy [167]. However, the classification has yet to be modified to reflect this, and we rectify this situation here. We find that Calabariidae is nested within Boidae [150], but this is poorly supported, and contrary to most previous studies [47,48]. While Calabaria has been classified as an erycine boid in the past, this placement is strongly rejected here and in other studies [47,48]. If the current placement of Calabaria is supported in the future, it would require recognition as the subfamily Calabariinae.

The Malagasy boine genera Acrantophis and Sanzinia are placed as the sister taxa to a weakly-supported clade containing Calabariidae and a strongly supported clade (SHL = 99) comprising the currently recognized subfamilies Erycinae, Ungaliophiinae, and other boines (Figure 21). Regardless of the position of Calabariidae, this placement of Malagasy boines renders Boinae paraphyletic. We therefore resurrect the subfamily Sanziniinae [168] for Acrantophis and Sanzinia. This subfamily could be recognized as a distinct family if future studies also support placement of this clade as distinct from other Boidae + Calabariidae.

The genera Lichanura and Charina are currently classified as erycines [1], but are strongly supported as the sister group to Ungaliophiinae, as in previous studies [20,36,47,166]. We expand Ungaliophiinae to include these two genera (Figure 21), rather than erect a new subfamily for these taxa. The subfamily Ungaliophiinae is placed as the sister group to a well-supported clade (SHL = 87) containing the rest of the traditionally recognized Erycinae and Boinae. We restrict Erycinae to the Old World genus Eryx.

The genus Candoia (Boinae) from Oceania and New Guinea [1], is placed as the sister taxon to a moderately supported clade (SHL = 83) consisting of Erycinae (Eryx) and the remaining genera of Boinae (Boa, Corallus, Epicrates, and Eunectes). To solve the non-monophyly of Boinae with respect to Erycinae (due to Candoia), we place Candoia in a new subfamily (Candoiinae, subfam. nov.; see Appendix I). Boinae then comprises the four Neotropical genera that have traditionally been classified in this group (Boa, Corallus, Epicrates, and Eunectes). We acknowledge that non-monophyly of Boinae could be resolved in other ways (e.g. expanding it to include Erycinae). However, our taxonomy maintains the traditionally used subfamilies Boinae, Erycinae, and Ungaliophiinae, modifies them to reflect the phylogeny, and recognizes the phylogenetically distinct boine clades as separate subfamilies (Candoiinae, Sanziniinae). Within Boinae, Eunectes renders Epicrates paraphyletic, but this is not strongly supported see also ([48]).

Our results for advanced snakes (Caenophidia) are generally similar to those of other recent studies [41,42,169], and will only be briefly described. However, in contrast to most recent studies [20,36,41,42,81,159,160], Acrochordidae is here strongly placed (SHL = 95) as the sister group to Xenodermatidae. This clade is then the sister group to the remaining Colubroidea, which form a strongly supported clade (SHL = 100; Figures 1, 22). This relationship has been found in some previous studies [169,170], and was hypothesized by early authors [171]. Further evidence will be required to resolve this conclusively. Analyses based on concatenation of 20–44 loci do not support this grouping [20,36], though preliminary species-tree analyses of >400 loci do (Pyron et al., in prep.). Relationships in Pareatidae are similar to recent studies [172], and the group is strongly placed as the sister taxon to colubroids excluding xenodermatids (SHL = 100; Figures 1 , 22), as in most recent analyses (e.g. [41,43,44]).

The family Viperidae is the sister group to all colubroids excluding xenodermatids and pareatids (Figure 1), as in other recent studies. The family Viperidae is strongly supported (Figure 22), as is the subfamily Viperinae, and the sister-group relationship between Azemiopinae and Crotalinae (SHL = 100). Our results generally support the existing generic-level taxonomy within Viperinae (Figure 22). However, we recover a strongly supported clade within Viperinae consisting of Daboia russelii, D. palaestinae, Macrovipera mauritanica, and M. deserti (Figure 22), as in previous studies [173]. We corroborate previous suggestions that these taxa be included in Daboia [174], though this has not been widely adopted [1]. The other Macrovipera species (including the type species) remain in that genus (Figure 22).

Within Crotalinae (Figure 22), a number of genera appear to be non-monophyletic. The species Trimeresurus gracilis is strongly supported as the sister taxon to Ovophis okinavensis and distantly related to other Trimeresurus, whereas the other Ovophis are strongly placed as the sister group to Protobothrops. A well-supported clade (SHL = 90) containing Atropoides picadoi, Cerrophidion, and Porthidium renders Atropoides paraphyletic (see also [175]). The species Bothrops pictus, considered incertae sedis in previous studies [176], is here strongly

supported as the sister taxon to a clade containing Rhinocerophis, Bothropoides, Bothriopsis, and Bothrops (Figure 22). Most of these relationships are strongly supported.

Viperidae is strongly placed (SHL = 95) as the sister taxon to a well-supported clade (SHL = 100) containing Colubridae, Elapidae, Homalopsidae, and Lamprophiidae (Figure 1). Monophyly of Homalopsidae is also strongly supported (Figure 23). Within Homalopsidae, the non-monophyly of the genus Enhydris is strongly supported (Figure 23), and should likely be split into multiple genera. Homalopsidae is weakly supported (SHL = 58) as the sister group of Elapidae + Lamprophiidae (Figure 1). This same relationship was also weakly supported by previous analyses [41,44], but other studies have found strong support for placing Homalopsidae as the sister group of a strongly supported clade including Elapidae, Lamprophiidae, and Colubridae [20,36], including data from >400 loci (Pyron et al., in prep.).

Support for the monophyly of Lamprophiidae is strong (but excluding Micrelaps; see below), and most of its subfamilies are well-supported [40,41,177,178] including Atractaspidinae, Aparallactinae, Lamprophiinae, Prosymninae (weakly placed as the sister-group to Oxyrhabdium), Pseudaspidinae, Psammophiinae, and Pseudoxyrhophiinae (Figure 23). In Lamprophiidae, most genera are monophyletic based on our sampling (Figure 23). However, within Aparallactinae, Xenocalamus is strongly placed within Amblyodipsas, and in Atractaspidinae, Homoroselaps is weakly placed in Atractaspis. In Lamprophiinae, Lamprophis is paraphyletic with respect to Lycodonomorphus but support for the relevant clades is weak.

The enigmatic genera Buhoma from Africa and Psammodynastes from Asia were both previously considered incertae sedis within Lamprophiidae [41]. Here they are weakly placed as sister taxa, and more importantly, they form a strongly supported clade with the African genus Pseudaspis (Pseudaspidinae; SHL = 95; Figure 23). Therefore, we expand Pseudaspidinae to include these two genera.

The genus Micrelaps (putatively an aparallactine; [1]) is weakly placed as the sister taxon to Lamprophiidae + Elapidae. Along with Oxyrhabdium (see above) and Montaspis [40], this genus is treated as incertae sedis in our classification (Appendix I). If future studies strongly support these relationships, they may require a new family for Micrelaps and possibly a new subfamily for Oxyrhabdium, though placement of these taxa has been highly variable in previous studies [40,41,44,81].

Monophyly of Elapidae is strongly supported (Figure 24), and Calliophis melanurus is strongly supported as the sister group to all other elapids (see also [44]). Within Elapidae (Figure 24), relationships are generally concordant with previous taxonomy, with some exceptions. The genera Toxicocalamus, Simoselaps, and Echiopsis are all divided across multiple clades, with strong support for many of the relevant branches. A recent study has provided a generic re-classification of the sea snakes (Hydrophis group) to resolve the extensive paraphyly of genera found in previous studies (e.g. [46,179,180]). Our results support this classification.

Monophyly of Colubridae and most of its subfamilies (sensu [41,44]) are strongly supported (Figures 1, 25, 26, 27, 28). However, relationships among many of these subfamilies are weakly supported (Figure 1), as in most previous studies [41,43,45,181]. The subfamilies Calamariinae and Pseudoxenodontinae are strongly supported as sister taxa, and weakly

placed as the sister-group to the rest of Colubridae (Figure 25). There is a weakly supported clade (Figure 1) comprising Natricinae + (Dipsadinae + Thermophis), but the clade uniting the New World Dipsadinae with the Asian genus Thermophis is strongly supported (SHL = 100; Figure 28). Here, we place Thermophis (recently in Pseudoxenodontinae [41]) in Dipsadinae (following [182]), making it the first and only Asian member of this otherwise exclusively New World subfamily. However, despite the strong support for its placement here, placement of this taxon has been variable in previous analyses [41,182,183], and we acknowledge that future analyses may support recognition of a distinct subfamily (Thermophiinae).

The clade of Natricinae and Dipsadinae is weakly supported as the sister group (Figures 1, 25, 26, 27, 28) to a clade containing Sibynophiinae [181] + (Colubrinae + Grayiinae). The subfamily Colubrinae is weakly supported; we find that the colubrine genera Ahaetulla, Chrysopelea, and Dendrelaphis form a strongly supported clade that is weakly placed as the sister group to the rest of Colubrinae, which form a strongly supported clade (Figure 25). This clade was also placed with Grayiinae or Sibynophiinae in many preliminary analyses, rendering Colubrinae paraphyletic. This group of three genera has been strongly supported in the past, and only weakly placed with Colubrinae [41,44]. It is possible that future analyses will reveal that the clade of Ahaetulla, Chrysopelea, and Dendrelaphis is placed elsewhere in Colubridae with strong support, and thus merits recognition as a distinct subfamily (Ahaetuliinae). A notable feature of this clade is the presence of gliding flight in most species of Chrysopelea, less-developed non-flight jumping with similar locomotor origins in Dendrelaphis, and homologous glide-related traits in Ahaetulla [184].

Numerous colubroid genera are not included in our tree and are not clearly placed in subfamilies based on previous morphological evidence. In our classification, these genera are also considered incertae sedis within Colubridae, including Blythia, Cyclocorus, Elapoidis, Gongylosoma, Helophis, Myersophis, Oreocalamus, Poecilopholis, Rhabdops, and Tetralepis, as in previous classifications [1].

Our phylogeny reveals numerous taxonomic problems within Colubrinae (Figures 25, 26). The genus Boiga is paraphyletic with respect to Crotaphopeltis, Dipsadoboa, Telescopus, Toxicodryas, and Dasypeltis, with strong support (Figure 25). The genus Philothamnus is paraphyletic with respect to Hapsidophrys (Figure 25). The genus Coluber is split between Old World and New World clades (Figures 25, 26). The species Hierophis spinalis is sister to Eirenis to the exclusion of the other Hierophis species (Figure 25). The genus Dryocalamus is nested within Lycodon (Figure 26). The species Chironius carinatus and C. quadricarinatus are weakly placed in a clade of Neotropical colubrines only distantly related to the other Chironius species (Figure 26). The genus Drymobius renders Dendrophidion paraphyletic (Figure 26). The monotypic genus Rhynchophis renders the two species of Rhadinophis paraphyletic (Figure 26). The genus Coronella is rendered paraphyletic (Figure 26) by Oocatochus with weak support see also [185]. Finally, the genus Rhinechis is nested within Zamenis (Figure 26).

We find numerous non-monophyletic genera within Natricinae (Figure 27), as in previous studies [41,44,78,186]. These non-monophyletic genera include the Asian genera Amphiesma, Atretium, and Xenocrophis. Among New World genera, we find Regina to be non-monophyletic with respect to most other genera, as in previous phylogenetic studies (e.g. [41,186]). Also, as in previous studies (e.g. [41,187]), we find that Adelophis [188] is nested deep within Thamnophis [189].

Finally, within a weakly supported Dipsadinae (Figure 28), we find non-monophyly of numerous genera, as in many earlier studies (e.g. [41-43,190]). These problems of non-monophyly include Leptodeira (with respect to Imantodes), Geophis (with respect to Atractus), Atractus (with respect to Geophis), Sibynomorphus (with respect to Dipsas), Dipsas (with respect to Sibynomorphus), Taeniophallus (with respect to Echinanthera), and Echinanthera (with respect to Taeniophallus). Recent revisions have begun to tackle these problems [42,43,190], but additional taxon and character sampling will be crucial to resolve relationships and taxonomy.

Discussion

In this study, we provide a phylogenetic estimate for 4161 species of squamates based on molecular data from up to 12 genes per species, combining much of the relevant data used in previous molecular phylogenetic analyses. This tree provides a framework for future evolutionary studies, spanning from the species level to relationships among families, utilizing a common set of branch lengths. These estimated branch lengths are critically important for most phylogenetic comparative methods. To further facilitate use of this phylogeny in comparative studies, we provide the Newick version of this tree (with estimated branch lengths) in DataDryad repository 10.5061/dryad.82h0m and Additional file 1 Data File S1. Our results also suggest that the branch lengths in this tree should not generally be compromised by missing data for some genes in some taxa.

Our results also reveal many problems in squamate classification at nearly all phylogenetic levels. We make several changes to higher-level taxonomy based on this phylogeny, including changes to the traditionally recognized subfamilies of boid snakes (i.e. resurrecting Sanziniinae for the boine genera Acrantophis and Sanzinia, erecting Candoiinae for the boine genus Candoia, and moving Lichanura and Charina from Erycinae to Ungaliophiinae), lamprophiid snakes (expansion of Pseudaspidinae to include the formerly incertae sedis genera Buhoma and Psammodynastes), colubrid snakes (expansion of Dipsadinae to include the Asian pseudoxenodontine genus Thermophis), and gymnophthalmid lizards (recognition of Bachiinae for the tribe cercosaurine Bachiini, containing Bachia) and scincid lizards (synonymizing Feylininae with Scincinae to yield a total of three scincid subfamilies: Acontiinae, Lygosominae, and Scincinae). In Appendix I, we list the generic content of all families and subfamilies. We also find dozens of problems at the genus level, many of which have been identified previously, and which we defer the resolution of to future studies. Our results also highlight potential problems in recent proposals to modify the classification of scincid [112] and teiid lizards [123].

In addition to synthesizing existing molecular data for squamate phylogeny, our analyses also reveal several apparently novel findings (Figures 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28). Given space constraints, we cannot detail every deviation from previous phylogenetic hypotheses (especially pre-molecular studies). Nevertheless, we focus on three sets of examples. First, we find some relatively novel, strongly-supported relationships at the family level. These include the placement of Helodermatidae (as sister to Xenosauridae, Anguidae, and Anniellidae) and the placement of Xenodermatidae as the sister taxon to Acrochordidae (rendering Colubroidea paraphyletic), in contrast to most recent analyses of anguimorphs and snakes (see above). We also find some novel, strongly supported relationships among pleurodont families, but we acknowledge that these may be overturned in future studies.

The second example is the higher-level relationships within Scincidae, the largest family of lizards [1]. No previous studies examining higher-level relationships within the group included more than ~50 species [50,51]. In this study, we sample 683 skink species (Figures 6, 7, 8, 9, 10), and our phylogeny provides a unique resolution of higher-level skink relationships. Previous researchers [51] placed acontiines as the sister group to all other skinks, but suggested that scincines and lygosomines were paraphyletic with respect to each other (with feyliniines placed with scincines). In contrast, others [50] suggested that acontiines, feyliniines, and lygosomines were all nested inside scincines (but with each of those three subfamilies as monophyletic), although many clades were only weakly supported. Here (Figures 1, 6, 7, 8, 9, 10), we find that acontiines are the sister group to a strongly supported clade consisting of a monophyletic Scincinae and a monophyletic Lygosominae (excepting the weakly supported placement of Ateuchosaurus and placement of Feyliniinae in Scincinae).

Third, our phylogeny reveals numerous genera that appear to be non-monophyletic, with many of these cases having strong support for the associated nodes. Our examples include genera in many families, including dibamids, diplodactylids, gekkonids, phyllodactylids, gerrhosaurids, scincids, teiids, gymnophthalmids, lacertids, anguids, chamaeleonids, agamids, tropidurids, oplurids, leiosaurids, typhlopids, pythonids, uropeltids, boids, viperids, lamprophiids, elapids, and colubrids (see Results). Although many problems noted here were found in previous studies, some seem to be new, such as placement of Crocodilurus and Draceana within Tupinambis (in Teiidae; Figure 11) and Coloptychon within Gerrhonotus (in Anguidae; Figure 14).

Our study also offers an important test of higher-level squamate relationships using a very different sampling strategy than that used in most previous analyses. Squamates have traditionally been divided into two clades based on morphology, Iguania and Scleroglossa (e.g. [13,21]). Despite considerable disagreement among morphology-based hypotheses, this basic division is supported by nearly all phylogenetic analyses based on morphological data [13-15,19,22,95,191]. In contrast, our results and those of most previous molecular analyses strongly support placement of iguanians with anguimorphs and snakes [16-20,23,24]. The causes of this conflict remain unclear, but may be related to morphological traits associated with different feeding strategies of iguanian and (traditional) scleroglossan squamates [3,17].

Additionally, analyses of morphology often place dibamids, amphisbaenians, snakes, and (in some cases) some scincids and anguids in a single clade [13-15]. Our analyses do not support such a clade (Figure 1), nor do other analyses of molecular data alone [17-20], or analyses of combined molecular and morphological data [19]. Instead, these morphological results seem to be explained by convergence associated with burrowing (e.g. [19]). Overall, molecular datasets have shown overwhelmingly strong support for placement of dibamids and gekkonids at the base of the tree, amphisbaenians with lacertoids, and iguanians with snakes and anguimorphs [17-20,23]. These results have now been corroborated with up to 22 genes (15794 bp) for 45 taxa [19], 25 genes (19020 bp) for 64 taxa [16], and 44 genes (33717 bp) for 161 taxa [20]. We now support this basic topology with 4161 species sampled for up to 12 genes each (up to 12896 bp).

Nevertheless, despite the overall strong support for most of the tree (i.e. 70% of all nodes have SHL > 85), certain clades remain poorly supported (e.g. relationships among many pleurodont iguanian families; Figures 1, 17, 18, 19). A potential criticism of the supermatrix approach used here is that this weak support may occur due to missing data. However,

previous studies of 8 datasets have shown explicitly that there is typically little relationship between branch support for terminal taxa and the amount of missing data [85]. Instead, these patterns of weak support are more likely to reflect short underlying branch lengths [20,36,41], and may be difficult to resolve even with more complete taxonomic and genomic sampling. Indeed, as noted above, many of the weakly supported nodes in our phylogeny are also weakly supported in analyses with little missing data (<20%) and large numbers of genes (e.g. 44 genes as in [20]), such as the relationships of many pleurodont lizard families and colubroid snake families and subfamilies.

We acknowledge that the differences between our results and previous studies (noted above) do not necessarily mean that our results are right and those of previous studies are wrong. In some cases, we provide strong support for novel relationships when previous, conflicting studies showed only weak support (as in scincids, see above). In other cases, our results disagree with other studies for clades that were strongly supported (e.g. placement of xenodermatids). In the best-case scenario, these conflicts may be resolved because our results are correct, possibly reflecting the beneficial effects of adding taxa and the associated subdivision of long branches [25,26,28,87,192-194]. Furthermore, in many cases, we are including more genes than used in previous studies of particular clades, increasing sampling of characters and loci. This should generally reduce spurious results caused by sampling few characters and by incongruence between gene and species trees.

However, other explanations for incongruence between our results and previous studies are also possible. Adding taxa can potentially lead to incorrect results in some cases (e.g. [195]), such as when a long terminal branch is added that further subdivides a short internal branch. In other cases, conflicts with our results might reflect the impact of our sampling fewer nuclear genes and a correspondingly increased influence of mitochondrial data. Mitochondrial genes have relatively fast evolutionary rates (potentially exacerbating the impacts of long branches), and their phylogenetic resolution for a particular node may also reflect introgression or incomplete lineage sorting rather than the species phylogeny (review in [196]). Many taxa in the matrix are represented only by mitochondrial data, and highly variable mitochondrial genes might also overcome the influence of less variable nuclear genes in combined analyses (although this scenario does not seem to be common [196]). Such cases might explain some strongly supported conflicts between our results and those based on multiple nuclear loci. Another possibility is that some cases may represent failure to find the optimal tree (although we assume that these cases will likely show only weak support). We acknowledge that there are many reasons why our results may differ from previous studies, and the ultimate test of these novel findings will be corroboration in future studies that include more taxa and characters.

This analysis also corroborates several recent studies suggesting that the supermatrix approach is a powerful strategy for large-scale phylogenetic inference [41,72,73,75,76,197]. For example, even though each species had 81% missing data on average, we found that most species were placed in the families and genera expected based on previous taxonomy, often with very strong support. Furthermore, we found that incompleteness of terminal taxa is not related to branch lengths (at least not terminal branch lengths), suggesting that missing data are not significantly biasing branch-length estimates (see also [84,86,87]). Also, the CAT-based models we used have been shown to be robust to missing data in large, sparse supermatrices [84].

Even though we did find some subfamilies and genera to be non-monophyletic, similar relationships were often found in previous studies based on data matrices with only limited missing data (e.g. non-monophyly of boid snake subfamilies [47], lacertid and scincid lizard genera [67,111], and scolecophidian, dipsadine, and natricine snake genera [38,43,186]). We suggest that further resolution of the squamate tree will be greatly facilitated if researchers deliberately sample mitochondrial genes and nuclear genes that include the set of genes used here and in recent phylogenomic studies (e.g. [20]), to increase overlap between genes and taxa, and decrease missing data.

With over 5000 species remaining to be included and only 12 genes sampled, our study is far from the last word on squamate phylogeny. We note that new data can easily be added to this matrix, in terms of both new taxa and new genes. Increased sampling of other nuclear genes is likely to be advantageous as well. Next-generation sequencing strategies and phylogenomic methods should help resolve difficult nodes [16,20,36,198-200], as should application of species-tree methods [201,202]. Species-tree analyses of 44 nuclear loci support many of these same clades across squamates [20], and data from >400 nuclear loci reinforces many of the relationships found here among the colubroid snake subfamilies (Pyron et al., in prep.). In addition, it would be useful to incorporate fossil taxa in future studies [15,19,22,86], utilizing the large morphological datasets that are now available [14,15]. Despite these areas for future studies, the present tree provides a framework for researchers analyzing patterns of squamate evolution at both lower and higher taxonomic levels (e.g. [10,11,203,204]), and for building a more complete picture of squamate phylogeny.

Conclusions

In this study, we provide a phylogenetic estimate for 4161 squamate species, based on a supermatrix approach. Our results provide important confirmation for previous studies based on more limited taxon sampling, and reveal new relationships at the level of families, genera, and species. We also provide a phylogenetic framework for future comparative studies, with a large-scale tree including a common set of estimated branch lengths. Finally, we provide a revised classification for squamates based on this tree, including changes in the higher-level taxonomy of gymnophthalmid and scincid lizards and boid, colubrid, and lamprophiid snakes.

Methods

Initial classification

Our initial squamate classification is based on the June 2009 version of the Reptile Database (http://www.reptile-database.org/), accessed in September of 2009 when this research was begun. Minor modifications to this scheme were made, primarily to update changes in colubroid snake taxonomy [41-44,205]. This initial taxonomic database consists of 8650 species (169 amphisbaenians, 5270 lizards, 3209 snakes, and 2 tuataras), against which the classification of species in the molecular sequence database was fixed. While modifications and updates (i.e. new species, revisions) have been made to squamate taxonomy subsequently, these are minor and should have no impact on our phylogenetic results. This database represents ~92% of the current estimated diversity of squamates (~9400 species as of December 2012).

Throughout the paper, we refer to the updated version of squamate taxonomy from the December 2012 update of the Reptile Database, incorporating major, well-accepted changes from recent studies (summarized in [1]). However, for large, taxonomic groups that have recently been broken up for reasons other than resolving paraphyly or matters of priority (e.g. in dactyloid and scincid lizards; see Results), we generally retain the older, more inclusive name in the interest of clarity, while providing references to the recent revision. We attempt to alter existing classifications as little as possible (see also [113]). Therefore, we generally only make changes when there is strong support for non-monophyly of currently recognized taxa and our proposed changes yield strongly supported monophyletic groups. Similarly, we only erect new taxa if they are strongly supported. Finally, although numerous genera are identified as being non-monophyletic in our tree, we refrain from changing genus-level taxonomy, given that our taxon sampling within many genera is limited.

Molecular data

Preliminary literature searches were conducted to identify candidate genes for which a substantial number of squamate species were sequenced and available on GenBank (with the sampled species spread across multiple families), and which were demonstrably useful in previous phylogenetic studies of squamates (see Introduction for references). Twelve genes were identified as meeting these criteria: seven nuclear genes (brain-derived neurotrophic factor [BDNF], oocyte maturation factor [c-mos], neurotrophin-3 [NT3], phosducin [PDC], G protein-coupled receptor 35 [R35], and recombination-activating genes 1 [RAG-1] and 2 [RAG-2]), and five mitochondrial genes (12S/16S long and short subunit RNAs, cytochrome b [cyt-b], and nicotinamide adenine dehydrogenase subunits 2 [ND2] and 4 [ND4]). This sampling of genes does not include all available markers. For example, we omitted several nuclear and mitochondrial genes because they were available only for a limited subset of taxa. We also excluded tRNAs associated with the protein-coding sequences, given their short lengths and difficulty in alignment across the large time scales considered here.

To ensure maximal taxonomic coverage from the available data, searches were conducted on GenBank by family (stopping in October 2012), and the longest sequence for every species was gathered. Sequences totaling less than 250 bp for any species were not included. Only species in the taxonomic database were included in the sequence matrix, which resulted in the exclusion of numerous named taxa of ambiguous status, a few taxa described very recently, and many sequences labeled 'sp.' Some recently described phylogeographic lineages were also omitted. Species and GenBank accession numbers are available in Additional file 2 Table S1.

With respect to the December 2012 update of the Reptile Database, we sampled 52 of 183 amphisbaenian species (28%) from 11 of 19 (58%) genera; 2847 of 5799 lizard species (49%) from 448 of 499 genera (90%); and 1262 of 3434 snake species (39%) in 396 of 500 genera (80%). This yielded a total of 4161 species in 855 genera in the final matrix, 44% of the 9416 known, extant squamate species in 84% of 1018 genera [1]. The species-level classification of squamates is in constant flux, and the numbers of species and genera changed even as this paper was under review. The extant species of tuatara (Sphenodon punctatus) was included as a non-squamate outgroup taxon (see below). We acknowledge that our sampling of outgroup taxa is not extensive. However, placement of Sphenodon as the sister group to squamates is well-established by molecular analyses with extensive taxon sampling (e.g. [16,128,206]) and morphological data (e.g. [13]).

Alignment for protein-coding sequences was relatively straightforward. We converted them to amino acids, and then used the translation alignment algorithm in the program Geneious v4.8.4 (GeneMatters Corp.), with the default cost matrix (Blosum62) and gap penalties (open=12, extension=3). Alignments were relatively unambiguous after being trimmed for quality and maximum coverage (i.e. ambiguous end regions were removed, and most sequences began and ended at the same point).

For the ribosomal RNA sequences (12S and 16S sequences), alignment was more challenging. Preliminary global alignments using the algorithms MUSCLE [207] and CLUSTAL [208] under a variety of gap-cost parameters yielded low-quality results (i.e. alignments with large numbers of gaps and little overlap of potentially homologous characters). We subsequently employed a two-step strategy for these data. We first grouped sequences by higher taxa (i.e. Amphisbaenia, Anguimorpha, Gekkota, Iguania, Scincomorpha, and Serpentes, though these are not all monophyletic as previously defined), for which alignments were relatively straightforward under the default MUSCLE parameters.

These were then combined using the profile alignment feature of MUSCLE, and the global alignment was subsequently updated using the "refine alignment" option. Minor adjustments were then made by eye, and ambiguously aligned end-regions were trimmed for maximum coverage and quality. We did not include partitions for stems and loops for the ribosomal sequences, although this has been shown to improve model fit in previous squamate studies (e.g. [82]). Although it is possible to assign individual nucleotide positions to these partitions, this would have been challenging given the large number of sequences, and the potential for stems and loops to shift across the many species and large time scales involved.

Each species was represented by a single terminal taxon in the matrix. In many cases, sequences from multiple individuals of the same species were combined, to allow us to combine data from different genes for the same species. We acknowledge the possibility that in some cases this approach may cause us to combine genes from different species in the same terminal taxon (e.g. due to changing taxonomy or incorrect identifications). Additionally, many sequences are not from vouchered specimens, and it is possible that misidentified species are present on GenBank and in our matrix. However, most of our data came from lower-level phylogenetic studies, in which the identification of species by previous authors should be highly accurate. In addition, any such mistakes should be among closely related species, and lead to minimal phylogenetic distortion, as the grossest errors are easily identified.

Some species were removed after preliminary analyses, due either to obvious sequencing errors (e.g. high BLAST homology with unrelated families or non-squamates, excessive ambiguities) or a lack of overlap in genes sampled with other members of the same genus (leading to seemingly artificial paraphyly). We also excluded species with identical sequences between taxa across all genes, arbitrarily choosing the first taxon in alphabetical order to remain in the matrix. Additionally, we also removed a few apparent "rogue taxa" [75,77]. These were identified by their poor support and suspect placement (e.g. in a clearly incorrect family), and were typically represented in the matrix by short fragments of single genes (e.g. an ND4 fragment from the enigmatic colubroid snake Oreocalamus hanitchsi).

The final combined matrix contained sequence data for: 2335 species for 12S (including 56% of all 4162 taxa, 1395 bp), 2377 for 16S (57%, 1970 bp), 730 for BDNF (18%, 714 bp), 1671 for c-mos (40%, 903 bp), 1985 for cyt-b (48%, 1000 bp), 437 for NT3 (10%, 675 bp), 1860

for ND2 (45%, 960 bp), 1556 for ND4 (37%, 696 bp), 393 for PDC (9%, 395 bp), 401 for R35 (10%, 768 bp), 1379 for RAG-1 (33%, 2700 bp), and 471 for RAG2 (11%, 720 bp). The total alignment consists of 12896 bp for 4162 taxa (4161 squamates and 1 outgroup). The mean length is 2497 bp of sequence data present per species from 3.75 genes (19% of the total matrix length of 12896 bp, or 81% missing data), and ranges from 270–11153 bp (2–86% complete). The matrix and phylogeny (see below) are available in DataDryad repository 10.5061/dryad.82h0m.

Clearly, many taxa had large amounts of missing data (some >95%), and on average each species had 81% missing cells. However, several lines of evidence suggest that these missing data are not generally problematic. First, a large body of empirical and theoretical studies has shown that highly incomplete taxa can be accurately placed in model-based phylogenetic analyses (and with high levels of branch support), especially if a large number of characters have been sampled (recent reviews in [84,85]). Second, several recent empirical studies have shown that the supermatrix approach (with extensive missing data in some taxa) yields generally well-supported large-scale trees that are generally congruent with previous taxonomies and phylogenetic estimates (e.g. [41,48,72,73,75,76,197]). Third, recent studies have also shown that there is generally little relationship between the amount of missing data in individual taxa and the support for their placement on the tree [41,73,85]. Finally, we note that some highly incomplete taxa were unstable in their placement (“rogue taxa”;[ 75]), but these were removed prior to the analysis of the final matrix (see above).

Our sampling design should be especially robust to the impacts of missing data for several reasons. Most importantly, most terminal taxon (species) had substantial data present (mean of 2497 bp per species) regardless of the number of missing data cells. Simulations (see reviews in [84,85]) suggest that the amount of data present is a key parameter in determining the accuracy with which incomplete taxa are placed in phylogenies, not the amount of data absent. Additionally, several genes (e.g. 12S/16S, cyt-b, and c-mos) were shared by many (>40%) of taxa. Thus, there was typically extensive overlap among the genes present for each taxon (as also indicated by the mean bp per species being much greater than the length of most genes). Limited overlap in gene sampling among taxa could be highly problematic, irrespective of the amount of missing data per se, but this does not appear to be a problem in our dataset. Finally, several nuclear genes (e.g. BDNF, c-mos, R35, and RAG-1) were congruently sampled in previous studies to represent most (>80%) squamate families and subfamilies (e.g. [20]), providing a scaffold of well-sampled taxa spanning all major clades, as recommended by recent authors [84].

Phylogenetic analyses

We performed phylogenetic analyses of the 12-gene concatenated matrix using Maximum Likelihood (ML). We assessed node support using the non-parametric Shimodaira-Hasegawa-Like (SHL) implementation of the approximate likelihood-ratio test (aLRT; [94]). This involved a two-stage strategy. We first performed initial ML tree inference using the program RAxML-Light v1.0.7 [209], a modification of the original RAxML algorithm [210]. This program uses the GTRCAT strategy for all genes and partitions, a high-speed approximation of the GTR+Γ model (general time-reversible with gamma-distribution of rate heterogeneity among sites). The GTR model is the only substitution model implemented in RAxML [210], and all other substitution models are simply special cases of the GTR model [211]. Previous analyses suggest that GTR is generally the best-fitting model for these genes and that they should be partitioned by gene and codon position [16,17,19,20,36,81].

To generate an initial ML estimate for final optimization and support estimation, we performed 11 ML searches from 11 parsimony starting trees generated under the default parsimony model in RAxMLv7.2.8. This number is likely to be sufficient when datasets contain many characters that have strong phylogenetic signal (A. Stamatakis, pers. comm.). Additionally, the dataset was analyzed with these settings (GTRCAT search from a randomized parsimony starting tree) numerous times (>20) as the final matrix was assembled and tested, representing hundreds of independent searches from random starting points. All of the estimated trees from these various analyses showed high overall congruence with the final topology. The concordance between the preliminary and final results suggests that the tree was not strongly impacted by searches stuck on local optima, and that it should be a good approximation of the ML tree.

We then performed a final topology optimization and assessed support. We passed our best ML estimate of the phylogeny (based on GTRCAT) from RAxML-Light to RAxMLv7.2.8, which does an additional search (using the GTRGAMMA model) to produce a nearest-neighbor interchange (NNI)-optimized estimate of the ML tree. This optimization is needed to calculate the SHL version of the aLRT for estimating support values [94]. The SHL-aLRT strategy approximates a test of the null hypothesis that the branch length subtending each node equals 0 (i.e. that the node can be resolved, rather than estimated as a polytomy) with a test of the more general null hypothesis that "the branch is incorrect" relative to the four next suboptimal arrangements of that node relative to the NNI-optimal arrangement [94]. Based on initial analyses, generating sufficient ML bootstrap replicates for a tree of this size proved computationally intractable, so we rely on SHL values alone to assess support.

The SHL approach has at least two major advantages over non-parametric bootstrapping for large ML trees: (i) values are apparently robust to many potential model violations and have the same properties as bootstrap proportions for all but the shortest branches [41,94,212], and (ii) values for short branches may be more accurate than bootstrap proportions, as support is evaluated based on whole-alignment likelihoods, rather than the frequency of re-sampled characters [94,213]. Additionally, the SHL approach is orders of magnitude faster than traditional bootstrapping [94,212,213], and it appears to be similarly robust to matrices with extensive missing data [41]. As in previous studies, we take a conservative view, considering SHL values of 85 or greater (i.e. a 15% chance that a branch is "incorrect") as strong support [41,212,213].

These analyses were performed on a 360-core SGI ICE supercomputing system ("ANDY") at the High Performance Computing Center at the City University of New York (CUNY). The final analysis was completed in 8.8 days of computer time using 188 nodes of the CUNY supercomputing cluster.

Finally, we assessed the potential impact of missing data on our branch-length estimates. We performed linear regression (in R) of the proportional completeness of each terminal taxa (non-missing data in bp / maximum amount of non-missing data, 12896 bp) against the length of its terminal branch. This test addresses whether incomplete taxa have branch-length estimates that are consistently biased in one direction (shorter vs. longer) relative to more complete terminals. However, it does not directly test whether branch length estimates are correct or not, nor how branch length estimates are impacted by replacing non-missing data with missing data (see [87] for results suggesting that such replacements have little effect in real data sets).

Authors' contributions

RAP and JJW conceived the study. RAP, FTB, and JJW conducted analyses and checked results. RAP, FTB, and JJW wrote the MS. All authors read and approved the final manuscript.

Acknowledgements

We thank the many researchers who made this study possible through their detailed studies of squamate phylogeny with a (mostly) shared set of molecular markers, and uploading their sequence data to GenBank. We thank E. Paradis, J. Lombardo T. Guiher, R. Walsh, and P. Muzio for computational assistance, T. Gamble, D. Frost, D. Cannatella, H. Zaher, F. Grazziotin, P. Uetz, T. Jackman, and A. Bauer for taxonomic advice, and A. Larson, M. Vences, and five anonymous reviewers for comments on this manuscript. The research was supported in part by the U.S. National Science Foundation, including a Bioinformatics Postdoctoral grant to R.A.P. (DBI-0905765), an AToL grant to J.J.W. (EF-0334923), and grants to the CUNY HPCC (CNS-0958379 and CNS-0855217).

Appendix I

Note that we only provide here an account for the one subfamily newly erected in this study. We do not provide accounts for subfamilies with changes in content (Boinae, Erycinae, Dipsadinae, Pseudaspidinae, Scincinae, Ungaliophiinae), that have been resurrrected (Sanziniinae), or that represent elevation of lower-ranked taxa (tribe Bachiini here recognized as Bachiinae).

Candoiinae subfam. nov. (family Boidae)

Type: genus and species Candoia carinata [214].

Content: one genus, 4 species; C. aspera, C. bibroni, C. carinata, C. paulsoni.

Definition: this subfamily consists of the most recent common ancestor of the extant species of Candoia, and all its descendants. These species are morphologically distinguished in part from other boid snakes by a flattened rostrum leading to an angular snout [215] and a wide premaxillary floor [167].

Distribution: these snakes are primarily restricted to the South Pacific islands of New Guinea and Melanesia, and the eastern Indonesian archipelago [150].

Remarks: the three species from this subfamily that are sampled in our tree are strongly supported as monophyletic (SHL = 100), and are well supported (SHL = 87) as the sister taxon to a moderately supported clade consisting of Erycinae + Boinae (SHL = 83).

Proposed Generic Composition of Higher Taxa

Below, we list the familial and subfamilial assignment of all squamate genera from the December, 2012 update of the Reptile Database, updated to reflect some recent changes and

the proposed subfamily level changes listed above. As this classification includes numerous taxa not sampled in our tree, we deal with this conservatively. For traditionally recognized families and subfamilies that we found to be monophyletic, we include all taxa traditionally assigned to them. Taxa are denoted incertae sedis if they are of ambiguous familial or subfamilial assignment due to uncertain placement in our tree, or due to absence from our tree and lack of assignment by previous authors. This classification includes 67 families and 56 subfamilies, and accounts for >9400 squamate species in 1018 genera [1]. Higher taxa are listed (more-or-less) phylogenetically (starting closest to the root; Figure 1), families are listed alphabetically within higher taxa, and subfamilies and genera are listed alphabetically within families.

Dibamidae (Anelytropsis, Dibamus)

Gekkota

Carphodactylidae (Carphodactylus, Nephrurus, Orraya, Phyllurus, Saltuarius, Underwoodisaurus, Uvidicolus); Diplodactylidae (Amalosia, Bavayia, Correlophus, Crenadactylus, Dactylocnemis, Dierogekko, Diplodactylus, Eurydactylodes, Hesperoedura, Hoplodactylus, Lucasium, Mniarogekko, Mokopirirakau, Naultinus, Nebulifera, Oedodera, Oedura, Paniegekko, Pseudothecadactylus, Rhacodactylus, Rhynchoedura, Strophurus, Toropuku, Tukutuku, Woodworthia); Eublepharidae (Aeluroscalabotes, Coleonyx, Eublepharis, Goniurosaurus, Hemitheconyx, Holodactylus); Gekkonidae (Afroedura, Afrogecko, Agamura, Ailuronyx, Alsophylax, Asiocolotes, Blaesodactylus, Bunopus, Calodactylodes, Chondrodactylus, Christinus, Cnemaspis, Colopus, Crossobamon, Cryptactites, Cyrtodactylus, Cyrtopodion, Dixonius, Ebenavia, Elasmodactylus, Geckolepis, Gehyra, Gekko, Goggia, Hemidactylus, Hemiphyllodactylus, Heteronotia, Homopholis, Lepidodactylus, Luperosaurus, Lygodactylus, Matoatoa, Mediodactylus, Nactus, Narudasia, Pachydactylus, Paragehyra, Paroedura, Perochirus, Phelsuma, Pseudoceramodactylus, Pseudogekko, Ptenopus, Ptychozoon, Rhinogecko, Rhoptropella, Rhoptropus, Stenodactylus, Tropiocolotes, Urocotyledon, Uroplatus); Phyllodactylidae (Asaccus, Gymnodactylus, Haemodracon, Homonota, Phyllodactylus, Phyllopezus, Ptyodactylus, Tarentola, Thecadactylus); Pygopodidae (Aprasia, Delma, Lialis, Ophidiocephalus, Paradelma, Pletholax, Pygopus); Spha (Aristelliger, Chatogekko, Coleodactylus, Euleptes, Gonatodes, Lepidoblepharis, Pristurus, Pseudogonatodes, Quedenfeldtia, Saurodactylus, Sphaerodactylus, Teratoscincus)

Scincoidea

Cordylidae, Cordylinae (Chamaesaura, Cordylus, Hemicordylus, Karusasaurus, Namazonurus, Ninurta, Ouroborus, Pseudocordylus, Smaug), Platysaurinae (Platysaurus); Gerrhosauridae, Gerrhosaurinae (Cordylosaurus, Gerrhosaurus, Tetradactylus), Zonosaurinae (Tracheloptychus, Zonosaurus); Scincidae, Acontiinae (Acontias, Typhlosaurus), Lygosominae (Ablepharus, Afroablepharus, Anomalopus, Asymblepharus, Ateuchosaurus, Bartleia, Bassiana, Bellatorias, Caledoniscincus, Calyptotis, Carlia, Cautula, Celatiscincus, Chioninia, Coeranoscincus, Coggeria, Cophoscincopus, Corucia, Cryptoblepharus, Ctenotus, Cyclodomorphus, Dasia, Egernia, Emoia, Eremiascincus, Eroticoscincus, Eugongylus, Eulamprus, Eumecia, Eutropis, Fojia, Geomyersia, Geoscincus, Glaphyromorphus, Gnypetoscincus, Graciliscincus, Haackgreerius, Hemiergis, Hemisphaeriodon, Insulasaurus, Isopachys, Kaestlea, Kanakysaurus, Lacertaspis,

Lacertoides, Lamprolepis, Lampropholis, Lankascincus, Larutia, Leiolopisma, Lepidothyris, Leptoseps, Leptosiaphos, Lerista, Liburnascincus, Liopholis, Lioscincus, Lipinia, Lissolepis, Lobulia, Lygisaurus, Lygosoma, Mabuya, Marmorosphax, Menetia, Mochlus, Morethia, Nangura, Nannoscincus, Niveoscincus, Notoscincus, Oligosoma, Ophioscincus, Otosaurus, Panaspis, Papuascincus, Parvoscincus, Phoboscincus, Pinoyscincus, Prasinohaema, Proablepharus, Pseudemoia, Ristella, Saiphos, Saproscincus, Scincella, Sigaloseps, Simiscincus, Sphenomorphus, Tachygyia, Tiliqua, Trachylepis, Tribolonotus, Tropidophorus, Tropidoscincus, Tytthoscincus, Vietnascincus), Scincinae (Amphiglossus, Androngo, Barkudia, Brachymeles, Chabanaudia, Chalcides, Chalcidoseps, Eumeces, Eurylepis, Feylinia, Gongylomorphus, Hakaria, Janetaescincus, Jarujinia, Madascincus, Melanoseps, Mesoscincus, Nessia, Ophiomorus, Pamelaescincus, Paracontias, Plestiodon, Proscelotes, Pseudoacontias, Pygomeles, Scelotes, Scincopus, Scincus, Scolecoseps, Sepsina, Sepsophis, Sirenoscincus, Typhlacontias, Voeltzkowia); Xantusiidae, Cricosaurinae (Cricosaura), Lepidophyminae (Lepidophyma), Xantusiinae (Xantusia)

Lacertoidea (including Amphisbaenia)

Amphisbaenidae (Amphisbaena, Ancylocranium, Baikia, Chirindia, Cynisca, Dalophia, Geocalamus, Loveridgea, Mesobaena, Monopeltis, Zygaspis); Bipedidae (Bipes); Blanidae (Blanus); Cadeidae (Cadea); Gymnophthalmidae, Alopoglossinae (Alopoglossus, Ptychoglossus), Bachiinae (Bachia), Cercosaurinae (Anadia, Cercosaura, Echinosaura, Euspondylus, Macropholidus, Neusticurus, Opipeuter, Petracola, Pholidobolus, Placosoma, Potamites, Proctoporus, Riama, Riolama, Teuchocercus), Ecpleopinae (Adercosaurus, Amapasaurus, Anotosaura, Arthrosaura, Colobosauroides, Dryadosaura, Ecpleopus, Kaieteurosaurus, Leposoma, Marinussaurus, Pantepuisaurus), Gymnophthalminae (Acratosaura, Alexandresaurus, Calyptommatus, Caparaonia, Colobodactylus, Colobosaura, Gymnophthalmus, Heterodactylus, Iphisa, Micrablepharus, Nothobachia, Procellosaurinus, Psilophthalmus, Scriptosaura, Stenolepis, Tretioscincus, Vanzosaura), Rhachisaurinae (Rhachisaurus); Lacertidae, Gallotiinae (Gallotia, Psammodromus), Lacertinae (Acanthodactylus, Adolfus, Algyroides, Anatololacerta, Apathya, Archaeolacerta, Atlantolacerta, Australolacerta, Congolacerta, Dalmatolacerta, Darevskia, Dinarolacerta, Eremias, Gastropholis, Heliobolus, Hellenolacerta, Holaspis, Iberolacerta, Ichnotropis, Iranolacerta, Lacerta, Latastia, Meroles, Mesalina, Nucras, Omanosaura, Ophisops, Parvilacerta, Pedioplanis, Philochortus, Phoenicolacerta, Podarcis, Poromera, Pseuderemias, Scelarcis, Takydromus, Teira, Timon, Tropidosaura, Zootoca); Rhineuridae (Rhineura); Teiidae, Teiinae (Ameiva, Aspidoscelis, Cnemidophorus, Dicrodon, Kentropyx, Teius), Tupinambinae (Callopistes, Crocodilurus, Dracaena, Tupinambis); Trogonophiidae (Agamodon, Diplometopon, Pachycalamus, Trogonophis)

Iguania

Agamidae, Agaminae (Acanthocercus, Agama, Brachysaura, Bufoniceps, Laudakia, Phrynocephalus, Pseudotrapelus, Trapelus, Xenagama), Amphibolurinae (Amphibolurus, Chelosania, Chlamydosaurus, Cryptagama, Ctenophorus, Diporiphora, Hypsilurus, Intellagama, Lophognathus, Moloch, Physignathus, Pogona, Rankinia, Tympanocryptis), Draconinae (Acanthosaura, Aphaniotis, Bronchocela, Calotes, Ceratophora, Complicitus, Cophotis, Coryphophylax, Dendragama, Draco, Gonocephalus, Harpesaurus, Hypsicalotes, Japalura, Lophocalotes, Lyriocephalus, Mantheyus, Oriocalotes, Otocryptis, Phoxophrys, Psammophilus, Pseudocalotes, Pseudocophotis, Ptyctolaemus, Salea, Sitana, Thaumatorhynchus), Hydrosaurinae (Hydrosaurus), Leiolepidinae (Leiolepis),

Uromastycinae (Uromastyx); Chamaeleonidae, Brookesiinae (Brookesia), Chamaeleoninae (Archaius, Bradypodion, Calumma, Chamaeleo, Furcifer, Kinyongia, Nadzikambia, Rhampholeon, Rieppeleon, Trioceros); Corytophanidae (Basiliscus, Corytophanes, Laemanctus); Crotaphytidae (Crotaphytus, Gambelia); Dactyloidae (Anolis); Hoplocercidae (Enyalioides, Hoplocercus, Morunasaurus); Iguanidae (Amblyrhynchus, Brachylophus, Conolophus, Ctenosaura, Cyclura, Dipsosaurus, Iguana, Sauromalus); Leiocephalidae (Leiocephalus); Leiosauridae, Enyaliinae (Anisolepis, Enyalius, Urostrophus), Leiosaurinae (Diplolaemus, Leiosaurus, Pristidactylus); Liolaemidae (Ctenoblepharys, Liolaemus, Phymaturus); Opluridae (Chalarodon, Oplurus); Phrynosomatidae (Callisaurus, Cophosaurus, Holbrookia, Petrosaurus, Phrynosoma, Sceloporus, Uma, Urosaurus, Uta); Polychrotidae (Polychrus); Tropiduridae (Eurolophosaurus, Microlophus, Plica, Stenocercus, Strobilurus, Tropidurus, Uracentron, Uranoscodon)

Anguimorpha

Anguidae, Anguinae (Anguis, Dopasia, Ophisaurus, Pseudopus), Diploglossinae (Celestus, Diploglossus, Ophiodes), Gerrhonotinae (Abronia, Barisia, Coloptychon, Elgaria, Gerrhonotus, Mesaspis); Anniellidae (Anniella); Helodermatidae (Heloderma); Lanthanotidae (Lanthanotus); Shinisauridae (Shinisaurus); Varanidae (Varanus); Xenosauridae (Xenosaurus)

Serpentes

Acrochordidae (Acrochordus); Aniliidae (Anilius); Anomalepididae (Anomalepis, Helminthophis, Liotyphlops, Typhlophis); Anomochilidae (Anomochilus); Boidae, Boinae (Boa, Corallus, Epicrates, Eunectes), Candoiinae (Candoia), Erycinae (Eryx), Sanziniinae (Acrantophis, Sanzinia), Ungaliophiinae (Charina, Exiliboa, Lichanura, Ungaliophis); Bolyeriidae (Bolyeria, Casarea); Calabariidae (Calabaria); Colubridae incertae sedis (Blythia, Cyclocorus, Elapoidis, Gongylosoma, Helophis, Myersophis, Oreocalamus, Poecilopholis, Rhabdops, Tetralepis), Calamariinae (Calamaria, Calamorhabdium, Collorhabdium, Etheridgeum, Macrocalamus, Pseudorabdion, Rabdion), Colubrinae (Aeluroglena, Ahaetulla, Aprosdoketophis, Archelaphe, Argyrogena, Arizona, Bamanophis, Bogertophis, Boiga, Cemophora, Chilomeniscus, Chionactis, Chironius, Chrysopelea, Coelognathus, Coluber, Colubroelaps, Conopsis, Coronella, Crotaphopeltis, Cyclophiops, Dasypeltis, Dendrelaphis, Dendrophidion, Dipsadoboa, Dispholidus, Dolichophis, Drymarchon, Drymobius, Drymoluber, Dryocalamus, Dryophiops, Eirenis, Elachistodon, Elaphe, Euprepiophis, Ficimia, Geagras, Gonyophis, Gonyosoma, Gyalopion, Hapsidophrys, Hemerophis, Hemorrhois, Hierophis, Lampropeltis, Leptodrymus, Leptophis, Lepturophis, Limnophis, Liopeltis, Lycodon, Lytorhynchus, Macroprotodon, Mastigodryas, Meizodon, Oligodon, Oocatochus, Opheodrys, Oreocryptophis, Orthriophis, Oxybelis, Pantherophis, Philothamnus, Phyllorhynchus, Pituophis, Platyceps, Pseudelaphe, Pseudoficimia, Pseustes, Ptyas, Rhadinophis, Rhamnophis, Rhinechis, Rhinobothryum, Rhinocheilus, Rhynchocalamus, Rhynchophis, Salvadora, Scaphiophis, Scolecophis, Senticolis, Simophis, Sonora, Spalerosophis, Spilotes, Stegonotus, Stenorrhina, Symphimus, Sympholis, Tantilla, Tantillita, Telescopus, Thelotornis, Thrasops, Toxicodryas, Trimorphodon, Xenelaphis, Xyelodontophis, Zamenis), Dipsadinae (Adelphicos, Alsophis, Amastridium, Amnesteophis, Antillophis, Apostolepis, Arrhyton, Atractus, Boiruna, Borikenophis, Caaeteboia, Calamodontophis, Caraiba, Carphophis, Cercophis, Chapinophis, Chersodromus, Clelia, Coniophanes, Conophis, Contia, Coronelaps, Crisantophis, Cryophis, Cubophis,

Darlingtonia, Diadophis, Diaphorolepis, Dipsas, Ditaxodon, Drepanoides, Echinanthera, Elapomorphus, Emmochliophis, Enuliophis, Enulius, Erythrolamprus, Farancia, Geophis, Gomesophis, Haitiophis, Helicops, Heterodon, Hydrodynastes, Hydromorphus, Hydrops, Hypsiglena, Hypsirhynchus, Ialtris, Imantodes, Leptodeira, Lioheterophis, Lygophis, Magliophis, Manolepis, Mussurana, Ninia, Nothopsis, Ocyophis, Omoadiphas, Oxyrhopus, Paraphimophis, Phalotris, Philodryas, Phimophis, Plesiodipsas, Pliocercus, Pseudalsophis, Pseudoboa, Pseudoeryx, Pseudoleptodeira, Pseudotomodon, Psomophis, Ptychophis, Rhachidelus, Rhadinaea, Rhadinella, Rhadinophanes, Rodriguesophis, Saphenophis, Schwartzophis, Sibon, Sibynomorphus, Siphlophis, Sordellina, Synophis, Tachymenis, Taeniophallus, Tantalophis, Thamnodynastes, Thermophis, Tomodon, Tretanorhinus, Trimetopon, Tropidodipsas, Tropidodryas, Uromacer, Uromacerina, Urotheca, Xenodon, Xenopholis), Grayiinae (Grayia), Natricinae (Adelophis, Afronatrix, Amphiesma, Amphiesmoides, Anoplohydrus, Aspidura, Atretium, Balanophis, Clonophis, Hologerrhum, Hydrablabes, Hydraethiops, Iguanognathus, Lycognathophis, Macropisthodon, Natriciteres, Natrix, Nerodia, Opisthotropis, Parahelicops, Pararhabdophis, Paratapinophis, Regina, Rhabdophis, Seminatrix, Sinonatrix, Storeria, Thamnophis, Trachischium, Tropidoclonion, Tropidonophis, Virginia, Xenochrophis), Pseudoxenodontinae (Plagiopholis, Pseudoxenodon), Sibynophiinae (Scaphiodontophis, Sibynophis); Cylindrophiidae (Cylindrophis); Elapidae (Acanthophis, Aipysurus, Aspidelaps, Aspidomorphus, Austrelaps, Bungarus, Cacophis, Calliophis, Cryptophis, Demansia, Dendroaspis, Denisonia, Drysdalia, Echiopsis, Elapognathus, Elapsoidea, Emydocephalus, Ephalophis, Furina, Hemachatus, Hemiaspis, Hemibungarus, Hoplocephalus, Hydrelaps, Hydrophis, Kolpophis, Laticauda, Loveridgelaps, Maticora, Micropechis, Micruroides, Micrurus, Naja, Notechis, Ogmodon, Ophiophagus, Oxyuranus, Parahydrophis, Parapistocalamus, Parasuta, Pseudechis, Pseudohaje, Pseudolaticauda, Pseudonaja, Rhinoplocephalus, Salomonelaps, Simoselaps, Sinomicrurus, Suta, Thalassophis, Toxicocalamus, Tropidechis, Vermicella, Walterinnesia); Gerrhopilidae (Gerrhopilus); Homalopsidae (Bitia, Brachyorrhos, Cantoria, Cerberus, Djokoiskandarus, Enhydris, Erpeton, Fordonia, Gerarda, Heurnia, Homalopsis, Myron, Pseudoferania); Lamprophiidae incertae sedis (Micrelaps, Montaspis, Oxyrhabdium), Aparallactinae (Amblyodipsas, Aparallactus, Brachyophis, Chilorhinophis, Elapotinus, Hypoptophis, Macrelaps, Polemon, Xenocalamus), Atractaspidinae (Atractaspis, Homoroselaps), Lamprophiinae (Boaedon, Bothrophthalmus, Chamaelycus, Dendrolycus, Gonionotophis, Hormonotus, Inyoka, Lamprophis, Lycodonomorphus, Lycophidion, Pseudoboodon), Prosymninae (Prosymna), Psammophiinae (Dipsina, Hemirhagerrhis, Malpolon, Mimophis, Psammophis, Psammophylax, Rhagerhis, Rhamphiophis), Pseudaspidinae (Buhoma, Psammodynastes, Pseudaspis, Pythonodipsas), Pseudoxyrhophiine (Alluaudina, Amplorhinus, Bothrolycus, Brygophis, Compsophis, Ditypophis, Dromicodryas, Duberria, Exallodontophis, Heteroliodon, Ithycyphus, Langaha, Leioheterodon, Liophidium, Liopholidophis, Lycodryas, Madagascarophis, Micropisthodon, Pararhadinaea, Parastenophis, Phisalixella, Pseudoxyrhopus, Thamnosophis); Leptotyphlopidae (Epacrophis, Epictia, Leptotyphlops, Mitophis, Myriopholis, Namibiana, Rena, Rhinoleptus, Siagonodon, Tetracheilostoma, Tricheilostoma, Trilepida); Loxocemidae (Loxocemus); Pareatidae (Aplopeltura, Asthenodipsas, Pareas); Pythonidae (Antaresia, Apodora, Aspidites, Bothrochilus, Broghammerus, Leiopython, Liasis, Morelia, Python); Tropidophiidae (Trachyboa, Tropidophis); Typhlopidae (Acutotyphlops, Afrotyphlops, Austrotyphlops, Cyclotyphlops, Grypotyphlops, Letheobia, Megatyphlops, Ramphotyphlops, Rhinotyphlops, Typhlops); Uropeltidae (Brachyophidium, Melanophidium, Platyplectrurus, Plectrurus, Pseudotyphlops, Rhinophis, Teretrurus, Uropeltis); Viperidae, Azemiopinae (Azemiops), Crotalinae (Agkistrodon, Atropoides, Bothriechis, Bothriopsis, Bothrocophias, Bothropoides, Bothrops, Calloselasma, Cerrophidion, Crotalus, Deinagkistrodon, Garthius,

Gloydius, Hypnale, Lachesis, Mixcoatlus, Ophryacus, Ovophis, Porthidium, Protobothrops, Rhinocerophis, Sistrurus, Trimeresurus, Tropidolaemus), Viperinae (Atheris, Bitis, Causus, Cerastes, Daboia, Echis, Eristicophis, Macrovipera, Montatheris, Montivipera, Proatheris, Pseudocerastes, Vipera); Xenodermatidae (Achalinus, Fimbrios, Stoliczkia, Xenodermus, Xylophis); Xenopeltidae (Xenopeltis); Xenophidiidae (Xenophidion); Xenotyphlopidae (Xenotyphlops)

Additional files

Additional_file_1 as TXT Additional file 1: Data File S1 The 4162-species ML phylogeny in Newick format; taxonomic changes are given in Additional file 2: Table S1.

Additional_file_2 as DOCX Additional file 2: Table S1 GenBank accession numbers for all taxa included in this analysis.

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177. Kelly CMR, Branch WR, Broadley DG, Barker NP, Villet MH: Molecular systematics of the African snake family Lamprophiidae Fitzinger, 1843 (Serpentes: Elapoidea), with particular focus on the genera Lamprophis Fitzinger 1843 and Mehelya Csiki 1903. Mol Phylogenet Evol 2011, 58:415–426.

178. Vidal N, Branch WR, Pauwels OSG, Hedges SB, Broadley DG, Wink M, Cruaud C, Joger U, Nagy ZT: Dissecting the major African snake radiation: a molecular phylogeny of the Lamprophiidae Fitzinger (Serpentes, Caenophidia). Zootaxa 2008, 1945:51–66.

179. Sanders KL, Lee MSY, Leys R, Foster R, Keogh JS: Molecular phylogeny and divergence dates for Australasian elapids and sea snakes (Hydrophiinae): evidence from seven genes for rapid evolutionary radiations. J Evol Biol 2008, 21:682–695.

180. Sanders KL, Lee MSY: Molecular evidence for a rapid late-Miocene radiation of Australasian venomous snakes (Elapidae, Colubroidea). Mol Phylogenet Evol 2008, 46:1165–1173.

181. Chen X, Huang S, Guo P, Colli GR, de Oca AN M, Vitt LJ, Pyron RA, Burbrink FT: Understanding the formation of ancient intertropical disjunct distributions using Asian and Neotropical hinged-teeth snakes (Sibynophis and Scaphiodontophis: Serpentes: Colubridae). Mol Phylogenet Evol 2012, 66:254–261.

182. Huang S, Liu SY, Guo P, Zhang YP, Zhao EM: What are the closest relatives of the hot-spring snakes (Colubridae, Thermophis), the relict species endemic to the Tibetan Plateau? Mol Phylogenet Evol 2009, 51:438–446.

183. He M, Feng JC, Liu SY, Guo P, Zhao EM: The phylogenetic position of Thermophis (Serpentes: Colubridae), an endemic snake from the Qinghai-Xizang Plateau, China. J Nat Hist 2009, 43:479–488.

184. Socha JJ: Gliding flight in Chrysopelea: turning a snake into a wing. Integr Comp Biol 2011, 51:969–982.

185. Helfenberger N: Phylogenetic relationship of Old World ratsnakes based on visceral organ topography, osteology, and allozyme variation. Russ J Herp 2001, 8:1–56.

186. Alfaro ME, Arnold SJ: Molecular systematics and evolution of Regina and the Thamnophiine snakes. Mol Phylogenet Evol 2001, 21:408–423.

187. de Queiroz A, Lawson R, Lemos-Espinal JA: Phylogenetic relationships of North American garter snakes (Thamnophis) based on four mitochondrial genes: How much DNA sequence is enough? Mol Phylogenet Evol 2002, 22:315–329.

188. Cope ED: Eleventh contribution to the herpetology of tropical America: Dugés, A. Proc Amer Philos Soc 1879, 18:261–277.

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0.2 subst./site

Scincidae

Xantusiidae

Gerrhosauridae

Teiidae

Gymnophthalmidae

Lacertidae

Anguidae

Chamaeleonidae

Agamidae

Leiosauridae

Boidae

Viperidae

Colubridae

Lamprophiidae

A

B

C

D

E

F

G

A) Gekkota

B) Scincoidea

C) Episquamata

D) Lacertoidea

E) Toxicofera

F) Anguimorpha

G) Iguania

H) Serpentes

H

Dipsadinae

Gekkonidae

Cercosaurinae

Acontiinae

Lacertinae

Hydrosaurinae

Xenodermatidae

Anniellidae

Crotaphytidae

Hoplocercidae

Sphenodontidae

Leiolepidinae

Polychrotidae

Pseudoxyrhophiinae

Loxocemidae

Dibamidae

Prosymninae

Lygosominae

Natricinae

Xantusiinae

Tropiduridae

Corytophanidae

Ecpleopinae

Anomochilidae

Amphisbaenidae

Leiosaurinae

Xenophiidae

Scincinae

Draconinae

Bipedidae

Gerrhosaurinae

Rhineuridae

Anomalepididae

Trogonophiidae

Aniliidae

Azemiopinae

Alopoglossinae

Lanthanotidae

Pseudaspidinae

Tupinambinae

Xenotyphlopidae

Blanidae

Gerrhopilidae

Liolaemidae

Candoiinae

Gallotiinae

Leptotyphlopidae

Platysaurinae

Pythonidae

Boinae

Colubrinae

Opluridae

Elapidae

Typhlopidae

Pareatidae

Cadeidae

Crotalinae

Sibynophiinae

Chamaeleoninae

Rhachisaurinae

Grayiinae

Ungaliophiinae

Erycinae

Phyllodactylidae

Anguinae

Helodermatidae

Phrynosomatidae

Sanziniinae

Tropidophiidae

Viperinae

Cricosaurinae

Shinisauridae

Teiinae

Diplodactylidae

Cylindrophiidae

Brookesiinae

Lepidophyminae

Enyaliinae

Varanidae

Bachiinae

Aparallactinae

Sphaerodactylidae

Atractaspidinae

Uropeltidae

LeiocephalidaeIguanidae

Homalopsidae

Amphibolurinae

Xenopeltidae

Diploglossinae

Calamariinae

Xenosauridae

Uromasticinae

Agaminae

Acrochordidae

Pygopodidae

Calabariidae

Psammophiinae

Carphodactylidae

Cordylinae

Gymnophthalminae

Pseudoxenodontinae

Bolyeriidae

Dactyloidae

Gerrhonotinae

Eublepharidae

Lamprophiinae

Zonosaurinae

83

98

100

100

98

99

100

99

100

99

83

54

98

99

84

100

68

100

100

95

100

94

63

84

71

90

100

100

100

100

100

81

100

100

100

100

87

9969

90

100

100

88

65

97

72

89

100

90

100

100

100

100

96

100

100

96

100

94

100

95

100

97

100

100

100

100

100

100

100

100

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100

77

100

74

100

95

95

100

99

95

54

100

95

96

79

95

100

99

87

100

100

100

Squamata

Cordylidae

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BTarentola gigas

Tarentola caboverdianaTarentola rudis

Tarentola darwiniTarentola chazaliae

Tarentola delalandiiTarentola gomerensis

Tarentola annularisTarentola ephippiata

Tarentola boettgeriTarentola mindiae

Tarentola neglectaTarentola angustimentalisTarentola mauritanica

Tarentola desertiTarentola boehmei

Tarentola americanaPhyllopezus maranjonensis

Phyllopezus lutzaePhyllopezus pollicaris

Phyllopezus periosusPhyllodactylus homolepidurus

Phyllodactylus davisiPhyllodactylus duellmani

Phyllodactylus delcampoiPhyllodactylus paucituberculatus

Phyllodactylus nocticolusPhyllodactylus bugastrolepisPhyllodactylus unctus

Phyllodactylus xantiPhyllodactylus bordai

Phyllodactylus laneiPhyllodactylus tuberculosus

Phyllodactylus reissiiPhyllodactylus wirshingi

Homonota andicolaHomonota darwinii

Homonota borelliiHomonota underwoodi

Homonota fasciataHomonota gaudichaudii

Ptyodactylus guttatusPtyodactylus hasselquistii

Ptyodactylus oudriiPtyodactylus ragazzii

Asaccus platyrhynchusHaemodracon riebeckii

Thecadactylus rapicaudaThecadactylus solimoensis

Sphaerodactylus nicholsiSphaerodactylus ocoae

Sphaerodactylus gaigeaeSphaerodactylus klauberi

Sphaerodactylus semasiopsSphaerodactylus goniorhynchus

Sphaerodactylus townsendiSphaerodactylus armstrongi

Sphaerodactylus macrolepisSphaerodactylus argus

Sphaerodactylus rooseveltiSphaerodactylus altavelensis

Sphaerodactylus notatusSphaerodactylus darlingtoni

Sphaerodactylus cryphiusSphaerodactylus shrevei

Sphaerodactylus elegansSphaerodactylus leucaster

Sphaerodactylus copeiSphaerodactylus nigropunctatus

Sphaerodactylus intermediusSphaerodactylus torrei

Sphaerodactylus cinereusSphaerodactylus thompsoni

Sphaerodactylus glaucusSphaerodactylus molei

Sphaerodactylus oliveriSphaerodactylus richardi

Sphaerodactylus cricoderusSphaerodactylus ramsdeni

Sphaerodactylus schwartziSphaerodactylus kirbyiSphaerodactylus vincenti

Sphaerodactylus microlepisSphaerodactylus parvus

Sphaerodactylus sabanusSphaerodactylus elegantulus

Sphaerodactylus sputatorSphaerodactylus fantasticus

Pseudogonatodes guianensisPseudogonatodes lunulatus

Pseudogonatodes manessiColeodactylus natalensis

Coleodactylus meridionalisColeodactylus brachystoma

Coleodactylus septentrionalisGonatodes ocellatusGonatodes ceciliaeGonatodes seigliei

Gonatodes concinnatusGonatodes antillensis

Gonatodes humeralisGonatodes falconensis

Gonatodes taniaeGonatodes purpurogularis

Gonatodes alexandermendesiGonatodes superciliaris

Gonatodes annularisGonatodes hasemani

Gonatodes infernalisGonatodes vittatus

Gonatodes petersiGonatodes albogularis

Gonatodes daudiniGonatodes caudiscutatus

Gonatodes eladioiLepidoblepharis festae

Lepidoblepharis xanthostigmaChatogekko amazonicus

Saurodactylus mauritanicusTeratoscincus roborowskii

Teratoscincus przewalskiiTeratoscincus scincusTeratoscincus microlepisEuleptes europaea

Saurodactylus fasciatusAristelliger georgeensis

Aristelliger praesignisAristelliger lar

Quedenfeldtia moerensQuedenfeldtia trachyblepharus

Pristurus somalicusPristurus crucifer

Pristurus carteriPristurus minimusPristurus rupestrisPristurus flavipunctatus

Pristurus abdelkuriPristurus guichardi

Pristurus sokotranusPristurus insignis

Pristurus celerrimusGoniurosaurus araneus

Goniurosaurus luiiGoniurosaurus catbaensis

Goniurosaurus lichtenfelderiGoniurosaurus kuroiwae

Hemitheconyx tayloriHemitheconyx caudicinctus

Holodactylus africanusEublepharis turcmenicusEublepharis macularius

Coleonyx elegansColeonyx mitratus

Coleonyx variegatusColeonyx brevis

Aeluroscalabotes felinus

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Eublepharidae

Sphaerodactylidae

CFigure 3

CPhelsuma kely

Phelsuma lineataPhelsuma comorensis

Phelsuma pusillaPhelsuma quadriocellata

Phelsuma antanosyPhelsuma klemmeri

Phelsuma robertmertensiPhelsuma laticaudaPhelsuma serraticaudaPhelsuma malamakibo

Phelsuma berghofiPhelsuma hielscheriPhelsuma flavigularis

Phelsuma ravenalaPhelsuma dubiaPhelsuma modesta

Phelsuma nigristriataPhelsuma inexpectata

Phelsuma ornataPhelsuma guimbeaui

Phelsuma cepedianaPhelsuma borbonica

Phelsuma guentheriPhelsuma gigas

Phelsuma edwardnewtoniPhelsuma standingi

Phelsuma andamanensePhelsuma mutabilis

Phelsuma brevicepsPhelsuma pronkiPhelsuma barbouri

Phelsuma seippiPhelsuma parkeri

Phelsuma abbottiPhelsuma madagascariensis

Phelsuma guttataPhelsuma sundbergiPhelsuma astriata

Phelsuma vanheygeniLygodactylus keniensis

Lygodactylus kimhowelliLygodactylus luteopicturatusLygodactylus picturatus

Lygodactylus williamsiLygodactylus chobiensis

Lygodactylus gutturalisLygodactylus angularis

Lygodactylus thomensisLygodactylus conraui

Lygodactylus klugeiLygodactylus bradfieldiLygodactylus capensisLygodactylus stevensoni

Lygodactylus lawrenceiLygodactylus pictus

Lygodactylus mirabilisLygodactylus tuberosus

Lygodactylus montanusLygodactylus gravis

Lygodactylus paulianiLygodactylus arnoulti

Lygodactylus blancaeLygodactylus verticillatusLygodactylus heterurus

Lygodactylus tolampyaeLygodactylus guibei

Lygodactylus miopsLygodactylus madagascariensis

Lygodactylus rarusLygodactylus expectatus

Rhoptropella ocellataCnemaspis tropidogaster

Cnemaspis kandianaCnemaspis podihuna

Pachydactylus affinisPachydactylus vansoni

Pachydactylus capensisPachydactylus oshaughnessyi

Pachydactylus tigrinusPachydactylus montanus

Pachydactylus vanzyliPachydactylus rangei

Pachydactylus austeniPachydactylus mariquensis

Pachydactylus mclachlaniPachydactylus monicaePachydactylus weberi

Pachydactylus servalPachydactylus griffini

Pachydactylus carinatusPachydactylus fasciatus

Pachydactylus tsodiloensisPachydactylus waterbergensis

Pachydactylus purcelliPachydactylus oculatus

Pachydactylus maculatusPachydactylus geitje

Pachydactylus labialisPachydactylus barnardi

Pachydactylus formosusPachydactylus rugosus

Pachydactylus punctatusPachydactylus scherzi

Pachydactylus sansteynaePachydactylus caraculicus

Pachydactylus bicolorPachydactylus oreophilus

Pachydactylus gaiasensisPachydactylus reconditus

Pachydactylus parascutatusPachydactylus scutatus

Pachydactylus namaquensisPachydactylus kladaroderma

Pachydactylus haackeiColopus kochii

Colopus wahlbergiiPachydactylus robertsi

Chondrodactylus bibroniiChondrodactylus fitzsimonsi

Chondrodactylus turneriPachydactylus laevigatus

Chondrodactylus anguliferElasmodactylus tuberculosus

Elasmodactylus tetensisRhoptropus barnardi

Rhoptropus biporosusRhoptropus boultoni

Rhoptropus bradfieldiRhoptropus afer

Goggia lineataBlaesodactylus sakalava

Blaesodactylus antongilensisBlaesodactylus boiviniHomopholis mulleri

Homopholis walbergiiHomopholis fasciataGeckolepis maculataGeckolepis typica

Afroedura karroicaAfroedura pondolia

Afrogecko porphyreusMatoatoa brevipes

Cryptactites peringueyiAfrogecko swartbergensis

Christinus marmoratusParagehyra gabriellae

Uroplatus fimbriatusUroplatus giganteus

Uroplatus henkeliUroplatus sikorae

Uroplatus lineatusUroplatus pietschmanni

Uroplatus alluaudiUroplatus phantasticus

Uroplatus ebenauiUroplatus malama

Uroplatus malaheloUroplatus guentheri

Cnemaspis africanaCnemaspis dickersonae

Cnemaspis uzungwaeNarudasia festiva

Ptenopus carpiCalodactylodes aureusCalodactylodes illingworthorum

Ailuronyx trachygasterAiluronyx seychellensis

Ailuronyx tachyscopaeusParoedura bastardi

Paroedura tanjakaParoedura vazimba

Paroedura androyensisParoedura picta

Paroedura sanctijohannisParoedura stumpffi

Paroedura lohatsaraParoedura karstophila

Paroedura ovicepsParoedura homalorhina

Paroedura gracilisParoedura masobe

Ebenavia inunguisUrocotyledon inexpectata

Perochirus ateles

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Hemidactylus homoeolepisHemidactylus forbesii

Hemidactylus oxyrhinusHemidactylus macropholis

Hemidactylus mindiaeHemidactylus lemurinus

Hemidactylus turcicusHemidactylus robustus

Hemidactylus yerburiiHemidactylus persicus

Hemidactylus grantiHemidactylus dracaenacolus

Hemidactylus pumilioHemidactylus foudaii

Hemidactylus citerniiHemidactylus modestus

Hemidactylus agriusHemidactylus palaichthusHemidactylus bouvieri

Hemidactylus brasilianusHemidactylus greeffiiHemidactylus platycephalus

Hemidactylus longicephalusHemidactylus mercatoriusHemidactylus mabouia

Hemidactylus haitianusHemidactylus angulatus

Hemidactylus gracilisHemidactylus reticulatus

Hemidactylus albofasciatusHemidactylus imbricatus

Hemidactylus sataraensisHemidactylus brookii

Hemidactylus frenatusHemidactylus flaviviridis

Hemidactylus leschenaultiiHemidactylus maculatus

Hemidactylus prashadiHemidactylus triedrus

Hemidactylus depressusHemidactylus giganteus

Hemidactylus aaronbaueriHemidactylus fasciatus

Hemidactylus platyurusHemidactylus karenorum

Hemidactylus garnotiiHemidactylus bowringii

Cyrtodactylus louisiadensisCyrtodactylus epiroticusCyrtodactylus tripartitus

Cyrtodactylus robustusCyrtodactylus klugei

Cyrtodactylus tuberculatusCyrtodactylus novaeguineae

Cyrtodactylus loriaeCyrtodactylus sermowaiensis

Cyrtodactylus pulchellusCyrtodactylus intermedius

Cyrtodactylus agusanensisCyrtodactylus philippinicus

Cyrtodactylus annulatusCyrtodactylus consobrinus

Cyrtodactylus irregularisCyrtodactylus marmoratus

Cyrtodactylus triedrusCyrtodactylus jarujini

Cyrtodactylus angularisCyrtodactylus ayeyarwadyensis

Cyrtodactylus oldhamiCyrtopodion gastropholeCyrtopodion agamuroides

Cyrtopodion caspiumCyrtopodion longipes

Cyrtopodion scabrumCyrtopodion sistanensis

Agamura persicaBunopus crassicauda

Crossobamon orientalisBunopus tuberculatus

Mediodactylus heteropholisMediodactylus heterocercum

Mediodactylus sagittiferumMediodactylus kotschyi

Stenodactylus sthenodactylusStenodactylus yemenensis

Stenodactylus doriaeStenodactylus leptocosymbotus

Stenodactylus petriiStenodactylus arabicus

Tropiocolotes tripolitanusPseudoceramodactylus khobarensis

Mediodactylus russowiiMediodactylus spinicaudum

Cnemaspis kendalliiCnemaspis limi

Tropiocolotes helenaeAlsophylax pipiens

Gehyra minutaGehyra montium

Gehyra pilbaraGehyra punctata

Gehyra variegataGehyra purpurascensGehyra nana

Gehyra xenopusGehyra australis

Gehyra occidentalisGehyra koira

Gehyra robustaGehyra borroloola

Gehyra pamelaGehyra catenata

Gehyra dubiaGehyra membranacruralis

Gehyra oceanicaGehyra marginata

Gehyra bareaGehyra baliola

Gehyra brevipalmataGehyra lacerata

Gehyra mutilataGehyra fehlmanni

Hemiphyllodactylus aurantiacusHemiphyllodactylus yunnanensis

Hemiphyllodactylus typusNactus pelagicusNactus multicarinatus

Nactus chevertiNactus galgajuga

Nactus vankampeniNactus eboracensisNactus acutus

Heteronotia speleaHeteronotia binoeiHeteronotia planiceps

Dixonius siamensisDixonius vietnamensis

Dixonius melanostictusGekko grossmanni

Gekko badeniiGekko petricolus

Gekko vittatusLuperosaurus iskandari

Ptychozoon lionotumPtychozoon kuhli

Ptychozoon rhacophorusGekko porosusGekko crombota

Gekko romblonGekko mindorensis

Gekko monarchusGekko athymus

Gekko swinhonisGekko auriverrucosus

Gekko hokouensisGekko japonicus

Gekko chinensisGekko gecko

Gekko smithiiLepidodactylus moestusLepidodactylus lugubris

Luperosaurus joloensisLuperosaurus cumingii

Luperosaurus macgregoriLepidodactylus orientalis

Pseudogekko compressicorpusPseudogekko smaragdinus

Lepidodactylus novaeguineae

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ae

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Figure 4

DCordylus cordylusCordylus tasmani

Cordylus oelofseniCordylus mclachlani

Cordylus nigerCordylus minorCordylus aridusCordylus imkeae

Cordylus macropholisCordylus rhodesianus

Cordylus jonesiiCordylus beraducciiCordylus ukingensisCordylus vittifer

Cordylus meculaeCordylus tropidosternum

Hemicordylus capensisHemicordylus nebulosusNinurta coeruleopunctatusPseudocordylus melanotusPseudocordylus spinosus

Pseudocordylus microlepidotusPseudocordylus langi

Chamaesaura anguinaChamaesaura aenea

Smaug giganteusSmaug warreni

Namazonurus peersiNamazonurus lawrenci

Namazonurus namaquensisNamazonurus pustulatus

Namazonurus campbelliKarusasaurus polyzonus

Karusasaurus jordaniOuroborus cataphractus

Platysaurus monotropisPlatysaurus minor

Platysaurus intermediusPlatysaurus capensis

Platysaurus broadleyiPlatysaurus mitchelli

Platysaurus pungweensisZonosaurus rufipes

Zonosaurus aeneusZonosaurus bemaraha

Zonosaurus subunicolorZonosaurus brygooiZonosaurus tsingy

Zonosaurus boettgeriZonosaurus laticaudatus

Zonosaurus anelanelanyZonosaurus karsteni

Zonosaurus quadrilineatusZonosaurus trilineatus

Zonosaurus ornatusZonosaurus madagascariensis

Zonosaurus haraldmeieriTracheloptychus petersi

Tracheloptychus madagascariensisGerrhosaurus flavigularis

Gerrhosaurus multilineatusGerrhosaurus nigrolineatus

Gerrhosaurus typicusGerrhosaurus skoogi

Gerrhosaurus validusTetradactylus tetradactylus

Tetradactylus africanusTetradactylus seps

Cordylosaurus subtessellatusGerrhosaurus major

Lepidophyma dontomasiLepidophyma radula

Lepidophyma loweiLepidophyma cuicatecaLepidophyma smithii

Lepidophyma lineriLepidophyma gaigeae

Lepidophyma sylvaticumLepidophyma micropholis

Lepidophyma occulorLepidophyma pajapanensis

Lepidophyma reticulatumLepidophyma flavimaculatumLepidophyma lipetziLepidophyma tuxtlae

Lepidophyma mayaeXantusia wigginsi

Xantusia bezyiXantusia vigilis

Xantusia arizonaeXantusia riversiana

Xantusia sancheziXantusia bolsonaeXantusia henshawi

Xantusia gracilisCricosaura typica

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Platysaurinae

Cordylinae

Cordylidae

Gerrhosauridae

Gerrhosaurinae

Zonosaurinae

Lepidophyminae

Xantusiinae

Cricosaurinae

Xantusiidae

Figure 5

EAmphiglossus frontoparietalisAmphiglossus punctatus

Amphiglossus macrocercusAmphiglossus anosyensis

Amphiglossus splendidusVoeltzkowia rubrocaudataVoeltzkowia lineata

Voeltzkowia fierinensisAmphiglossus astrolabi

Amphiglossus reticulatusAmphiglossus tsaratananensis

Androngo trivittatusPygomeles braconnieri

Amphiglossus tanysomaAmphiglossus mandokava

Amphiglossus ornaticepsAmphiglossus melanurus

Madascincus intermediusMadascincus polleni

Madascincus stumpffiMadascincus nanus

Madascincus mouroundavaeMadascincus igneocaudatus

Pseudoacontias menamaintyMadascincus melanopleura

Paracontias rothschildiParacontias hildebrandti

Paracontias manifyParacontias brocchii

Paracontias holomelasScelotes kasneri

Scelotes montispectusScelotes gronovii

Scelotes sexlineatusScelotes bipes

Scelotes arenicolusScelotes mirus

Scelotes anguineusScelotes caffer

Proscelotes eggeliHakaria simonyi

Melanoseps loveridgeiMelanoseps ater

Melanoseps occidentalisFeylinia currori

Feylinia polylepisFeylinia grandisquamis

Typhlacontias punctatissimusTyphlacontias brevipes

Sepsina angolensisChalcides montanus

Chalcides polylepisChalcides manueli

Chalcides mionectonChalcides sphenopsiformis

Chalcides viridanusChalcides coeruleopunctatus

Chalcides sexlineatusChalcides lanzaiChalcides parallelus

Chalcides boulengeriChalcides bedriagaiChalcides colosii

Chalcides sepsoidesChalcides ocellatus

Chalcides striatusChalcides pseudostriatusChalcides chalcides

Chalcides guentheriChalcides minutus

Chalcides mauritanicusGongylomorphus bojerii

Janetaescincus braueriJanetaescincus veseyfitzgeraldi

Pamelaescincus gardineriScincus mitranusScincus scincus

Eumeces algeriensisScincopus fasciatus

Eumeces schneideriEurylepis taeniolatus

Plestiodon dugesiiPlestiodon brevirostris

Plestiodon copeiPlestiodon parvulus

Plestiodon ochoterenaePlestiodon lynxe

Plestiodon sumichrastiPlestiodon parviauriculatus

Plestiodon skiltonianusPlestiodon lagunensis

Plestiodon gilbertiPlestiodon longirostris

Plestiodon septentrionalisPlestiodon multivirgatus

Plestiodon fasciatusPlestiodon obsoletus

Plestiodon callicephalusPlestiodon tetragrammus

Plestiodon laticepsPlestiodon inexpectatus

Plestiodon anthracinusPlestiodon egregius

Plestiodon reynoldsiPlestiodon stimpsonii

Plestiodon marginatusPlestiodon elegans

Plestiodon latiscutatusPlestiodon japonicusPlestiodon barbouri

Plestiodon capitoPlestiodon tunganus

Plestiodon quadrilineatusPlestiodon chinensis

Plestiodon kishinouyeiPlestiodon tamdaoensis

Brachymeles pathfinderiBrachymeles gracilis

Brachymeles bicolorBrachymeles boulengeri

Brachymeles schadenbergiBrachymeles eleraeBrachymeles talinis

Brachymeles samarensisBrachymeles cebuensis

Brachymeles minimusBrachymeles bonitae

Brachymeles tridactylusBrachymeles miriamae

Brachymeles apusOphiomorus latastiiOphiomorus punctatissimus

Mesoscincus managuaeMesoscincus schwartzei

Acontias poecilusAcontias plumbeus

Acontias gracilicaudaAcontias breviceps

Acontias rieppeliAcontias percivali

Acontias meleagrisAcontias kgalagadi

Acontias litoralisAcontias lineatus

Acontias gariepensisTyphlosaurus lomiaeTyphlosaurus vermisTyphlosaurus caecusTyphlosaurus meyeri

Typhlosaurus braini

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Scincidae

Acontiinae

Scincinae

F-I

Figure 6

Lygosominae

Lygosominae

cont.FPapuascincus stanleyanus

Lipinia noctua

Lipinia pulchella

Insulasaurus victoria

Insulasaurus wrighti

Insulasaurus arborens

Prasinohaema virens

Sphenomorphus buenloicus

Scincella assatus

Scincella cherriei

Scincella gemmingeri

Scincella lateralis

Asymblepharus sikimmensis

Scincella reevesii

Sphenomorphus sabanus

Sphenomorphus cyanolaemus

Sphenomorphus variegatus

Sphenomorphus multisquamatus

Sphenomorphus indicus

Sphenomorphus maculatus

Larutia seribuatensis

Parvoscincus lawtoni

Parvoscincus kitangladensis

Parvoscincus luzonense

Parvoscincus laterimaculatus

Parvoscincus beyeri

Parvoscincus sisoni

Parvoscincus tagapayo

Parvoscincus leucospilos

Parvoscincus decipiens

Parvoscincus steerei

Sphenomorphus acutus

Sphenomorphus diwata

Pinoyscincus llanosi

Pinoyscincus abdictus

Pinoyscincus coxi

Pinoyscincus jagori

Pinoyscincus mindanensis

Otosaurus cumingi

Sphenomorphus maindroni

Sphenomorphus cranei

Sphenomorphus leptofasciatus

Sphenomorphus fasciatus

Sphenomorphus solomonis

Sphenomorphus scutatus

Sphenomorphus concinnatus

Tytthoscincus atrigularis

Tytthoscincus hallieri

Tytthoscincus parvus

Tytthoscincus aesculeticola

Sphenomorphus muelleri

Sphenomorphus jobiensis

Sphenomorphus melanopogon

Isopachys anguinoides

Lipinia vittigera

Tropidophorus misaminius

Tropidophorus partelloi

Tropidophorus brookei

Tropidophorus beccarii

Tropidophorus baconi

Tropidophorus grayi

Tropidophorus microlepis

Tropidophorus cocincinensis

Tropidophorus thai

Tropidophorus robinsoni

Tropidophorus sinicus

Tropidophorus baviensis

Tropidophorus hainanus

Tropidophorus murphyi

Tropidophorus noggei

Tropidophorus latiscutatus

Tropidophorus matsuii

Tropidophorus berdmorei

Sphenomorphus simus

Sphenomorphus praesignis

Ablepharus pannonicus

Asymblepharus alaicus

Ateuchosaurus pellopleurus

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Lerista kennedyensisLerista onsloviana

Lerista uniduoLerista connivens

Lerista variaLerista lineopunctulata

Lerista yunaLerista kendricki

Lerista nichollsiLerista gascoynensis

Lerista petersoniLerista humphriesi

Lerista praepeditaLerista bougainvillii

Lerista viduataLerista muelleri

Lerista haroldiLerista allochira

Lerista stictopleuraLerista planiventralis

Lerista lineataLerista christinae

Lerista distinguendaLerista elegans

Lerista emmottiLerista punctatovittata

Lerista dorsalisLerista terdigitata

Lerista tridactylaLerista elongata

Lerista speciosaLerista zietzi

Lerista flammicaudaLerista picturata

Lerista baynesiLerista edwardsae

Lerista arenicolaLerista microtis

Lerista macropisthopusLerista axillaris

Lerista gerrardiiLerista eupoda

Lerista desertorumLerista puncticaudaLerista neander

Lerista zonulataLerista ingrami

Lerista orientalisLerista taeniata

Lerista aericepsLerista xanthura

Lerista chordaeLerista fragilis

Lerista frostiLerista borealis

Lerista walkeriLerista simillima

Lerista vermicularisLerista robusta

Lerista greeriLerista labialis

Lerista bipesLerista ips

Lerista griffiniLerista apoda

Lerista kalumburuLerista wilkinsiLerista cinerea

Lerista amelesLerista carpentariae

Lerista karlschmidtiLerista stylis

Ctenotus pulchellusCtenotus gagudju

Ctenotus hilliCtenotus hebetior

Ctenotus essingtoniiCtenotus piankai

Ctenotus hanloniCtenotus angusticeps

Ctenotus grandisCtenotus atlas

Ctenotus maryaniCtenotus olympicus

Ctenotus regiusCtenotus septenarius

Ctenotus astarteCtenotus mimetes

Ctenotus tanamiensisCtenotus greeri

Ctenotus serventyiCtenotus quattuordecimlineatus

Ctenotus leonhardiiCtenotus leae

Ctenotus australisCtenotus uber

Ctenotus rutilansCtenotus taeniolatus

Ctenotus robustusCtenotus spaldingi

Ctenotus inornatusCtenotus saxatilis

Ctenotus fallensCtenotus rawlinsoni

Ctenotus calurusCtenotus schomburgkiiCtenotus youngsoni

Ctenotus strauchiiCtenotus pantherinus

Ctenotus nasutusCtenotus rubicundus

Ctenotus brooksiCtenotus labillardieri

Notoscincus ornatusEulamprus tympanum

Eulamprus heatwoleiEulamprus kosciuskoi

Eulamprus leuraensisEulamprus quoyii

Glaphyromorphus darwiniensisGlaphyromorphus cracens

Glaphyromorphus pumilusGlaphyromorphus fuscicaudis

Glaphyromorphus mjobergiGlaphyromorphus punctulatus

Hemiergis decresiensisHemiergis millewae

Hemiergis gracilipesHemiergis quadrilineatum

Hemiergis peroniiHemiergis initialis

Eremiascincus isolepisEremiascincus douglasiEremiascincus richardsoniiEremiascincus pardalis

Eremiascincus fasciolatusAnomalopus leuckartii

Anomalopus verreauxiAnomalopus mackayi

Anomalopus swansoniOphioscincus truncatus

Coeranoscincus reticulatusSaiphos equalis

Ophioscincus ophioscincusCoeranoscincus frontalis

Coggeria naufragusEulamprus murrayi

Eulamprus tryoniEulamprus luteilateralis

Eulamprus brachyosomaEulamprus sokosoma

Eulamprus martiniEulamprus tigrinus

Eulamprus tenuisEulamprus amplus

Gnypetoscincus queenslandiaeCalyptotis ruficauda

Calyptotis scutirostrumCalyptotis lepidorostrum

Nangura spinosaEulamprus frerei

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G

Lygosominae

cont.

Figure 8

Mabuya heathiMabuya caissara

Mabuya agilisMabuya guaporicola

Mabuya macrorhynchaMabuya agmosticha

Mabuya frenataMabuya bistriata

Mabuya falconensisMabuya unimarginata

Mabuya mabouyaMabuya meridensis

Mabuya dorsivittataMabuya cochabambae

Mabuya nigropunctataMabuya altamazonica

Mabuya sloaniiMabuya nigropalmata

Mabuya croizatiMabuya carvalhoiChioninia stangeri

Chioninia fogoensisChioninia spinalis

Chioninia cocteiChioninia delalandii

Chioninia vaillantiiEumecia anchietae

Trachylepis dumasiTrachylepis aureopunctata

Trachylepis vatoTrachylepis boettgeriTrachylepis madagascariensis

Trachylepis elegansTrachylepis gravenhorstiiTrachylepis acutilabris

Trachylepis homalocephalaTrachylepis sulcata

Trachylepis variegataTrachylepis hoeschi

Trachylepis striataTrachylepis spilogaster

Trachylepis occidentalisTrachylepis capensis

Trachylepis variaTrachylepis atlantica

Trachylepis margaritiferaTrachylepis quinquetaeniata

Trachylepis perrotetiiTrachylepis affinis

Trachylepis sechellensisTrachylepis wrightii

Trachylepis maculilabrisTrachylepis socotrana

Trachylepis brevicollisTrachylepis vittata

Trachylepis aurataDasia olivacea

Dasia griseaDasia vittata

Eutropis trivittataEutropis nagarjuniEutropis beddomii

Eutropis bibroniiEutropis clivicola

Eutropis multicarinataEutropis cumingi

Eutropis multifasciataEutropis macrophthalma

Eutropis rudisEutropis macularia

Eutropis longicaudataLankascincus fallax

Ristella rurkiiLiopholis montana

Liopholis guthegaLiopholis whitiiLiopholis margaretae

Liopholis modestaLiopholis pulchra

Liopholis kintoreiLiopholis multiscutata

Liopholis inornataLiopholis striata

Tiliqua scincoidesTiliqua gigas

Tiliqua nigroluteaTiliqua occipitalis

Tiliqua rugosaTiliqua adelaidensisCyclodomorphus branchialis

Cyclodomorphus casuarinaeCyclodomorphus michaeli

Egernia hosmeriEgernia stokesii

Lissolepis luctuosaEgernia napoleonis

Egernia richardiBellatorias frerei

Egernia kingiiEgernia depressa

Bellatorias majorEgernia saxatilis

Corucia zebrataTribolonotus pseudoponceleti

Tribolonotus ponceletiTribolonotus brongersmai

Tribolonotus schmidtiTribolonotus blanchardi

Tribolonotus gracilisTribolonotus novaeguineae

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66

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74

73

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100

Lygosominae

cont.

HFigure 9

Carlia vivaxCarlia dogare

Carlia rostralisCarlia amax

Carlia tetradactylaCarlia rubrigularis

Carlia rhomboidalisCarlia rufilatus

Carlia pectoralisCarlia munda

Carlia mysiCarlia longipes

Carlia fuscaCarlia storri

Carlia schmeltziiLygisaurus malleolus

Lygisaurus tanneriLygisaurus absconditaLygisaurus foliorum

Lygisaurus laevisLygisaurus aeratus

Lygisaurus novaeguineaeLygisaurus macfarlani

Lygisaurus parrhasiusLygisaurus sesbrauna

Carlia gracilisCarlia bicarinata

Carlia jarnoldaeCarlia johnstonei

Carlia triacanthaMenetia timlowi

Liburnascincus mundivensisLiburnascincus scirtetis

Liburnascincus coensisCautula zia

Niveoscincus metallicusNiveoscincus pretiosus

Niveoscincus ocellatusNiveoscincus greeni

Proablepharus reginaeLampropholis robertsi

Lampropholis coggeriLampropholis delicata

Lampropholis guichenotiSaproscincus spectabilis

Saproscincus roseiSaproscincus challengeri

Saproscincus mustelinusSaproscincus oriarus

Saproscincus hannahaeSaproscincus tetradactylus

Saproscincus czechuraiSaproscincus lewisi

Saproscincus basiliscusBartleia jigurru

Morethia adelaidensisMorethia butleri

Morethia ruficaudaBassiana trilineata

Emoia isolataEmoia pseudocyanura

Emoia cyanuraEmoia impar

Emoia physicaeEmoia jakati

Emoia atrocostataEmoia caeruleocauda

Emoia cyanogasterEmoia schmidti

Menetia alanaeMenetia greyii

Cryptoblepharus novocaledonicusCryptoblepharus boutonii

Cryptoblepharus nigropunctatusCaledoniscincus terma

Caledoniscincus aquiloniusCaledoniscincus chazeaui

Caledoniscincus atropunctatusCaledoniscincus haplorhinus

Caledoniscincus austrocaledonicusCaledoniscincus festivus

Caledoniscincus auratusCaledoniscincus renevieri

Caledoniscincus orestesSimiscincus aurantiacus

Graciliscincus shonaeTropidoscincus variabilis

Tropidoscincus boreus

Tropidoscincus aubrianusLioscincus tillieri

Lioscincus maruiaLioscincus novaecaledoniaeSigaloseps deplanchei

Sigaloseps ruficaudaPhoboscincus garnieri

Lacertoides pardalisLioscincus nigrofasciolatum

Kanakysaurus viviparusLioscincus steindachneri

Lioscincus vivaeCelatiscincus euryotis

Celatiscincus similisMarmorosphax tricolor

Marmorosphax montanaNannoscincus humectus

Nannoscincus hanchisteusNannoscincus greeriNannoscincus mariei

Nannoscincus gracilisNannoscincus slevini

Nannoscincus garrulusOligosoma whitakeri

Oligosoma oliveriOligosoma townsi

Oligosoma ornatumOligosoma macgregori

Oligosoma mocoOligosoma alani

Oligosoma fallaiOligosoma hardyi

Oligosoma levidensumOligosoma aeneum

Oligosoma microlepisOligosoma smithi

Oligosoma striatumOligosoma homalonotumOligosoma zelandicum

Oligosoma notosaurusOligosoma inconspicuumOligosoma maccanni

Oligosoma stenotisOligosoma grande

Oligosoma nigriplantareOligosoma longipes

Oligosoma lineoocellatumOligosoma chloronoton

Oligosoma otagenseOligosoma waimatenseOligosoma infrapunctatum

Oligosoma acrinasumOligosoma taumakaeOligosoma pikitanga

Oligosoma suteriOligosoma lichenigera

Pseudemoia entrecasteauxiiBassiana duperreyi

Pseudemoia pagenstecheriLeptosiaphos vigintiserierumLeptosiaphos kilimensis

Leptosiaphos amietiLeptosiaphos graueri

Leptosiaphos hackarsiLacertaspis lepesmei

Lacertaspis gemmiventrisLacertaspis chriswildi

Lacertaspis rohdeiLacertaspis reichenowi

Afroablepharus africanusAfroablepharus annobonensis

Afroablepharus wahlbergiPanaspis togoensis

Panaspis brevicepsLeiolopisma mauritianaLeiolopisma telfairii

Emoia loyaltiensisEugongylus albofasciolatusEugongylus rufescens

Lygosoma bowringiiMochlus brevicaudisLygosoma punctata

Lygosoma sundevalliMochlus afer

Lygosoma lineolatumLepidothyris fernandi

Lygosoma albopunctataLygosoma koratense

Lygosoma quadrupesLamprolepis smaragdina

Emoia tonganaEmoia concolor

Sphenomorphus stellatusAblepharus kitaibelii

Ablepharus chernoviAblepharus budaki

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52

79

100

72

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80

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7653

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76

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61

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53

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8585

92

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9696

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8293

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57

9893

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63

93

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100

86

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9891

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84

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9396

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63

60

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I

Lygosominae

cont.

Figure 10

Gymnophthalmus cryptusGymnophthalmus underwoodi

Gymnophthalmus speciosusGymnophthalmus vanzoiGymnophthalmus leucomystax

Gymnophthalmus pleeiPsilophthalmus paeminosus

Calyptommatus nicterusCalyptommatus leiolepis

Calyptommatus confusionibusCalyptommatus sinebrachiatus

Nothobachia ablepharaProcellosaurinus tetradactylusProcellosaurinus erythrocercus

Vanzosaura rubricaudaMicrablepharus maximiliani

Micrablepharus atticolusTretioscincus oriximinensis

Tretioscincus agilisAcratosaura mentalisStenolepis ridleyi

Colobosaura modestaIphisa elegans

Colobodactylus taunayiColobodactylus dalcyanus

Heterodactylus imbricatusRhachisaurus brachylepis

Bachia heteropaBachia intermediaBachia barbouriBachia bicolorBachia peruana

Bachia panopliaBachia trisanale

Bachia scolecoidesBachia huallagana

Bachia dorbignyiBachia bresslaui

Bachia flavescensPetracola ventrimaculatus

Proctoporus bolivianusProctoporus unsaacae

Proctoporus guentheriProctoporus pachyurus

Proctoporus subsolanusProctoporus sucullucu

Cercosaura eigenmanniCercosaura schreibersii

Cercosaura ocellataCercosaura argulus

Cercosaura oshaughnessyiCercosaura quadrilineata

Potamites juruazensisPotamites ecpleopus

Pholidobolus macbrydeiPholidobolus montium

Placosoma glabellumPlacosoma cordylinum

Neusticurus bicarinatusNeusticurus rudis

Riama simoterusRiama colomaromani

Riama unicolorLeposoma guianense

Leposoma southiLeposoma parietale

Leposoma osvaldoiLeposoma percarinatum

Arthrosaura kockiiArthrosaura reticulata

Anotosaura collarisColobosauroides cearensis

Leposoma annectansLeposoma scincoides

Leposoma pukLeposoma baturitensis

Leposoma nanodactylusEcpleopus gaudichaudii

Alopoglossus angulatusAlopoglossus copii

Alopoglossus atriventrisPtychoglossus brevifrontalis

Cnemidophorus lacertoidesCnemidophorus longicaudus

Dicrodon guttulatumAmeiva fuscataAmeiva erythrocephala

Ameiva griswoldiAmeiva pluvianotata

Ameiva coraxAmeiva plei

Ameiva maynardiAmeiva lineolata

Ameiva taeniuraAmeiva chrysolaema

Ameiva leberiAmeiva wetmorei

Ameiva exsulAmeiva polops

Ameiva dorsalisAmeiva auberi

Aspidoscelis ceralbensisAspidoscelis hyperythra

Aspidoscelis tigrisAspidoscelis marmorata

Aspidoscelis lineattissimaAspidoscelis guttata

Aspidoscelis deppeiAspidoscelis velox

Aspidoscelis laredoensisAspidoscelis gularis

Aspidoscelis costataAspidoscelis communis

Aspidoscelis burtiAspidoscelis sexlineata

Aspidoscelis inornataCnemidophorus arenivagus

Cnemidophorus lemniscatusCnemidophorus gramivagus

Cnemidophorus vanzoiAmeiva festivaAmeiva quadrilineataAmeiva undulata

Kentropyx viridistrigaKentropyx vanzoi

Kentropyx paulensisKentropyx pelviceps

Kentropyx altamazonicaKentropyx striata

Kentropyx calcarataCnemidophorus ocellifer

Ameiva bifrontataAmeiva ameivaTeius teyou

Dracaena guianensisCrocodilurus amazonicus

Tupinambis teguixinTupinambis longilineus

Tupinambis quadrilineatusTupinambis duseni

Tupinambis merianaeTupinambis rufescens

Callopistes maculatusCallopistes flavipunctatus

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84

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50

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J

Teiidae

Gymnophthalmidae

Tupinambinae

Teiinae

Alopoglossinae

Ecpleopinae

Cercosaurinae

Bachiinae

Rhachisaurinae

Gymnophthalminae

Figure 11

Amphisbaena xera

Amphisbaena bakeri

Amphisbaena caeca

Amphisbaena fenestrata

Amphisbaena manni

Amphisbaena schmidti

Amphisbaena carlgansi

Amphisbaena cubana

Amphisbaena barbouri

Amphisbaena anaemariae

Amphisbaena silvestrii

Amphisbaena leeseri

Amphisbaena angustifrons

Amphisbaena darwini

Amphisbaena munoai

Amphisbaena kingii

Amphisbaena cuiabana

Amphisbaena hastata

Amphisbaena infraorbitale

Amphisbaena microcephalum

Amphisbaena polystegum

Amphisbaena anomala

Amphisbaena bolivica

Amphisbaena camura

Amphisbaena alba

Amphisbaena vermicularis

Amphisbaena roberti

Amphisbaena kraoh

Amphisbaena saxosa

Amphisbaena ignatiana

Amphisbaena leali

Amphisbaena innocens

Amphisbaena hyporissor

Amphisbaena mertensii

Amphisbaena cunhai

Amphisbaena fuliginosa

Amphisbaena brasiliana

Monopeltis capensis

Geocalamus acutus

Chirindia swynnertoni

Cynisca leucura

Trogonophis wiegmanni

Diplometopon zarudnyi

Cadea blanoides

Blanus tingitanus

Blanus mettetali

Blanus cinereus

Blanus strauchi

Bipes canaliculatus

Bipes biporus

Bipes tridactylus

Rhineura floridana

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Blanidae

Cadeidae

Trogonophiidae

Amphisbaenidae

K

Bipedidae

Rhineuridae

Figure 12

Darevskia derjuginiDarevskia caucasica

Darevskia daghestanicaDarevskia mixta

Darevskia clarkorumDarevskia armeniaca

Darevskia bendimahiensisDarevskia sapphirina

Darevskia uzzelliDarevskia raddei

Darevskia rostombekoviDarevskia saxicola

Darevskia brauneriDarevskia lindholmi

Darevskia alpinaDarevskia chlorogaster

Darevskia praticolaDarevskia valentini

Darevskia portschinskiiDarevskia rudis

Darevskia parvulaIranolacerta zagrosicaIranolacerta brandtii

Algyroides fitzingeriAlgyroides marchi

Dinarolacerta montenegrinaDinarolacerta mosorensis

Algyroides nigropunctatusAlgyroides moreoticus

Anatololacerta danfordiAnatololacerta oertzeni

Anatololacerta anatolicaParvilacerta parva

Parvilacerta fraasiiIberolacerta aranicaIberolacerta bonnali

Iberolacerta aurelioiIberolacerta horvathi

Iberolacerta monticolaIberolacerta cyreni

Iberolacerta galaniApathya cappadocica

Archaeolacerta bedriagaeHellenolacerta graecaDalmatolacerta oxycephala

Podarcis carbonelliPodarcis bocagei

Podarcis hispanicusPodarcis vaucheri

Podarcis liolepisPodarcis peloponnesiacusPodarcis erhardii

Podarcis raffoneaePodarcis lilfordi

Podarcis pityusensisPodarcis siculus

Podarcis muralisPodarcis tiliguerta

Podarcis filfolensisPodarcis gaigeae

Podarcis milensisPodarcis tauricus

Podarcis melisellensisScelarcis perspicillata

Teira dugesiiLacerta pamphylicaLacerta trilineata

Lacerta mediaLacerta agilis

Lacerta schreiberiLacerta strigata

Lacerta bilineataLacerta viridis

Timon tangitanusTimon lepidusTimon pater

Timon princepsTakydromus stejnegeriTakydromus septentrionalisTakydromus toyamaiTakydromus wolteriTakydromus formosanus

Takydromus hsuehshanensisTakydromus amurensis

Takydromus sylvaticusTakydromus dorsalis

Takydromus intermediusTakydromus sauteri

Takydromus smaragdinusTakydromus tachydromoides

Takydromus sexlineatusTakydromus kuehnei

Zootoca viviparaPhoenicolacerta cyanisparsa

Phoenicolacerta laevisPhoenicolacerta kulzeri

Acanthodactylus schreiberiAcanthodactylus boskianus

Acanthodactylus opheodurusAcanthodactylus gongrorhynchatus

Acanthodactylus masiraeAcanthodactylus cantoris

Acanthodactylus schmidtiAcanthodactylus longipes

Acanthodactylus scutellatusAcanthodactylus aureus

Acanthodactylus maculatusAcanthodactylus pardalis

Acanthodactylus beershebensisAcanthodactylus busacki

Acanthodactylus erythrurusAcanthodactylus blanci

Acanthodactylus tristramiAcanthodactylus orientalisOphisops elegans

Ophisops occidentalisMesalina rubropunctata

Mesalina brevirostrisMesalina adramitana

Mesalina balfouriMesalina guttulata

Mesalina bahaeldiniMesalina olivieri

Mesalina simoniOmanosaura jayakariOmanosaura cyanura

Congolacerta vauereselliEremias grammica

Eremias pleskeiEremias multiocellata

Eremias przewalskiiEremias arguta

Eremias nigrolateralisEremias persica

Eremias montanusEremias velox

Eremias vermiculataEremias argus

Eremias brenchleyiAdolfus jacksoni

Adolfus alleniAdolfus africanus

Gastropholis prasinaGastropholis vittata

Holaspis guentheriHolaspis laevis

Pedioplanis gaerdesiPedioplanis inornata

Pedioplanis rubensPedioplanis undata

Pedioplanis husabensisPedioplanis namaquensis

Pedioplanis brevicepsPedioplanis burchelli

Pedioplanis laticepsNucras tessellata

Pedioplanis lineoocellataMeroles cuneirostrisMeroles micropholidotus

Meroles ctenodactylusMeroles anchietaeIchnotropis squamulosa

Meroles suborbitalisMeroles knoxii

Meroles reticulatusIchnotropis capensis

Tropidosaura gularisAustralolacerta australis

Heliobolus spekiiHeliobolus lugubris

Pseuderemias smithiiPhilochortus spinalis

Latastia longicaudataNucras lalandii

Poromera fordiiAtlantolacerta andreanskyiGallotia bravoana

Gallotia simonyiGallotia intermedia

Gallotia caesarisGallotia galloti

Gallotia atlanticaGallotia stehlini

Psammodromus blanciPsammodromus algirus

Psammodromus hispanicus

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Lacertidae

Gallotiinae

Lacertinae

LFigure 13

Varanus baritjiVaranus acanthurus

Varanus storriVaranus primordius

Varanus kingorumVaranus bushiVaranus gilleni

Varanus caudolineatusVaranus eremius

Varanus brevicaudaVaranus semiremex

Varanus mitchelliVaranus timorensis

Varanus scalarisVaranus glauerti

Varanus tristisVaranus pilbarensis

Varanus glebopalmaVaranus komodoensis

Varanus variusVaranus salvadoriiVaranus gouldiiVaranus panoptes

Varanus rosenbergiVaranus giganteus

Varanus spenceriVaranus mertensi

Varanus bengalensisVaranus flavescens

Varanus dumeriliiVaranus rudicollis

Varanus salvatorVaranus marmoratus

Varanus finschiVaranus doreanusVaranus yuwonoiVaranus jobiensis

Varanus caerulivirensVaranus cerambonensisVaranus melinusVaranus indicus

Varanus rainerguentheriVaranus prasinusVaranus macraeiVaranus boehmei

Varanus beccariiVaranus keithhornei

Varanus olivaceusVaranus yemenensis

Varanus albigularisVaranus exanthematicusVaranus niloticus

Varanus griseusLanthanotus borneensis

Shinisaurus crocodilurusAbronia auritaAbronia campbelliAbronia anzuetoiAbronia matudai

Abronia fimbriataAbronia lythrochilaAbronia ornelasi

Abronia frostiAbronia graminea

Abronia oaxacaeAbronia chiszari

Mesaspis gadoviiMesaspis moreletiiBarisia rudicollis

Barisia herreraeBarisia imbricataBarisia levicollis

Abronia mixtecaGerrhonotus infernalisGerrhonotus liocephalusColoptychon rhombifer

Gerrhonotus parvusElgaria multicarinataElgaria panamintinaElgaria paucicarinataElgaria kingii

Elgaria coeruleaDopasia harti

Dopasia gracilisOphisaurus attenuatus

Anguis fragilisPseudopus apodus

Ophisaurus koellikeriOphisaurus ventralis

Celestus haetianusCelestus agasepsoides

Ophiodes striatusDiploglossus pleii

Diploglossus bilobatusCelestus enneagrammus

Anniella geronimensisAnniella pulchra

Heloderma horridumHeloderma suspectum

Xenosaurus grandisXenosaurus platyceps

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M

Xenosauridae

Helodermatidae

Anniellidae

Anguidae

Shinisauridae Lanthanotidae

Varanidae

Gerrhonotinae

Anguinae

Diploglossinae

Figure 14

Trioceros sternfeldiTrioceros rudis

Trioceros elliotiTrioceros hoehneliiTrioceros schubotzi

Trioceros narraiocaTrioceros jacksonii

Trioceros bitaeniatusTrioceros fuelleborni

Trioceros goetzeiTrioceros tempeli

Trioceros werneriTrioceros deremensis

Trioceros melleriTrioceros johnstoni

Trioceros oweniTrioceros pfefferiTrioceros quadricornisTrioceros wiedersheimi

Trioceros cristatusTrioceros montiumTrioceros feae

Trioceros balebicornutusTrioceros harennae

Trioceros affinisChamaeleo arabicus

Chamaeleo calyptratusChamaeleo zeylanicus

Chamaeleo chamaeleonChamaeleo calcaricarensChamaeleo africanus

Chamaeleo monachusChamaeleo senegalensis

Chamaeleo roperiChamaeleo dilepis

Chamaeleo quilensisChamaeleo gracilis

Chamaeleo necasiChamaeleo laevigatus

Chamaeleo namaquensisCalumma globifer

Calumma parsoniiCalumma oshaughnessyi

Calumma capuroniRhampholeon chapmanorum

Rhampholeon platycepsRhampholeon nchisiensis

Rhampholeon beraducciiRhampholeon boulengeriRhampholeon acuminatus

Rhampholeon uluguruensisRhampholeon moyeri

Rhampholeon marshalliRhampholeon viridis

Rhampholeon spinosusRhampholeon temporalis

Rhampholeon spectrumNadzikambia mlanjensis

Calumma nasutumCalumma boettgeri

Calumma fallaxCalumma gallus

Calumma maltheCalumma guibei

Calumma hilleniusiCalumma tsaratananense

Calumma brevicorneCalumma crypticum

Calumma cucullatumRieppeleon brevicaudatus

Rieppeleon brachyurusRieppeleon kerstenii

Calumma gastrotaeniaCalumma furcifer

Bradypodion ventraleBradypodion karrooicumBradypodion taeniabronchum

Bradypodion gutturaleBradypodion atromontanum

Bradypodion occidentaleBradypodion setaroi

Bradypodion nemoraleBradypodion dracomontanumBradypodion transvaalense

Bradypodion thamnobatesBradypodion melanocephalum

Bradypodion cafferBradypodion damaranumBradypodion pumilum

Kinyongia fischeriKinyongia vosseleri

Kinyongia multituberculataKinyongia matschiei

Kinyongia boehmeiKinyongia tavetana

Kinyongia uthmoelleriKinyongia carpenteri

Kinyongia xenorhinaKinyongia excubitor

Kinyongia adolfifridericiKinyongia tenue

Kinyongia oxyrhinaFurcifer antimenaFurcifer labordi

Furcifer lateralisFurcifer belalandaensis

Furcifer verrucosusFurcifer oustaleti

Furcifer angeliFurcifer pardalis

Furcifer polleniFurcifer cephalolepis

Furcifer campaniFurcifer petteri

Furcifer willsiiFurcifer minor

Furcifer bifidusFurcifer balteatus

Brookesia lineataBrookesia betschiBrookesia thieliBrookesia vadoni

Brookesia ebenauiBrookesia antakaranaBrookesia ambreensis

Brookesia stumpffiBrookesia griveaudi

Brookesia valerieaeBrookesia superciliaris

Brookesia therezieniBrookesia bonsiBrookesia brygooi

Brookesia decaryiBrookesia perarmata

Brookesia peyrierasiBrookesia karchei

Brookesia tuberculataBrookesia minima

Brookesia exarmataBrookesia dentata

Brookesia nasusBrookesia lolontany

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ChamaeleonidaeBrookesiinae

Chamaeleoninae

NFigure 15

Pseudocalotes flavigulaPseudocalotes brevipes

Pseudocalotes kakhienensisJapalura splendida

Japalura flavicepsOtocryptis wiegmanniSitana ponticeriana

Acanthosaura lepidogasterAcanthosaura capraAcanthosaura armataAcanthosaura crucigera

Salea horsfieldiiCalotes htunwiniCalotes calotes

Calotes irawadiCalotes versicolor

Calotes liolepisCalotes nigrilabris

Calotes ceylonensisCalotes liocephalusCalotes emma

Calotes chincolliumCalotes mystaceus

Ceratophora erdeleniCeratophora stoddartii

Ceratophora karuCeratophora aspera

Cophotis ceylanicaCophotis dumbara

Lyriocephalus scutatusGonocephalus kuhliiGonocephalus chamaeleontinus

Gonocephalus grandisBronchocela cristatella

Coryphophylax subcristatusAphaniotis fusca

Gonocephalus robinsoniiJapalura polygonata

Phoxophrys nigrilabrisDraco ornatusDraco palawanensisDraco spilopterus

Draco cornutusDraco guentheri

Draco quadrasiDraco cyanopterusDraco reticulatusDraco boschmai

Draco timorensisDraco volans

Draco bimaculatusDraco rhytismaDraco bourouniensis

Draco beccariiDraco biaroDraco caerulhians

Draco spilonotusDraco obscurusDraco taeniopterus

Draco blanfordiiDraco indochinensisDraco haematopogon

Draco melanopogonDraco quinquefasciatus

Draco mindanensisDraco maximus

Draco cristatellusDraco fimbriatus

Draco maculatusDraco lineatus

Draco dussumieriPtyctolaemus collicristatus

Ptyctolaemus gularisJapalura tricarinata

Japalura variegataMantheyus phuwuanensis

Agama paragamaAgama planiceps

Agama finchiAgama agama

Agama doriaeAgama sankaranicaAgama mwanzae

Agama kaimosaeAgama lionotus

Agama rueppelliAgama caudospinosa

Agama aculeataAgama armata

Agama hispidaAgama atraAgama anchietae

Agama weidholziAgama gracilimembris

Agama insularisAgama boulengeri

Agama castroviejoiAgama impalearis

Agama bouetiAgama spinosa

Trapelus savigniiTrapelus flavimaculatus

Trapelus pallidusTrapelus ruderatus

Trapelus agilisTrapelus mutabilisTrapelus sanguinolentus

Bufoniceps laungwalaensisXenagama taylori

Acanthocercus atricollisPseudotrapelus sinaitus

Phrynocephalus guttatusPhrynocephalus albolineatus

Phrynocephalus melanurusPhrynocephalus przewalskiiPhrynocephalus versicolorPhrynocephalus raddei

Phrynocephalus mystaceusPhrynocephalus helioscopus

Phrynocephalus axillarisPhrynocephalus lidskiiPhrynocephalus vlangalii

Phrynocephalus putjataiPhrynocephalus theobaldiPhrynocephalus forsythiiPhrynocephalus interscapularis

Phrynocephalus scutellatusLaudakia erythrogasterLaudakia caucasia

Laudakia microlepisLaudakia stoliczkana

Laudakia himalayanaLaudakia lehmanni

Laudakia nuptaLaudakia tuberculataLaudakia sacra

Laudakia stellio

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Diporiphora lalliae

Diporiphora arnhemica

Diporiphora albilabris

Diporiphora bennettii

Diporiphora nobbi

Diporiphora australis

Diporiphora amphiboluroides

Diporiphora valens

Diporiphora pindan

Diporiphora bilineata

Diporiphora magna

Diporiphora reginae

Diporiphora winneckei

Diporiphora linga

Diporiphora superba

Pogona vitticeps

Pogona minor

Pogona minima

Pogona henrylawsoni

Pogona nullarbor

Pogona barbata

Rankinia diemensis

Tympanocryptis lineata

Tympanocryptis pinguicolla

Tympanocryptis cephalus

Tympanocryptis tetraporophora

Tympanocryptis intima

Tympanocryptis uniformis

Amphibolurus norrisi

Amphibolurus muricatus

Lophognathus gilberti

Chlamydosaurus kingii

Lophognathus longirostris

Lophognathus temporalis

Ctenophorus femoralis

Ctenophorus fordi

Ctenophorus maculatus

Ctenophorus pictus

Ctenophorus mckenziei

Ctenophorus scutulatus

Ctenophorus isolepis

Ctenophorus ornatus

Ctenophorus caudicinctus

Ctenophorus fionni

Ctenophorus decresii

Ctenophorus vadnappa

Ctenophorus tjantjalka

Ctenophorus rufescens

Ctenophorus reticulatus

Ctenophorus nuchalis

Ctenophorus cristatus

Ctenophorus salinarum

Ctenophorus gibba

Ctenophorus clayi

Ctenophorus adelaidensis

Ctenophorus maculosus

Intellagama lesueurii

Hypsilurus bruijnii

Hypsilurus nigrigularis

Hypsilurus papuensis

Hypsilurus modestus

Chelosania brunnea

Moloch horridus

Hypsilurus dilophus

Hypsilurus boydii

Hypsilurus spinipes

Physignathus cocincinus

Hydrosaurus amboinensis

Leiolepis guentherpetersi

Leiolepis guttata

Leiolepis reevesii

Leiolepis belliana

Uromastyx yemenensis

Uromastyx benti

Uromastyx ocellata

Uromastyx ornata

Uromastyx leptieni

Uromastyx aegyptia

Uromastyx thomasi

Uromastyx dispar

Uromastyx acanthinura

Uromastyx geyri

Uromastyx macfadyeni

Uromastyx princeps

Uromastyx asmussi

Uromastyx loricata

Uromastyx hardwickii

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Uromasticinae

Leiolepidinae

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Hydrosaurinae Agam

inae

Draconinae

O

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Figure 16

Ctenosaura oaxacanaCtenosaura quinquecarinataCtenosaura flavidorsalisCtenosaura palearis

Ctenosaura bakeriCtenosaura oedirhinaCtenosaura melanosterna

Ctenosaura pectinataCtenosaura acanthuraCtenosaura hemilophaCtenosaura similis

Conolophus pallidusConolophus subcristatusAmblyrhynchus cristatus

Cyclura cychluraCyclura nubila

Cyclura rileyiCyclura colleiCyclura carinataCyclura ricordiCyclura cornuta

Cyclura pinguisSauromalus variusSauromalus hispidusSauromalus klauberiSauromalus aterIguana delicatissima

Iguana iguanaBrachylophus vitiensisBrachylophus fasciatus

Dipsosaurus dorsalisTropidurus torquatusTropidurus hispidus

Tropidurus oreadicusTropidurus insulanus

Tropidurus erythrocephalusTropidurus mucujensis

Tropidurus etheridgeiTropidurus cocorobensis

Tropidurus itambereTropidurus psammonastes

Tropidurus montanusTropidurus hygomi

Eurolophosaurus nanuzaeEurolophosaurus amathites

Eurolophosaurus divaricatusTropidurus spinulosus

Tropidurus callathelysPlica plica

Plica lumariaPlica umbra

Strobilurus torquatusTropidurus bogerti

Uracentron flavicepsUranoscodon superciliosus

Microlophus duncanensisMicrolophus albemarlensisMicrolophus pacificusMicrolophus grayii

Microlophus delanonisMicrolophus stolzmanni

Microlophus habeliiMicrolophus bivittatus

Microlophus occipitalisMicrolophus koepckeorum

Microlophus yaneziMicrolophus theresioidesMicrolophus atacamensis

Microlophus quadrivittatusMicrolophus peruvianus

Microlophus tigrisMicrolophus heterolepis

Microlophus theresiaeMicrolophus thoracicus

Stenocercus stigmosusStenocercus melanopygus

Stenocercus latebrosusStenocercus orientalis

Stenocercus ornatissimusStenocercus chrysopygus

Stenocercus cupreusStenocercus boettgeriStenocercus empetrusStenocercus eunetopsisStenocercus imitator

Stenocercus variusStenocercus torquatus

Stenocercus crassicaudatusStenocercus marmoratus

Stenocercus humeralisStenocercus angel

Stenocercus guentheriStenocercus festae

Stenocercus chotaStenocercus rhodomelasStenocercus anguliferStenocercus iridescens

Stenocercus puyangoStenocercus percultusStenocercus ornatus

Stenocercus caducusStenocercus limitaris

Stenocercus doellojuradoiStenocercus azureusStenocercus roseiventris

Stenocercus ochoaiStenocercus formosus

Stenocercus apurimacusStenocercus scapularis

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PQ-RFigure 17

Sceloporus adleriSceloporus stejnegeriSceloporus formosusSceloporus subpictusSceloporus cryptus

Sceloporus lundelliSceloporus malachiticusSceloporus smaragdinus

Sceloporus taeniocnemisSceloporus spinosusSceloporus edwardtaylori

Sceloporus horridusSceloporus cautusSceloporus undulatus

Sceloporus consobrinusSceloporus woodiSceloporus virgatus

Sceloporus occidentalisSceloporus olivaceus

Sceloporus clarkiiSceloporus cyanogenysSceloporus serriferSceloporus ornatus

Sceloporus minorSceloporus dugesii

Sceloporus poinsettiiSceloporus macdougalli

Sceloporus mucronatusSceloporus bulleri

Sceloporus torquatusSceloporus jarrovii

Sceloporus insignisSceloporus megalepidurus

Sceloporus goldmaniSceloporus samcolemani

Sceloporus chaneyiSceloporus slevini

Sceloporus scalarisSceloporus bicanthalis

Sceloporus aeneusSceloporus heterolepis

Sceloporus palaciosiSceloporus grammicus

Sceloporus melanorhinusSceloporus hunsakeriSceloporus orcuttiSceloporus lickiSceloporus lineatulus

Sceloporus zosteromusSceloporus magister

Sceloporus arenicolusSceloporus graciosusSceloporus vandenburgianus

Sceloporus ochoterenaeSceloporus jalapae

Sceloporus maculosusSceloporus gadoviae

Sceloporus nelsoniSceloporus pyrocephalus

Sceloporus merriamiSceloporus siniferus

Sceloporus squamosusSceloporus carinatus

Sceloporus utiformisSceloporus angustus

Sceloporus grandaevusSceloporus cozumelae

Sceloporus smithiSceloporus variabilis

Sceloporus teapensisSceloporus chrysostictus

Sceloporus couchiiSceloporus parvus

Urosaurus auriculatusUrosaurus clarionensisUrosaurus ornatus

Urosaurus graciosusUrosaurus nigricaudusUrosaurus lahtelaiUrosaurus bicarinatus

Urosaurus gadoviUta stejnegeri

Uta stansburianaUta palmeriUta squamataPetrosaurus thalassinusPetrosaurus repens

Petrosaurus mearnsiPhrynosoma hernandesi

Phrynosoma douglassiiPhrynosoma ditmarsiPhrynosoma orbiculare

Phrynosoma modestumPhrynosoma taurusPhrynosoma braconnieri

Phrynosoma asioPhrynosoma wigginsiPhrynosoma cerroense

Phrynosoma blainvilliiPhrynosoma coronatum

Phrynosoma platyrhinosPhrynosoma mcalliiPhrynosoma solare

Phrynosoma cornutumHolbrookia maculataHolbrookia propinquaHolbrookia lacerata

Cophosaurus texanusCallisaurus draconoides

Uma notataUma inornataUma scoparia

Uma paraphygasUma exsul

Crotaphytus collarisCrotaphytus nebriusCrotaphytus bicinctores

Crotaphytus grismeriCrotaphytus insularis

Crotaphytus vestigiumCrotaphytus reticulatus

Crotaphytus antiquusGambelia copeiiGambelia sila

Gambelia wislizeniiLeiocephalus barahonensisLeiocephalus schreibersii

Leiocephalus personatusLeiocephalus psammodromus

Leiocephalus ravicepsLeiocephalus carinatus

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Liolaemus lavillaiLiolaemus ornatusLiolaemus calchaquiLiolaemus albicepsLiolaemus irregularis

Liolaemus crepuscularisLiolaemus abaucanLiolaemus espinozai

Liolaemus quilmesLiolaemus koslowskyi

Liolaemus laurentiLiolaemus darwiniiLiolaemus grosseorum

Liolaemus olongastaLiolaemus chacoensis

Liolaemus uspallatensisLiolaemus hermannuneziLiolaemus xanthoviridisLiolaemus fitzingerii

Liolaemus chehuachekenkLiolaemus morenoiLiolaemus canqueli

Liolaemus melanopsLiolaemus donosobarrosiLiolaemus cuyanus

Liolaemus telsenLiolaemus inacayali

Liolaemus boulengeriLiolaemus rothi

Liolaemus wiegmanniiLiolaemus azarai

Liolaemus scapularisLiolaemus multimaculatusLiolaemus riojanusLiolaemus salinicola

Liolaemus lutzaeLiolaemus occipitalis

Liolaemus pseudoanomalusLiolaemus andinus

Liolaemus multicolorLiolaemus molinaiLiolaemus dorbignyiLiolaemus huacahuasicusLiolaemus fabianiLiolaemus audituvelatus

Liolaemus ruibaliLiolaemus vallecurensisLiolaemus famatinae

Liolaemus orientalisLiolaemus stolzmanni

Liolaemus archeforusLiolaemus tristisLiolaemus zullyaeLiolaemus scolaroi

Liolaemus sarmientoiLiolaemus gallardoi

Liolaemus kingiiLiolaemus escarchadosiLiolaemus tari

Liolaemus bagualiLiolaemus somuncurae

Liolaemus uptoniLiolaemus magellanicus

Liolaemus kolenghLiolaemus silvanaeLiolaemus lineomaculatus

Liolaemus hatcheriLiolaemus saxatilis

Liolaemus gracilisLiolaemus robertmertensiLiolaemus ramirezae

Liolaemus yanalcuLiolaemus walkeriLiolaemus puna

Liolaemus chaltinLiolaemus bitaeniatus

Liolaemus pagaburoiLiolaemus bibronii

Liolaemus hernaniLiolaemus pictusLiolaemus cyanogaster

Liolaemus chiliensisLiolaemus schroederi

Liolaemus gravenhorstiiLiolaemus belliiLiolaemus coeruleusLiolaemus elongatus

Liolaemus kriegiLiolaemus leopardinus

Liolaemus ceiiLiolaemus buergeriLiolaemus petrophilusLiolaemus umbriferLiolaemus capillitasLiolaemus heliodermis

Liolaemus dicktracyiLiolaemus thermarum

Liolaemus austromendocinusLiolaemus paulinaeLiolaemus plateiLiolaemus nigromaculatus

Liolaemus pseudolemniscatusLiolaemus zapallarensisLiolaemus atacamensis

Liolaemus fuscusLiolaemus nigroviridisLiolaemus nitidus

Liolaemus monticolaLiolaemus lemniscatus

Liolaemus tenuisPhymaturus antofagastensisPhymaturus mallimacciiPhymaturus punaePhymaturus palluma

Phymaturus dorsimaculatusPhymaturus patagonicusPhymaturus somuncurensis

Phymaturus indistinctusCtenoblepharys adspersa

Leiosaurus catamarcensisLeiosaurus paronae

Leiosaurus belliiPristidactylus torquatus

Diplolaemus darwiniiPristidactylus scapulatus

Urostrophus vautieriAnisolepis longicauda

Urostrophus gallardoiEnyalius leechii

Enyalius bilineatusOplurus fierinensis

Oplurus grandidieriOplurus saxicola

Oplurus quadrimaculatusOplurus cuvieri

Oplurus cyclurusChalarodon madagascariensis

Enyalioides praestabilisEnyalioides microlepisEnyalioides palpebralis

Enyalioides oshaughnessyiEnyalioides heterolepis

Enyalioides laticepsMorunasaurus annularis

Hoplocercus spinosusPolychrus marmoratus

Polychrus femoralisPolychrus acutirostris

Polychrus gutturosus

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Po

lych

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dae

Ho

plo

cerc

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Opluridae

En

yaliid

ae

Lio

laem

idae

Leiosaurinae

Enyaliinae

(i)

(ii)

(i)(ii)

QRFigure 18

Anolis smaragdinusAnolis allisoniAnolis maynardi

Anolis brunneusAnolis longiceps

Anolis porcatusAnolis carolinensisAnolis isolepisAnolis oporinus

Anolis argillaceusAnolis centralis

Anolis pumilusAnolis loysiana

Anolis guazumaAnolis garridoi

Anolis angusticepsAnolis paternusAnolis alayoniAnolis sheplaniAnolis placidus

Anolis alutaceusAnolis inexpectatus

Anolis vanidicusAnolis alfaroi

Anolis macilentusAnolis cupeyalensisAnolis cyanopleurusAnolis rejectus

Anolis clivicolaAnolis lucius

Anolis whitemaniAnolis cybotes

Anolis armouriAnolis shreveiAnolis haetianusAnolis longitibialis

Anolis strahmiAnolis marcanoi

Anolis barahonaeAnolis baleatus

Anolis ricordiAnolis eugenegrahami

Anolis christopheiAnolis cuvieri

Anolis guamuhayaAnolis chamaeleonides

Anolis porcusAnolis barbatus

Anolis argenteolusAnolis alumina

Anolis semilineatusAnolis olssoni

Anolis barbouriAnolis insolitus

Anolis fowleriAnolis etheridgei

Anolis equestrisAnolis luteogularis

Anolis baracoaeAnolis nobleiAnolis smallwoodi

Anolis alinigerAnolis singularisAnolis chlorocyanusAnolis coelestinus

Anolis hendersoniAnolis dolichocephalus

Anolis bahorucoensisAnolis darlingtoni

Anolis monticolaAnolis occultus

Anolis vermiculatusAnolis bartschi

Anolis maculigulaAnolis casildae

Anolis frenatusAnolis princeps

Anolis chocorumAnolis fraseri

Anolis danieliAnolis insignisAnolis microtus

Anolis agassiziAnolis neblininusAnolis calimae

Anolis anatolorosAnolis jacare

Anolis tigrinusAnolis transversalisAnolis punctatus

Anolis inderenaeAnolis vanzoliniiAnolis heterodermusAnolis nicefori

Anolis euskalerriariAnolis gemmosusAnolis aequatorialisAnolis ventrimaculatusAnolis chlorisAnolis festae

Anolis peraccaeAnolis huilaeAnolis fitchi

Anolis extremusAnolis roquet

Anolis aeneusAnolis richardii

Anolis trinitatisAnolis griseus

Anolis bonairensisAnolis luciae

Anolis boettgeriBasiliscus basiliscus

Basiliscus plumifronsBasiliscus vittatus

Basiliscus galeritusCorytophanes cristatus

Corytophanes percarinatusLaemanctus longipes

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Anolis trachyderma

Anolis poecilopus

Anolis tropidogaster

Anolis lionotus

Anolis oxylophus

Anolis zeus

Anolis limifrons

Anolis lemurinus

Anolis bicaorum

Anolis carpenteri

Anolis ocelloscapularis

Anolis tropidonotus

Anolis capito

Anolis polylepis

Anolis cupreus

Anolis fuscoauratus

Anolis kemptoni

Anolis altae

Anolis humilis

Anolis pachypus

Anolis sericeus

Anolis isthmicus

Anolis intermedius

Anolis laeviventris

Anolis ortonii

Anolis quercorum

Anolis aquaticus

Anolis woodi

Anolis biporcatus

Anolis bitectus

Anolis uniformis

Anolis polyrhachis

Anolis sminthus

Anolis crassulus

Anolis utilensis

Anolis purpurgularis

Anolis loveridgei

Anolis chrysolepis

Anolis bombiceps

Anolis nitens

Anolis meridionalis

Anolis lineatus

Anolis onca

Anolis annectens

Anolis auratus

Anolis grahami

Anolis conspersus

Anolis garmani

Anolis opalinus

Anolis valencienni

Anolis reconditus

Anolis lineatopus

Anolis bremeri

Anolis quadriocellifer

Anolis sagrei

Anolis ophiolepis

Anolis mestrei

Anolis homolechis

Anolis jubar

Anolis confusus

Anolis guafe

Anolis ahli

Anolis allogus

Anolis rubribarbaris

Anolis imias

Anolis cristatellus

Anolis desechensis

Anolis ernestwilliamsi

Anolis scriptus

Anolis cooki

Anolis monensis

Anolis krugi

Anolis pulchellus

Anolis gundlachi

Anolis poncensis

Anolis evermanni

Anolis stratulus

Anolis acutus

Anolis caudalis

Anolis marron

Anolis brevirostris

Anolis websteri

Anolis distichus

Anolis marmoratus

Anolis sabanus

Anolis nubilus

Anolis lividus

Anolis ferreus

Anolis terraealtae

Anolis oculatus

Anolis gingivinus

Anolis bimaculatus

Anolis leachii

Anolis pogus

Anolis wattsi

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Corytophanidae

Dactyloidae

(i)

(ii)

(i)

(ii)

RFigure 19

Austrotyphlops pilbarensis

Austrotyphlops hamatus

Austrotyphlops endoterus

Austrotyphlops australis

Austrotyphlops waitii

Austrotyphlops splendidus

Austrotyphlops pinguis

Ramphotyphlops bicolor

Austrotyphlops ligatus

Austrotyphlops ganei

Austrotyphlops troglodytes

Austrotyphlops kimberleyensis

Austrotyphlops ammodytes

Austrotyphlops unguirostris

Austrotyphlops leptosomus

Austrotyphlops longissimus

Austrotyphlops grypus

Austrotyphlops bituberculatus

Austrotyphlops guentheri

Austrotyphlops howi

Austrotyphlops diversus

Ramphotyphlops polygrammicus

Acutotyphlops kunuaensis

Acutotyphlops subocularis

Ramphotyphlops acuticaudus

Ramphotyphlops lineatus

Typhlopidae sp. (Sri Lanka)

Ramphotyphlops braminus

Typhlops pammeces

Ramphotyphlops albiceps

Typhlops ruber

Typhlops luzonensis

Typhlops arenarius

Typhlops vermicularis

Afrotyphlops punctatus

Afrotyphlops congestus

Afrotyphlops lineolatus

Afrotyphlops bibronii

Afrotyphlops fornasinii

Megatyphlops schlegelii

Afrotyphlops angolensis

Typhlops elegans

Letheobia obtusa

Letheobia newtoni

Letheobia feae

Rhinotyphlops lalandei

Typhlops catapontus

Typhlops richardi

Typhlops platycephalus

Typhlops hypomethes

Typhlops granti

Typhlops dominicanus

Typhlops monastus

Typhlops notorachius

Typhlops anousius

Typhlops anchaurus

Typhlops contorhinus

Typhlops arator

Typhlops caymanensis

Typhlops agoralionis

Typhlops sylleptor

Typhlops jamaicensis

Typhlops capitulatus

Typhlops rostellatus

Typhlops sulcatus

Typhlops titanops

Typhlops schwartzi

Typhlops lumbricalis

Typhlops eperopeus

Typhlops syntherus

Typhlops hectus

Typhlops pusillus

Typhlops biminiensis

Typhlops reticulatus

Typhlops brongersmianus

Xenotyphlops grandidieri

Gerrhopilus mirus

Gerrhopilus hedraeus

Leptotyphlops scutifrons

Leptotyphlops distanti

Leptotyphlops conjunctus

Leptotyphlops sylvicolus

Leptotyphlops nigricans

Leptotyphlops nigroterminus

Namibiana occidentalis

Myriopholis adleri

Myriopholis macrorhyncha

Myriopholis blanfordi

Myriopholis boueti

Myriopholis rouxestevae

Myriopholis algeriensis

Myriopholis longicauda

Mitophis leptipileptus

Mitophis pyrites

Mitophis asbolepis

Tetracheilostoma breuili

Tetracheilostoma carlae

Rena humilis

Rena dulcis

Trilepida macrolepis

Epictia columbi

Epictia goudotii

Epictia albifrons

Siagonodon septemstriatus

Tricheilostoma bicolor

Typhlophis squamosus

Liotyphlops albirostris

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988174

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100 Anomalepididae

Leptotyphlopidae

Gerrhopilidae

Xenotyphlopidae

Typ

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ae

ST-AAFigure 20

Antaresia childreniAntaresia stimsoniAntaresia perthensisAntaresia maculosaMorelia bredliMorelia spilota

Morelia carinataMorelia viridisBothrochilus boaLeiopython albertisii

Liasis fuscusLiasis mackloti

Apodora papuanaLiasis olivaceus

Aspidites melanocephalusAspidites ramsayi

Morelia amethistinaMorelia boeleniMorelia oenpelliensisBroghammerus timoriensisBroghammerus reticulatus

Python molurusPython sebaePython curtusPython regius

Python brongersmaiLoxocemus bicolor

Xenopeltis unicolorRhinophis blythiiRhinophis homolepisPseudotyphlops philippinusRhinophis oxyrhynchus

Rhinophis philippinusRhinophis dorsimaculatus

Rhinophis drummondhayiUropeltis phillipsiUropeltis melanogaster

Rhinophis travancoricusUropeltis ceylanicus

Uropeltis liuraBrachyophidium rhodogaster

Melanophidium punctatumCylindrophis ruffus

Cylindrophis maculatusAnomochilus leonardi

Epicrates striatusEpicrates exsulEpicrates chrysogasterEpicrates subflavus

Epicrates fordiEpicrates monensisEpicrates inornatus

Epicrates anguliferEunectes notaeusEunectes murinus

Epicrates cenchriaCorallus annulatus

Corallus caninusCorallus hortulanusBoa constrictorEryx tataricusEryx miliaris

Eryx elegansEryx jaculusEryx johnii

Eryx conicusEryx colubrinus

Eryx jayakariCandoia bibroni

Candoia carinataCandoia aspera

Lichanura trivirgataCharina bottae

Ungaliophis continentalisExiliboa placata

Calabaria reinhardtiiAcrantophis dumeriliAcrantophis madagascariensisSanzinia madagascariensisCasarea dussumieriXenophidion schaeferiTropidophis melanurusTropidophis feicki

Tropidophis haetianusTropidophis greenwayi

Tropidophis wrightiTropidophis pardalis

Trachyboa boulengeriTrachyboa gularis

Anilius scytale

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5398

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100 Aniliidae

Tropidophiidae

Xenophidiidae

Bolyeriidae

Boidae

Anomochilidae

Cylindrophiidae

Uropeltidae

XenopeltidaeLoxocemidae

Pythonidae

Calabariidae

Sanziniinae

Ungaliophiinae

Candoiinae

Erycinae

Boinae

TU-AAFigure 21

Bitis rubida

Bitis cornuta

Bitis atropos

Bitis xeropaga

Bitis caudalis

Bitis peringueyi

Bitis gabonica

Bitis nasicornis

Bitis arietans

Bitis worthingtoni

Atheris desaixi

Atheris nitschei

Atheris squamigera

Atheris hispida

Atheris chlorechis

Atheris barbouri

Atheris ceratophora

Echis pyramidum

Echis leucogaster

Echis coloratus

Echis omanensis

Echis jogeri

Echis ocellatus

Echis carinatus

Causus defilippii

Causus rhombeatus

Causus resimus

Cerastes gasperettii

Cerastes cerastes

Cerastes vipera

Proatheris superciliaris

Vipera lotievi

Vipera renardi

Vipera dinniki

Vipera ursinii

Vipera eriwanensis

Vipera kaznakovi

Vipera barani

Vipera berus

Vipera nikolskii

Vipera seoanei

Vipera aspis

Vipera latastei

Vipera ammodytes

Macrovipera mauritanica

Macrovipera deserti

Daboia russelii

Daboia palaestinae

Montivipera wagneri

Montivipera albizona

Montivipera bornmuelleri

Montivipera raddei

Montivipera xanthina

Macrovipera schweizeri

Macrovipera lebetina

Pseudocerastes fieldi

Pseudocerastes persicus

Eristicophis macmahoni

Pareas nuchalis

Pareas carinatus

Pareas hamptoni

Pareas macularius

Pareas margaritophorus

Pareas formosensis

Pareas boulengeri

Pareas monticola

Aplopeltura boa

Asthenodipsas vertebralis

Achalinus rufescens

Achalinus meiguensis

Xenodermus javanicus

Stoliczkia borneensis

Acrochordus arafurae

Acrochordus granulatus

Acrochordus javanicus

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Crotalus adamanteusCrotalus tigris

Crotalus mitchelliiCrotalus viridis

Crotalus oreganusCrotalus scutulatusCrotalus tortugensis

Crotalus atroxCrotalus catalinensis

Crotalus ruberCrotalus totonacusCrotalus molossus

Crotalus basiliscusCrotalus simusCrotalus durissus

Crotalus horridusCrotalus willardi

Crotalus ravusCrotalus cerastesCrotalus polystictus

Crotalus enyoCrotalus aquilus

Crotalus lepidusCrotalus pusillus

Crotalus triseriatusCrotalus tancitarensis

Crotalus transversusCrotalus intermedius

Crotalus priceiSistrurus miliarius

Sistrurus catenatusAgkistrodon bilineatus

Agkistrodon tayloriAgkistrodon piscivorus

Agkistrodon contortrixBothriechis rowleyi

Bothriechis auriferBothriechis bicolor

Bothriechis thalassinusBothriechis marchi

Bothriechis lateralisBothriechis nigroviridis

Bothriechis schlegeliiLachesis mutaLachesis stenophrys

Mixcoatlus melanurusMixcoatlus barbouri

Ophryacus undulatusBothrops leucurus

Bothrops moojeniBothrops atrox

Bothrops colombiensisBothrops marajoensis

Bothrops asperBothrops lanceolatus

Bothrops caribbaeusBothrops punctatusBothrops jararacussu

Bothrops braziliBothriopsis bilineata

Bothriopsis taeniataBothriopsis chloromelasBothriopsis pulchra

Bothropoides alcatrazBothropoides insularis

Bothropoides jararacaBothropoides neuwiedi

Bothropoides diporusBothropoides erythromelas

Rhinocerophis itapetiningaeRhinocerophis alternatus

Rhinocerophis fonsecaiRhinocerophis cotiara

Rhinocerophis ammodytoidesBothrops pictus

Bothrocophias hyoproraBothrocophias microphthalmus

Bothrocophias campbelliPorthidium lansbergii

Porthidium porrasiPorthidium nasutum

Porthidium yucatanicumPorthidium dunni

Porthidium ophryomegasCerrophidion petlalcalensis

Cerrophidion tzotzilorumCerrophidion godmani

Atropoides picadoiAtropoides olmec

Atropoides nummiferAtropoides occiduus

Gloydius saxatilisGloydius intermedius

Gloydius shedaoensisGloydius halys

Gloydius strauchiGloydius blomhoffiiGloydius ussuriensis

Gloydius brevicaudusGloydius tsushimaensis

Trimeresurus gracilisOvophis okinavensis

Protobothrops tokarensisProtobothrops flavoviridis

Protobothrops mucrosquamatusProtobothrops elegans

Protobothrops jerdoniiProtobothrops xiangchengensis

Protobothrops cornutusProtobothrops mangshanensis

Protobothrops sieversorumProtobothrops kaulbacki

Ovophis tonkinensisOvophis zayuensisOvophis monticola

Trimeresurus purpureomaculatusTrimeresurus erythrurus

Trimeresurus cantoriTrimeresurus albolabris

Trimeresurus andersoniiTrimeresurus septentrionalis

Trimeresurus insularisTrimeresurus fasciatus

Trimeresurus macropsTrimeresurus venustus

Trimeresurus kanburiensisTrimeresurus vogeli

Trimeresurus stejnegeriTrimeresurus gumprechti

Trimeresurus yunnanensisTrimeresurus medoensis

Trimeresurus tibetanusTrimeresurus popeiorum

Trimeresurus sumatranusTrimeresurus schultzei

Trimeresurus flavomaculatusTrimeresurus malcolmiTrimeresurus hageni

Trimeresurus trigonocephalusTrimeresurus gramineus

Trimeresurus malabaricusTrimeresurus borneensis

Trimeresurus puniceusHypnale zara

Hypnale hypnaleHypnale nepa

Calloselasma rhodostomaDeinagkistrodon acutus

Tropidolaemus wagleriGarthius chaseni

Azemiops feae

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Acrochordidae

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Vip

erinae

Azemiopinae

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(i)

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Figure 22

Liophidium chabaudiLiophidium mayottensis

Liophidium torquatumLiophidium therezieni

Liophidium vaillantiLiophidium rhodogaster

Liopholidophis sexlineatusLiopholidophis dolicocercus

Liopholidophis dimorphusHeteroliodon occipitalis

Pseudoxyrhopus ambreensisThamnosophis lateralis

Thamnosophis stumpffiThamnosophis epistibes

Thamnosophis martaeThamnosophis infrasignatus

Dromicodryas bernieriDromicodryas quadrilineatus

Lycodryas granulicepsLycodryas pseudogranuliceps

Lycodryas inopinaeLycodryas sanctijohannis

Lycodryas citrinusLycodryas inornatus

Madagascarophis meridionalisMadagascarophis colubrinus

Ithycyphus oursiIthycyphus miniatus

Micropisthodon ochraceusLangaha madagascariensis

Leioheterodon modestusLeioheterodon madagascariensis

Leioheterodon geayiParastenophis betsileanus

Alluaudina bellyiCompsophis infralineatus

Compsophis laphystiusCompsophis albiventris

Compsophis boulengeriDitypophis vivaxDuberria lutrix

Duberria variegataAmplorhinus multimaculatus

Lycodonomorphus whytiiLycodonomorphus laevissimus

Lycodonomorphus rufulusLycodonomorphus inornatus

Lamprophis fiskiiLamprophis aurora

Lamprophis fuscusLamprophis guttatus

Boaedon olivaceusBoaedon fuliginosus

Boaedon lineatusBoaedon virgatus

Bothrophthalmus lineatusBothrophthalmus brunneus

Bothrolycus aterPseudoboodon lemniscatus

Gonionotophis capensisGonionotophis poensis

Gonionotophis brussauxiGonionotophis nyassae

Gonionotophis stenophthalmusInyoka swazicus

Hormonotus modestusLycophidion ornatum

Lycophidion capenseLycophidion laterale

Lycophidion nigromaculatumBuhoma depressiceps

Buhoma procteraePsammodynastes pictus

Psammodynastes pulverulentusPseudaspis cana

Pythonodipsas carinataAparallactus guentheri

Aparallactus capensisAparallactus werneriAparallactus modestus

Polemon acanthiasPolemon collaris

Polemon notatusAmblyodipsas dimidiata

Xenocalamus transvaalensisAmblyodipsas polylepis

Macrelaps microlepidotusAtractaspis corpulenta

Atractaspis micropholisAtractaspis bibronii

Atractaspis boulengeriAtractaspis microlepidota

Atractaspis irregularisHomoroselaps lacteus

Psammophis phillipsiPsammophis mossambicusPsammophis leopardinus

Psammophis sibilansPsammophis rukwae

Psammophis orientalisPsammophis sudanensis

Psammophis subtaeniatusPsammophis lineatusPsammophis biseriatus

Psammophis tanganicusPsammophis praeornatus

Psammophis punctulatusPsammophis schokari

Psammophis angolensisPsammophis notostictusPsammophis leightoniPsammophis jallae

Psammophis trigrammusPsammophis condanarus

Psammophis lineolatusPsammophis crucifer

Psammophylax tritaeniatusPsammophylax variabilis

Psammophylax rhombeatusPsammophylax acutus

Hemirhagerrhis hildebrandtiiHemirhagerrhis kelleri

Hemirhagerrhis viperinaDipsina multimaculata

Mimophis mahfalensisRhagerhis moilensis

Malpolon monspessulanusRhamphiophis rubropunctatus

Rhamphiophis oxyrhynchusProsymna meleagris

Prosymna greigertiProsymna janii

Prosymna visseriProsymna ruspolii

Oxyrhabdium leporinumMicrelaps bicoloratus

Cerberus rynchopsCerberus microlepis

Cerberus australisHomalopsis buccataEnhydris punctata

Fordonia leucobaliaGerarda prevostiana

Cantoria violaceaBitia hydroides

Enhydris bocourtiErpeton tentaculatum

Pseudoferania polylepisMyron richardsonii

Enhydris innominataEnhydris longicauda

Enhydris jagoriiEnhydris enhydris

Enhydris matannensisEnhydris plumbea

Enhydris chinensis

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Homalopsidae

Prosymninae

Psammophiinae

Atractaspidinae

Aparallactinae

Pseudaspidinae

Lamprophiinae

Pseudoxyrhophiinae

Lamprophiidae

VX-AA WFigure 23

Hydrophis ornataHydrophis peronii

Hydrophis kingiiHydrophis macdowelli

Hydrophis schistosaHydrophis majorHydrophis czeblukovi

Hydrophis caerulescensHydrophis brooki

Hydrophis atricepsHydrophis stokesii

Hydrophis platuraHydrophis curtus

Hydrophis parvicepsHydrophis melanocephala

Hydrophis cyanocinctaHydrophis pacificaHydrophis semperi

Hydrophis spiralisHydrophis lapemoides

Hydrophis elegansHydrelaps darwiniensis

Ephalophis greyaeParahydrophis mertoni

Aipysurus laevisAipysurus fuscusAipysurus apraefrontalisAipysurus duboisii

Aipysurus eydouxiiEmydocephalus annulatus

Hemiaspis dameliiHemiaspis signata

Tropidechis carinatusNotechis scutatus

Echiopsis atricepsHoplocephalus bitorquatus

Austrelaps superbusAustrelaps labialis

Drysdalia coronoidesDrysdalia mastersii

Echiopsis curtaPseudonaja textilisPseudonaja modesta

Oxyuranus scutellatusOxyuranus microlepidotus

Denisonia devisiSimoselaps calonotus

Vermicella intermediaSuta spectabilis

Suta sutaSuta monachus

Suta fasciataRhinoplocephalus bicolor

Cryptophis nigrescensElapognathus coronata

Cacophis squamulosusPseudechis guttatus

Pseudechis papuanusPseudechis colletti

Pseudechis australisPseudechis butleri

Pseudechis porphyriacusAcanthophis antarcticusAcanthophis praelongus

Aspidomorphus muelleriAspidomorphus lineaticollis

Aspidomorphus schlegeliSimoselaps bertholdi

Simoselaps anomalusSimoselaps semifasciatus

Furina diademaFurina ornata

Toxicocalamus loriaeDemansia psammophis

Demansia papuensisDemansia vestigiata

Toxicocalamus preussiMicropechis ikaheka

Laticauda colubrinaLaticauda guineai

Laticauda saintgironsiLaticauda laticaudata

Bungarus candidusBungarus multicinctus

Bungarus nigerBungarus caeruleus

Bungarus ceylonicusBungarus sindanus

Bungarus fasciatusBungarus bungaroidesBungarus flavicepsElapsoidea sundevalliiElapsoidea semiannulata

Elapsoidea nigraNaja ashei

Naja nigricollisNaja mossambica

Naja katiensisNaja pallida

Naja nubiaeNaja haje

Naja annuliferaNaja nivea

Naja annulataNaja melanoleuca

Naja multifasciataNaja sumatranaNaja siamensis

Naja mandalayensisNaja naja

Naja atraNaja kaouthia

Hemachatus haemachatusAspidelaps scutatus

Walterinnesia aegyptiaDendroaspis polylepis

Dendroaspis angusticepsOphiophagus hannah

Hemibungarus calligasterMicrurus brasiliensisMicrurus frontalisMicrurus spixii

Micrurus ibibobocaMicrurus altirostris

Micrurus pyrrhocryptusMicrurus baliocoryphus

Micrurus decoratusMicrurus lemniscatusMicrurus hemprichii

Micrurus surinamensisMicrurus dissoleucus

Micrurus mipartitusMicrurus narduccii

Micrurus diastemaMicrurus fulvius

Micrurus psychesMicrurus albicinctus

Micrurus corallinusSinomicrurus macclellandi

Sinomicrurus kelloggiSinomicrurus japonicus

Micruroides euryxanthusMaticora bivirgata

Calliophis melanurus

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WFigure 24

Eirenis punctatolineatusEirenis barani

Eirenis collarisEirenis eiselti

Eirenis coronelloidesEirenis rothiiEirenis lineomaculatus

Eirenis thospitisEirenis medus

Eirenis levantinusEirenis decemlineatus

Eirenis persicusEirenis aurolineatus

Eirenis modestusHierophis spinalisHierophis gemonensis

Hierophis viridiflavusDolichophis caspius

Dolichophis schmidtiDolichophis jugularis

Platyceps florulentusPlatyceps collaris

Platyceps najadumPlatyceps ventromaculatus

Platyceps kareliniPlatyceps rogersi

Platyceps rhodorachisSpalerosophis diadema

Spalerosophis microlepisHemorrhois ravergieri

Hemorrhois nummiferHemorrhois algirus

Hemorrhois hippocrepisHemerophis socotrae

Macroprotodon abubakeriMacroprotodon cucullatus

Bamanophis dorriColuber zebrinus

Lytorhynchus diademaHapsidophrys principis

Hapsidophrys smaragdinaHapsidophrys lineatus

Philothamnus hoplogasterPhilothamnus natalensisPhilothamnus thomensis

Philothamnus girardiPhilothamnus angolensis

Philothamnus semivariegatusPhilothamnus nitidus

Philothamnus heterodermusPhilothamnus carinatus

Thelotornis capensisDispholidus typus

Thrasops jacksoniiCoelognathus flavolineatus

Coelognathus subradiatusCoelognathus erythrurus

Coelognathus helenaCoelognathus radiatus

Oligodon planicepsOligodon torquatus

Oligodon theobaldiOligodon cruentatus

Oligodon splendidusOligodon maculatus

Oligodon cinereusOligodon formosanus

Oligodon ocellatusOligodon chinensisOligodon taeniatusOligodon barroniOligodon cyclurus

Oligodon octolineatusOligodon taeniolatusOligodon sublineatus

Oligodon arnensisScaphiophis albopunctatus

Dasypeltis fasciataDasypeltis gansi

Dasypeltis sahelensisDasypeltis scabra

Dasypeltis atraDasypeltis confusa

Toxicodryas pulverulentaBoiga multomaculata

Boiga beddomeiBoiga ceylonensisBoiga trigonata

Boiga barnesiiBoiga cynodon

Boiga forsteniBoiga dendrophila

Boiga irregularisTelescopus fallax

Dipsadoboa unicolorCrotaphopeltis tornieri

Boiga kraepeliniDendrelaphis tristis

Dendrelaphis schokariDendrelaphis caudolineatus

Dendrelaphis caudolineolatusDendrelaphis bifrenalis

Chrysopelea paradisiChrysopelea ornata

Chrysopelea taprobanicaAhaetulla nasuta

Ahaetulla pulverulentaAhaetulla fronticincta

Grayia smithiiGrayia ornataGrayia tholloni

Sibynophis chinensisSibynophis collaris

Sibynophis triangularisSibynophis subpunctatus

Sibynophis bistrigatusScaphiodontophis annulatus

Pseudoxenodon karlschmidtiPseudoxenodon macrops

Pseudoxenodon bambusicolaPlagiopholis styani

Calamaria yunnanensisCalamaria pavimentata

Pseudorabdion oxycephalum

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Lampropeltis californiaeLampropeltis splendidaLampropeltis holbrooki

Lampropeltis getulaLampropeltis nigraLampropeltis alterna

Lampropeltis extenuatumLampropeltis triangulumLampropeltis ruthveniLampropeltis mexicanaLampropeltis elapsoidesLampropeltis zonataLampropeltis pyromelana

Lampropeltis webbiLampropeltis calligaster

Cemophora coccineaPseudelaphe flavirufa

Arizona elegansRhinocheilus lecontei

Bogertophis rosaliaeBogertophis subocularis

Pantherophis bairdiPantherophis obsoletusPantherophis alleghaniensis

Pantherophis spiloidesPantherophis slowinskii

Pantherophis emoryiPantherophis guttatus

Pantherophis vulpinusPituophis cateniferPituophis ruthveniPituophis melanoleucus

Pituophis lineaticollisPituophis vertebralis

Pituophis deppeiSenticolis triaspis

Oocatochus rufodorsatusCoronella austriaca

Coronella girondicaElaphe sauromates

Elaphe quatuorlineataElaphe quadrivirgata

Elaphe schrenckiiElaphe climacophora

Elaphe dioneElaphe bimaculata

Elaphe carinataElaphe davidi

Zamenis situlaRhinechis scalaris

Zamenis lineatusZamenis longissimus

Zamenis persicusZamenis hohenackeri

Orthriophis cantorisOrthriophis moellendorffi

Orthriophis hodgsoniOrthriophis taeniurus

Oreocryptophis porphyraceusEuprepiophis mandarinus

Euprepiophis conspicillataArchelaphe bella

Lycodon aulicusLycodon zawi

Lycodon osmanhilliLycodon capucinus

Lycodon carinatusDryocalamus nympha

Lycodon semicarinatumLycodon rufozonatum

Lycodon paucifasciatusLycodon fasciatus

Lycodon laoensisLycodon ruhstrati

Rhadinophis frenatusRhynchophis boulengeri

Rhadinophis prasinusGonyosoma jansenii

Gonyosoma oxycephalumSympholis lippiens

Pseudoficimia frontalisGyalopion canum

Ficimia streckeriConopsis nasusConopsis biserialis

Sonora semiannulataChilomeniscus stramineus

Chionactis occipitalisStenorrhina freminvillei

Rhinobothryum lentiginosumMastigodryas bifossatus

Mastigodryas boddaertiMastigodryas melanolomus

Drymoluber braziliDrymoluber dichrous

Chironius multiventrisChironius laurenti

Chironius exoletusChironius monticola

Chironius bicarinatusChironius flavolineatus

Chironius grandisquamisChironius laevicollisChironius scurrulus

Chironius fuscusDrymarchon corais

Pseustes sulphureusSpilotes pullatus

Phyllorhynchus decurtatusTrimorphodon biscutatus

Drymobius rhombiferDendrophidion percarinatum

Dendrophidion dendrophisLeptophis ahaetulla

Chironius carinatusChironius quadricarinatus

Coluber flagellumColuber constrictor

Coluber taeniatusTantilla melanocephala

Salvadora mexicanaOpheodrys aestivusOpheodrys vernalisOxybelis aeneus

Oxybelis fulgidusPtyas mucosa

Ptyas korrosCyclophiops major

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YFigure 26

Thamnophis butleri

Thamnophis radix

Thamnophis brachystoma

Thamnophis elegans

Thamnophis gigas

Thamnophis atratus

Thamnophis couchii

Thamnophis ordinoides

Thamnophis hammondii

Thamnophis marcianus

Thamnophis eques

Thamnophis cyrtopsis

Thamnophis chrysocephalus

Thamnophis fulvus

Thamnophis mendax

Thamnophis sumichrasti

Thamnophis scaliger

Thamnophis godmani

Thamnophis exsul

Thamnophis melanogaster

Thamnophis valida

Adelophis foxi

Thamnophis rufipunctatus

Thamnophis proximus

Thamnophis sauritus

Thamnophis sirtalis

Nerodia sipedon

Nerodia fasciata

Nerodia harteri

Nerodia erythrogaster

Nerodia rhombifer

Nerodia taxispilota

Nerodia floridana

Nerodia cyclopion

Tropidoclonion lineatum

Regina grahami

Regina septemvittata

Regina alleni

Regina rigida

Seminatrix pygaea

Storeria dekayi

Storeria occipitomaculata

Virginia striatula

Clonophis kirtlandii

Natrix tessellata

Natrix natrix

Natrix maura

Sinonatrix annularis

Sinonatrix percarinata

Sinonatrix aequifasciata

Opisthotropis cheni

Opisthotropis latouchii

Opisthotropis lateralis

Opisthotropis guangxiensis

Aspidura guentheri

Aspidura ceylonensis

Aspidura trachyprocta

Aspidura drummondhayi

Atretium yunnanensis

Xenochrophis asperrimus

Xenochrophis punctulatus

Atretium schistosum

Xenochrophis piscator

Xenochrophis flavipunctatus

Xenochrophis vittatus

Amphiesma stolatum

Rhabdophis nuchalis

Rhabdophis tigrinus

Rhabdophis subminiatus

Balanophis ceylonensis

Macropisthodon rudis

Lycognathophis seychellensis

Afronatrix anoscopus

Natriciteres olivacea

Amphiesma craspedogaster

Amphiesma sauteri

Trachischium monticola

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Natricinae

ZFigure 27

Sibynomorphus neuwiedi

Sibynomorphus ventrimaculatus

Dipsas albifrons

Dipsas articulata

Sibynomorphus turgidus

Sibynomorphus mikanii

Dipsas pratti

Dipsas variegata

Dipsas neivai

Dipsas catesbyi

Dipsas indica

Tropidodipsas sartorii

Sibon nebulatus

Ninia atrata

Atractus zebrinus

Atractus trihedrurus

Atractus reticulatus

Atractus badius

Atractus flammigerus

Atractus elaps

Atractus albuquerquei

Atractus schach

Atractus wagleri

Atractus zidoki

Geophis godmani

Geophis carinosus

Cryophis hallbergi

Tretanorhinus nigroluteus

Hydromorphus concolor

Adelphicos quadrivirgatum

Leptodeira rubricata

Leptodeira maculata

Leptodeira bakeri

Leptodeira annulata

Leptodeira septentrionalis

Leptodeira punctata

Leptodeira splendida

Leptodeira frenata

Leptodeira uribei

Imantodes cenchoa

Imantodes gemmistratus

Imantodes lentiferus

Imantodes inornatus

Leptodeira nigrofasciata

Tretanorhinus variabilis

Hypsiglena chlorophaea

Hypsiglena torquata

Hypsiglena ochrorhyncha

Hypsiglena affinis

Hypsiglena jani

Hypsiglena slevini

Trimetopon gracile

Pseudoleptodeira latifasciata

Rhadinaea fulvivittis

Rhadinaea flavilata

Coniophanes fissidens

Tantalophis discolor

Amastridium veliferum

Nothopsis rugosus

Farancia erytrogramma

Farancia abacura

Carphophis amoenus

Diadophis punctatus

Heterodon nasicus

Heterodon simus

Heterodon platirhinos

Contia tenuis

Thermophis baileyi

Thermophis zhaoermii

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Pseudoboa coronataPseudoboa nigra

Pseudoboa neuwiediiRhachidelus brazili

Boiruna maculataDrepanoides anomalus

Mussurana bicolorClelia clelia

Phimophis gueriniParaphimophis rusticus

Rodriguesophis iglesiasiOxyrhopus guibei

Oxyrhopus melanogenysOxyrhopus rhombifer

Oxyrhopus clathratusOxyrhopus trigeminus

Oxyrhopus formosusOxyrhopus petolarius

Siphlophis longicaudatusSiphlophis pulcher

Siphlophis compressusSiphlophis cervinus

Hydrodynastes gigasHydrodynastes bicinctus

Caaeteboia amaraliXenopholis scalarisXenopholis undulatus

Tropidodryas striaticepsTropidodryas serra

Thamnodynastes rutilusThamnodynastes strigatus

Thamnodynastes hypoconiaThamnodynastes laneiThamnodynastes pallidusTomodon dorsatus

Ptychophis flavovirgatusTachymenis peruviana

Pseudotomodon trigonatusCalamodontophis paucidens

Gomesophis brasiliensisHelicops angulatus

Helicops gomesiHelicops carinicaudus

Helicops hagmanniHelicops infrataeniatus

Pseudoeryx plicatilisHydrops triangularis

Manolepis putnamiApostolepis cearensisApostolepis sanctaeritae

Apostolepis flavotorquataApostolepis albicollaris

Apostolepis dimidiataApostolepis assimilis

Elapomorphus quinquelineatusPhalotris mertensi

Phalotris lativittatusPhalotris nasutusPhalotris lemniscatusTaeniophallus affinisEchinanthera undulataEchinanthera melanostigma

Taeniophallus nicagusTaeniophallus brevirostris

Sordellina punctataPhilodryas patagoniensis

Philodryas agassiziiPhilodryas aestiva

Philodryas psammophideaPhilodryas mattogrossensis

Philodryas georgeboulengeriPhilodryas argentea

Philodryas olfersiiPhilodryas viridissima

Philodryas nattereriPhilodryas baroni

Erythrolamprus aesculapiiErythrolamprus mimus

Eryrthrolamprus typhlusEryrthrolamprus pygmaea

Eryrthrolamprus brevicepsEryrthrolamprus reginae

Eryrthrolamprus miliarisEryrthrolamprus juliae

Eryrthrolamprus epinephelusEryrthrolamprus poecilogyrusEryrthrolamprus ceii

Eryrthrolamprus almadensisEryrthrolamprus jaegeri

Eryrthrolamprus atraventerXenodon pulcherXenodon matogrossensisXenodon semicinctusXenodon guentheri

Xenodon nattereriXenodon histricus

Xenodon dorbignyiXenodon neuwiedii

Xenodon werneriXenodon merremi

Xenodon severusLygophis meridionalis

Lygophis flavifrenatusLygophis paucidens

Lygophis lineatusLygophis elegantissimus

Lygophis anomalusUromacer frenatusUromacer oxyrhynchusUromacer catesbyi

Schwartzophis funereumSchwartzophis polylepis

Schwartzophis callilaemumAntillophis parvifrons

Hypsirhynchus feroxDarlingtonia haetiana

Ialtris dorsalisAlsophis rufiventrisAlsophis antiguaeAlsophis rijgersmaei

Alsophis antillensisBorikenophis portoricensisHaitiophis anomalusCaraiba andreae

Cubophis vudiiCubophis cantherigerus

Magliophis exiguumArrhyton dolichura

Arrhyton tanyplectumArrhyton procerum

Arrhyton landoiArrhyton vittatum

Arrhyton supernumArrhyton taeniatum

Pseudalsophis elegansPseudalsophis biserialis

Psomophis jobertiPsomophis genimaculatus

Psomophis obtususCrisantophis nevermanni

Conophis lineatus

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Figure 28

Additional files provided with this submission:

Additional file 1: 2046042875907394_add1.txt, 264Khttp://www.biomedcentral.com/imedia/1032288879981940/supp1.txtAdditional file 2: 2046042875907394_add2.docx, 681Khttp://www.biomedcentral.com/imedia/7057154239819418/supp2.docx