BMC Evolutionary Biology

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

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

Robert Alexander Pyron ([email protected]) Frank T Burbrink ([email protected]) John J Wiens ([email protected])

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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© 2013 Pyron et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

Robert Alexander Pyron 1* * Corresponding author Email: [email protected]

Frank T Burbrink 2,3 Email: [email protected]

John J Wiens 4 Email: [email protected]

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. References

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Sphenodontidae Dibamidae 77 Carphodactylidae Pygopodidae A 100 Diplodactylidae 100 Eublepharidae 100 Sphaerodactylidae Phyllodactylidae 100 Gekkonidae Cricosaurinae Squamata 100 Xantusiinae Xantusiidae 99 100 Lepidophyminae Gerrhosaurinae Gerrhosauridae 100 Zonosaurinae B Platysaurinae 100 100 Cordylidae 100 Cordylinae Acontiinae 95 100 Scincinae Scincidae 94 Lygosominae 54 Tupinambinae Teiidae Teiinae Alopoglossinae 100 84 Bachiinae Rhachisaurinae 98 Gymnophthalmidae 99 Gymnophthalminae 100 100 Ecpleopinae D Cercosaurinae 99 Rhineuridae 100 Bipedidae Blanidae 100 Cadeidae 100 84 Trogonophiidae 100 Amphisbaenidae 100 Gallotiinae Lacertinae Lacertidae 100 Xenosauridae Helodermatidae Anniellidae 95 F 100 Diploglossinae Anguinae Anguidae 100 90 100 Gerrhonotinae C Shinisauridae 100 94 Lanthanotidae 100 Varanidae 79 100 Brookesiinae Chamaeleoninae Chamaeleonidae 100 Uromasticinae Leiolepidinae 100 Hydrosaurinae 96 Amphibolurinae Agamidae 100 100 Agaminae G 100 Draconinae Tropiduridae 100 Iguanidae Leiocephalidae Crotaphytidae 72 87 E 54 Phrynosomatidae 96 Polychrotidae 99 81 Hoplocercidae Opluridae 99 Enyaliinae 63 Leiosauridae 95 100 Leiosaurinae Liolaemidae Corytophanidae 99 Dactyloidae Anomalepididae 90 Leptotyphlopidae H 100 Gerrhopilidae 100 Xenotyphlopidae 83 Typhlopidae 98 Aniliidae Tropidophiidae Xenophiidae Bolyeriidae 100 Sanziniinae 100 Calabariidae Ungaliophiinae 69 Boidae 99 Candoiinae 97 87 Erycinae 83 88 Boinae Anomochilidae 65 Cylindrophiidae 100 89 Uropeltidae Xenopeltidae 98 Loxocemidae 100 Pythonidae A) Gekkota Acrochordidae 95 Xenodermatidae B) Scincoidea Pareatidae Viperinae 100 100 C) Episquamata Azemiopinae Viperidae D) Lacertoidea 100 Crotalinae 100 Homalopsidae Prosymninae E) Toxicofera 95 58 Psammophiinae F) Anguimorpha 95 95 Atractaspidinae 100 Aparallactinae G) Iguania 96 Pseudaspidinae Lamprophiidae H) Serpentes Lamprophiinae 90 Pseudoxyrhophiinae 100 Elapidae Calamariinae 97 Pseudoxenodontinae Sibynophiinae 100 74 Grayiinae Colubridae 71 Colubrinae 68 Natricinae Figure 1 0.2 subst./site Dipsadinae &∃&##% #$$ &∃%&∃ ! #$ &$' &∃## #$$ ∗%#!∃∃!!∃&∃ &∃%∃∃ && &∃∋& #$$ &∃∃#∃∃ #$$ &∃∃∃ #$$ ** ∗&#&∃ ∗&#&∃!%&#&∃ # & ∗&#&∃ '" %&#&∃#&%&∃ %&#&∃∃#∃&∃ %&#&∃(∗# ($ &$- &$' #$$ %&#&∃% " %&#&∃∃( #$$ &* %&#&∃#%+ ##∗&%&∃ #!%∗&∃∋∃ "( ∋&∃∃!∗#&#&∃ &" #(∃&#&∃ % !#&#&∃(# #$$ !#&#&∃∃!# !#&#&∃∗ * #$$ !#&#&∃∃ '& !#&#&∃∋∃ !#&#&∃∃%%&∃ && #$$ !#&#&∃∋#%#∃ #$$ !#&#&∃∋∃∃&∃ $ !#&#&∃ #$$ %#∀&% &∃%#∃ #$$ "$ ∃ # !) #$$ %% % " # * !# ∃&% ' #$$ &%# #$$ #% '% #∃# #∗ !!&∃%%&∃ #$$ ∃&#%∃ 12& &$' ∃# %)#∃ "( #$$ ##%∃ ∗!&∃#!∃ % ∗!&∃!!&∃ !#∃&#% &' !#∃∃%#% "% !#∃&#% #$$ # !#∃!#!& #$$ !#∃!∃&!& #$$ !#∃!%&#% #$$ !#∃!& &( !#∃&∃ &# !#∃∃% * !#∃#!∃ ∃&%%∗&∃# ( %∗&∃%#∗#∗&∃ ###% #!&∃∃ ) #)!%%&∃ #∋∋∃ #&∃∃ *# #∃&#∃ ' # '& #%∃(% % #∃∃ '& ∋∗!& #$$ ∋∗∃&∋ * ∋∗% '& %∗&∃&∃ &( ∋∗#% ∋∗#∃∃ ∋∗% ( ∋∗∗&# #$$ %∗&∃&#&%&∃ " ##!&∃%&∃ ##!&∃∃#∃#& #& &#∗%∗∃∃∗%#&∃ '" &#∗%∗∃%∃ ' &#∗%∗∃∋# #$$ &#∗%∗∃# #%∗&∃%&∃ #$$ !%∗&∃&∋& (#%&%&∃ &% (#%#∗∃∃#%&∃ #$$ %∗∃!&∃ #!&&∃%!∃ #$$ !##&&%# !##&#&%&∃ ) !##&&∃&∃ % #$$ !##&#∗!%+&∃ &&%&&#&# #$$ &%&∃&∃ & &%&∃#∗ #$$ &%&∃∃ &%&∃∃%%&∃ ( &%&∃%&#&%&∃ '' &%&∃&&∃ #$$ * &%&∃#&∃ '# &%&∃!#&∃ &##&∃% &$ #$$ %#!&#&∃%& ∃∃&&# ' ∃∃&# '% ∃## ∃!#&##%&% ( &#∃ &#%#∗ &## #$$ #$$ #$$ &#∃%& &##∃ !  &$- &$' &#! 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'% !%∗&∃% !%∗&∃∃∋ "#!! $#% &( !%∗&∃!&# Figure 2 & !%∗&∃& Aeluroscalabotes felinus 79 100 Coleonyx brevis Coleonyx variegatus 100 Coleonyx mitratus Eublepharidae 100 Coleonyx elegans 100 Eublepharis macularius 100 100 Eublepharis turcmenicus Holodactylus africanus Hemitheconyx caudicinctus 100 100 Hemitheconyx taylori 100 Goniurosaurus kuroiwae Goniurosaurus lichtenfelderi 97 100 Goniurosaurus catbaensis 96 Goniurosaurus luii 90 Goniurosaurus araneus Pristurus celerrimus 100 Pristurus insignis 100 Pristurus sokotranus Pristurus guichardi 76 92 Pristurus abdelkuri 100 Pristurus flavipunctatus Pristurus rupestris 60 100 Pristurus minimus Pristurus carteri 63 98 Pristurus crucifer 85 Pristurus somalicus 100 Quedenfeldtia trachyblepharus 100 Quedenfeldtia moerens 100 Aristelliger lar Aristelliger praesignis 91 Aristelliger georgeensis 75 Saurodactylus fasciatus 100 Euleptes europaea 78 Teratoscincus microlepis 100 Teratoscincus scincus 97 Teratoscincus przewalskii 98 Teratoscincus roborowskii Saurodactylus mauritanicus Chatogekko amazonicus 100 Lepidoblepharis xanthostigma Lepidoblepharis festae 99 97 Gonatodes eladioi 83 Gonatodes caudiscutatus 89 Gonatodes daudini 100 Gonatodes albogularis 100 96 Gonatodes petersi Gonatodes vittatus 100 98 Gonatodes infernalis Sphaerodactylidae Gonatodes hasemani 70 Gonatodes annularis 60 Gonatodes superciliaris 100 Gonatodes alexandermendesi 60 Gonatodes purpurogularis 100 Gonatodes taniae 95 Gonatodes falconensis 79 Gonatodes humeralis 97 100 Gonatodes antillensis 93 Gonatodes concinnatus 89 Gonatodes seigliei 100 Gonatodes ceciliae 99 Gonatodes ocellatus Coleodactylus septentrionalis 100 Coleodactylus brachystoma 99 Coleodactylus meridionalis 100 Coleodactylus natalensis 100 Pseudogonatodes manessi 96 Pseudogonatodes lunulatus 82 Pseudogonatodes guianensis Sphaerodactylus fantasticus 98 Sphaerodactylus sputator 87 Sphaerodactylus elegantulus 87 Sphaerodactylus sabanus 81 Sphaerodactylus parvus Sphaerodactylus microlepis Sphaerodactylus vincenti 100 82 100 Sphaerodactylus kirbyi 100 Sphaerodactylus schwartzi Sphaerodactylus ramsdeni 84 84 Sphaerodactylus cricoderus 83 Sphaerodactylus richardi 100 Sphaerodactylus oliveri 91 Sphaerodactylus molei 84 Sphaerodactylus glaucus Sphaerodactylus thompsoni 69 81 Sphaerodactylus cinereus Sphaerodactylus torrei 100 Sphaerodactylus intermedius 100 Sphaerodactylus nigropunctatus 93 Sphaerodactylus copei 83 Sphaerodactylus leucaster Sphaerodactylus elegans Sphaerodactylus shrevei 85 99 Sphaerodactylus cryphius 90 Sphaerodactylus darlingtoni Sphaerodactylus notatus Sphaerodactylus altavelensis 52 Sphaerodactylus roosevelti 85 Sphaerodactylus argus Sphaerodactylus macrolepis 93 Sphaerodactylus armstrongi 84 Sphaerodactylus townsendi 83 79 Sphaerodactylus goniorhynchus 66 Sphaerodactylus semasiops Sphaerodactylus klauberi Phyllodactylidae 94 Sphaerodactylus gaigeae Sphaerodactylus ocoae 99 Sphaerodactylus nicholsi 100 Thecadactylus solimoensis Thecadactylus rapicauda 98 Haemodracon riebeckii Asaccus platyrhynchus 65 100 Ptyodactylus ragazzii Ptyodactylus oudrii 100 Ptyodactylus hasselquistii Ptyodactylus guttatus Homonota gaudichaudii Homonota fasciata 93 Homonota underwoodi 100 Homonota borellii 100 85 Homonota darwinii 100 92 Homonota andicola Phyllodactylus wirshingi Phyllodactylus reissii 100 86 Phyllodactylus tuberculosus 65 Phyllodactylus lanei Phyllodactylus bordai 100 97 Phyllodactylus xanti Phyllodactylus unctus 99 100 92 97 Phyllodactylus bugastrolepis 100 Phyllodactylus nocticolus 100 Phyllodactylus paucituberculatus 67 Phyllodactylus delcampoi 75 Phyllodactylus duellmani 96 Phyllodactylus davisi 57 Phyllodactylus homolepidurus Phyllopezus periosus 100 Phyllopezus pollicaris 90 Phyllopezus lutzae 92 Phyllopezus maranjonensis Tarentola americana 73 Tarentola boehmei 100 100 Tarentola deserti Tarentola mauritanica 99 Tarentola angustimentalis 87 Tarentola neglecta 99 100 Tarentola mindiae Tarentola boettgeri 100 Tarentola ephippiata 93 Tarentola annularis 76 Tarentola gomerensis 91 Tarentola delalandii Tarentola chazaliae 62 Tarentola darwini B 100 99 Tarentola rudis Tarentola caboverdiana Figure 3 C 73 Tarentola gigas Lepidodactylus novaeguineae Perochirus ateles Pseudogekko smaragdinus Urocotyledon inexpectata 100 100 Pseudogekko compressicorpus 93 Ebenavia inunguis Lepidodactylus orientalis 83 Paroedura masobe 100 Luperosaurus macgregori 100 Paroedura gracilis Luperosaurus cumingii 98 99 Paroedura homalorhina Paroedura oviceps 79 Luperosaurus joloensis Lepidodactylus lugubris 73 Paroedura karstophila 100 91 100 100 100 Paroedura lohatsara Lepidodactylus moestus Paroedura stumpffi 100 Gekko smithii 85 Paroedura sanctijohannis Gekko gecko 99 Paroedura picta 100 Gekko chinensis 100 Paroedura androyensis Gekko japonicus Paroedura vazimba 92 99 Gekko hokouensis 61 Paroedura tanjaka 100 95 Gekko auriverrucosus Paroedura bastardi 98 100 Ailuronyx tachyscopaeus 54 Gekko swinhonis Gekko athymus Ailuronyx seychellensis 100 Ailuronyx trachygaster 100 Gekko monarchus Calodactylodes illingworthorum (i) Gekko mindorensis 100 100 Calodactylodes aureus 99 Gekko romblon 98 Ptenopus carpi Gekko crombota 80 (ii) 65 Narudasia festiva 100 Gekko porosus Cnemaspis uzungwae 100 89 Ptychozoon rhacophorus 53 100 Cnemaspis dickersonae Ptychozoon kuhli 69 Cnemaspis africana 64 87 Uroplatus guentheri (ii) 95 Ptychozoon lionotum 92 Luperosaurus iskandari Uroplatus malahelo 100 Uroplatus malama 97 Gekko vittatus 100 Uroplatus ebenaui Gekko petricolus Uroplatus phantasticus 94 Gekko badenii 85 100 96 Uroplatus alluaudi Gekko grossmanni 50 100 Uroplatus pietschmanni Dixonius melanostictus Uroplatus lineatus 100 Dixonius vietnamensis 100 Uroplatus sikorae 100 100 Dixonius siamensis 77 100 Uroplatus henkeli 100 Heteronotia planiceps 100 Uroplatus giganteus Heteronotia binoei 100 Uroplatus fimbriatus 100 Paragehyra gabriellae Heteronotia spelea 56 97 Christinus marmoratus Nactus acutus Afrogecko swartbergensis Nactus eboracensis 100 Cryptactites peringueyi 100 Nactus vankampeni 100 Matoatoa brevipes 83 100 Nactus galgajuga 52 Afrogecko porphyreus Nactus cheverti 100 Afroedura pondolia 98 100 Nactus multicarinatus 52 Afroedura karroica Nactus pelagicus 79 Geckolepis typica Hemiphyllodactylus typus 100 Geckolepis maculata Hemiphyllodactylus yunnanensis 89 99 Homopholis fasciata 100 93 100 Homopholis walbergii 85 Hemiphyllodactylus aurantiacus Homopholis mulleri 100 Gehyra fehlmanni 100 Blaesodactylus boivini Gehyra mutilata Blaesodactylus antongilensis 100 98 99 97 Gehyra lacerata 100 Blaesodactylus sakalava Gehyra brevipalmata Goggia lineata 100 Gehyra baliola Rhoptropus afer

Gekkonidae 100 Gehyra barea Rhoptropus bradfieldi 99 84 Rhoptropus boultoni 59 Gehyra marginata 100 Gehyra oceanica 99 Rhoptropus biporosus (i) 91 98 98 Rhoptropus barnardi 96 Gehyra membranacruralis 86 Elasmodactylus tetensis 100 Gehyra dubia 100 Elasmodactylus tuberculosus Gehyra catenata Chondrodactylus angulifer 100 Gehyra pamela 100 Pachydactylus laevigatus 55 Gehyra borroloola 100 Chondrodactylus turneri 97 Gehyra robusta 96 100 86 Chondrodactylus fitzsimonsi 70 Gehyra koira Chondrodactylus bibronii 100 Gehyra occidentalis Pachydactylus robertsi Gehyra australis 100 93 Colopus wahlbergii Gehyra xenopus Colopus kochii 98 Pachydactylus haackei Gehyra nana Pachydactylus kladaroderma 98 Gehyra purpurascens 89 100 Pachydactylus namaquensis 98 100 Gehyra variegata 68 Pachydactylus scutatus Gehyra punctata 74 100 Pachydactylus parascutatus Gehyra pilbara Pachydactylus reconditus 98 Gehyra montium 70 95 Pachydactylus gaiasensis 92 Gehyra minuta 90 Pachydactylus oreophilus Alsophylax pipiens 100 91 Pachydactylus bicolor Tropiocolotes helenae Pachydactylus caraculicus 65 100 Cnemaspis limi 63 Pachydactylus sansteynae 86 Pachydactylus scherzi Cnemaspis kendallii Pachydactylus punctatus 100 Mediodactylus spinicaudum 96 85 100 Pachydactylus rugosus 98 Mediodactylus russowii 99 Pachydactylus formosus Pseudoceramodactylus khobarensis 95 Pachydactylus barnardi Tropiocolotes tripolitanus 84 Pachydactylus labialis 96 Stenodactylus arabicus Pachydactylus geitje 92 Stenodactylus petrii 52 Pachydactylus maculatus 100 Stenodactylus leptocosymbotus 93 Pachydactylus oculatus 96 100 Stenodactylus doriae Pachydactylus purcelli Stenodactylus yemenensis 61 100 Pachydactylus waterbergensis 100 97 Pachydactylus tsodiloensis 85 Stenodactylus sthenodactylus Pachydactylus fasciatus Mediodactylus kotschyi 98 Pachydactylus carinatus Mediodactylus sagittiferum 85 99 Pachydactylus griffini 69 Mediodactylus heterocercum 68 Pachydactylus serval 99 Mediodactylus heteropholis 74 Pachydactylus weberi 75 100 Bunopus tuberculatus Pachydactylus monicae Crossobamon orientalis 69 Pachydactylus mclachlani 86 Bunopus crassicauda Pachydactylus mariquensis Agamura persica 99 Pachydactylus austeni 95 Pachydactylus rangei Cyrtopodion sistanensis 100 Pachydactylus vanzyli 99 Cyrtopodion scabrum Pachydactylus montanus Cyrtopodion longipes Pachydactylus tigrinus 79 100 Cyrtopodion caspium 100 Pachydactylus oshaughnessyi Cyrtopodion agamuroides 72 Pachydactylus capensis 99 Cyrtopodion gastrophole 100 Pachydactylus vansoni Cyrtodactylus oldhami 100 Pachydactylus affinis 100 87 Cyrtodactylus ayeyarwadyensis Cnemaspis podihuna Cnemaspis kandiana 100 Cyrtodactylus angularis 100 Cyrtodactylus jarujini 99 Cnemaspis tropidogaster Cyrtodactylus triedrus Rhoptropella ocellata 88 Lygodactylus expectatus Cyrtodactylus marmoratus Lygodactylus rarus 92 Cyrtodactylus irregularis Lygodactylus madagascariensis 99 71 100 Cyrtodactylus consobrinus 98 Lygodactylus miops 52 Cyrtodactylus annulatus 92 Lygodactylus guibei Lygodactylus tolampyae 97 Cyrtodactylus philippinicus 100 92 98 Cyrtodactylus agusanensis Lygodactylus heterurus Cyrtodactylus intermedius 100 100 Lygodactylus verticillatus Cyrtodactylus pulchellus 81 Lygodactylus blancae 79 Cyrtodactylus sermowaiensis 90 91 Lygodactylus arnoulti 94 85 Lygodactylus pauliani Cyrtodactylus loriae Lygodactylus gravis 77 Cyrtodactylus novaeguineae 81 99 Lygodactylus montanus 96 Cyrtodactylus tuberculatus 82 Lygodactylus tuberosus 98 97 Cyrtodactylus klugei 73 Lygodactylus mirabilis Cyrtodactylus robustus 98 Lygodactylus pictus Cyrtodactylus tripartitus Lygodactylus lawrencei 98 Lygodactylus stevensoni 98 Cyrtodactylus epiroticus 68 89 99 Cyrtodactylus louisiadensis 93 Lygodactylus capensis Hemidactylus bowringii 84 Lygodactylus bradfieldi 100 Lygodactylus klugei 100 Hemidactylus garnotii Lygodactylus conraui Hemidactylus karenorum 100 97 Lygodactylus thomensis Hemidactylus platyurus 78 Lygodactylus angularis Hemidactylus fasciatus Lygodactylus gutturalis 100 Hemidactylus aaronbaueri 67 Lygodactylus chobiensis 81 93 Hemidactylus giganteus 94 Lygodactylus williamsi Hemidactylus depressus 94 Lygodactylus picturatus Hemidactylus triedrus 68 100 Lygodactylus luteopicturatus 89 Hemidactylus prashadi 97 Lygodactylus kimhowelli 88 93 Lygodactylus keniensis 100 93 76 Hemidactylus maculatus 92 100 Hemidactylus leschenaultii Phelsuma vanheygeni 100 Phelsuma astriata Hemidactylus flaviviridis 100 Phelsuma sundbergi Hemidactylus frenatus Phelsuma guttata Hemidactylus brookii Phelsuma madagascariensis 100 Hemidactylus sataraensis 100 Phelsuma abbotti 100 Hemidactylus imbricatus 100 Phelsuma parkeri 99 Hemidactylus albofasciatus 87 Phelsuma seippi 56 Phelsuma barbouri Hemidactylus reticulatus 100 Hemidactylus gracilis 96 100 Phelsuma pronki 97 Phelsuma breviceps Hemidactylus angulatus Phelsuma mutabilis 100 Hemidactylus haitianus 85 57 92 Phelsuma andamanense Hemidactylus mabouia Phelsuma standingi 100 Hemidactylus mercatorius 82 Phelsuma edwardnewtoni Hemidactylus longicephalus 94 Phelsuma gigas 100 Hemidactylus platycephalus 99 Phelsuma guentheri 97 Hemidactylus greeffii 99 Phelsuma borbonica 100 Hemidactylus brasilianus 95 Phelsuma cepediana Hemidactylus bouvieri 100 Phelsuma guimbeaui 96 Phelsuma ornata 99 95 Hemidactylus palaichthus 100 55 100 Phelsuma inexpectata 97 Hemidactylus agrius Phelsuma nigristriata 96 Hemidactylus modestus 98 100 Phelsuma modesta Hemidactylus citernii Phelsuma dubia Hemidactylus foudaii 100 Phelsuma ravenala Hemidactylus pumilio 98 Phelsuma flavigularis 98 Hemidactylus dracaenacolus 94 Phelsuma hielscheri 100 Hemidactylus granti 100 99 Phelsuma berghofi Phelsuma malamakibo 97 Hemidactylus persicus 82 Hemidactylus yerburii 95 Phelsuma serraticauda Phelsuma laticauda 91 Hemidactylus robustus 95 99 Hemidactylus turcicus Phelsuma robertmertensi 99 96 Phelsuma klemmeri 91 Hemidactylus lemurinus Phelsuma antanosy Hemidactylus mindiae 87 Phelsuma quadriocellata C 96 Hemidactylus macropholis 99 Phelsuma pusilla 66 Hemidactylus oxyrhinus 100 Phelsuma comorensis Figure 4 97 Hemidactylus forbesii 57 Phelsuma lineata 98 Hemidactylus homoeolepis 94 Phelsuma kely Cricosaura typica Cricosaurinae 100 Xantusia gracilis Xantusia henshawi Xantusiidae Xantusiinae 100 Xantusia bolsonae 100 100 Xantusia sanchezi Xantusia riversiana 84 97 Xantusia arizonae 92 Xantusia vigilis 100 100 Xantusia bezyi 66 Xantusia wigginsi Lepidophyma mayae 100 Lepidophyma tuxtlae 100 Lepidophyma lipetzi Lepidophyminae 100 Lepidophyma flavimaculatum 100 Lepidophyma reticulatum Lepidophyma pajapanensis 94 Lepidophyma occulor 87 Lepidophyma micropholis 100 Lepidophyma sylvaticum 95 Lepidophyma gaigeae Lepidophyma lineri Lepidophyma smithii 95 Lepidophyma cuicateca 94 Lepidophyma lowei 100 Lepidophyma radula 99 100 Lepidophyma dontomasi Gerrhosaurus major Gerrhosaurinae 100 Cordylosaurus subtessellatus 95 Tetradactylus seps 98 Tetradactylus africanus 69 Tetradactylus tetradactylus Gerrhosaurus validus Gerrhosaurus skoogi Gerrhosauridae 79 Gerrhosaurus typicus Gerrhosaurus nigrolineatus 100 91 100 Gerrhosaurus multilineatus 76 Gerrhosaurus flavigularis 100 Tracheloptychus madagascariensis Tracheloptychus petersi 100 100 Zonosaurus haraldmeieri Zonosaurus madagascariensis Zonosaurinae Zonosaurus ornatus 100 Zonosaurus trilineatus 91 Zonosaurus quadrilineatus Zonosaurus karsteni 100 Zonosaurus anelanelany 96 100 Zonosaurus laticaudatus Zonosaurus boettgeri 100 Zonosaurus tsingy Zonosaurus brygooi 66 73 Zonosaurus subunicolor 82 Zonosaurus bemaraha 89 Zonosaurus aeneus 87 Zonosaurus rufipes Platysaurinae Platysaurus pungweensis Platysaurus mitchelli 92 Platysaurus broadleyi 100 Platysaurus capensis 91 Platysaurus intermedius Platysaurus minor 100 Platysaurus monotropis Ouroborus cataphractus Cordylidae 100 Karusasaurus jordani Karusasaurus polyzonus 99 Namazonurus campbelli 100 Namazonurus pustulatus 100 Namazonurus namaquensis Cordylinae Namazonurus lawrenci 100 Namazonurus peersi 94 Smaug warreni Smaug giganteus 100 55 Chamaesaura aenea Chamaesaura anguina Pseudocordylus langi 93 Pseudocordylus microlepidotus 100 Pseudocordylus spinosus 99 Pseudocordylus melanotus 95 86 Ninurta coeruleopunctatus 100 Hemicordylus nebulosus Hemicordylus capensis 95 Cordylus tropidosternum 99 Cordylus meculae 96 Cordylus vittifer 81 88 Cordylus ukingensis Cordylus beraduccii 82 Cordylus jonesii 83 99 Cordylus rhodesianus 92 Cordylus macropholis Cordylus imkeae 83 Cordylus aridus 100 Cordylus minor 100 84 Cordylus niger Cordylus mclachlani 85 Cordylus oelofseni D 86 Cordylus tasmani 100 Figure 5 Cordylus cordylus 89 Typhlosaurus braini Typhlosaurus meyeri 95 Typhlosaurus caecus Typhlosaurus vermis Acontiinae 99 100 Typhlosaurus lomiae 100 Acontias gariepensis Acontias lineatus 100 Acontias litoralis Acontias kgalagadi 96 Acontias meleagris 94 Acontias percivali 98 Acontias rieppeli 98 Acontias breviceps Acontias gracilicauda 92 Acontias plumbeus 100 Acontias poecilus 98 Mesoscincus schwartzei 91 Mesoscincus managuae Ophiomorus punctatissimus 99 Ophiomorus latastii Brachymeles apus Brachymeles miriamae 100 99 Brachymeles tridactylus Brachymeles bonitae 94 94 Brachymeles minimus 95 Brachymeles cebuensis Brachymeles samarensis 83 Brachymeles talinis Brachymeles elerae 88 Brachymeles schadenbergi 85 Brachymeles boulengeri 85 73 Brachymeles bicolor Brachymeles gracilis 85 Brachymeles pathfinderi Plestiodon tamdaoensis 100 Plestiodon kishinouyei 100 Plestiodon chinensis Plestiodon quadrilineatus 98 Plestiodon tunganus 100 Plestiodon capito 100 86 Plestiodon barbouri Plestiodon japonicus 97 Plestiodon latiscutatus Scincidae 70 93 Plestiodon elegans Plestiodon marginatus 100 100 Plestiodon stimpsonii Plestiodon reynoldsi 97 100 Plestiodon egregius 88 Plestiodon anthracinus 74 Plestiodon inexpectatus 97 56 Plestiodon laticeps Plestiodon tetragrammus Scincinae 100 Plestiodon callicephalus 74 Plestiodon obsoletus 76 Plestiodon fasciatus 100 71 Plestiodon multivirgatus 98 86 Plestiodon septentrionalis Plestiodon longirostris 92 Plestiodon gilberti Plestiodon lagunensis 100 Plestiodon skiltonianus Plestiodon parviauriculatus Plestiodon sumichrasti 100 91 Plestiodon lynxe 73 Plestiodon ochoterenae 73 Plestiodon parvulus 76 Plestiodon copei Plestiodon brevirostris 98 Plestiodon dugesii Eurylepis taeniolatus Eumeces schneideri 77 Scincopus fasciatus 100 Eumeces algeriensis 100 100 Scincus scincus Scincus mitranus 99 Pamelaescincus gardineri Janetaescincus veseyfitzgeraldi 100 Janetaescincus braueri Gongylomorphus bojerii Chalcides mauritanicus 81 55 92 Chalcides minutus 57 Chalcides guentheri 100 Chalcides chalcides 86 Chalcides pseudostriatus 94 75 Chalcides striatus 74 Chalcides ocellatus 100 Chalcides sepsoides 91 Chalcides colosii 100 Chalcides bedriagai 74 Chalcides boulengeri 87 Chalcides parallelus 88 99 Chalcides lanzai 98 Chalcides sexlineatus 99 Chalcides coeruleopunctatus Chalcides viridanus 100 Chalcides sphenopsiformis Chalcides mionecton 94 Chalcides manueli 95 Chalcides polylepis 96 Chalcides montanus Sepsina angolensis 97 97 100 Typhlacontias brevipes Typhlacontias punctatissimus 100 100 Feylinia grandisquamis 96 Feylinia polylepis 93 98 Feylinia currori 96 Melanoseps occidentalis 100 Melanoseps ater Melanoseps loveridgei Hakaria simonyi Proscelotes eggeli 80 Scelotes caffer 89 Scelotes anguineus 100 Scelotes mirus 99 87 Scelotes arenicolus Scelotes bipes 97 Scelotes sexlineatus 100 Scelotes gronovii 75 Scelotes montispectus 92 94 Scelotes kasneri 100 Paracontias holomelas Paracontias brocchii 60 Paracontias manify 100 69 Paracontias hildebrandti Paracontias rothschildi Madascincus melanopleura 89 Pseudoacontias menamainty 52 Madascincus igneocaudatus 97 Madascincus mouroundavae Madascincus nanus 64 100 Madascincus stumpffi 100 Madascincus polleni 87 Madascincus intermedius 100 Amphiglossus melanurus 90 Amphiglossus ornaticeps F-I 100 Amphiglossus mandokava Amphiglossus tanysoma 100 Pygomeles braconnieri 100 Androngo trivittatus 93 Amphiglossus tsaratananensis 85 Amphiglossus reticulatus 86 Amphiglossus astrolabi 93 Voeltzkowia fierinensis 100 Voeltzkowia lineata 95 Voeltzkowia rubrocaudata 24 Amphiglossus splendidus E 80 Amphiglossus anosyensis 70 Amphiglossus macrocercus 90 Amphiglossus punctatus Figure 6 96 Amphiglossus frontoparietalis Ateuchosaurus pellopleurus Asymblepharus alaicus 100 Ablepharus pannonicus Sphenomorphus praesignis 81 Sphenomorphus simus Tropidophorus berdmorei 98 60 100 Tropidophorus matsuii Tropidophorus latiscutatus 90 Tropidophorus noggei 99 Tropidophorus murphyi Tropidophorus hainanus 89 100 98 Tropidophorus baviensis Tropidophorus sinicus Tropidophorus robinsoni 98 Tropidophorus thai Tropidophorus cocincinensis 83 89 Tropidophorus microlepis Tropidophorus grayi 97 95 Tropidophorus baconi 100 94 Tropidophorus beccarii Tropidophorus brookei 100 Tropidophorus partelloi 95 Tropidophorus misaminius 86 Lipinia vittigera Isopachys anguinoides 77 Sphenomorphus melanopogon 98 Sphenomorphus jobiensis Sphenomorphus muelleri Tytthoscincus aesculeticola 100 Tytthoscincus parvus 100 Tytthoscincus hallieri 92 Tytthoscincus atrigularis 94 Sphenomorphus concinnatus 99 95 100 Sphenomorphus scutatus Sphenomorphus solomonis 100 Sphenomorphus fasciatus 100 Sphenomorphus leptofasciatus 90 87 Sphenomorphus cranei 76 Sphenomorphus maindroni 93 Otosaurus cumingi 100 Pinoyscincus mindanensis 96 Pinoyscincus jagori 100 80 Pinoyscincus coxi Pinoyscincus abdictus 100 100 Pinoyscincus llanosi Sphenomorphus diwata Sphenomorphus acutus 89 Parvoscincus steerei Lygosominae Parvoscincus decipiens 100 Parvoscincus leucospilos Parvoscincus tagapayo 100 Parvoscincus sisoni 76 Parvoscincus beyeri 97 100 Parvoscincus laterimaculatus 99 Parvoscincus luzonense 68 Parvoscincus kitangladensis 83 Parvoscincus lawtoni Larutia seribuatensis Sphenomorphus maculatus Sphenomorphus indicus 91 100 100 Sphenomorphus multisquamatus Sphenomorphus variegatus 100 Sphenomorphus cyanolaemus 100 Sphenomorphus sabanus 65 Scincella reevesii Asymblepharus sikimmensis 96 Scincella lateralis 93 Scincella gemmingeri 54 Scincella cherriei 99 99 Scincella assatus 99 Sphenomorphus buenloicus Prasinohaema virens 100 Insulasaurus arborens 98 Insulasaurus wrighti 80 Insulasaurus victoria 99 Lygosominae Lipinia pulchella F cont. 94 Lipinia noctua Figure 7 H-I G 100 Papuascincus stanleyanus Eulamprus frerei Nangura spinosa Calyptotis lepidorostrum Calyptotis scutirostrum 100 77 Calyptotis ruficauda 97 98 Gnypetoscincus queenslandiae Eulamprus amplus Eulamprus tenuis 78 Eulamprus tigrinus 96 Eulamprus martini 88 100 Eulamprus sokosoma 80 Eulamprus brachyosoma Eulamprus luteilateralis 85 Eulamprus tryoni 83 Eulamprus murrayi 77 Coggeria naufragus 91 Coeranoscincus frontalis Ophioscincus ophioscincus 95 Saiphos equalis Coeranoscincus reticulatus Lygosominae 95 Ophioscincus truncatus Anomalopus swansoni cont. 100 Anomalopus mackayi 100 Anomalopus verreauxi 100 Anomalopus leuckartii Eremiascincus fasciolatus Eremiascincus pardalis 100 Eremiascincus richardsonii 97 91 Eremiascincus douglasi 62 88 Eremiascincus isolepis 100 Hemiergis initialis 100 Hemiergis peronii 100 Hemiergis quadrilineatum 70 Hemiergis gracilipes Hemiergis millewae 82 60 Hemiergis decresiensis Glaphyromorphus punctulatus Glaphyromorphus mjobergi 95 Glaphyromorphus fuscicaudis 93 Glaphyromorphus pumilus 99 Glaphyromorphus cracens 78 Glaphyromorphus darwiniensis Eulamprus quoyii 93 100 Eulamprus leuraensis Eulamprus kosciuskoi 82 Eulamprus heatwolei 87 Eulamprus tympanum Notoscincus ornatus Ctenotus labillardieri 76 Ctenotus brooksi 95 99 Ctenotus rubicundus Ctenotus nasutus 100 Ctenotus pantherinus 95 Ctenotus strauchii Ctenotus youngsoni 81 Ctenotus schomburgkii 85 Ctenotus calurus Ctenotus rawlinsoni 84 Ctenotus fallens Ctenotus saxatilis 67 Ctenotus inornatus 85 Ctenotus spaldingi 99 Ctenotus robustus 76 Ctenotus taeniolatus Ctenotus rutilans 55 89 Ctenotus uber Ctenotus australis 88 Ctenotus leae 95 Ctenotus leonhardii 100 Ctenotus quattuordecimlineatus Ctenotus serventyi 100 Ctenotus greeri 83 Ctenotus tanamiensis 86 Ctenotus mimetes 88 Ctenotus astarte 73 Ctenotus septenarius 63 Ctenotus regius Ctenotus olympicus 97 Ctenotus maryani 66 Ctenotus atlas 90 Ctenotus grandis 51 Ctenotus angusticeps 79 Ctenotus hanloni 92 Ctenotus piankai 85 Ctenotus essingtonii Ctenotus hebetior 78 Ctenotus hilli 91 Ctenotus gagudju 65 Ctenotus pulchellus 95 Lerista stylis Lerista karlschmidti 81 Lerista carpentariae 100 Lerista ameles 99 Lerista cinerea 97 Lerista wilkinsi 98 Lerista kalumburu 91 Lerista apoda 100 Lerista griffini Lerista ips 88 Lerista bipes 99 Lerista labialis 93 Lerista greeri 98 Lerista robusta 90 100 Lerista vermicularis Lerista simillima 99 Lerista walkeri 96 Lerista borealis Lerista frosti 97 Lerista fragilis 89 Lerista chordae Lerista xanthura 99 90 100 Lerista aericeps Lerista taeniata 100 100 Lerista orientalis 100 Lerista ingrami Lerista zonulata 100 87 Lerista neander Lerista puncticauda 100 Lerista desertorum 99 79 Lerista eupoda Lerista gerrardii 100 Lerista axillaris 93 Lerista macropisthopus Lerista microtis 100 Lerista arenicola Lerista edwardsae Lerista baynesi 100 Lerista picturata Lerista flammicauda 85 100 Lerista zietzi 61 Lerista speciosa 100 Lerista elongata 100 Lerista tridactyla 99 Lerista terdigitata 82 90 Lerista dorsalis Lerista punctatovittata 100 Lerista emmotti 100 Lerista elegans 90 Lerista distinguenda 87 Lerista christinae Lerista lineata 92 Lerista planiventralis 93 Lerista stictopleura 90 Lerista allochira 89 Lerista haroldi 96 Lerista muelleri Lerista viduata 93 100 Lerista bougainvillii Lerista praepedita 100 Lerista humphriesi 93 Lerista petersoni 56 Lerista gascoynensis 89 100 Lerista nichollsi 81 Lerista kendricki 77 Lerista yuna 98 Lerista lineopunctulata 100 Lerista varia 100 Lerista connivens G 84 Lerista uniduo 100 Lerista onsloviana Figure 8 96 Lerista kennedyensis 100 Tribolonotus novaeguineae 100 Tribolonotus gracilis Tribolonotus blanchardi Tribolonotus schmidti 86 97 Tribolonotus brongersmai 93 96 Tribolonotus ponceleti 93 Tribolonotus pseudoponceleti Corucia zebrata Egernia saxatilis 86 Bellatorias major 77 Egernia depressa Egernia kingii Bellatorias frerei 100 74 90 Egernia richardi Egernia napoleonis Lissolepis luctuosa 73 Egernia stokesii Egernia hosmeri 96 66 Cyclodomorphus michaeli Cyclodomorphus casuarinae 97 Cyclodomorphus branchialis 81 Tiliqua adelaidensis 95 Tiliqua rugosa 84 Tiliqua occipitalis Lygosominae 71 Tiliqua nigrolutea cont. Tiliqua gigas 91 100 Tiliqua scincoides 88 Liopholis striata Liopholis inornata 98 Liopholis multiscutata 90 Liopholis kintorei 85 Liopholis pulchra 99 73 Liopholis modesta Liopholis margaretae 56 Liopholis whitii 52 Liopholis guthega 90 Liopholis montana 94 Ristella rurkii Lankascincus fallax Eutropis longicaudata 96 Eutropis macularia 95 Eutropis rudis 88 Eutropis macrophthalma Eutropis multifasciata 83 90 100 Eutropis cumingi Eutropis multicarinata 73 Eutropis clivicola 97 Eutropis bibronii 96 100 Eutropis beddomii Eutropis nagarjuni 97 80 Eutropis trivittata 97 Dasia vittata Dasia grisea Dasia olivacea 93 Trachylepis aurata Trachylepis vittata 99 Trachylepis brevicollis Trachylepis socotrana 98 83 Trachylepis maculilabris 91 100 Trachylepis wrightii Trachylepis sechellensis 99 Trachylepis affinis 92 Trachylepis perrotetii 100 Trachylepis quinquetaeniata Trachylepis margaritifera 99 84 Trachylepis atlantica 54 Trachylepis varia Trachylepis capensis 78 100 Trachylepis occidentalis Trachylepis spilogaster 89 100 Trachylepis striata 99 Trachylepis hoeschi 90 100 Trachylepis variegata Trachylepis sulcata 95 Trachylepis homalocephala Trachylepis acutilabris Trachylepis gravenhorstii 74 100 Trachylepis elegans 95 Trachylepis madagascariensis 98 Trachylepis boettgeri 100 Trachylepis vato 97 Trachylepis aureopunctata 95 Trachylepis dumasi Eumecia anchietae 90 91 Chioninia vaillantii 98 Chioninia delalandii Chioninia coctei 80 Chioninia spinalis Chioninia fogoensis 87 100 Chioninia stangeri Mabuya carvalhoi Mabuya croizati Mabuya nigropalmata 100 78 Mabuya sloanii Mabuya altamazonica 98 Mabuya nigropunctata Mabuya cochabambae 97 100 Mabuya dorsivittata 89 Mabuya meridensis 96 Mabuya mabouya Mabuya unimarginata 81 95 Mabuya falconensis Mabuya bistriata Mabuya frenata 70 100 Mabuya agmosticha Mabuya macrorhyncha 77 Mabuya guaporicola 80 Mabuya agilis H 100 Mabuya caissara Figure 9 99 Mabuya heathi Ablepharus budaki Ablepharus chernovi 100 Ablepharus kitaibelii Sphenomorphus stellatus Emoia concolor 96 Emoia tongana Lamprolepis smaragdina 63 Lygosoma quadrupes 60 98 Lygosoma koratense Lygosoma albopunctata 95 Lepidothyris fernandi 93 Lygosoma lineolatum 92 Mochlus afer 100 Lygosoma sundevalli Lygosoma punctata Mochlus brevicaudis 76 70 Lygosoma bowringii Eugongylus rufescens Lygosominae 100 Eugongylus albofasciolatus Emoia loyaltiensis cont. 90 Leiolopisma telfairii 75 100 Leiolopisma mauritiana Panaspis breviceps 100 Panaspis togoensis Afroablepharus wahlbergi 84 99 99 Afroablepharus annobonensis 85 Afroablepharus africanus 90 Lacertaspis reichenowi 85 Lacertaspis rohdei 93 Lacertaspis chriswildi 91 Lacertaspis gemmiventris 96 Lacertaspis lepesmei 100 Leptosiaphos hackarsi 95 Leptosiaphos graueri Leptosiaphos amieti 81 Leptosiaphos kilimensis 95 99 Leptosiaphos vigintiserierum 100 Pseudemoia pagenstecheri 80 Bassiana duperreyi 99 Pseudemoia entrecasteauxii Oligosoma lichenigera Oligosoma suteri Oligosoma pikitanga 100 99 95 Oligosoma taumakae Oligosoma acrinasum 98 Oligosoma infrapunctatum 100 Oligosoma waimatense 86 91 Oligosoma otagense 98 100 Oligosoma chloronoton Oligosoma lineoocellatum 61 99 Oligosoma longipes 99 Oligosoma nigriplantare 98 Oligosoma grande Oligosoma stenotis 85 Oligosoma maccanni 100 90 100 Oligosoma inconspicuum 98 Oligosoma notosaurus Oligosoma zelandicum 100 Oligosoma homalonotum 100 Oligosoma striatum 100 Oligosoma smithi 93 Oligosoma microlepis 94 Oligosoma aeneum 99 99 Oligosoma levidensum Oligosoma hardyi 57 Oligosoma fallai Oligosoma alani 98 63 Oligosoma moco 93 Oligosoma macgregori Oligosoma ornatum Oligosoma townsi 89 Oligosoma oliveri 9796 Oligosoma whitakeri 98 Nannoscincus garrulus 98 Nannoscincus slevini 89 Nannoscincus gracilis Nannoscincus mariei Nannoscincus greeri 82 94 Nannoscincus hanchisteus 93 Nannoscincus humectus Marmorosphax montana 90 100 Marmorosphax tricolor 96 100 Celatiscincus similis Celatiscincus euryotis 96 Lioscincus vivae 96 Lioscincus steindachneri Kanakysaurus viviparus 84 Lioscincus nigrofasciolatum 80 80 Lacertoides pardalis 96 Phoboscincus garnieri Sigaloseps ruficauda 100 Sigaloseps deplanchei 85 Lioscincus novaecaledoniae 85 Lioscincus maruia 98 92 Tropidoscincus aubrianus Lioscincus tillieri Tropidoscincus boreus 100 100 Tropidoscincus variabilis 87 Graciliscincus shonae Simiscincus aurantiacus 97 Caledoniscincus orestes 100 Caledoniscincus renevieri Caledoniscincus auratus 95 95 Caledoniscincus festivus 83 Caledoniscincus austrocaledonicus 97 Caledoniscincus haplorhinus 53 Caledoniscincus atropunctatus Caledoniscincus chazeaui 87 98 Caledoniscincus aquilonius 95 Caledoniscincus terma 100 Cryptoblepharus nigropunctatus Cryptoblepharus boutonii 93 79 Cryptoblepharus novocaledonicus 93 Menetia greyii Menetia alanae Emoia schmidti 100 Emoia cyanogaster 91 Emoia caeruleocauda 98 Emoia atrocostata 100 100 Emoia jakati Emoia physicae 77 Emoia impar Emoia cyanura 98 71 98 52 Emoia pseudocyanura Emoia isolata Bassiana trilineata 73 Morethia ruficauda Morethia butleri Morethia adelaidensis Bartleia jigurru Saproscincus basiliscus 96 96 Saproscincus lewisi 72 Saproscincus czechurai 79 Saproscincus tetradactylus 98 Saproscincus hannahae 76 100 Saproscincus oriarus Saproscincus mustelinus Saproscincus challengeri 71 Saproscincus rosei 100 100 97 Saproscincus spectabilis Lampropholis guichenoti 92 Lampropholis delicata 100 Lampropholis coggeri Lampropholis robertsi Proablepharus reginae Niveoscincus greeni 72 Niveoscincus ocellatus 76 Niveoscincus pretiosus 100 Niveoscincus metallicus 87 Cautula zia 96 Liburnascincus coensis Liburnascincus scirtetis 88 91 Liburnascincus mundivensis Menetia timlowi 100 98 Carlia triacantha Carlia johnstonei Carlia jarnoldae 90 Carlia bicarinata Carlia gracilis 79 Lygisaurus sesbrauna 75 Lygisaurus parrhasius 88 Lygisaurus macfarlani 98 99 Lygisaurus novaeguineae Lygisaurus aeratus 85 100 Lygisaurus laevis 100 Lygisaurus foliorum 78 68 Lygisaurus abscondita 89 100 Lygisaurus tanneri Lygisaurus malleolus 91 Carlia schmeltzii Carlia storri 98 Carlia fusca 100 Carlia longipes 73 Carlia mysi 80 93 Carlia munda Carlia pectoralis Carlia rufilatus 85 100 Carlia rhomboidalis Carlia rubrigularis 92 Carlia tetradactyla I Carlia amax 76 Carlia rostralis Figure 10 53 Carlia dogare 62 Carlia vivax Callopistes flavipunctatus 97 Callopistes maculatus Tupinambinae Tupinambis rufescens 100 Tupinambis merianae 100 Tupinambis duseni 97 Tupinambis quadrilineatus Tupinambis longilineus 98 Tupinambis teguixin Teiidae 87 54 66 Crocodilurus amazonicus 91 Dracaena guianensis Teius teyou 99 Ameiva ameiva Ameiva bifrontata 100 Cnemidophorus ocellifer 82 Kentropyx calcarata Teiinae 71 Kentropyx striata 100 Kentropyx altamazonica Kentropyx pelviceps 56 91 Kentropyx paulensis 96 Kentropyx vanzoi Kentropyx viridistriga Ameiva undulata 97 100 Ameiva quadrilineata Ameiva festiva 93 Cnemidophorus vanzoi Cnemidophorus gramivagus 99 Cnemidophorus lemniscatus 94 Cnemidophorus arenivagus Aspidoscelis inornata 100 Aspidoscelis sexlineata 99 Aspidoscelis burti 99 Aspidoscelis communis 93 Aspidoscelis costata 98 99 81 Aspidoscelis gularis 83 Aspidoscelis laredoensis Aspidoscelis velox 98 Aspidoscelis deppei Aspidoscelis guttata Aspidoscelis lineattissima 84 100 Aspidoscelis marmorata 92 Aspidoscelis tigris Aspidoscelis hyperythra 98 Aspidoscelis ceralbensis Ameiva auberi 100 100 Ameiva dorsalis Ameiva polops 86 Ameiva exsul 99 Ameiva wetmorei 97 Ameiva leberi 59 100 Ameiva chrysolaema 96 Ameiva taeniura 95 100 Ameiva lineolata Ameiva maynardi 100 Ameiva plei Ameiva corax 98 Ameiva pluvianotata 100 Ameiva griswoldi 93 Ameiva erythrocephala 94 Ameiva fuscata 55 Dicrodon guttulatum 85 Cnemidophorus longicaudus Alopoglossinae 97 Cnemidophorus lacertoides Ptychoglossus brevifrontalis Alopoglossus atriventris 100 99 100 Alopoglossus copii Alopoglossus angulatus Ecpleopus gaudichaudii Leposoma nanodactylus Ecpleopinae Leposoma baturitensis 100 100 Leposoma puk 98 Leposoma scincoides 97 Leposoma annectans 97 Colobosauroides cearensis 100 Anotosaura collaris Arthrosaura reticulata 99 86 Arthrosaura kockii 65 Leposoma percarinatum 96 Leposoma osvaldoi 98 100 Leposoma parietale 95 Leposoma southi Leposoma guianense Gymnophthalmidae Cercosaurinae 100 Riama unicolor Riama colomaromani 91 Riama simoterus Neusticurus rudis 94 Neusticurus bicarinatus 99 98 Placosoma cordylinum 100 Placosoma glabellum Pholidobolus montium 80 100 Pholidobolus macbrydei Potamites ecpleopus 92 Potamites juruazensis 100 Cercosaura quadrilineata 98 100 Cercosaura oshaughnessyi 97 Cercosaura argulus 99 Cercosaura ocellata 100 Cercosaura schreibersii 55 82 Cercosaura eigenmanni Proctoporus sucullucu Proctoporus subsolanus 98 Proctoporus pachyurus 100 Proctoporus guentheri Proctoporus unsaacae 94 99 Proctoporus bolivianus Bachiinae Petracola ventrimaculatus Bachia flavescens Bachia bresslaui 100 Bachia dorbignyi 77 100 Bachia huallagana 100 Bachia scolecoides 88 Bachia trisanale Bachia panoplia 97 Bachia peruana 95 100 84 Bachia bicolor 78 Bachia barbouri 74 Bachia intermedia Rhachisaurinae 98 Bachia heteropa Rhachisaurus brachylepis 100 Heterodactylus imbricatus Colobodactylus dalcyanus 99 93 Colobodactylus taunayi 100 Iphisa elegans 100 Colobosaura modesta 91 Stenolepis ridleyi Gymnophthalminae 96 Acratosaura mentalis Tretioscincus agilis 72 98 Tretioscincus oriximinensis Micrablepharus atticolus 100 Micrablepharus maximiliani 98 Vanzosaura rubricauda 61 Procellosaurinus erythrocercus 100 Procellosaurinus tetradactylus 100 93 Nothobachia ablephara Calyptommatus sinebrachiatus 88 Calyptommatus confusionibus 93 Calyptommatus leiolepis 50 86 Calyptommatus nicterus Psilophthalmus paeminosus Gymnophthalmus pleei Gymnophthalmus leucomystax 100 Gymnophthalmus vanzoi J 100 Gymnophthalmus speciosus 87 Gymnophthalmus underwoodi Figure 11 100 Gymnophthalmus cryptus Rhineura floridana Rhineuridae Bipes tridactylus 100 Bipes biporus Bipedidae 99 73 Bipes canaliculatus

100 Blanus strauchi 100 Blanus cinereus Blanidae 100 Blanus mettetali 97 Blanus tingitanus Cadeidae 84 Cadea blanoides 100 Diplometopon zarudnyi Trogonophiidae Trogonophis wiegmanni Cynisca leucura 100 100 Chirindia swynnertoni Geocalamus acutus 91 Monopeltis capensis Amphisbaenidae Amphisbaena brasiliana 89 Amphisbaena fuliginosa 55 Amphisbaena cunhai 95 86 Amphisbaena mertensii Amphisbaena hyporissor 96 Amphisbaena innocens 67 81 Amphisbaena leali 91 Amphisbaena ignatiana Amphisbaena saxosa 100 Amphisbaena kraoh 100 100 Amphisbaena roberti Amphisbaena vermicularis 98 Amphisbaena alba 95 Amphisbaena camura 100 Amphisbaena bolivica Amphisbaena anomala 89 Amphisbaena polystegum 100 Amphisbaena microcephalum 100 Amphisbaena infraorbitale 90 Amphisbaena hastata 100 Amphisbaena cuiabana 78 Amphisbaena kingii 100 Amphisbaena munoai 99 Amphisbaena darwini 93 Amphisbaena angustifrons 95 Amphisbaena leeseri 100 Amphisbaena silvestrii Amphisbaena anaemariae Amphisbaena barbouri 100 Amphisbaena cubana 90 Amphisbaena carlgansi Amphisbaena schmidti Amphisbaena manni 92 97 Amphisbaena fenestrata 87 Amphisbaena caeca K 100 Amphisbaena bakeri Figure 12 100 Amphisbaena xera Psammodromus hispanicus Psammodromus algirus 99 Gallotiinae 95 Psammodromus blanci 100 Gallotia stehlini Gallotia atlantica 99 Gallotia galloti Gallotia caesaris 95 Gallotia intermedia 68 Gallotia simonyi 100 97 Gallotia bravoana Atlantolacerta andreanskyi 73 Poromera fordii Nucras lalandii Latastia longicaudata 96 Philochortus spinalis 99 Pseuderemias smithii 88 100 Heliobolus lugubris 90 Heliobolus spekii 99 84 Australolacerta australis 54 Tropidosaura gularis Ichnotropis capensis Meroles reticulatus Meroles knoxii 92 Meroles suborbitalis 100 Ichnotropis squamulosa 76 80 Meroles anchietae 97 Meroles ctenodactylus 100 97 Meroles micropholidotus Meroles cuneirostris Pedioplanis lineoocellata Nucras tessellata 100 Pedioplanis laticeps Lacertidae 100 Pedioplanis burchelli Pedioplanis breviceps 100 Pedioplanis namaquensis 96 Pedioplanis husabensis 100 69 Pedioplanis undata 76 Pedioplanis rubens 96 96 Pedioplanis inornata 56 Pedioplanis gaerdesi 100 Holaspis laevis 100 Holaspis guentheri 100 Gastropholis vittata Gastropholis prasina 72 Adolfus africanus 96 89 Adolfus alleni 99 Adolfus jacksoni Eremias brenchleyi 97 Eremias argus Eremias vermiculata 76 Eremias velox 100 99 Eremias montanus Eremias persica Eremias nigrolateralis 95 Eremias arguta Eremias przewalskii 93 93 100 Eremias multiocellata 56 Eremias pleskei 86 Eremias grammica Congolacerta vauereselli Omanosaura cyanura 98 Omanosaura jayakari 100 97 Mesalina simoni Mesalina olivieri Mesalina bahaeldini Lacertinae 100 91 Mesalina guttulata Mesalina balfouri 89 93 Mesalina adramitana 63 Mesalina brevirostris Mesalina rubropunctata Ophisops occidentalis Ophisops elegans 100 Acanthodactylus orientalis 100 Acanthodactylus tristrami Acanthodactylus blanci 73 95 99 Acanthodactylus erythrurus 94 Acanthodactylus busacki Acanthodactylus beershebensis 100 76 Acanthodactylus pardalis 100 86 Acanthodactylus maculatus Acanthodactylus aureus 95 Acanthodactylus scutellatus 93 Acanthodactylus longipes 80 Acanthodactylus schmidti 99 Acanthodactylus cantoris 96 Acanthodactylus masirae 100 Acanthodactylus gongrorhynchatus Acanthodactylus opheodurus 85 75 Acanthodactylus boskianus 99 Acanthodactylus schreiberi 100 Phoenicolacerta kulzeri 98 Phoenicolacerta laevis Phoenicolacerta cyanisparsa Zootoca vivipara 95 Takydromus kuehnei 100 Takydromus sexlineatus Takydromus tachydromoides 100 Takydromus smaragdinus 95 Takydromus sauteri 85 Takydromus intermedius 100 Takydromus dorsalis 100 Takydromus sylvaticus 79 Takydromus amurensis 100 99 Takydromus hsuehshanensis 100 Takydromus formosanus 97 Takydromus wolteri 100 Takydromus toyamai 99 Takydromus septentrionalis 75 Takydromus stejnegeri Timon princeps 94 Timon pater Timon lepidus 99 98 69 Timon tangitanus Lacerta viridis 58 100 100 Lacerta bilineata Lacerta strigata 80 Lacerta schreiberi Lacerta agilis 92 98 Lacerta media 99 Lacerta trilineata 98 Lacerta pamphylica 100 Teira dugesii Scelarcis perspicillata 85 Podarcis melisellensis Podarcis tauricus 62 74 Podarcis milensis 55 Podarcis gaigeae Podarcis filfolensis 99 85 Podarcis tiliguerta 100 Podarcis muralis 92 Podarcis siculus 95 Podarcis pityusensis 94 Podarcis lilfordi 78 Podarcis raffoneae Podarcis erhardii 79 Podarcis peloponnesiacus 88 Podarcis liolepis Podarcis vaucheri 97 93 Podarcis hispanicus 92 100 Podarcis bocagei Podarcis carbonelli 97 Dalmatolacerta oxycephala Hellenolacerta graeca 92 Archaeolacerta bedriagae Apathya cappadocica 91 Iberolacerta galani 86 86 Iberolacerta cyreni Iberolacerta monticola 100 Iberolacerta horvathi 100 Iberolacerta aurelioi Iberolacerta bonnali 93 Iberolacerta aranica 100 Parvilacerta fraasii 64 99 Parvilacerta parva 100 Anatololacerta anatolica Anatololacerta oertzeni 89 Anatololacerta danfordi 96 Algyroides moreoticus 100 Algyroides nigropunctatus 73 100 Dinarolacerta mosorensis Dinarolacerta montenegrina 94 Algyroides marchi 98 Algyroides fitzingeri 53 Iranolacerta brandtii 99 Iranolacerta zagrosica Darevskia parvula 97 Darevskia rudis 100 100 Darevskia portschinskii 94 Darevskia valentini Darevskia praticola Darevskia chlorogaster 100 Darevskia alpina 96 Darevskia lindholmi 100 Darevskia brauneri 87 Darevskia saxicola 100 Darevskia rostombekovi 97 Darevskia raddei Darevskia uzzelli Darevskia sapphirina 100 Darevskia bendimahiensis 93 94 Darevskia armeniaca Darevskia clarkorum L 98 Darevskia mixta 70 Darevskia daghestanica 99 Darevskia caucasica Figure 13 90 Darevskia derjugini Xenosauridae 100 Xenosaurus platyceps Xenosaurus grandis Helodermatidae Heloderma suspectum 100 100 Heloderma horridum Anniellidae Anniella pulchra 100 Anniella geronimensis 95 Celestus enneagrammus 98 Diploglossus bilobatus Diploglossus pleii 100 Ophiodes striatus Diploglossinae 100 93 100 Celestus agasepsoides Celestus haetianus Ophisaurus ventralis 90 100 83 Ophisaurus koellikeri Anguidae Pseudopus apodus 99 Anguis fragilis Anguinae 87 Ophisaurus attenuatus Dopasia gracilis 100 Dopasia harti 100 100 Elgaria coerulea Elgaria kingii 99 Elgaria paucicarinata 85 Elgaria panamintina 100 84 Elgaria multicarinata 88 Gerrhonotus parvus Gerrhonotinae Coloptychon rhombifer 92 Gerrhonotus liocephalus 100 Gerrhonotus infernalis 97 Abronia mixteca 100 Barisia levicollis Barisia imbricata 89 95 Barisia herrerae 94 Barisia rudicollis Mesaspis moreletii 79 Mesaspis gadovii 72 Abronia chiszari 66 Abronia oaxacae 99 Abronia graminea Abronia frosti Abronia ornelasi 96 84 Abronia lythrochila 89 Abronia fimbriata 96 Abronia matudai 97 Abronia anzuetoi 95 Abronia campbelli Shinisauridae Abronia aurita Shinisaurus crocodilurus Lanthanotidae Lanthanotus borneensis Varanus griseus Varanus niloticus 94 95 Varanus exanthematicus 97 Varanus albigularis 99 Varanus yemenensis 100 Varanus olivaceus 98 Varanus keithhornei 95 100 Varanus beccarii 95 Varanus boehmei Varanidae Varanus macraei 100 75 Varanus prasinus 86 86 Varanus rainerguentheri 78Varanus indicus Varanus melinus 88 Varanus cerambonensis 100 Varanus caerulivirens Varanus jobiensis 76 Varanus yuwonoi 100 79 Varanus doreanus 74 Varanus finschi 86 Varanus marmoratus Varanus salvator 100 69 Varanus rudicollis Varanus dumerilii 85 Varanus flavescens 72 Varanus bengalensis 100 Varanus mertensi Varanus spenceri 84 Varanus giganteus 92 Varanus rosenbergi 96 Varanus panoptes 94 Varanus gouldii 100 100 Varanus salvadorii Varanus varius 99 Varanus komodoensis 99 Varanus glebopalma Varanus pilbarensis 100 Varanus tristis 87 Varanus glauerti 96 Varanus scalaris 76 Varanus timorensis 100 86 Varanus mitchelli 100 Varanus semiremex Varanus brevicauda 100 Varanus eremius Varanus caudolineatus 88 100 Varanus gilleni 100 Varanus bushi 97 99 Varanus kingorum Varanus primordius 99 Varanus storri M 100 Varanus acanthurus Figure 14 99 Varanus baritji Brookesia lolontany 79 Brookesia nasus 100 Brookesia dentata 100 Brookesia exarmata 63 Brookesia minima Brookesia tuberculata 83 100 Brookesia karchei 100 Brookesia peyrierasi 100 Brookesia perarmata Brookesia decaryi 100 98 Brookesia brygooi Brookesia bonsi 100 Brookesia therezieni Brookesiinae 99 Brookesia superciliaris Chamaeleonidae 93 Brookesia valerieae 100 100 Brookesia griveaudi Brookesia stumpffi 100 Brookesia ambreensis Brookesia antakarana Brookesia ebenaui Brookesia vadoni 100 Brookesia thieli Brookesia betschi 51 Brookesia lineata Furcifer balteatus 99 Furcifer bifidus 99 62 Furcifer minor Furcifer willsii 86 Furcifer petteri Furcifer campani 93 96 Furcifer cephalolepis 91 Furcifer polleni 94 100 Furcifer pardalis Furcifer angeli 99 93 Furcifer oustaleti Furcifer verrucosus 98 Furcifer belalandaensis Furcifer lateralis 98 94 100 Furcifer labordi Furcifer antimena 100 Kinyongia oxyrhina Kinyongia tenue 95 100 Kinyongia adolfifriderici Kinyongia excubitor 67 Kinyongia xenorhina 98 Kinyongia carpenteri 82 Kinyongia uthmoelleri Kinyongia tavetana 100 92 100 Kinyongia boehmei 55 100 Kinyongia matschiei Chamaeleoninae 100 Kinyongia multituberculata 59 Kinyongia vosseleri 100 Kinyongia fischeri 96 Bradypodion pumilum Bradypodion damaranum Bradypodion caffer 100 100 Bradypodion melanocephalum 94 Bradypodion thamnobates 98 Bradypodion transvaalense 72 Bradypodion dracomontanum 87 Bradypodion nemorale Bradypodion setaroi Bradypodion occidentale 85 Bradypodion atromontanum 98 Bradypodion gutturale 74 Bradypodion taeniabronchum 95 Bradypodion karrooicum 95 Bradypodion ventrale 100 Calumma furcifer 99 Calumma gastrotaenia Rieppeleon kerstenii 100 Rieppeleon brachyurus 58 Rieppeleon brevicaudatus Calumma cucullatum 82 100 88 Calumma crypticum Calumma brevicorne 98 Calumma tsaratananense 100 75 Calumma hilleniusi Calumma guibei 91 Calumma malthe 78 93 Calumma gallus 85 Calumma fallax 97 Calumma boettgeri 94 Calumma nasutum Nadzikambia mlanjensis 73 Rhampholeon spectrum 88 Rhampholeon temporalis 98 Rhampholeon spinosus 98 Rhampholeon viridis 99 Rhampholeon marshalli Rhampholeon moyeri 86 Rhampholeon uluguruensis 100 Rhampholeon acuminatus 81 Rhampholeon boulengeri 73 Rhampholeon beraduccii 91 Rhampholeon nchisiensis 90 Rhampholeon platyceps 100 Rhampholeon chapmanorum 100 Calumma capuroni Calumma oshaughnessyi 100 Calumma parsonii 95 61 Calumma globifer Chamaeleo namaquensis Chamaeleo laevigatus 99 100 Chamaeleo necasi 90 Chamaeleo gracilis Chamaeleo quilensis 100 Chamaeleo dilepis 99 Chamaeleo roperi Chamaeleo senegalensis Chamaeleo monachus 95 Chamaeleo africanus Chamaeleo calcaricarens 85 Chamaeleo chamaeleon 100 Chamaeleo zeylanicus 98 Chamaeleo calyptratus 100 Chamaeleo arabicus 100 Trioceros affinis Trioceros harennae 66 100 Trioceros balebicornutus Trioceros feae 100 Trioceros montium 85 Trioceros cristatus 100 Trioceros wiedersheimi 96 Trioceros quadricornis 100 50 Trioceros pfefferi 97 Trioceros oweni Trioceros johnstoni 93 Trioceros melleri 98 Trioceros deremensis 92 Trioceros werneri 92 Trioceros tempeli 97 Trioceros goetzei 91 Trioceros fuelleborni 70 Trioceros bitaeniatus Trioceros jacksonii 98 90 Trioceros narraioca Trioceros schubotzi 85 Trioceros hoehnelii N 87 Trioceros ellioti 97 Trioceros rudis Figure 15 66 Trioceros sternfeldi Laudakia stellio Uromastyx hardwickii 94 99 Laudakia sacra 94 Laudakia tuberculata Uromastyx loricata Laudakia nupta Uromasticinae 95 Uromastyx asmussi Laudakia lehmanni 85 Laudakia himalayana 100 Uromastyx princeps 84 99 Laudakia stoliczkana Uromastyx macfadyeni 84 Laudakia microlepis Laudakia caucasia 86 Uromastyx geyri 88 Laudakia erythrogaster 100 100 Uromastyx acanthinura Phrynocephalus scutellatus 74 Phrynocephalus interscapularis Uromastyx dispar Phrynocephalus forsythii 94 100 100 Uromastyx thomasi Phrynocephalus theobaldi 64 90 Phrynocephalus putjatai 100 Uromastyx aegyptia 75 Phrynocephalus vlangalii 73 Phrynocephalus lidskii 91 Uromastyx leptieni Phrynocephalus axillaris 99 Uromastyx ornata Phrynocephalus helioscopus 70 91 Phrynocephalus mystaceus Uromastyx ocellata Phrynocephalus raddei 100 89 100 Uromastyx benti 100 Phrynocephalus versicolor 94 Phrynocephalus przewalskii 100 Uromastyx yemenensis 100 Phrynocephalus melanurus Phrynocephalus albolineatus 100 Leiolepis belliana 96 90 Phrynocephalus guttatus Leiolepidinae Leiolepis reevesii 100 Pseudotrapelus sinaitus Acanthocercus atricollis 100 100 Leiolepis guttata 66 95 Xenagama taylori Leiolepis guentherpetersi Bufoniceps laungwalaensis 100 Hydrosaurinae Agaminae Trapelus sanguinolentus (i) Hydrosaurus amboinensis 100 Trapelus mutabilis Physignathus cocincinus 99 Trapelus agilis Trapelus ruderatus Hypsilurus spinipes 93 92 99 Trapelus pallidus Hypsilurus boydii 89 Trapelus flavimaculatus 97 100 100 Trapelus savignii 85 Hypsilurus dilophus Agama spinosa Agama boueti Moloch horridus 100 98 100 Agama impalearis 100 Chelosania brunnea 96 Agama castroviejoi

Agamidae Hypsilurus modestus 76 Agama boulengeri 100 Agama insularis Hypsilurus papuensis 100 84 Agama gracilimembris 69 Agama weidholzi 100 Hypsilurus nigrigularis 51 Agama anchietae Hypsilurus bruijnii (ii) 100 100 Agama atra 91 Agama hispida Intellagama lesueurii 100 50 Agama armata Ctenophorus maculosus 100 Agama aculeata 100 75 Agama caudospinosa Ctenophorus adelaidensis 100 Agama rueppelli Ctenophorus clayi Agama lionotus 100 Agama kaimosae Amphibolurinae Ctenophorus gibba 91 96 65 Agama mwanzae Ctenophorus salinarum 98 Agama sankaranica 99 Agama doriae 96 Ctenophorus cristatus 100 Agama agama 100 Ctenophorus nuchalis 100 Agama finchi 98 68 Agama planiceps Ctenophorus reticulatus 68 Agama paragama 71 Ctenophorus rufescens Mantheyus phuwuanensis 99 Japalura variegata Ctenophorus tjantjalka 70 Japalura tricarinata 100 Ptyctolaemus gularis Ctenophorus vadnappa Ptyctolaemus collicristatus 99 Ctenophorus decresii 100 Draco dussumieri Draco lineatus 79 90 Ctenophorus fionni 95 Draco maculatus (i) Ctenophorus caudicinctus Draco fimbriatus 100 86 99 97 Draco cristatellus Ctenophorus ornatus 53 Draco maximus Ctenophorus isolepis 100 Draco mindanensis 100 92 92 Draco quinquefasciatus 53 Ctenophorus scutulatus Draconinae 100 Draco melanopogon 100 65 (ii) Ctenophorus mckenziei 59 Draco haematopogon 95 Draco indochinensis 76 Ctenophorus pictus 96 Draco blanfordii Ctenophorus maculatus 61 Draco taeniopterus 90 86 100 Draco obscurus 100 Ctenophorus fordi 100 Draco spilonotus 94 Draco caerulhians Ctenophorus femoralis 100 97 Draco biaro Lophognathus temporalis Draco beccarii 71 Draco bourouniensis Lophognathus longirostris 100 99 Draco rhytisma 95 100 Chlamydosaurus kingii Draco bimaculatus 100 Draco volans Lophognathus gilberti 100 94 Draco timorensis Amphibolurus muricatus 99 Draco boschmai 100 100 Draco reticulatus 97 Amphibolurus norrisi Draco cyanopterus 100 Tympanocryptis uniformis Draco quadrasi 100 91 Draco guentheri Tympanocryptis intima Draco cornutus 99 Tympanocryptis tetraporophora 85 Draco spilopterus Draco palawanensis Tympanocryptis cephalus 87 Draco ornatus Phoxophrys nigrilabris 71 100 Tympanocryptis pinguicolla Japalura polygonata 53 Tympanocryptis lineata 100 Gonocephalus robinsonii Aphaniotis fusca Rankinia diemensis 97 98 Coryphophylax subcristatus 63 Pogona barbata Bronchocela cristatella 100 Gonocephalus grandis Pogona nullarbor 85 99 87 Gonocephalus chamaeleontinus Pogona henrylawsoni 86 100 Gonocephalus kuhlii 52 97 Lyriocephalus scutatus Pogona minima Cophotis dumbara 99 99 Pogona minor 100 Cophotis ceylanica 100 Ceratophora aspera 94 Pogona vitticeps Ceratophora karu Diporiphora superba 90 Ceratophora stoddartii 100 Ceratophora erdeleni Diporiphora linga Calotes mystaceus 99 81 72 Diporiphora winneckei Calotes chincollium 81 100 Calotes emma Diporiphora reginae 55 Calotes liocephalus 90 Calotes ceylonensis Diporiphora magna 100 76 99Calotes nigrilabris Diporiphora bilineata Calotes liolepis 67 99 Calotes versicolor Diporiphora pindan 100 Calotes irawadi 95 100 Diporiphora valens 50 Calotes calotes 91 Calotes htunwini Diporiphora amphiboluroides Salea horsfieldii Diporiphora australis Acanthosaura crucigera 100 Acanthosaura armata 95 Diporiphora nobbi 96 Acanthosaura capra Diporiphora bennettii Acanthosaura lepidogaster 56 69 Sitana ponticeriana 100 Diporiphora albilabris 100 Otocryptis wiegmanni Japalura flaviceps 95 Diporiphora arnhemica 100 Japalura splendida Diporiphora lalliae 99 Pseudocalotes kakhienensis 100 Pseudocalotes brevipes O 95 Pseudocalotes flavigula Figure 16 94 Stenocercus scapularis 86 Stenocercus apurimacus Stenocercus formosus 94 Stenocercus ochoai Stenocercus roseiventris 64 Stenocercus azureus 100 100 Stenocercus doellojuradoi 69 Stenocercus limitaris Stenocercus caducus 88 Stenocercus ornatus 100 Stenocercus percultus 78 Stenocercus puyango 100 Stenocercus iridescens 89 Stenocercus angulifer 96 Stenocercus rhodomelas Stenocercus chota 84 82 99 Stenocercus festae 96 Stenocercus guentheri 100 Stenocercus angel Stenocercus humeralis Stenocercus marmoratus 71 Stenocercus crassicaudatus 100 100 Stenocercus torquatus 73 Stenocercus varius 89 Stenocercus imitator 94 Stenocercus eunetopsis Tropiduridae Stenocercus empetrus 100 Stenocercus boettgeri 100 88 Stenocercus cupreus 78 Stenocercus chrysopygus 79 Stenocercus ornatissimus Stenocercus orientalis 100 Stenocercus latebrosus 85 Stenocercus melanopygus 88 Stenocercus stigmosus Microlophus thoracicus 100 Microlophus theresiae 100 Microlophus heterolepis 99 96 Microlophus tigris Microlophus peruvianus 100 Microlophus quadrivittatus 100 Microlophus atacamensis 100 Microlophus theresioides 98 Microlophus yanezi Microlophus koepckeorum 100 Microlophus occipitalis 100 Microlophus bivittatus 100 Microlophus habelii Microlophus stolzmanni 100 Microlophus delanonis 100 Microlophus grayii 100 Microlophus pacificus 64 Microlophus albemarlensis 95 Microlophus duncanensis Uranoscodon superciliosus 74 Uracentron flaviceps 98 Tropidurus bogerti Strobilurus torquatus 78 Plica umbra Plica lumaria 99 Plica plica 100 Tropidurus callathelys 100 100 Tropidurus spinulosus 100 Eurolophosaurus divaricatus 100 Eurolophosaurus amathites Eurolophosaurus nanuzae Tropidurus hygomi Tropidurus montanus 100 100 Tropidurus psammonastes 73 Tropidurus itambere 98 Tropidurus cocorobensis 97 83 Tropidurus etheridgei Tropidurus mucujensis Tropidurus erythrocephalus Tropidurus insulanus 100 Tropidurus oreadicus 98 Tropidurus hispidus Iguanidae 89 Tropidurus torquatus Dipsosaurus dorsalis Brachylophus fasciatus 100 Brachylophus vitiensis 99 Iguana iguana 92 Iguana delicatissima Sauromalus ater 100 100 Sauromalus klauberi Sauromalus hispidus 61 Sauromalus varius Cyclura pinguis 100 94 Cyclura cornuta 100 Cyclura ricordi 97 Cyclura carinata 95 Cyclura collei 57 Cyclura rileyi 85 Cyclura nubila 56 86 Cyclura cychlura Amblyrhynchus cristatus 100 Conolophus subcristatus 72 Conolophus pallidus 62 Ctenosaura similis 100 Ctenosaura hemilopha 96 Ctenosaura acanthura 99 Ctenosaura pectinata 99 98 Ctenosaura melanosterna Ctenosaura oedirhina Ctenosaura bakeri 100 74 Ctenosaura palearis Ctenosaura flavidorsalis P 99 Ctenosaura quinquecarinata 72 Figure 17 Q-R Ctenosaura oaxacana 94 Leiocephalus carinatus 69 Polychrus gutturosus Leiocephalus raviceps 100 Polychrus acutirostris 100 93 Leiocephalus psammodromus Polychrus femoralis Leiocephalus personatus 99 92 Polychrus marmoratus Hoplocercus spinosus 92 Leiocephalus schreibersii 100 Morunasaurus annularis Leiocephalus barahonensis 100 Enyalioides laticeps Crotaphytidae Gambelia wislizenii 88 Enyalioides heterolepis Gambelia sila Enyalioides oshaughnessyi 100 Gambelia copeii Enyalioides palpebralis 96 Enyalioides microlepis 99 Crotaphytus antiquus 96 100 96 Enyalioides praestabilis Crotaphytus reticulatus Chalarodon madagascariensis 100 Crotaphytus vestigium 90 Oplurus cyclurus Crotaphytus insularis Opluridae 100 99 Oplurus cuvieri 82 Crotaphytus grismeri 100 Oplurus quadrimaculatus 83 Crotaphytus bicinctores Oplurus saxicola 73 93 Crotaphytus nebrius 96 Oplurus grandidieri Crotaphytus collaris 99 88 Oplurus fierinensis 100 Enyaliinae Enyalius bilineatus Uma exsul Enyalius leechii Leiocephalidae 100 100 Uma paraphygas 97 Urostrophus gallardoi Uma scoparia Anisolepis longicauda Uma inornata Polychrotidae 99 Urostrophus vautieri 100 100 100 100 Uma notata 98 Pristidactylus scapulatus Callisaurus draconoides 100 Diplolaemus darwinii Cophosaurus texanus Hoplocercidae Pristidactylus torquatus 99 Leiosaurinae Leiosaurus bellii 87 Holbrookia lacerata 78 Leiosaurus paronae 100 Holbrookia propinqua 77

Leiosaurus catamarcensis Enyaliidae 99 Holbrookia maculata 70 100 95 Ctenoblepharys adspersa Phrynosoma cornutum 100 Phymaturus indistinctus Phrynosoma solare Phymaturus somuncurensis 96 Phrynosoma mcallii 100 98 Phymaturus patagonicus 100 Phrynosoma platyrhinos 100 Phymaturus dorsimaculatus 100 Phrynosoma coronatum Phymaturus palluma 96 Phymaturus punae 100 Phrynosoma blainvillii Phymaturus mallimaccii Phrynosoma cerroense 89 88 Phymaturus antofagastensis 95 96 Phrynosoma wigginsi Liolaemus tenuis Phrynosoma asio Liolaemus lemniscatus 88 95 99 Liolaemus monticola Phrynosoma braconnieri 96 100 92 Phrynosoma taurus Liolaemus nitidus 68 Liolaemus nigroviridis (i) 100 Phrynosoma modestum 93 Liolaemus fuscus Phrynosoma orbiculare 100 Liolaemus atacamensis 100 Phrynosoma ditmarsi (ii) 54 97 Liolaemus zapallarensis 100 Phrynosoma douglassii 63 91 Liolaemus pseudolemniscatus 99 Phrynosoma hernandesi Liolaemus nigromaculatus 67 Liolaemus platei Petrosaurus mearnsi 66 97 100 Petrosaurus repens 99 Liolaemus paulinae 99 Liolaemus austromendocinus 100 Petrosaurus thalassinus Liolaemus thermarum Uta squamata 100 Liolaemus dicktracyi Uta palmeri 100 100 Liolaemus heliodermis Uta stansburiana 95 Liolaemus capillitas 76 Liolaemidae 98 100 Uta stejnegeri 83 Liolaemus umbrifer Urosaurus gadovi Liolaemus petrophilus Urosaurus bicarinatus 100 Liolaemus buergeri 100 100 59 Liolaemus ceii 100 99 Urosaurus lahtelai Liolaemus leopardinus Urosaurus nigricaudus 100 100 66 Liolaemus kriegi 100 Urosaurus graciosus 98 Liolaemus elongatus 99 Urosaurus ornatus Liolaemus coeruleus Phrynosomatidae Urosaurus clarionensis 98 Liolaemus bellii 100 Liolaemus gravenhorstii 100 Urosaurus auriculatus 97 96 Sceloporus parvus 100 Liolaemus schroederi 99 Liolaemus chiliensis 86 100 Sceloporus couchii Liolaemus cyanogaster Sceloporus chrysostictus 98 Liolaemus pictus Sceloporus teapensis 100 99 Liolaemus hernani Sceloporus variabilis 86 Liolaemus bibronii Liolaemus pagaburoi 91 Sceloporus smithi 56 97 Sceloporus cozumelae Liolaemus bitaeniatus Sceloporus grandaevus 100 53 Liolaemus chaltin 90 Liolaemus puna 100 100 Sceloporus angustus 100 100 97 68 Liolaemus walkeri Sceloporus utiformis Liolaemus yanalcu Sceloporus carinatus 91 Liolaemus ramirezae 100 Sceloporus squamosus 74 Liolaemus robertmertensi 100 Sceloporus siniferus 84 Liolaemus gracilis 75 Sceloporus merriami 100 Liolaemus saxatilis 95 Sceloporus pyrocephalus 94 Liolaemus hatcheri Liolaemus lineomaculatus Sceloporus nelsoni 70 Liolaemus silvanae 100 100 Sceloporus gadoviae 100 Liolaemus kolengh Sceloporus maculosus 100 Liolaemus magellanicus 82 Sceloporus jalapae Liolaemus uptoni (i) 96 99 Liolaemus somuncurae 100 Sceloporus ochoterenae 100 81 Sceloporus vandenburgianus 100 Liolaemus baguali Sceloporus graciosus Liolaemus tari 100 100 95 Liolaemus escarchadosi 89 99 Sceloporus arenicolus Liolaemus kingii Sceloporus magister (ii) 100 Liolaemus gallardoi 99 Sceloporus zosteromus 83 Liolaemus sarmientoi 100 99 Sceloporus lineatulus 99 Liolaemus scolaroi 100 Sceloporus licki 98 Liolaemus zullyae 100 Sceloporus orcutti 78 Liolaemus tristis 99 Sceloporus hunsakeri Liolaemus archeforus 100 Liolaemus stolzmanni Sceloporus melanorhinus 100 Liolaemus orientalis 100 Sceloporus grammicus Liolaemus famatinae 99 Sceloporus palaciosi 98 Liolaemus vallecurensis 97 Sceloporus heterolepis 82 82 Liolaemus ruibali 89 99 Sceloporus aeneus 78 99Liolaemus audituvelatus Sceloporus bicanthalis 72 Liolaemus fabiani Sceloporus scalaris Liolaemus huacahuasicus 100 Liolaemus dorbignyi 99 Sceloporus slevini 84 Liolaemus molinai 98 Sceloporus chaneyi 87 Liolaemus multicolor 98 Sceloporus samcolemani 100 Liolaemus andinus 100 Sceloporus goldmani 100 Liolaemus pseudoanomalus Sceloporus megalepidurus 97 99 Liolaemus occipitalis 96 Sceloporus insignis Liolaemus lutzae Liolaemus salinicola 96 92 Sceloporus jarrovii 65 Sceloporus torquatus 85 Liolaemus riojanus 100 Liolaemus multimaculatus 89 97 Sceloporus bulleri 99 Liolaemus scapularis 100 Sceloporus mucronatus 98 Liolaemus azarai Sceloporus macdougalli 100 Liolaemus wiegmannii Sceloporus poinsettii Liolaemus rothi 100 100 Sceloporus dugesii 99 Liolaemus boulengeri 98 Sceloporus minor Liolaemus inacayali Sceloporus ornatus 85 Liolaemus telsen 82 98 Liolaemus cuyanus 98 Sceloporus serrifer 99 Liolaemus donosobarrosi 100 Sceloporus cyanogenys Liolaemus melanops Sceloporus clarkii 100 Liolaemus canqueli Sceloporus olivaceus 98 93 Liolaemus morenoi Sceloporus occidentalis 64 Liolaemus chehuachekenk Sceloporus virgatus 95 Liolaemus fitzingerii 100 91 Sceloporus woodi 79 Liolaemus xanthoviridis 65 Liolaemus hermannunezi Sceloporus consobrinus Liolaemus uspallatensis 100 Sceloporus undulatus 94 100 Liolaemus chacoensis 99 Sceloporus cautus 78 Liolaemus olongasta 100 Sceloporus horridus 95 Liolaemus grosseorum Sceloporus edwardtaylori 99 Liolaemus darwinii 74 Sceloporus spinosus 100 100 Liolaemus laurenti Liolaemus koslowskyi 100 Sceloporus taeniocnemis 94 98 Liolaemus quilmes 100 Sceloporus smaragdinus 100 Liolaemus espinozai Sceloporus malachiticus 66 Liolaemus abaucan Sceloporus lundelli Liolaemus crepuscularis 100 100 Sceloporus cryptus 100Liolaemus irregularis Sceloporus subpictus 99 Liolaemus albiceps 61 Sceloporus formosus 67 Liolaemus calchaqui Q 86 Liolaemus ornatus 100 Sceloporus stejnegeri Liolaemus lavillai Figure 18 97 Sceloporus adleri R Laemanctus longipes Anolis wattsi 100 100 Corytophanes percarinatus Anolis pogus Corytophanes cristatus 100 Basiliscus galeritus Corytophanidae 100 56 Anolis leachii Basiliscus vittatus Anolis bimaculatus 90 98 Basiliscus plumifrons Anolis gingivinus Basiliscus basiliscus 92 Anolis oculatus Anolis boettgeri 99 77 67 Anolis luciae Anolis terraealtae Anolis bonairensis 99 Anolis ferreus 64 Anolis griseus Anolis lividus Anolis trinitatis 100 100 Anolis nubilus Anolis richardii 95 62 100 Anolis aeneus 57 Anolis sabanus 96 100 Anolis roquet Anolis marmoratus 100 100 Anolis extremus Anolis distichus Anolis fitchi 100 89 Anolis websteri Anolis huilae 96 Anolis peraccae 96 Anolis brevirostris Anolis festae 94 Anolis marron (i) Anolis chloris 100 Anolis caudalis 95 Anolis ventrimaculatus Anolis acutus 99 99 Anolis aequatorialis 95 100 96 Anolis gemmosus Anolis stratulus 90 Anolis euskalerriari Anolis evermanni Anolis nicefori 100 Anolis poncensis Anolis heterodermus 88 100 100 Anolis gundlachi 99 Anolis vanzolinii 91 Anolis pulchellus 65 Anolis inderenae 100 100 Anolis punctatus Anolis krugi 83 100 Anolis transversalis 98 100 Anolis monensis Anolis tigrinus Anolis cooki 99 Anolis jacare 100 Anolis anatoloros (ii) 100 Anolis scriptus 71 98 Anolis calimae 96 Anolis ernestwilliamsi Anolis neblininus 75 100 Anolis desechensis Anolis agassizi 100 100 Anolis microtus Anolis cristatellus Anolis insignis Anolis imias 100 98 100 80 Anolis danieli Anolis rubribarbaris Anolis fraseri Anolis allogus 98 Anolis chocorum 100 98 Anolis ahli Dactyloidae 87 Anolis princeps 90 Anolis guafe 100 Anolis frenatus 100 100 Anolis casildae Anolis confusus Anolis maculigula Anolis jubar 100 72 Anolis bartschi 94 75 Anolis vermiculatus 100 Anolis homolechis Anolis mestrei 79 Anolis occultus Anolis monticola Anolis ophiolepis 82 100 Anolis darlingtoni Anolis sagrei Anolis bahorucoensis 99 56 Anolis quadriocellifer 99 100 Anolis dolichocephalus 89 100 Anolis hendersoni 99 Anolis bremeri Anolis coelestinus Anolis lineatopus 94 Anolis chlorocyanus 100 Anolis reconditus 100 Anolis singularis 58 Anolis valencienni 59 99 Anolis aliniger 90 Anolis smallwoodi 100 Anolis opalinus 100 100 Anolis noblei Anolis garmani Anolis baracoae 95 90 Anolis conspersus 59 Anolis luteogularis 89 Anolis equestris 100 Anolis grahami 98 Anolis etheridgei Anolis auratus 98 Anolis fowleri 99 Anolis annectens 100 Anolis insolitus 100 97 Anolis onca Anolis barbouri 86 Anolis olssoni Anolis lineatus 97 Anolis semilineatus 52 Anolis meridionalis 99 Anolis alumina Anolis nitens Anolis argenteolus 84 Anolis bombiceps 95 Anolis barbatus 59 100 99 Anolis porcus 99 Anolis chrysolepis Anolis chamaeleonides Anolis loveridgei 86 100 86 66 Anolis guamuhaya Anolis purpurgularis Anolis cuvieri 90 Anolis christophei Anolis utilensis Anolis crassulus 93 90 Anolis eugenegrahami 96 (i) 90 Anolis ricordi Anolis sminthus 100 Anolis baleatus 72 Anolis polyrhachis 95 Anolis barahonae 94 (ii) Anolis marcanoi Anolis uniformis 100 Anolis strahmi Anolis bitectus 99 Anolis longitibialis Anolis biporcatus 96 Anolis haetianus 95 Anolis woodi Anolis shrevei 100 99 Anolis aquaticus 95 Anolis armouri Anolis cybotes Anolis quercorum 60 99 Anolis whitemani Anolis ortonii Anolis lucius Anolis laeviventris 97 Anolis clivicola 100 Anolis rejectus Anolis intermedius 92 93 Anolis cyanopleurus Anolis isthmicus 100 100 100 Anolis cupeyalensis Anolis sericeus Anolis macilentus 99 Anolis pachypus Anolis alfaroi 86 100 Anolis humilis 65 Anolis vanidicus 69 76 Anolis inexpectatus Anolis altae 100 Anolis alutaceus Anolis kemptoni 100 86 Anolis placidus Anolis fuscoauratus 86 100 Anolis sheplani 85 93 Anolis cupreus Anolis alayoni 98 Anolis paternus Anolis polylepis 100 100 Anolis angusticeps Anolis capito Anolis garridoi 90 99 80 Anolis tropidonotus 98 100 Anolis guazuma 89 Anolis loysiana Anolis ocelloscapularis 97 Anolis pumilus Anolis carpenteri 100 Anolis centralis 100 100 Anolis bicaorum Anolis argillaceus 95 Anolis lemurinus Anolis oporinus 56 91 100 Anolis limifrons Anolis isolepis 100 100 Anolis carolinensis Anolis zeus Anolis porcatus 94 Anolis oxylophus Anolis longiceps 86 Anolis lionotus 99 Anolis brunneus 100 Anolis maynardi 97 Anolis tropidogaster R 74 Anolis allisoni 96 Anolis poecilopus 97 Figure 19 Anolis smaragdinus 92 Anolis trachyderma 100 Liotyphlops albirostris Typhlophis squamosus Anomalepididae Tricheilostoma bicolor Siagonodon septemstriatus 97 93 Epictia albifrons 100 Epictia goudotii 100 Epictia columbi 97 100 Trilepida macrolepis Rena dulcis 100 Rena humilis 100 Tetracheilostoma carlae Tetracheilostoma breuili 100 Mitophis asbolepis 100 100 Mitophis pyrites 98 Mitophis leptipileptus Myriopholis longicauda Leptotyphlopidae 100 Myriopholis algeriensis Myriopholis rouxestevae 56 100 Myriopholis boueti 79 Myriopholis blanfordi 100 69 100 Myriopholis macrorhyncha Myriopholis adleri Namibiana occidentalis Leptotyphlops nigroterminus 90 100 99 Leptotyphlops nigricans 100 Leptotyphlops sylvicolus 100 Leptotyphlops conjunctus 51 Leptotyphlops distanti 100 Leptotyphlops scutifrons 91 Gerrhopilus hedraeus Gerrhopilus mirus Gerrhopilidae Xenotyphlops grandidieri Typhlops brongersmianus Xenotyphlopidae 100 96 Typhlops reticulatus 100 Typhlops biminiensis Typhlops pusillus 95 100 Typhlops hectus Typhlops syntherus 71 90 Typhlops eperopeus 87 Typhlops lumbricalis 84 Typhlops schwartzi 56 Typhlops titanops 92 100 83 Typhlops sulcatus 77 Typhlops rostellatus Typhlops capitulatus 77 Typhlops jamaicensis 92 Typhlops sylleptor 92 99 Typhlops agoralionis 100 Typhlops caymanensis Typhlops arator Typhlops contorhinus 74 Typhlops anchaurus 100 Typhlops anousius Typhlops notorachius Typhlops monastus 100 Typhlops dominicanus 86 Typhlops granti Typhlops hypomethes 84 99 Typhlops platycephalus 95 Typhlops richardi 75 Typhlops catapontus Rhinotyphlops lalandei

Typhlopidae Letheobia feae 100 Letheobia newtoni 87 Letheobia obtusa Typhlops elegans 100 100 Afrotyphlops angolensis 77 Megatyphlops schlegelii Afrotyphlops fornasinii 89 99 Afrotyphlops bibronii 87 87 Afrotyphlops lineolatus 99 Afrotyphlops congestus 72 Afrotyphlops punctatus Typhlops vermicularis Typhlops arenarius 100 Typhlops luzonensis Typhlops ruber 76 Ramphotyphlops albiceps 84 Typhlops pammeces 99 100 Ramphotyphlops braminus 97 Typhlopidae sp. (Sri Lanka) Ramphotyphlops lineatus 65 72 Ramphotyphlops acuticaudus 100 Acutotyphlops subocularis Acutotyphlops kunuaensis Ramphotyphlops polygrammicus 91 74 Austrotyphlops diversus Austrotyphlops howi 87 75 Austrotyphlops guentheri Austrotyphlops bituberculatus 100 Austrotyphlops grypus Austrotyphlops longissimus 100 52 Austrotyphlops leptosomus Austrotyphlops unguirostris 59 98 Austrotyphlops ammodytes 92 Austrotyphlops kimberleyensis 96 Austrotyphlops troglodytes 93 Austrotyphlops ganei 87 Austrotyphlops ligatus 76 96 Ramphotyphlops bicolor Austrotyphlops pinguis 90 Austrotyphlops splendidus 99 Austrotyphlops waitii 98 Austrotyphlops australis 81 Austrotyphlops endoterus S 74 Austrotyphlops hamatus Figure 20 T-AA 91 Austrotyphlops pilbarensis Anilius scytale 98 100 Trachyboa gularis Aniliidae Trachyboa boulengeri 100 Tropidophis pardalis 100 Tropidophis wrighti Tropidophiidae 100 Tropidophis greenwayi 100 Tropidophis haetianus 53 Tropidophis feicki 98 Tropidophis melanurus Xenophidion schaeferi Xenophidiidae Casarea dussumieri Bolyeriidae 100 Sanzinia madagascariensis Acrantophis madagascariensis Sanziniinae 100 100 Acrantophis dumerili Calabaria reinhardtii Calabariidae Exiliboa placata 100 Ungaliophis continentalis 99 Ungaliophiinae Charina bottae 100 100 Lichanura trivirgata 100 Candoia aspera Candoia carinata Candoiinae 99 81 Candoia bibroni Eryx jayakari 69 Eryx colubrinus 100 53 87 Eryx conicus Eryx johnii 87 95 Eryx jaculus Erycinae 96 Eryx elegans Boidae 83 93 Eryx miliaris 100 Eryx tataricus Boa constrictor 99 Corallus hortulanus Corallus caninus 97 98 Corallus annulatus Epicrates cenchria 88 100 100 Eunectes murinus Eunectes notaeus 94 Epicrates angulifer Boinae 96 Epicrates inornatus 85 Epicrates monensis 90 Epicrates fordi Epicrates subflavus 95 Epicrates chrysogaster 100 Epicrates exsul 92 Epicrates striatus 65 Anomochilus leonardi Anomochilidae Cylindrophis maculatus 100 Cylindrophis ruffus Cylindrophiidae Melanophidium punctatum Brachyophidium rhodogaster 98 Uropeltis liura 86 Uropeltis ceylanicus 90 Rhinophis travancoricus 73 100 Uropeltis melanogaster 80 Uropeltis phillipsi Rhinophis drummondhayi Uropeltidae 82 89 69 Rhinophis dorsimaculatus Rhinophis philippinus 77 Rhinophis oxyrhynchus 84 Pseudotyphlops philippinus 85 Rhinophis homolepis 80 Rhinophis blythii Xenopeltis unicolor Loxocemus bicolor Xenopeltidae Python brongersmai Loxocemidae 98 99 Python regius 99 Python curtus 100 86 96 Python sebae Python molurus 98 Broghammerus reticulatus 100 Broghammerus timoriensis Morelia oenpelliensis 76 97 Morelia boeleni Morelia amethistina 100 100 Aspidites ramsayi Aspidites melanocephalus 75 Liasis olivaceus Apodora papuana Pythonidae 98 96 Liasis mackloti 100 Liasis fuscus Leiopython albertisii 100 Bothrochilus boa Morelia viridis 71 84 Morelia carinata 96 100Morelia spilota Morelia bredli 85 Antaresia maculosa 51 Antaresia perthensis T 83 Antaresia stimsoni 100 Antaresia childreni Figure 21 U-AA Acrochordidae Acrochordus javanicus Azemiops feae 91 Garthius chaseni Azemiopinae 100 Acrochordus granulatus Tropidolaemus wagleri 95 50 Deinagkistrodon acutus 95 Acrochordus arafurae Calloselasma rhodostoma Hypnale nepa Stoliczkia borneensis 100 100 Hypnale hypnale 100 97 95 Hypnale zara 100 Xenodermus javanicus (ii) 99 Trimeresurus puniceus 98 Trimeresurus borneensis Achalinus meiguensis 100 Trimeresurus malabaricus 96 Trimeresurus gramineus 98 Achalinus rufescens 100 Trimeresurus trigonocephalus 100 Trimeresurus hageni Asthenodipsas vertebralis 99 Trimeresurus malcolmi Trimeresurus flavomaculatus 99 99 Aplopeltura boa 89 Trimeresurus schultzei 97 Trimeresurus sumatranus Pareas monticola 89 Trimeresurus popeiorum 98 Trimeresurus tibetanus 100 Pareas boulengeri Crotalinae 94 Trimeresurus medoensis Trimeresurus yunnanensis 96 Pareas formosensis Trimeresurus gumprechti 81 Trimeresurus stejnegeri Pareas margaritophorus 72 96 Trimeresurus vogeli 95 93 100 Trimeresurus kanburiensis 91 Pareas macularius Trimeresurus venustus Trimeresurus macrops Xenodermatidae Pareas hamptoni 96 Trimeresurus fasciatus 64 Trimeresurus insularis 85 Trimeresurus septentrionalis Pareatidae Pareas carinatus 100 100 Trimeresurus andersonii 100 Pareas nuchalis Trimeresurus albolabris 93 Trimeresurus cantori 77 Eristicophis macmahoni 100 Trimeresurus erythrurus 100 97 99 Trimeresurus purpureomaculatus Pseudocerastes persicus 100 Ovophis monticola Ovophis zayuensis 99 Pseudocerastes fieldi 98 Ovophis tonkinensis (i) 97 Protobothrops kaulbacki Macrovipera lebetina Protobothrops sieversorum 100 100 Protobothrops mangshanensis 99 92 Protobothrops cornutus Macrovipera schweizeri 100 Protobothrops xiangchengensis 100 100 90 Montivipera xanthina Protobothrops jerdonii 100 100 Protobothrops elegans Montivipera raddei Protobothrops mucrosquamatus 99 63 100 Protobothrops flavoviridis Protobothrops tokarensis Montivipera bornmuelleri 100 Ovophis okinavensis Trimeresurus gracilis 94 Montivipera albizona 85 100 Gloydius tsushimaensis Gloydius brevicaudus 83 Montivipera wagneri 100 88 99 Gloydius ussuriensis Gloydius blomhoffii Daboia palaestinae 100 Gloydius strauchi 96 97 Gloydius halys Daboia russelii 96 Gloydius shedaoensis 100 Gloydius intermedius 59 Macrovipera deserti 99 95 Gloydius saxatilis 100 100 Atropoides occiduus Macrovipera mauritanica 100 Atropoides nummifer 95 99 Atropoides olmec Vipera ammodytes Atropoides picadoi Cerrophidion godmani Vipera latastei 94 Cerrophidion tzotzilorum 100 90 Cerrophidion petlalcalensis Vipera aspis 99 100 78 Porthidium ophryomegas 96 Porthidium dunni Vipera seoanei Porthidium yucatanicum 93 100 Porthidium nasutum 100 77 Vipera nikolskii 86 Porthidium porrasi 100 90 Porthidium lansbergii Vipera berus Bothrocophias campbelli 99 Bothrocophias microphthalmus 100 Vipera barani Bothrocophias hyoprora 99 Bothrops pictus Vipera kaznakovi 100 Rhinocerophis ammodytoides 100 96 100 Rhinocerophis cotiara Vipera eriwanensis Rhinocerophis fonsecai 97 90 94 Rhinocerophis alternatus Vipera ursinii 99 Rhinocerophis itapetiningae 99 100 Bothropoides erythromelas Vipera dinniki Bothropoides diporus 85 91 100 94 Bothropoides neuwiedi 59 Vipera renardi 100 Bothropoides jararaca

Viperinae 80 Bothropoides insularis Vipera lotievi 90 Bothropoides alcatraz 99 100 Bothriopsis pulchra Proatheris superciliaris Bothriopsis chloromelas 98 Bothriopsis taeniata Cerastes vipera 95 Bothriopsis bilineata 100 Bothrops brazili 100 Cerastes cerastes 100 Bothrops jararacussu Bothrops punctatus 100 Cerastes gasperettii 100 97 Bothrops caribbaeus Bothrops lanceolatus 86 Causus resimus Bothrops asper 100 87 Bothrops marajoensis 100 Causus rhombeatus 90 Bothrops colombiensis 99 Bothrops atrox Causus defilippii 72 Bothrops moojeni 89 Bothrops leucurus 100 Ophryacus undulatus Echis carinatus Mixcoatlus barbouri 85 100 Mixcoatlus melanurus 100 Echis ocellatus 100 Lachesis stenophrys 100 Lachesis muta Echis jogeri Bothriechis schlegelii 53 Echis omanensis 51 Bothriechis nigroviridis 62 98 Bothriechis lateralis 100 98 Bothriechis marchi Echis coloratus 100 100 Bothriechis thalassinus (i) 97 Bothriechis bicolor 91 Echis leucogaster 91 Bothriechis aurifer 100 Bothriechis rowleyi 100 Echis pyramidum 84 100 Agkistrodon contortrix (ii) Agkistrodon piscivorus 93 Atheris ceratophora 99 Agkistrodon taylori 99 Agkistrodon bilineatus Atheris barbouri Sistrurus catenatus 100 97 Sistrurus miliarius Atheris chlorechis 96 Crotalus pricei Crotalus intermedius Atheris hispida 100 100 Crotalus transversus 100 98 51 100 Crotalus tancitarensis

Viperidae Atheris squamigera 52 Crotalus triseriatus 100 77 Crotalus pusillus Atheris nitschei Crotalus lepidus 87 53 95 Crotalus aquilus 94 Atheris desaixi 74 56 Crotalus enyo Crotalus polystictus Bitis worthingtoni 99 Crotalus cerastes 63 Crotalus ravus Bitis arietans 63 Crotalus willardi 95 Crotalus horridus Bitis nasicornis 97 82 100 Crotalus durissus 100 100 Crotalus simus Bitis gabonica 100 Crotalus basiliscus 100 Crotalus molossus 100 Bitis peringueyi 91 Crotalus totonacus 96 99 Crotalus ruber Bitis caudalis Crotalus catalinensis 100 Crotalus atrox 98 Bitis xeropaga 100 Crotalus tortugensis Crotalus scutulatus 100 98 99 Bitis atropos Crotalus oreganus 58 Crotalus viridis U 98 Bitis cornuta 77 Crotalus mitchellii 89 Crotalus tigris Figure 22 V-AA 100 Bitis rubida 90 Crotalus adamanteus Enhydris chinensis 53 Enhydris plumbea 97 100 Enhydris matannensis Enhydris enhydris Enhydris jagorii 100 Enhydris longicauda 100 Homalopsidae 100 Enhydris innominata 100 Myron richardsonii 100 Pseudoferania polylepis 71 Erpeton tentaculatum 89 Enhydris bocourti 96 Bitia hydroides 85 Cantoria violacea Gerarda prevostiana 70 Fordonia leucobalia 88 98 Enhydris punctata Homalopsis buccata 88 Cerberus australis 97 100 Cerberus microlepis 100 Cerberus rynchops Micrelaps bicoloratus Oxyrhabdium leporinum 100 Prosymna ruspolii 86 Prosymna visseri Prosymna janii Prosymninae 100 Prosymna greigerti Prosymna meleagris 95 99 Rhamphiophis oxyrhynchus 99 Rhamphiophis rubropunctatus 96 Malpolon monspessulanus Rhagerhis moilensis 54 Mimophis mahfalensis Dipsina multimaculata 97 100 Hemirhagerrhis viperina 58 100 Hemirhagerrhis kelleri Hemirhagerrhis hildebrandtii 65 Psammophylax acutus Psammophylax rhombeatus 97 100 Psammophylax variabilis 90 95 Psammophylax tritaeniatus 70 Psammophis crucifer Psammophis lineolatus 100 Psammophis condanarus Psammophis trigrammus 100 Psammophis jallae 100 Psammophis leightoni Psammophiinae 8550 Psammophis notostictus 100 Psammophis angolensis 76 Psammophis schokari Psammophis punctulatus 80 Psammophis praeornatus 100 Psammophis tanganicus 69 Psammophis biseriatus Psammophis lineatus 95 96 97 Psammophis subtaeniatus 73 Psammophis sudanensis 60 Psammophis orientalis 100 Psammophis rukwae Psammophis sibilans 80 Psammophis leopardinus Lamprophiidae 71 100 Psammophis mossambicus 100 Psammophis phillipsi Homoroselaps lacteus Atractaspis irregularis 98 98 Atractaspis microlepidota Atractaspis boulengeri Atractaspidinae 96 Atractaspis bibronii 98 Atractaspis micropholis 100 58 99 Atractaspis corpulenta 96 Macrelaps microlepidotus Amblyodipsas polylepis Xenocalamus transvaalensis 100 94 Amblyodipsas dimidiata Polemon notatus 97 Polemon collaris 100 Aparallactinae 93 Polemon acanthias 54 Aparallactus modestus Aparallactus werneri 100 100 Aparallactus capensis 92 Aparallactus guentheri 100 Pythonodipsas carinata 96 Pseudaspis cana 95 Psammodynastes pulverulentus 100 Psammodynastes pictus Pseudaspidinae 64 Buhoma procterae 92 Buhoma depressiceps 100 Lycophidion nigromaculatum Lycophidion laterale 69 Lycophidion capense 92 Lycophidion ornatum 97 Hormonotus modestus Inyoka swazicus 93 Gonionotophis stenophthalmus Gonionotophis nyassae 100 Gonionotophis brussauxi 100 Gonionotophis poensis 100 Gonionotophis capensis 100 Pseudoboodon lemniscatus Bothrolycus ater 97 Bothrophthalmus brunneus Lamprophiinae 92 100 Bothrophthalmus lineatus Boaedon virgatus Boaedon lineatus 98 100 100 Boaedon fuliginosus Boaedon olivaceus 95 Lamprophis guttatus 99 Lamprophis fuscus Lamprophis aurora 95 Lamprophis fiskii Lycodonomorphus inornatus 90 Lycodonomorphus rufulus 100 Lycodonomorphus laevissimus 98 Lycodonomorphus whytii 99 Amplorhinus multimaculatus 100 Duberria variegata 82 Duberria lutrix Ditypophis vivax 99 Compsophis boulengeri 98 Compsophis albiventris 100 Compsophis laphystius 94 Compsophis infralineatus Alluaudina bellyi Parastenophis betsileanus 100 Leioheterodon geayi 100 Leioheterodon madagascariensis Leioheterodon modestus 100 90 Langaha madagascariensis 100 Micropisthodon ochraceus Ithycyphus miniatus 100 Ithycyphus oursi 97 100 Madagascarophis colubrinus Madagascarophis meridionalis Lycodryas inornatus 94 Lycodryas citrinus 100 Lycodryas sanctijohannis Pseudoxyrhophiinae 95 98 Lycodryas inopinae 100 Lycodryas pseudogranuliceps 54 Lycodryas granuliceps 100 Dromicodryas quadrilineatus Dromicodryas bernieri 98 Thamnosophis infrasignatus 95 Thamnosophis martae 100 93 Thamnosophis epistibes 98 Thamnosophis stumpffi Thamnosophis lateralis 76 95 Pseudoxyrhopus ambreensis 94 Heteroliodon occipitalis Liopholidophis dimorphus 98 Liopholidophis dolicocercus 100 Liopholidophis sexlineatus 99 Liophidium rhodogaster Liophidium vaillanti 100 99 Liophidium therezieni V 89 99 Liophidium torquatum W Liophidium mayottensis Figure 23 X-AA 73 Liophidium chabaudi Calliophis melanurus Maticora bivirgata 61 Micruroides euryxanthus Sinomicrurus japonicus 100 Sinomicrurus kelloggi 85 95 Sinomicrurus macclellandi Micrurus corallinus 100 Micrurus albicinctus 90 Micrurus psyches Micrurus fulvius 100 99 Micrurus diastema 100 Micrurus narduccii 98 Micrurus mipartitus Elapidae Micrurus dissoleucus 91 Micrurus surinamensis 97 Micrurus hemprichii Micrurus lemniscatus Micrurus decoratus Micrurus baliocoryphus 94 97 Micrurus pyrrhocryptus 98 Micrurus altirostris Micrurus ibiboboca 88 Micrurus spixii 98 89 Micrurus frontalis 59 Micrurus brasiliensis 84 Hemibungarus calligaster Ophiophagus hannah 84 100 Dendroaspis angusticeps 87 Dendroaspis polylepis 63 Walterinnesia aegyptia Aspidelaps scutatus Hemachatus haemachatus Naja kaouthia 100 100 Naja atra Naja naja 91 Naja mandalayensis 99 Naja siamensis 87 Naja sumatrana 90 69 Naja multifasciata Naja melanoleuca 58 Naja annulata 100 Naja nivea 83 Naja annulifera 95 88 Naja haje 92 78 Naja nubiae Naja pallida 99 Naja katiensis 96 Naja mossambica 96 Naja nigricollis 76 Naja ashei 100 Elapsoidea nigra 99 Elapsoidea semiannulata Elapsoidea sundevallii Bungarus flaviceps 98 Bungarus bungaroides Bungarus fasciatus 90 Bungarus sindanus 100 97 Bungarus ceylonicus 97 Bungarus caeruleus 100 Bungarus niger 99 100 Bungarus multicinctus Bungarus candidus Laticauda laticaudata 100 Laticauda saintgironsi 98 Laticauda guineai 100 Laticauda colubrina Micropechis ikaheka Toxicocalamus preussi 100 100 Demansia vestigiata 100 Demansia papuensis 91 Demansia psammophis Toxicocalamus loriae 82 100 92 Furina ornata Furina diadema 99 Simoselaps semifasciatus 100 Simoselaps anomalus Simoselaps bertholdi 85 100 Aspidomorphus schlegeli Aspidomorphus lineaticollis 68 Aspidomorphus muelleri 100 Acanthophis praelongus Acanthophis antarcticus 67 Pseudechis porphyriacus Pseudechis butleri 100 100 100 Pseudechis australis 100 Pseudechis colletti Pseudechis papuanus Pseudechis guttatus Cacophis squamulosus 89 Elapognathus coronata 88 88 Cryptophis nigrescens 95 Rhinoplocephalus bicolor 98 Suta fasciata 100 Suta monachus Suta suta 90 Suta spectabilis 94 Vermicella intermedia 75 Simoselaps calonotus 71 Denisonia devisi 100 Oxyuranus microlepidotus Oxyuranus scutellatus 100 97 Pseudonaja modesta Pseudonaja textilis Echiopsis curta 78 100 Drysdalia mastersii Drysdalia coronoides 100 Austrelaps labialis 97 Austrelaps superbus 98 Hoplocephalus bitorquatus 98 Echiopsis atriceps 99 Notechis scutatus 99 98 Tropidechis carinatus 100 Hemiaspis signata Hemiaspis damelii 100 Emydocephalus annulatus Aipysurus eydouxii 91 97 Aipysurus duboisii 94 Aipysurus apraefrontalis 90 100 Aipysurus fuscus 100 Aipysurus laevis 96 Parahydrophis mertoni Ephalophis greyae Hydrelaps darwiniensis 98 Hydrophis elegans 72 Hydrophis lapemoides 94 Hydrophis spiralis 94 100 Hydrophis semperi 100 Hydrophis pacifica 97 Hydrophis cyanocincta 95 100 Hydrophis melanocephala 75 Hydrophis parviceps Hydrophis curtus Hydrophis platura Hydrophis stokesii Hydrophis atriceps 67 98 Hydrophis brooki 54 Hydrophis caerulescens 83 83 Hydrophis czeblukovi 77 Hydrophis major Hydrophis schistosa 93 Hydrophis macdowelli W 88 Hydrophis kingii 74 Hydrophis peronii Figure 24 100 Hydrophis ornata Calamariinae Pseudorabdion oxycephalum Calamaria pavimentata 99 100 97 Calamaria yunnanensis Plagiopholis styani 100 97 Pseudoxenodon bambusicola 85 Pseudoxenodon macrops Pseudoxenodontinae Pseudoxenodon karlschmidti Scaphiodontophis annulatus 96 100 Sibynophis bistrigatus 68 Sibynophis subpunctatus Sibynophis triangularis 100 Sibynophis collaris Sibynophiinae 100 Sibynophis chinensis Grayia tholloni 100 Grayia ornata Grayiinae Grayia smithii 74 Ahaetulla fronticincta 100 Ahaetulla pulverulenta Ahaetulla nasuta 100 100 Chrysopelea taprobanica 100 Chrysopelea ornata Chrysopelea paradisi 69 Dendrelaphis bifrenalis Dendrelaphis caudolineolatus 100 Dendrelaphis caudolineatus 97 Dendrelaphis schokari 71 91 Dendrelaphis tristis 71 Boiga kraepelini 99 Crotaphopeltis tornieri 73 Dipsadoboa unicolor Telescopus fallax 89 Boiga irregularis 96 Boiga dendrophila Boiga forsteni 100 96 68 Boiga cynodon Boiga barnesii 100 100 85 Boiga trigonata Boiga ceylonensis 74 Boiga beddomei 79 Boiga multomaculata Toxicodryas pulverulenta Dasypeltis confusa Dasypeltis atra 98 Dasypeltis scabra 70 Dasypeltis sahelensis 92 Colubrinae 77 Dasypeltis gansi 90 Dasypeltis fasciata Colubridae Scaphiophis albopunctatus 100 Oligodon arnensis 86 Oligodon sublineatus 83 Oligodon taeniolatus Oligodon octolineatus 85 Oligodon cyclurus 100 100 Oligodon barroni 99 Oligodon taeniatus 89 100 Oligodon chinensis 99 Oligodon ocellatus 99 90 Oligodon formosanus 93 Oligodon cinereus Oligodon maculatus 56 Oligodon splendidus 98 97 Oligodon cruentatus Oligodon theobaldi 98 100 Oligodon torquatus Oligodon planiceps 100 Coelognathus radiatus Coelognathus helena 100 Coelognathus erythrurus 99 Coelognathus subradiatus Coelognathus flavolineatus 90 Thrasops jacksonii 98 Dispholidus typus 68 Thelotornis capensis 52 Philothamnus carinatus Philothamnus heterodermus 60 94 Philothamnus nitidus 57 90 Philothamnus semivariegatus 88 Philothamnus angolensis 99 Philothamnus girardi 68 99 Philothamnus thomensis Philothamnus natalensis 69 Philothamnus hoplogaster 87 Hapsidophrys lineatus 68 99 Hapsidophrys smaragdina Hapsidophrys principis Lytorhynchus diadema Coluber zebrinus 92 Bamanophis dorri 86 100 Macroprotodon cucullatus 100 Macroprotodon abubakeri Hemerophis socotrae 100 Hemorrhois hippocrepis 94 100 Hemorrhois algirus Hemorrhois nummifer 99 100 Hemorrhois ravergieri Spalerosophis microlepis 60 95 Spalerosophis diadema 86 Platyceps rhodorachis 100 Platyceps rogersi Platyceps karelini 100 61 Platyceps ventromaculatus 94 Platyceps najadum 100 98 Platyceps collaris 52 Platyceps florulentus 100 Dolichophis jugularis Dolichophis schmidti 100 Dolichophis caspius 100 100 Hierophis viridiflavus Hierophis gemonensis Hierophis spinalis 92 100 Eirenis modestus 83 Eirenis aurolineatus 100 Eirenis persicus Eirenis decemlineatus 86 Eirenis levantinus Eirenis medus 83 82 Eirenis thospitis Eirenis lineomaculatus 97 86 59 Eirenis rothii Eirenis coronelloides Eirenis eiselti X 100 Eirenis collaris Y 91 Eirenis barani Figure 25 Z-AA Colubrinae cont. Eirenis punctatolineatus 100 Cyclophiops major Ptyas korros 81 Ptyas mucosa Oxybelis fulgidus 82 Oxybelis aeneus 96 100 Opheodrys vernalis Opheodrys aestivus 93 Salvadora mexicana Tantilla melanocephala 93 Coluber taeniatus 88 Coluber constrictor Coluber flagellum 92 Chironius quadricarinatus Chironius carinatus 97 Leptophis ahaetulla 93 92 Dendrophidion dendrophis 99 Dendrophidion percarinatum Colubrinae cont. 66 Drymobius rhombifer Trimorphodon biscutatus 91 Phyllorhynchus decurtatus 82 Spilotes pullatus 98 Pseustes sulphureus 100 Drymarchon corais Chironius fuscus Chironius scurrulus 87 Chironius laevicollis Chironius grandisquamis 86 74 Chironius flavolineatus Chironius bicarinatus 81 Chironius monticola 83 Chironius exoletus 54 Chironius laurenti 99 Chironius multiventris 100 Drymoluber dichrous 100 Drymoluber brazili 92 Mastigodryas melanolomus 64 87 Mastigodryas boddaerti Mastigodryas bifossatus 71 Rhinobothryum lentiginosum 87 Stenorrhina freminvillei Chionactis occipitalis 89 Chilomeniscus stramineus 94 Sonora semiannulata 99 Conopsis biserialis Conopsis nasus 100 Ficimia streckeri Gyalopion canum Pseudoficimia frontalis Sympholis lippiens 100 Gonyosoma oxycephalum 98 Gonyosoma jansenii 100 Rhadinophis prasinus 100 Rhynchophis boulengeri 53 Rhadinophis frenatus Lycodon ruhstrati 86 Lycodon laoensis Lycodon fasciatus 83 92 Lycodon paucifasciatus 93 Lycodon rufozonatum 60 Lycodon semicarinatum Dryocalamus nympha 83 Lycodon carinatus Lycodon capucinus 98 94 76 Lycodon osmanhilli Lycodon zawi Lycodon aulicus Archelaphe bella 100 Euprepiophis conspicillata Euprepiophis mandarinus 100 Oreocryptophis porphyraceus 99 Orthriophis taeniurus Orthriophis hodgsoni 88 Orthriophis moellendorffi 98 Orthriophis cantoris 99 Zamenis hohenackeri Zamenis persicus 100 Zamenis longissimus 99 64 Zamenis lineatus 100 Rhinechis scalaris 100 Zamenis situla Elaphe davidi Elaphe carinata 93 90 100 Elaphe bimaculata 100 Elaphe dione 61 Elaphe climacophora 55 Elaphe schrenckii Elaphe quadrivirgata 83 100 Elaphe quatuorlineata 75 Elaphe sauromates Coronella girondica 98 Coronella austriaca 83 Oocatochus rufodorsatus Senticolis triaspis 100 Pituophis deppei 84 Pituophis vertebralis 91 Pituophis lineaticollis Pituophis melanoleucus 100 94 Pituophis ruthveni 98 99 Pituophis catenifer Pantherophis vulpinus 100 Pantherophis guttatus Pantherophis emoryi 99 Pantherophis slowinskii 96 Pantherophis spiloides 100 100 Pantherophis alleghaniensis 100 98 Pantherophis obsoletus Pantherophis bairdi 100 Bogertophis subocularis Bogertophis rosaliae Rhinocheilus lecontei 87 98 Arizona elegans Pseudelaphe flavirufa Cemophora coccinea Lampropeltis calligaster 100 Lampropeltis webbi 75 100 Lampropeltis pyromelana Lampropeltis zonata 92 72 Lampropeltis elapsoides 79 Lampropeltis mexicana 82 94 Lampropeltis ruthveni Lampropeltis triangulum 100 Lampropeltis extenuatum 96 Lampropeltis alterna 98 Lampropeltis nigra 74 Lampropeltis getula Y 96 Lampropeltis holbrooki 60 Lampropeltis splendida Figure 26 98 Lampropeltis californiae 99 Trachischium monticola Amphiesma sauteri 100 Amphiesma craspedogaster 99 98 Natriciteres olivacea Afronatrix anoscopus Lycognathophis seychellensis Macropisthodon rudis 68 100 Balanophis ceylonensis Rhabdophis subminiatus 69 62 Rhabdophis tigrinus 96 Rhabdophis nuchalis 98 88 Amphiesma stolatum Xenochrophis vittatus Natricinae Xenochrophis flavipunctatus 100 Xenochrophis piscator 100 Atretium schistosum Xenochrophis punctulatus Xenochrophis asperrimus 88 Atretium yunnanensis 100 Aspidura drummondhayi 100 Aspidura trachyprocta Aspidura ceylonensis 99 Aspidura guentheri 100 Opisthotropis guangxiensis Opisthotropis lateralis 86 Opisthotropis latouchii 100 Opisthotropis cheni 100 Sinonatrix aequifasciata 98 Sinonatrix percarinata 82 Sinonatrix annularis 100 Natrix maura Natrix natrix 88 Natrix tessellata Clonophis kirtlandii 72 Virginia striatula 100 Storeria occipitomaculata 98 97 Storeria dekayi Seminatrix pygaea 80 100 Regina rigida 100 Regina alleni 76 Regina septemvittata Regina grahami 50 Tropidoclonion lineatum 96 100 Nerodia cyclopion Nerodia floridana 100 100 Nerodia taxispilota Nerodia rhombifer 99 Nerodia erythrogaster Nerodia harteri 100 Nerodia fasciata 100 Nerodia sipedon Thamnophis sirtalis 69 Thamnophis sauritus 100 Thamnophis proximus 93 Thamnophis rufipunctatus Adelophis foxi 100 Thamnophis valida Thamnophis melanogaster 100 Thamnophis exsul 72 Thamnophis godmani 85 Thamnophis scaliger 96 100 Thamnophis sumichrasti 98 Thamnophis mendax Thamnophis fulvus 100 Thamnophis chrysocephalus 86 Thamnophis cyrtopsis Thamnophis eques 99 99 Thamnophis marcianus 100 Thamnophis hammondii Thamnophis ordinoides 92 99Thamnophis couchii 63 69Thamnophis atratus Thamnophis gigas 73 Thamnophis elegans 94 Thamnophis brachystoma Z 100 Thamnophis radix Figure 27 89 Thamnophis butleri Conophis lineatus Thermophis zhaoermii 95 Crisantophis nevermanni 100 Psomophis obtusus Thermophis baileyi 94 Psomophis genimaculatus 100 Psomophis joberti Contia tenuis 100 Pseudalsophis biserialis 72 Pseudalsophis elegans Heterodon platirhinos Arrhyton taeniatum 100 100 Arrhyton supernum Heterodon simus Arrhyton vittatum 58 Arrhyton landoi 99 Heterodon nasicus 73 Arrhyton procerum 91 75 100 Arrhyton tanyplectum Diadophis punctatus 98 Arrhyton dolichura (ii) 81 Magliophis exiguum 87 Carphophis amoenus 100 Cubophis cantherigerus 100 Cubophis vudii 80 Farancia abacura 99 Caraiba andreae 93 Haitiophis anomalus 98 Farancia erytrogramma Borikenophis portoricensis 80 100 Alsophis antillensis Nothopsis rugosus Alsophis rijgersmaei 97 97 Alsophis antiguae 68 Amastridium veliferum 100 Alsophis rufiventris (i) 99 Ialtris dorsalis Tantalophis discolor 89 Darlingtonia haetiana 100 99 Hypsirhynchus ferox Coniophanes fissidens 83 Antillophis parvifrons 98 Schwartzophis callilaemum 96 Rhadinaea flavilata 100 Schwartzophis polylepis 93 100 Schwartzophis funereum 86 Rhadinaea fulvivittis 100 Uromacer catesbyi Uromacer oxyrhynchus Pseudoleptodeira latifasciata 99 Uromacer frenatus Lygophis anomalus

Dipsadinae 80 Trimetopon gracile 100 Lygophis elegantissimus 99 Lygophis lineatus 99 Lygophis paucidens Hypsiglena slevini 78 76 73 Lygophis flavifrenatus Hypsiglena jani 70 Lygophis meridionalis Xenodon severus 63 Xenodon merremi 100 Hypsiglena affinis 98 100 52 Xenodon werneri 100 Xenodon neuwiedii 99 Hypsiglena ochrorhyncha 98 Xenodon dorbignyi 75 Xenodon histricus 84 Hypsiglena torquata 99 Xenodon nattereri Xenodon guentheri 85 Hypsiglena chlorophaea 71 98 Xenodon semicinctus 90 94 61 Xenodon matogrossensis Tretanorhinus variabilis 62 Xenodon pulcher 92 Eryrthrolamprus atraventer 64 Leptodeira nigrofasciata Eryrthrolamprus jaegeri 73 Eryrthrolamprus almadensis Imantodes inornatus Eryrthrolamprus ceii 89 71 99 100 Eryrthrolamprus poecilogyrus Imantodes lentiferus Eryrthrolamprus epinephelus 67 87 94 Eryrthrolamprus juliae 100 Imantodes gemmistratus Eryrthrolamprus miliaris 86 96 Eryrthrolamprus reginae Imantodes cenchoa Eryrthrolamprus breviceps 88 Eryrthrolamprus pygmaea Leptodeira uribei 97 Eryrthrolamprus typhlus 87 Erythrolamprus mimus 100 Leptodeira frenata 100 Erythrolamprus aesculapii 51 Philodryas baroni Leptodeira splendida Philodryas nattereri 100 100 88 Philodryas viridissima Leptodeira punctata Philodryas olfersii Philodryas argentea Leptodeira septentrionalis 68 100 Philodryas georgeboulengeri 91 Philodryas mattogrossensis 90 68 98 Leptodeira annulata 96 Philodryas psammophidea 97 Philodryas aestiva Leptodeira bakeri 62 Philodryas agassizii 94 Philodryas patagoniensis 88 Leptodeira maculata Sordellina punctata 95 Taeniophallus brevirostris 100 Leptodeira rubricata 100 Taeniophallus nicagus 66 Echinanthera melanostigma Adelphicos quadrivirgatum 67 Echinanthera undulata 79 75 Taeniophallus affinis 90 Hydromorphus concolor 95 Phalotris lemniscatus 100 Phalotris nasutus Tretanorhinus nigroluteus 100 Phalotris lativittatus 100 Phalotris mertensi 100 Elapomorphus quinquelineatus 100 Cryophis hallbergi Apostolepis assimilis 56 Apostolepis dimidiata Geophis carinosus 95 91 Apostolepis albicollaris 97 Apostolepis flavotorquata Geophis godmani 94 94 69 Apostolepis sanctaeritae 99 Apostolepis cearensis Atractus zidoki Manolepis putnami 55 Hydrops triangularis Atractus wagleri Pseudoeryx plicatilis 83 86 Helicops infrataeniatus Atractus schach 100 Helicops hagmanni 68 91 98 Helicops carinicaudus 96 Atractus albuquerquei 91 99 Helicops gomesi 68 Helicops angulatus Atractus elaps Gomesophis brasiliensis Calamodontophis paucidens 73 Atractus flammigerus 97 89 100 Pseudotomodon trigonatus Tachymenis peruviana 70 Atractus badius 87 Ptychophis flavovirgatus Tomodon dorsatus 75 Atractus reticulatus 86 Thamnodynastes pallidus 94 90 Thamnodynastes lanei 73 Atractus trihedrurus 90 Thamnodynastes hypoconia 91 93 99 Thamnodynastes strigatus 97 Atractus zebrinus Thamnodynastes rutilus 100 Tropidodryas serra Ninia atrata Tropidodryas striaticeps 87 100 Xenopholis undulatus Sibon nebulatus Xenopholis scalaris 90 Caaeteboia amarali 100 Tropidodipsas sartorii 56 Hydrodynastes bicinctus 100 Hydrodynastes gigas Dipsas indica Siphlophis cervinus 68 98 91 Siphlophis compressus Dipsas catesbyi Siphlophis pulcher 84 100 Siphlophis longicaudatus Dipsas neivai Oxyrhopus petolarius 82 95 Oxyrhopus formosus 100 Dipsas variegata 100 Oxyrhopus trigeminus 67 Oxyrhopus clathratus Dipsas pratti Oxyrhopus rhombifer 70 63 Oxyrhopus melanogenys 95 95 Sibynomorphus mikanii 67 Oxyrhopus guibei Rodriguesophis iglesiasi 96 96 Sibynomorphus turgidus Paraphimophis rusticus Phimophis guerini 75 87 (i) 87 Clelia clelia Dipsas articulata 96 Mussurana bicolor 90 Drepanoides anomalus 79 Dipsas albifrons 74 Boiruna maculata (ii) Rhachidelus brazili AA 88 Sibynomorphus ventrimaculatus 92 Pseudoboa neuwiedii 79 100 Pseudoboa nigra Figure 28 Sibynomorphus neuwiedi Pseudoboa coronata Additional files provided with this submission:

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