A phylogeny and revised classification of Squamata ...

A phylogeny and revised classification ofSquamata, including 4161 species of lizardsand snakesPyron et al.

Pyron et al. BMC Evolutionary Biology 2013, 13:93http://www.biomedcentral.com/1471-2148/13/93

Pyron et al. BMC Evolutionary Biology 2013, 13:93http://www.biomedcentral.com/1471-2148/13/93

RESEARCH ARTICLE Open Access

A phylogeny and revised classification ofSquamata, including 4161 species of lizardsand snakesR Alexander Pyron1*, Frank T Burbrink2,3 and John J Wiens4

Abstract

Background: The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse andconspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for thegroup with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and toaddress 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 andsubfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrialgenes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates ofhigher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates thatare very different from previous morphology-based hypotheses. The tree also includes many relationships that differfrom 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 forfuture comparative studies. We also present a revised classification of squamates at the family and subfamily levelto 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, andlamprophiid snakes.

Keywords: Amphisbaenia, Lacertilia, Likelihood support measures, Missing data, Serpentes, Squamata,Phylogenetics, Reptilia, Supermatrices, Systematics

BackgroundSquamate reptiles (lizards, snakes, and amphisbaenians["worm lizards"]) are among the most diverse radiationsof terrestrial vertebrates. Squamata includes more than9400 species as of December 2012 [1]. The rate of newspecies descriptions shows no signs of slowing, with arecord 168 new species described in 2012 [1], greaterthan the highest yearly rates of the 18th and 19th cen-turies (e.g. 1758, 118 species; 1854, 144 species [1]).Squamates are presently found on every continent ex-cept Antarctica, and in the Indian and Pacific Oceans,and span many diverse ecologies and body forms,

* Correspondence: [email protected] of Biological Sciences, The George Washington University,2023 G St. NW, Washington, DC 20052, USAFull list of author information is available at the end of the article

© 2013 Pyron et al.; licensee BioMed Central LCommons Attribution License (http://creativecreproduction in any medium, provided the or

from limbless burrowers to arboreal gliders (summa-rized 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 ofmany pioneering studies using phylogenies to address ques-tions about trait evolution (e.g. [8,9]). Phylogenies are nowrecognized as being integral to all comparative studies ofsquamate biology (e.g. [10,11]). However, hypotheses aboutsquamate phylogeny have changed radically in recent years[12], especially when comparing trees generated from mor-phological [13-15] and molecular data [16-20]. Further-more, despite extensive work on squamate phylogeny at alltaxonomic levels, a large-scale phylogeny (i.e. includingthousands of species and multiple genes) has never beenattempted using morphological or molecular data.

td. This is an Open Access article distributed under the terms of the Creativeommons.org/licenses/by/2.0), which permits unrestricted use, distribution, andiginal work is properly cited.

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Pyron et al. BMC Evolutionary Biology 2013, 13:93 Page 2 of 53http://www.biomedcentral.com/1471-2148/13/93

Squamate phylogenetics has changed radically in thelast 10 years, revealing major conflicts between the re-sults of morphological and molecular analyses [12]. Earlyestimates of squamate phylogeny [21] and recent studiesbased on morphological data [13-15,22] consistentlysupported a basal division between Iguania (includingchameleons, agamids, and iguanids, sensu lato), andScleroglossa, which comprises all other squamates (in-cluding skinks, geckos, snakes, and amphisbaenians).Within Scleroglossa, many phylogenetic analyses of mor-phological data have also supported a clade containinglimb-reduced taxa, including various combinations ofsnakes, dibamids, amphisbaenians, and (in some ana-lyses) limb-reduced skinks and anguids [13-15,19,22],though some of these authors also acknowledged thatthis clade was likely erroneous.In contrast, recent molecular analyses have estimated

very different relationships. Novel arrangements includeplacement of dibamids and gekkotans near the root ofthe squamate tree, a sister-group relationship betweenamphisbaenians and lacertids, and a clade (Toxicofera)uniting Iguania with snakes and anguimorphs withinScleroglossa [16-20,23,24]. These molecular results (andthe results of combined morphological and molecularanalyses) suggest that some estimates of squamate phy-logeny based on morphology may have been misled, es-pecially by convergence associated with adaptations toburrowing [19]. However, there have also been disagree-ments among molecular studies, such as placement ofdibamids relative to gekkotans and other squamates, andrelationships 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 repre-sentatives from all described families and subfamilies[17-20,23,24]. This limited taxon sampling makesexisting molecular phylogenies difficult to use for broad-scale comparative studies, with some exceptions basedon supertrees [10,11]. In addition, limited taxon sam-pling is potentially a serious issue for phylogenetic ac-curacy [25-28]. Thus, an analysis with extensive taxonsampling is critically important to test hypotheses basedon molecular datasets with more limited sampling, andto provide a framework for comparative analyses.Despite the lack of a large-scale phylogeny across

squamates, recent molecular studies have producedphylogenetic estimates for many of the major groups ofsquamates, including iguanian lizards [29-34], higher-level snake groups [35-37], typhlopoid snakes [38,39],colubroid snakes [40-46], booid snakes [47,48], scincidlizards [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 ofcharacters and taxa that they sampled (and which wereavailable at the time for sequencing).Here, we present a phylogenetic estimate for Squamata

based on combining much of the existing sequence data forsquamate reptiles, using the increasingly well-establishedsupermatrix approach [41,72-77]. We present a newphylogenetic estimate including 4161 squamate species.The dataset includes up to 12896 bp per species from12 genes (7 nuclear, 5 mitochondrial). We include speciesfrom all currently described families and subfamilies.In terms of species sampled, this is 5 times larger than anyprevious 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 ofhigher-level squamate relationships [20]. While we didnot sequence any new taxa specifically for this project,much of the data in the combined matrix were gene-rated in our labs or from our previous collaborative pro-jects [16,19,20,34,36,37,41,44,78-82], including thousandsof gene sequences from hundreds of species (>550 spe-cies; ~13% of the total).The supermatrix approach can provide a relatively

comprehensive phylogeny, and uncover novel relation-ships not seen in any of the separate analyses in whichthe data were generated. Such novel relationships can berevealed via three primary mechanisms. First, differentstudies may have each sampled different species from agiven group for the same genes, and combining thesedata may reveal novel relationships not apparent in theseparate analyses. Second, different studies may haveused different genetic markers for the same taxa, andcombining these markers can dramatically increase char-acter sampling, potentially revealing new relationshipsand providing stronger support for previous hypotheses.Third, even for clades that were previously studied usingcomplete taxon sampling and multiple loci, novel rela-tionships may be revealed by including these lineageswith other related groups in a large-scale phylogeny.The estimated tree and branch-lengths should be use-

ful for comparative studies of squamate biology. How-ever, this phylogeny is based on a supermatrix withextensive missing data (mean = 81% per species). Someauthors have suggested that matrices with missing cellsmay yield misleading estimates of topology, support, andbranch lengths [83]. Nevertheless, most empirical andsimulation studies have not found this to be the case, atleast for topology and support [41,73,84,85]. Thoughfewer studies have examined the effects of missing dataon branch lengths [44,86,87], these also suggest thatmissing data do not strongly impact estimates. Here, wetest whether branch lengths for terminal taxa are relatedto their completeness.


In general, our results corroborate those of many recentmolecular studies with regard to higher-level relationships,species-level relationships, and the monophyly, compo-sition, and relationships of most families, subfamilies, andgenera. However, our results differ from previous estimatesfor some groups, and reveal (or corroborate) numerousproblems in the existing classification of squamates. Wetherefore provide a conservative, updated classification ofextant squamates at the family and subfamily level basedon the new phylogeny, while highlighting problematic ta-xonomy at the genus level, without making changes. Thegeneric composition of all families and subfamilies underour revised taxonomy are provided in Appendix I.We note dozens of problems in the genus-level tax-

onomy suggested by our tree, but we acknowledge in ad-vance that we do not provide a comprehensive review ofthe previous literature dealing with all these taxonomic is-sues (this would require a monographic treatment). Simi-larly, we do not attempt to fix these genus-level problemshere, as most will require more extensive taxon (and po-tentially character) sampling to adequately resolve.Throughout the paper, we address only extant squa-

mates. Squamata also includes numerous extinct spe-cies classified in both extant and extinct families,subfamilies, and genera. Relationships and classificationof extinct squamates based on morphological datafrom fossils have been addressed by numerous authors(e.g. [14,15,19,22,88-93]). A classification based only onliving taxa may create some problems for classifyingfossil taxa, but these can be addressed in future studiesthat integrate molecular and fossil data [19,86].

ResultsSupermatrix phylogenyWe generated the final tree (lnL = −2609551.07) usingMaximum Likelihood (ML) in RAxMLv7.2.8. Supportwas assessed using the non-parametric Shimodaira-Hasegawa-Like (SHL) implementation of the approximatelikelihood-ratio test (aLRT; see [94]). The tree and datamatrix are available in NEXUS format in DataDryad re-pository 10.5061/dryad.82h0m and as Additional file 1:Data File S1. A skeletal representation of the tree (exclud-ing several species which are incertae sedis) is shown inFigure 1. The full species-level phylogeny (minus theoutgroup 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-supportedphylogenetic estimate for squamates (i.e. 70% of nodes haveSHL values >85, indicating they are strongly supported).There is no relationship between proportional complete-ness (bp of non-missing data in species / 12896 bp ofcomplete data) and branch length (r = −0.29, P = 0.14) forterminal taxa, strongly suggesting that the estimatedbranch lengths are not consistently biased by missing data.

Higher-level relationshipsOur tree (Figure 1) is broadly congruent with most previ-ous molecular studies of higher-level squamate phylogenyusing both nuclear data and combined nuclear and mito-chondrial data (e.g. [16-20]), providing important confirm-ation of previous molecular studies based on more limitedtaxon sampling. Specifically we support (Figure 1): (i) theplacement of dibamids and gekkotans near the base of thetree (Figure 1A); (ii) a sister-group relationship betweenScincoidea (scincids, cordylids, gerrhosaurids, and xantu-siids; Figure 1B) and a clade (Episquamata; Figure 1C)containing the rest of the squamates excluding dibamidsand 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 sistertaxon to Lacertoidea.These relationships are strongly supported in general

(Figure 1), but differ sharply from most trees based onmorphological data [13-15,19,22,95]. Nevertheless, manyclades found in previous morphological taxonomies andphylogenies are also present in this tree in someform, including Amphisbaenia, Anguimorpha, Gekkota,Iguania, Lacertoidea (but including amphisbaenians),Scincoidea, Serpentes, and many families and subfamilies.In contrast, the relationships among these groups differstrongly between molecular analyses [17-20] and morpho-logical analyses [14,15]. Our results demonstrate that thisincongruence is not explained by limited taxon sampling inthe molecular data sets. In fact, our species-level samplingis 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 strong-

ly supported in our tree. The family Dibamidae is the sistergroup to all other squamates, and Gekkota is the sistergroup to all squamates excluding Dibamidae (Figure 1), asin some previous studies (e.g. [16,18]). Other recent mo-lecular analyses have also placed Dibamidae near the squa-mate root, but differed in placing it as either the sistertaxon to all squamates excluding Gekkota [17], or thesister- group of Gekkota [19,20]. Our results also corrobor-ate that the New World genus Anelytropsis is nested withinthe Old World genus Dibamus [96], but the associatedbranches are weakly supported (Figure 2).

GekkotaWithin Gekkota, we corroborate both earlier morpho-logical [97] and recent molecular estimates [55,56,59,98]in supporting a clade containing the Australian radiation of"diplodactylid" geckos (Carphodactylidae and Diplodac-tylidae) and the snakelike pygopodids (Figures 1, 2).As in previous studies [55], Carphodactylidae is theweakly supported sister group to Pygopodidae, andthis clade is the sister group of Diplodactylidae

0.2 subst./site

Scincidae

Xantusiidae

Gerrhosauridae

Teiidae

Gymnophthalmidae

Lacertidae

Anguidae

Chamaeleonidae

Agamidae

Leiosauridae

Boidae

Viperidae

Colubridae

Lamprophiidae

A

B

C

D

E

F

G

A) GekkotaB) ScincoideaC) EpisquamataD) LacertoideaE) ToxicoferaF) AnguimorphaG) IguaniaH) Serpentes

H

Dipsadinae

Gekkonidae

Cercosaurinae

Acontiinae

Lacertinae

Hydrosaurinae

Xenodermatidae

Anniellidae

Crotaphytidae

Hoplocercidae

Sphenodontidae

Leiolepidinae

Polychrotidae

Pseudoxyrhophiinae

Loxocemidae

Dibamidae

Prosymninae

Lygosominae

Natricinae

Xantusiinae

Tropiduridae

Corytophanidae

Ecpleopinae

Anomochilidae

Amphisbaenidae

Leiosaurinae

Xenophiidae

Scincinae

Draconinae

Bipedidae

Gerrhosaurinae

Rhineuridae

Anomalepididae

Trogonophiidae

Aniliidae

Azemiopinae

Alopoglossinae

Lanthanotidae

Pseudaspidinae

Tupinambinae

Xenotyphlopidae

Blanidae

Gerrhopilidae

Liolaemidae

Candoiinae

Gallotiinae

Leptotyphlopidae

Platysaurinae

Pythonidae

Boinae

Colubrinae

Opluridae

Elapidae

Typhlopidae

Pareatidae

Cadeidae

Crotalinae

Sibynophiinae

Chamaeleoninae

Rhachisaurinae

Grayiinae

Ungaliophiinae

Erycinae

Phyllodactylidae

Anguinae

Helodermatidae

Phrynosomatidae

Sanziniinae

Tropidophiidae

Viperinae

Cricosaurinae

Shinisauridae

Teiinae

Diplodactylidae

Cylindrophiidae

Brookesiinae

Lepidophyminae

Enyaliinae

Varanidae

Bachiinae

Aparallactinae

Sphaerodactylidae

Atractaspidinae

Uropeltidae

LeiocephalidaeIguanidae

Homalopsidae

Amphibolurinae

Xenopeltidae

Diploglossinae

Calamariinae

Xenosauridae

Uromastycinae

Agaminae

Acrochordidae

Pygopodidae

Calabariidae

Psammophiinae

Carphodactylidae

Cordylinae

Gymnophthalminae

Pseudoxenodontinae

Bolyeriidae

Dactyloidae

Gerrhonotinae

Eublepharidae

Lamprophiinae

Zonosaurinae

83

98

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98

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83

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68

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95

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65

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100

Squamata

Cordylidae

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 atnodes are SHL values greater than 50%. The full tree is presented in Figures 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,24, 25, 26, 27, 28.


A

Figure 2 (See legend on next page.)


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


(Figures 1, 2). We recover clades within the formerGekkonidae that correspond to the strongly supportedfamilies Eublepharidae, Sphaerodactylidae, Phyllodactylidae,and Gekkonidae as in previous studies, and similar rela-tionships among these groups [55-57,59,60,98-100].Within Gekkota, we find evidence for non-monophyly

of many genera. Many relationships among the NewCaledonian diplodactylids are weakly supported (Figure 2),and there is apparent non-monophyly of the generaRhacodactylus, Bavayia, and Eurydactylodes with respectto each other and Oedodera, Dierogekko, Paniegekko,Correlophus, and Mniarogekko [101]. In the Australiandiplodactylids, Strophurus taenicauda is strongly sup-ported as belonging to a clade that is only distantly relatedto the other sampled Strophurus species (Figure 2). Thetwo species of the North African sphaerodactylid genusSaurodactylus are divided between the two majorsphaerodactylid clades (Figure 3), but the associatedbranches are weakly supported. The South Americanphyllodactylid genus Homonota is strongly supportedas being paraphyletic with respect to Phyllodactylus(Figure 3).A number of gekkonid genera (Figure 4) also appear

to be non-monophyletic, including the Asian generaCnemaspis (sampled species divided into two non-sisterclades), Lepidodactylus (with respect to Pseudogekko andsome Luperosaurus), Gekko (with respect to Ptychozoonand Lu. iskandari), Luperosaurus (with respect toLepidodactylus and Gekko), Mediodactylus (with respectto Pseudoceramodactylus, Tropiocolotes, Stenodactylus,Cyrtopodion, Bunopus, Crossobamon, and Agamura), andBunopus (with respect to Crossobamon), and the AfricanAfrogecko (with respect to Afroedura, Christinus, Cryp-tactites, and Matoatoa), Afroedura (with respect toAfrogecko, Blaesodactylus, Christinus, Geckolepis, Pachy-dactylus, Rhoptropus, and numerous other genera),Chondrodactylus (with respect to Pachydactylus laevi-gatus), and Pachydactylus (with respect to Chondro-dactylus and Colopus). Many of these taxonomicproblems in gekkotan families have been identified inprevious studies (e.g. [59,99,102]), and extensive changeswill likely be required to fix them.

ScincoideaWe 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 stu-dies [16-20]. All four families are strongly supported(Figures 5, 6, 7, 8, 9, 10). A similar clade is also re-

cognized in morphological phylogenies [14], thoughwithout Xantusiidae in some [13].Within the New World family Xantusiidae, we corrob-

orate previous analyses [103,104] that found strong sup-port for a sister-group relationship between Xantusia andLepidophyma, excluding Cricosaura (Figure 5). These re-lationships support the subfamily Cricosaurinae forCricosaura [105]. We also recognize Xantusiinae for theNorth American genus Xantusia and Lepidophyminae forthe Central American genus Lepidophyma [106,107].Within the African and Madagascan family Gerrho-

sauridae (Figure 5), the genus Gerrhosaurus is weakly sup-ported as being paraphyletic with respect to the cladecomprising Tetradactylus + Cordylosaurus, with G. majorplaced as the sister group to all other gerrhosaurids.Within Cordylidae (Figure 5), we use the generic ta-xonomy from a recent phylogenetic analysis and re-classification based on multiple nuclear and mitochondrialgenes [108]. This classification broke up the non-monophyletic Cordylus [109] into several smaller genera,and we corroborate the non-monophyly of the formerCordylus and support the monophyly of the newly recog-nized genera (Figure 5). We support the distinctiveness ofPlatysaurus (Figure 5) and recognition of the subfamilyPlatysaurinae [108].We strong support (SHL = 100) for the monophyly of

Scincidae (Figure 6) as in previous studies (e.g.[20,50,51]). We strongly support the basal placement ofthe monophyletic subfamily Acontiinae (Figure 6), asfound in some previous studies (e.g. [20,51]) but notothers (e.g. [50]). Similar to earlier studies, we find thatthe subfamily Scincinae (sensu [110]) is non-monophyletic,as Feylininae is nested within Scincinae (also found in[20,50,51,111]). Based on these results, synonymizingFeylininae with Scincinae produces a monophyleticScincinae (SHL = 97), which is then sister to a monophy-letic 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 threesubfamilies (Acontiinae, Lygosominae, Scincinae) arestrongly supported. Importantly, these definitions approxi\mate the traditional content of the three subfamilies[50,110], except for recognition of Feylininae.We note that a recent revision of the New World

genus Mabuya introduced a nontraditional family-levelclassification for Scincidae [112]. These authors dividedScincidae into seven families: Acontiidae, Egerniidae,Eugongylidae, Lygosomidae, Mabuyidae, Scincidae andSphenomorphidae. However, there was no phylogenetic

BTarentola gigas

Tarentola caboverdianaTarentola rudis

Tarentola darwiniTarentola chazaliae

Tarentola delalandiiTarentola gomerensis

Tarentola annularisTarentola ephippiata

Tarentola boettgeriTarentola mindiae

Tarentola neglectaTarentola angustimentalisTarentola mauritanica

Tarentola desertiTarentola boehmei

Tarentola americanaPhyllopezus maranjonensis

Phyllopezus lutzaePhyllopezus pollicaris

Phyllopezus periosusPhyllodactylus homolepidurus

Phyllodactylus davisiPhyllodactylus duellmani

Phyllodactylus delcampoiPhyllodactylus paucituberculatus

Phyllodactylus nocticolusPhyllodactylus bugastrolepisPhyllodactylus unctus

Phyllodactylus xantiPhyllodactylus bordai

Phyllodactylus laneiPhyllodactylus tuberculosus

Phyllodactylus reissiiPhyllodactylus wirshingi

Homonota andicolaHomonota darwinii

Homonota borelliiHomonota underwoodi

Homonota fasciataHomonota gaudichaudii

Ptyodactylus guttatusPtyodactylus hasselquistii

Ptyodactylus oudriiPtyodactylus ragazzii

Asaccus platyrhynchusHaemodracon riebeckii

Thecadactylus rapicaudaThecadactylus solimoensis

Sphaerodactylus nicholsiSphaerodactylus ocoae

Sphaerodactylus gaigeaeSphaerodactylus klauberi

Sphaerodactylus semasiopsSphaerodactylus goniorhynchus

Sphaerodactylus townsendiSphaerodactylus armstrongi

Sphaerodactylus macrolepisSphaerodactylus argus

Sphaerodactylus rooseveltiSphaerodactylus altavelensis

Sphaerodactylus notatusSphaerodactylus darlingtoni

Sphaerodactylus cryphiusSphaerodactylus shrevei

Sphaerodactylus elegansSphaerodactylus leucaster

Sphaerodactylus copeiSphaerodactylus nigropunctatus

Sphaerodactylus intermediusSphaerodactylus torrei

Sphaerodactylus cinereusSphaerodactylus thompsoni

Sphaerodactylus glaucusSphaerodactylus molei

Sphaerodactylus oliveriSphaerodactylus richardi

Sphaerodactylus cricoderusSphaerodactylus ramsdeni

Sphaerodactylus schwartziSphaerodactylus kirbyiSphaerodactylus vincenti

Sphaerodactylus microlepisSphaerodactylus parvus

Sphaerodactylus sabanusSphaerodactylus elegantulus

Sphaerodactylus sputatorSphaerodactylus fantasticus

Pseudogonatodes guianensisPseudogonatodes lunulatus

Pseudogonatodes manessiColeodactylus natalensis

Coleodactylus meridionalisColeodactylus brachystoma

Coleodactylus septentrionalisGonatodes ocellatusGonatodes ceciliaeGonatodes seigliei

Gonatodes concinnatusGonatodes antillensis

Gonatodes humeralisGonatodes falconensis

Gonatodes taniaeGonatodes purpurogularis

Gonatodes alexandermendesiGonatodes superciliaris

Gonatodes annularisGonatodes hasemani

Gonatodes infernalisGonatodes vittatus

Gonatodes petersiGonatodes albogularis

Gonatodes daudiniGonatodes caudiscutatus

Gonatodes eladioiLepidoblepharis festae

Lepidoblepharis xanthostigmaChatogekko amazonicus

Saurodactylus mauritanicusTeratoscincus roborowskii

Teratoscincus przewalskiiTeratoscincus scincusTeratoscincus microlepisEuleptes europaea

Saurodactylus fasciatusAristelliger georgeensis

Aristelliger praesignisAristelliger lar

Quedenfeldtia moerensQuedenfeldtia trachyblepharus

Pristurus somalicusPristurus crucifer

Pristurus carteriPristurus minimusPristurus rupestrisPristurus flavipunctatus

Pristurus abdelkuriPristurus guichardi

Pristurus sokotranusPristurus insignis

Pristurus celerrimusGoniurosaurus araneus

Goniurosaurus luiiGoniurosaurus catbaensis

Goniurosaurus lichtenfelderiGoniurosaurus kuroiwae

Hemitheconyx tayloriHemitheconyx caudicinctus

Holodactylus africanusEublepharis turcmenicusEublepharis macularius

Coleonyx elegansColeonyx mitratus

Coleonyx variegatusColeonyx brevis

Aeluroscalabotes felinus

100

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92

73100

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9376

9162

100 99

73

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87100

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


CPhelsuma kely

Phelsuma lineataPhelsuma comorensis

Phelsuma pusillaPhelsuma quadriocellata

Phelsuma antanosyPhelsuma klemmeri

Phelsuma robertmertensiPhelsuma laticaudaPhelsuma serraticaudaPhelsuma malamakibo

Phelsuma berghofiPhelsuma hielscheriPhelsuma flavigularis

Phelsuma ravenalaPhelsuma dubiaPhelsuma modesta

Phelsuma nigristriataPhelsuma inexpectata

Phelsuma ornataPhelsuma guimbeaui

Phelsuma cepedianaPhelsuma borbonica

Phelsuma guentheriPhelsuma gigas

Phelsuma edwardnewtoniPhelsuma standingi

Phelsuma andamanensePhelsuma mutabilis

Phelsuma brevicepsPhelsuma pronkiPhelsuma barbouri

Phelsuma seippiPhelsuma parkeri

Phelsuma abbottiPhelsuma madagascariensis

Phelsuma guttataPhelsuma sundbergiPhelsuma astriata

Phelsuma vanheygeniLygodactylus keniensis

Lygodactylus kimhowelliLygodactylus luteopicturatusLygodactylus picturatus

Lygodactylus williamsiLygodactylus chobiensis

Lygodactylus gutturalisLygodactylus angularis

Lygodactylus thomensisLygodactylus conraui

Lygodactylus klugeiLygodactylus bradfieldiLygodactylus capensisLygodactylus stevensoni

Lygodactylus lawrenceiLygodactylus pictus

Lygodactylus mirabilisLygodactylus tuberosus

Lygodactylus montanusLygodactylus gravis

Lygodactylus paulianiLygodactylus arnoulti

Lygodactylus blancaeLygodactylus verticillatusLygodactylus heterurus

Lygodactylus tolampyaeLygodactylus guibei

Lygodactylus miopsLygodactylus madagascariensis

Lygodactylus rarusLygodactylus expectatus

Rhoptropella ocellataCnemaspis tropidogaster

Cnemaspis kandianaCnemaspis podihuna

Pachydactylus affinisPachydactylus vansoni

Pachydactylus capensisPachydactylus oshaughnessyi

Pachydactylus tigrinusPachydactylus montanus

Pachydactylus vanzyliPachydactylus rangei

Pachydactylus austeniPachydactylus mariquensis

Pachydactylus mclachlaniPachydactylus monicaePachydactylus weberi

Pachydactylus servalPachydactylus griffini

Pachydactylus carinatusPachydactylus fasciatus

Pachydactylus tsodiloensisPachydactylus waterbergensis

Pachydactylus purcelliPachydactylus oculatus

Pachydactylus maculatusPachydactylus geitje

Pachydactylus labialisPachydactylus barnardi

Pachydactylus formosusPachydactylus rugosus

Pachydactylus punctatusPachydactylus scherzi

Pachydactylus sansteynaePachydactylus caraculicus

Pachydactylus bicolorPachydactylus oreophilus

Pachydactylus gaiasensisPachydactylus reconditus

Pachydactylus parascutatusPachydactylus scutatus

Pachydactylus namaquensisPachydactylus kladaroderma

Pachydactylus haackeiColopus kochii

Colopus wahlbergiiPachydactylus robertsi

Chondrodactylus bibroniiChondrodactylus fitzsimonsi

Chondrodactylus turneriPachydactylus laevigatus

Chondrodactylus anguliferElasmodactylus tuberculosus

Elasmodactylus tetensisRhoptropus barnardi

Rhoptropus biporosusRhoptropus boultoni

Rhoptropus bradfieldiRhoptropus afer

Goggia lineataBlaesodactylus sakalava

Blaesodactylus antongilensisBlaesodactylus boiviniHomopho lis mulleri

Homopholis walbergiiHomopholis fasciataGeckolepis maculataGeckolepis typica

Afroedura karroicaAfroedura pondolia

Afrogecko porphyreusMatoatoa brevipes

Cryptactites peringueyiAfrogecko swartbergensis

Christinus marmoratusParagehyra gabriellae

Uroplatus fimbriatusUroplatus giganteus

Uroplatus henkeliUroplatus sikorae

Uroplatus lineatusUroplatus pietschmanni

Uroplatus alluaudiUroplatus phantasticus

Uroplatus ebenauiUroplatus malama

Uroplatus malaheloUroplatus guentheri

Cnemaspis africanaCnemaspis dickersonae

Cnemaspis uzungwaeNarudasia festiva

Ptenopus carpiCalodactylodes aureusCalodactylodes illingworthorum

Ailuronyx trachygasterAiluronyx seychellensis

Ailuronyx tachyscopaeusParoedura bastardi

Paroedura tanjakaParoedura vazimba

Paroedura androyensisParoedura picta

Paroedura sanctijohannisParoedura stumpffi

Paroedura lohatsaraParoedura karstophila

Paroedura ovicepsParoedura homalorhina

Paroedura gracilisParoedura masobe

Ebenavia inunguisUrocotyledon inexpectata

Perochirus ateles

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Hemidactylus homoeolepisHemidactylus forbesii

Hemidactylus oxyrhinusHemidactylus macropholis

Hemidactylus mindiaeHemidactylus lemurinus

Hemidactylus turcicusHemidactylus robustus

Hemidactylus yerburiiHemidactylus persicus

Hemidactylus grantiHemidactylus dracaenacolus

Hemidactylus pumilioHemidactylus foudaii

Hemidactylus citerniiHemidactylus modestus

Hemidactylus agriusHemidactylus palaichthusHemidactylus bouvieri

Hemidactylus brasilianusHemidactylus greeffiiHemidactylus platycephalus

Hemidactylus longicephalusHemidactylus mercatoriusHemidactylus mabouia

Hemidactylus haitianusHemidactylus angulatus

Hemidactylus gracilisHemidactylus reticulatus

Hemidactylus albofasciatusHemidactylus imbricatus

Hemidactylus sataraensisHemidactylus brookii

Hemidactylus frenatusHemidactylus flaviviridis

Hemidactylus leschenaultiiHemidactylus maculatu s

Hemidactylus prashadiHemidactylus triedrus

Hemidactylus depressusHemidactylus giganteus

Hemidactylus aaronbaueriHemidactylus fasciatus

Hemidactylus platyurusHemidactylus karenorum

Hemidactylus garnotiiHemidactylus bowringii

Cyrtodactylus louisiadensisCyrtodactylus epiroticusCyrtodactylus tripartitus

Cyrtodactylus robustusCyrtodactylus klugei

Cyrtodactylus tuberculatusCyrtodactylus novaeguineae

Cyrtodactylus loriaeCyrtodactylus sermowaiensis

Cyrtodactylus pulchellusCyrtodactylus intermedius

Cyrtodactylus agusanensisCyrtodactylus philippinicus

Cyrtodactylus annulatusCyrtodactylus consobrinus

Cyrtodactylus irregularisCyrtodactylus marmoratus

Cyrtodactylus triedrusCyrtodactylus jarujini

Cyrtodactylus angularisCyrtodactylus ayeyarwadyensis

Cyrtodactylus oldhamiCyrtopodion gastropholeCyrtopodion agamuroides

Cyrtopodion caspiumCyrtopodion longipes

Cyrtopodion scabrumCyrtopodion sistanensis

Agamura persicaBunopus crassicauda

Crossobamon orientalisBunopus tuberculatus

Mediodactylus heteropholisMediodactylus heterocercum

Mediodactylus sagittiferumMediodactylus kotschyi

Stenodactylus sthenodactylusStenodactylus yemenensis

Stenodactylus doriaeStenodactylus leptocosymbotus

Stenodactylus petriiStenodactylus arabicus

Tropiocolotes tripolitanusPseudoceramodactylus khobarensis

Mediodactylus russowiiMediodactylus spinicaudum

Cnemaspis kendalliiCnemaspis limi

Tropiocolotes helenaeAlsophylax pipiens

Gehyra minutaGehyra montium

Gehyra pilbaraGehyra punctata

Gehyra variegataGehyra purpurascensGehyra nana

Gehyra xenopusGehyra australis

Gehyra occidentalisGehyra koira

Gehyra robustaGehyra borroloola

Gehyra pamelaGehyra catenata

Gehyra dubiaGehyra membranacruralis

Gehyra oceanicaGehyra marginata

Gehyra bareaGehyra baliola

Gehyra brevipalmataGehyra lacerata

Gehyra mutilataGehyra fehlmanni

Hemiphyllodactylus aurantiacusHemiphyllodactylus yunnanensis

Hemiphyllodactylus typusNactus pelagicusNactus multicarinatus

Nactus chevertiNactus galgajuga

Nactus vankampeniNactus eboracensisNactus acutus

Heteronotia speleaHeteronotia binoeiHeteronotia planiceps

Dixonius siamensisDixonius vietnamensis

Dixonius melanostictusGekko grossmanni

Gekko badeniiGekko petricolus

Gekko vittatusLuperosaurus iskandari

Ptychozoon lionotumPtychozoon kuhli

Ptychozoon rhacophorusGekko porosusGekko crombota

Gekko romblonGekko mindorensis

Gekko monarchusGekko athymus

Gekko swinhonisGekko auriverrucosus

Gekko hokouensisGekko japonicus

Gekko chinensisGekko gecko

Gekko smithiiLepidodactylus moestusLepidodactylus lugubris

Luperosaurus joloensisLuperosaurus cumingii

Luperosaurus macgregoriLepidodactylus orientalis

Pseudogekko compressicorpusPseudogekko smaragdinus

Lepidodactylus novaeguineae

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Figure 4 Species-level squamate phylogeny continued (C).


DCordylus cordylusCordylus tasmani

Cordylus oelofseniCordylus mclachlani

Cordylus nigerCordylus minorCordylus aridusCordylus imkeae

Cordylus macropholisCordylus rhodesianus

Cordylus jonesiiCordylus beraducciiCordylus ukingensisCordylus vittifer

Cordylus meculaeCordylus tropidosternum

Hemicordylus capensisHemicordylus nebulosusNinurta coeruleopunctatusPseudocordylus melanotusPseudocordylus spinosus

Pseudocordylus microlepidotusPseudocordylus langi

Chamaesaura anguinaChamaesaura aenea

Smaug giganteusSmaug warreni

Namazonurus peersiNamazonurus lawrenci

Namazonurus namaquensisNamazonurus pustulatus

Namazonurus campbelliKarusasaurus polyzonus

Karusasaurus jordaniOuroborus cataphractus

Platysaurus monotropisPlatysaurus minor

Platysaurus intermediusPlatysaurus capensis

Platysaurus broadleyiPlatysaurus mitchelli

Platysaurus pungweensisZonosaurus rufipes

Zonosaurus aeneusZonosaurus bemaraha

Zonosaurus subunicolorZonosaurus brygooiZonosaurus tsingy

Zonosaurus boettgeriZonosaurus laticaudatus

Zonosaurus anelanelanyZonosaurus karsteni

Zonosaurus quadrilineatusZonosaurus trilineatus

Zonosaurus ornatusZonosaurus madagascariensis

Zonosaurus haraldmeieriTracheloptychus petersi

Tracheloptychus madagascariensisGerrhosaurus flavigularis

Gerrhosaurus multilineatusGerrhosaurus nigrolineatus

Gerrhosaurus typicusGerrhosaurus skoogi

Gerrhosaurus validusTetradactylus tetradactylus

Tetradactylus africanusTetradactylus seps

Cordylosaurus subtessellatusGerrhosaurus major

Lepidophyma dontomasiLepidophyma radula

Lepidophyma loweiLepidophyma cuicatecaLepidophyma smithii

Lepidophyma lineriLepidophyma gaigeae

Lepidophyma sylvaticumLepidophyma micropholis

Lepidophyma occulorLepidophyma pajapanensis

Lepidophyma reticulatumLepidophyma flavimaculatumLepidophyma lipetziLepidophyma tuxtlae

Lepidophyma mayaeXantusia wigginsi

Xantusia bezyiXantusia vigilis

Xantusia arizonaeXantusia riversiana

Xantusia sancheziXantusia bolsonaeXantusia henshawi

Xantusia gracilisCricosaura typica

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


EAmphiglossus frontoparietalisAmphiglossus punctatus

Amphiglossus macrocercusAmphiglossus anosyensis

Amphiglossus splendidusVoeltzkowia rubrocaudataVoeltzkowia lineata

Voeltzkowia fierinensisAmphiglossus astrolabi

Amphiglossus reticulatusAmphiglossus tsaratananensis

Androngo trivittatusPygomeles braconnieri

Amphiglossus tanysomaAmphiglossus mandokava

Amphiglossus ornaticepsAmphiglossus melanurus

Madascincus intermediusMadascincus polleni

Madascincus stumpffiMadascincus nanus

Madascincus mouroundavaeMadascincus igneocaudatus

Pseudoacontias menamaintyMadascincus melanopleura

Paracontias rothschildiParacontias hildebrandti

Paracontias manifyParacontias brocchii

Paracontias holomelasScelotes kasneri

Scelotes montispectusScelotes gronovii

Scelotes sexlineatusScelotes bipes

Scelotes arenicolusScelotes mirus

Scelotes anguineusScelotes caffer

Proscelotes eggeliHakaria simonyi

Melanoseps loveridgeiMelanoseps ater

Melanoseps occidentalisFeylinia currori

Feylinia polylepisFeylinia grandisquamis

Typhlacontias punctatissimusTyphlacontias brevipes

Sepsina angolensisChalcides montanus

Chalcides polylepisChalcides manueli

Chalcides mionectonChalcides sphenopsiformis

Chalcides viridanusChalcides coeruleopunctatus

Chalcides sexlineatusChalcides lanzaiChalcides parallelus

Chalcides boulengeriChalcides bedriagaiChalcides colosii

Chalcides sepsoidesChalcides ocellatus

Chalcides striatusChalcides pseudostriatusChalcides chalcides

Chalcides guentheriChalcides minutus

Chalcides mauritanicusGongylomorphus bojerii

Janetaescincus braueriJanetaescincus veseyfitzgeraldi

Pamelaescincus gardineriScincus mitranusScincus scincus

Eumeces algeriensisScincopus fasciatus

Eumeces schneideriEurylepis taeniolatus

Plestiodon dugesiiPlestiodon brevirostris

Plestiodon copeiPlestiodon parvulus

Plestiodon ochoterenaePlestiodon lynxe

Plestiodon sumichrastiPlestiodon parviauriculatus

Plestiodon skiltonianusPlestiodon lagunensis

Plestiodon gilbertiPlestiodon longirostris

Plestiodon septentrionalisPlestiodon multivirgatus

Plestiodon fasciatusPlestiodon obsoletus

Plestiodon callicephalusPlestiodon tetragrammus

Plestiodon laticepsPlestiodon inexpectatus

Plestiodon anthracinusPlestiodon egregius

Plestiodon reynoldsiPlestiodon stimpsonii

Plestiodon marginatusPlestiodon elegans

Plestiodon latiscutatusPlestiodon japonicusPlestiodon barbouri

Plestiodon capitoPlestiodon tunganus

Plestiodon quadrilineatusPlestiodon chinensis

Plestiodon kishinouyeiPlestiodon tamdaoensis

Brachymeles pathfinderiBrachymeles gracilis

Brachymeles bicolorBrachymeles boulengeri

Brachymeles schadenbergiBrachymeles eleraeBrachymeles talinis

Brachymeles samarensisBrachymeles cebuensis

Brachymeles minimusBrachymeles bonitae

Brachymeles tridactylusBrachymeles miriamae

Brachymeles apusOphiomorus latastiiOphiomorus punctatissimus

Mesoscincus managuaeMesoscincus schwartzei

Acontias poecilusAcontias plumbeus

Acontias gracilicaudaAcontias breviceps

Acontias rieppeliAcontias percivali

Acontias meleagrisAcontias kgalagadi

Acontias litoralisAcontias lineatus

Acontias gariepensisTyphlosaurus lomiaeTyphlosaurus vermisTyphlosaurus caecusTyphlosaurus meyeri

Typhlosaurus braini

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


Lygosominae

Lygosominaecont.F

Papuascincus stanleyanusLipinia noctuaLipinia pulchella

Insulasaurus victoriaInsulasaurus wrighti

Insulasaurus arborensPrasinohaema virens

Sphenomorphus buenloicusScincella assatus

Scincella cherrieiScincella gemmingeri

Scincella lateralisAsymblepharus sikimmensis

Scincella reevesiiSphenomorphus sabanusSphenomorphus cyanolaemus

Sphenomorphus variegatusSphenomorphus multisquamatus

Sphenomorphus indicusSphenomorphus maculatus

Larutia seribuatensisParvoscincus lawtoni

Parvoscincus kitangladensisParvoscincus luzonenseParvoscincus laterimaculatusParvoscincus beyeri

Parvoscincus sisoniParvoscincus tagapayo

Parvoscincus leucospilosParvoscincus decipiens

Parvoscincus steereiSphenomorphus acutusSphenomorphus diwataPinoyscincus llanosi

Pinoyscincus abdictusPinoyscincus coxi

Pinoyscincus jagoriPinoyscincus mindanen sis

Otosaurus cumingiSphenomorphus maindroni

Sphenomorphus craneiSphenomorphus leptofasciatus

Sphenomorphus fasciatusSphenomorphus solomonis

Sphenomorphus scutatusSphenomorphus concinnatus

Tytthoscincus atrigularisTytthoscincus hallieri

Tytthoscincus parvusTytthoscincus aesculeticola

Sphenomorphus muelleriSphenomorphus jobiensis

Sphenomorphus melanopogonIsopachys anguinoides

Lipinia vittigeraTropidophorus misaminiusTropidophorus partelloi

Tropidophorus brookeiTropidophorus beccarii

Tropidophorus baconiTropidophorus grayiTropidophorus microlepis

Tropidophorus cocincinensisTropidophorus thaiTropidophorus robinsoni

Tropidophorus sinicusTropidophorus baviensis

Tropidophorus hainanusTropidophorus murphyi

Tropidophorus noggeiTropidophorus latiscutatusTropidophorus matsuiiTropidophorus berdmorei

Sphenomorphus simusSphenomorphus praesignis

Ablepharus pannonicusAsymblepharus alaicus

Ateuchosaurus pellopleurus

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H-I GFigure 7 Species-level squamate phylogeny continued (F).


Lerista kennedyensisLerista onsloviana

Lerista uniduoLerista connivens

Lerista variaLerista lineopunctulata

Lerista yunaLerista kendricki

Lerista nichollsiLerista gascoynensis

Lerista petersoniLerista humphriesi

Lerista praepeditaLerista bougainvillii

Lerista viduataLerista muelleri

Lerista haroldiLerista allochira

Lerista stictopleuraLerista planiventralis

Lerista lineataLerista christinae

Lerista distinguendaLerista elegans

Lerista emmottiLerista punctatovittata

Lerista dorsalisLerista terdigitata

Lerista tridactylaLerista elongata

Lerista speciosaLerista zietzi

Lerista flammicaudaLerista picturata

Lerista baynesiLerista edwardsae

Lerista arenicolaLerista microtis

Lerista macropisthopusLerista axillaris

Lerista gerrardiiLerista eupoda

Lerista desertorumLerista puncticaudaLerista neander

Lerista zonulataLerista ingrami

Lerista orientalisLerista taeniata

Lerista aericepsLerista xanthura

Lerista chordaeLerista fragilis

Lerista frostiLerista borealis

Lerista walkeriLerista simillima

Lerista vermicularisLerista robusta

Lerista greeriLerista labialis

Lerista bipesLerista ips

Lerista griffiniLerista apoda

Lerista kalumburuLerista wilkinsiLerista cinerea

Lerista amelesLerista carpentariae

Lerista karlschmidtiLerista stylis

Ctenotus pulchellusCtenotus gagudju

Ctenotus hilliCtenotus hebetior

Ctenotus essingtoniiCtenotus piankai

Ctenotus hanloniCtenotus angusticeps

Ctenotus grandisCtenotus atlas

Ctenotus maryaniCtenotus olympicus

Ctenotus regiusCtenotus septenarius

Ctenotus astarteCtenotus mimetes

Ctenotus tanamiensisCtenotus greeri

Ctenotus serventyiCtenotus quattuordecimlineatus

Ctenotus leonhardiiCtenotus leae

Ctenotus australisCtenotus uber

Ctenotus rutilansCtenotus taeniolatus

Ctenotus robustusCtenotus spaldingi

Ctenotus inornatusCtenotus saxatilis

Ctenotus fallensCtenotus rawlinsoni

Ctenotus calurusCtenotus schomburgkiiCtenotus youngsoni

Ctenotus strauchiiCtenotus pantherinus

Ctenotus nasutusCtenotus rubicundus

Ctenotus brooksiCtenotus labillardieri

Notoscincus ornatusEulamprus tympanum

Eulamprus heatwoleiEulamprus kosciuskoi

Eulamprus leuraensisEulamprus quoyii

Glaphyromorphus darwiniensisGlaphyromorphus cracens

Glaphyromorphus pumilusGlaphyromorphus fuscicaudis

Glaphyromorphus mjobergiGlaphyromorphus punctulatus

Hemiergis decresiensisHemiergis millewae

Hemiergis gracilipesHemiergis quadrilineatum

Hemiergis peroniiHemiergis initialis

Eremiascincus isolepisEremiascincus douglasiEremiascincus richardsoniiEremiascincus pardal is

Eremiascincus fasciolatusAnomalopus leuckartii

Anomalopus verreauxiAnomalopus mackayi

Anomalopus swansoniOphioscincus truncatus

Coeranoscincus reticulatusSaiphos equalis

Ophioscincus ophioscincusCoeranoscincus frontalis

Coggeria naufragusEulamprus murrayi

Eulamprus tryoniEulamprus luteilateralis

Eulamprus brachyosomaEulamprus sokosoma

Eulamprus martiniEulamprus tigrinus

Eulamprus tenuisEulamprus amplus

Gnypetoscincus queenslandiaeCalyptotis ruficauda

Calyptotis scutirostrumCalyptotis lepidorostrum

Nangura spinosaEulamprus frerei

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Lygosominaecont.

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


Mabuya heathiMabuya caissara

Mabuya agilisMabuya guaporicola

Mabuya macrorhynchaMabuya agmosticha

Mabuya frenataMabuya bistriata

Mabuya falconensisMabuya unimarginata

Mabuya mabouyaMabuya meridensis

Mabuya dorsivittataMabuya cochabambae

Mabuya nigropunctataMabuya altamazonica

Mabuya sloaniiMabuya nigropalmata

Mabuya croizatiMabuya carvalhoiChioninia stangeri

Chioninia fogoensisChioninia spinalis

Chioninia cocteiChioninia delalandii

Chioninia vaillantiiEumecia anchietae

Trachylepis dumasiTrachylepis aureopunctata

Trachylepis vatoTrachylepis boettgeriTrachylepis madagascariensis

Trachylepis elegansTrachylepis gravenhorstiiTrachylepis acutilabris

Trachylepis homalocephalaTrachylepis sulcata

Trachylepis variegataTrachylepis hoeschi

Trachylepis striataTrachylepis spilogaster

Trachylepis occidentalisTrachylepis capensis

Trachylepis variaTrachylepis atlantica

Trachylepis margaritiferaTrachylepis quinquetaeniata

Trachylepis perrotetiiTrachylepis affinis

Trachylepis sechellensisTrachylepis wrightii

Trachylepis maculilabrisTrachylepis socotrana

Trachylepis brevicollisTrachylepis vittata

Trachylepis aurataDasia olivacea

Dasia griseaDasia vittata

Eutropis trivittataEutropis nagarjuniEutropis beddomii

Eutropis bibroniiEutropis clivicola

Eutropis multicarinataEutropis cumingi

Eutropis multifasciataEutropis macrophthalma

Eutropis rudisEutropis macularia

Eutropis longicaudataLankascincus fallax

Ristella rurkiiLiopholis montana

Liopholis guthegaLiopholis whitiiLiopholis margaretae

Liopholis modestaLiopholis pulchra

Liopholis kintoreiLiopholis multiscutata

Liopholis inornataLiopholis striata

Tiliqua scincoidesTiliqua gigas

Tiliqua nigroluteaTiliqua occipitalis

Tiliqua rugosaTiliqua adelaidensisCyclodomorphus branchialis

Cyclodomorphus casuarinaeCyclodomorphus michaeli

Egernia hosmeriEgernia stokesii

Lissolepis luctuosaEgernia napoleonis

Egernia richardiBellatorias frerei

Egernia kingiiEgernia depressa

Bellatorias majorEgernia saxatilis

Corucia zebrataTribolonotus pseudoponceleti

Tribolonotus ponceletiTribolonotus brongersmai

Tribolonotus schmidtiTribolonotus blanchardi

Tribolonotus gracilisTribolonotus novaeguineae

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H

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


Carlia vivaxCarlia dogare

Carlia rostralisCarlia amax

Carlia tetradactylaCarlia rubrigularis

Carlia rhomboidalisCarlia rufilatus

Carlia pectoralisCarlia munda

Carlia mysiCarlia longipes

Carlia fuscaCarlia storri

Carlia schmeltziiLygisaurus malleolus

Lygisaurus tanneriLygisaurus absconditaLygisaurus foliorum

Lygisaurus laevisLygisaurus aeratus

Lygisaurus novaeguineaeLygisaurus macfarlani

Lygisaurus parrhasiusLygisaurus sesbrauna

Carlia gracilisCarlia bicarinata

Carlia jarnoldaeCarlia johnstonei

Carlia triacanthaMenetia timlowi

Liburnascincus mundivensisLiburnascincus scirtetis

Liburnascincus coensisCautula zia

Niveoscincus metallicusNiveoscincus pretiosus

Niveoscincus ocellatusNiveoscincus greeni

Proablepharus reginaeLampropholis robertsi

Lampropholis coggeriLampropholis delicata

Lampropholis guichenotiSaproscincus spectabilis

Saproscincus roseiSaproscincus challengeri

Saproscincus mustelinusSaproscincus oriarus

Saproscincus hannahaeSaproscincus tetradactylus

Saproscincus czechuraiSaproscincus lewisi

Saproscincus basiliscusBartleia jigurru

Morethia adelaidensisMorethia butleri

Morethia ruficaudaBassiana trilineata

Emoia isolataEmoia pseudocyanura

Emoia cyanuraEmoia impar

Emoia physicaeEmoia jakati

Emoia atrocostataEmoia caeruleocauda

Emoia cyanogasterEmoia schmidti

Menetia alanaeMenetia greyii

Cryptoblepharus novocaledonicusCryptoblepharus boutonii

Cryptoblepharus nigropunctatusCaledoniscincus terma

Caledoniscincus aquiloniusCaledoniscincus chazeaui

Caledoniscincus atropunctatusCaledoniscincus haplorhinus

Caledoniscincus austrocaledonicusCaledoniscincus festivus

Caledoniscincus auratusCaledoniscincus renevieri

Caledoniscincus orestesSimiscincus aurantiacus

Graciliscincus shonaeTropidoscincus variabilis

Tropidoscincus boreus

Tropidoscincus aubrianusLioscincus tillieri

Lioscincus maruiaLioscincus novaecaledoniaeSigaloseps deplanchei

Sigaloseps ruficaudaPhoboscincus garnieri

Lacertoides pardalisLioscincus nigrofasciolatum

Kanakysaurus viviparusLioscincus steindachneri

Lioscincus vivaeCelatiscincus euryotis

Celatiscincus similisMarmorosphax tricolor

Marmorosphax montanaNannoscincus humectus

Nannoscincus hanchisteusNannoscincus greeriNannoscincus mariei

Nannoscincus gracilisNannoscincus slevini

Nannoscincus garrulusOligosoma whitakeri

Oligosoma oliveriOligosoma townsi

Oligosoma ornatumOligosoma macgregori

Oligosoma mocoOligosoma alani

Oligosoma fallaiOligosoma hardyi

Oligosoma levidensumOligosoma aeneum

Oligosoma microlepisOligosoma smithi

Oligosoma striatumOligosoma homalonotumOligosoma zelandicum

Oligosoma notosaurusOligosoma inconspicuumOligosoma maccanni

Oligosoma stenotisOligosoma grande

Oligosoma nigriplantareOligosoma longipes

Oligosoma lineoocellatumOligosoma chloronoton

Oligosoma otagenseOligosoma waimatenseOligosoma infrapunctatum

Oligosoma acrinasumOligosoma taumakaeOligosoma pikitanga

Oligosoma suteriOligosoma lichenigera

Pseudemoia entrecasteauxiiBassiana duperreyi

Pseudemoia pagenstecheriLeptosiaphos vigintiserierumLeptosiaphos kilimensis

Leptosiaphos amietiLeptosiaphos graueri

Leptosiaphos hackarsiLacertaspis lepesmei

Lacertaspis gemmiventrisLacertaspis chriswildi

Lacertaspis rohdeiLacertaspis reichenowi

Afroablepharus africanusAfroablepharus annobonensis

Afroablepharus wahlbergiPanaspis togoensis

Panaspis brevicepsLeiolopisma mauriti anaLeiolopisma telfairii

Emoia loyaltiensisEugongylus albofasciolatusEugongylus rufescens

Lygosoma bowringiiMochlus brevicaudisLygosoma punctata

Lygosoma sundevalliMochlus afer

Lygosoma lineolatumLepidothyris fernandi

Lygosoma albopunctataLygosoma koratense

Lygosoma quadrupesLamprolepis smaragdina

Emoia tonganaEmoia concolor

Sphenomorphus stellatusAblepharus kitaibelii

Ablepharus chernoviAblepharus budaki

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Lygosominaecont.

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


Gymnophthalmus cryptusGymnophthalmus underwoodi

Gymnophthalmus speciosusGymnophthalmus vanzoiGymnophthalmus leucomystax

Gymnophthalmus pleeiPsilophthalmus paeminosus

Calyptommatus nicterusCalyptommatus leiolepis

Calyptommatus confusionibusCalyptommatus sinebrachiatus

Nothobachia ablepharaProcellosaurinus tetradactylusProcellosaurinus erythrocercus

Vanzosaura rubricaudaMicrablepharus maximiliani

Micrablepharus atticolusTretioscincus oriximinensis

Tretioscincus agilisAcratosaura mentalisStenolepis ridleyi

Colobosaura modestaIphisa elegans

Colobodactylus taunayiColobodactylus dalcyanus

Heterodactylus imbricatusRhachisaurus brachylepis

Bachia heteropaBachia intermediaBachia barbouriBachia bicolorBachia peruana

Bachia panopliaBachia trisanale

Bachia scolecoidesBachia huallagana

Bachia dorbignyiBachia bresslaui

Bachia flavescensPetracola ventrimaculatus

Proctoporus bolivianusProctoporus unsaacae

Proctoporus guentheriProctoporus pachyurus

Proctoporus subsolanusProctoporus sucullucu

Cercosaura eigenmanniCercosaura schreibersii

Cercosaura ocellataCercosaura argulus

Cercosaura oshaughnessyiCercosaura quadrilineata

Potamites juruazensisPotamites ecpleopus

Pholidobolus macbrydeiPholidobolus montium

Placosoma glabellumPlacosoma cordylinum

Neusticurus bicarinatusNeusticurus rudis

Riama simoterusRiama colomaromani

Riama unicolorLeposoma guianense

Leposoma southiLeposoma parietale

Leposoma osvaldoiLeposoma percarinatum

Arthrosaura kockiiArthrosaura reticulata

Anotosaura collarisColobosauroides cearensis

Leposoma annectansLeposoma scincoides

Leposoma pukLeposoma baturitensis

Leposoma nanodactylusEcpleopus gaudichaudii

Alopoglossus angulatusAlopoglossus copii

Alopoglossus atriventrisPtychoglossus brevifrontalis

Cnemidophorus lacertoidesCnemidophorus longicaudus

Dicrodon guttulatumAmeiva fuscataAmeiva erythrocephala

Ameiva griswoldiAmeiva pluvianotata

Ameiva coraxAmeiva plei

Ameiva maynardiAmeiva lineolata

Ameiva taeniuraAmeiva chrysolaema

Ameiva leberiAmeiva wetmorei

Ameiva exsulAmeiva polops

Ameiva dorsalisAmeiva auberi

Aspidoscelis ceralbensisAspidoscelis hyperythra

Aspidoscelis tigrisAspidoscelis marmorata

Aspidoscelis lineattissimaAspidoscelis guttata

Aspidoscelis deppeiAspidoscelis velox

Aspidoscelis laredoensisAspidoscelis gularis

Aspidoscelis costataAspidoscelis communis

Aspidoscelis burtiAspidoscelis sexlineata

Aspidoscelis inornataCnemidophorus arenivagus

Cnemidophorus lemniscatusCnemidophorus gramivagus

Cnemidophorus vanzoiAmeiva festivaAmeiva quadrilineataAmeiva undulata

Kentropyx viridistrigaKentropyx vanzoi

Kentropyx paulensisKentropyx pelviceps

Kentropyx altamazonicaKentropyx striata

Kentropyx calcarataCnemidophorus ocellifer

Ameiva bifrontataAmeiva ameivaTeius teyou

Dracaena guianensisCrocodilurus amazonicus

Tupinambis teguixinTupinambis longilineus

Tupinambis quadrilineatusTupinambis duseni

Tupinambis merianaeTupinambis rufescens

Callopistes maculatusCallopistes flavipunctatus

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


Amphisbaena xeraAmphisbaena bakeriAmphisbaena caeca

Amphisbaena fenestrata

Amphisbaena manni

Amphisbaena schmidti

Amphisbaena carlgansi

Amphisbaena cubana

Amphisbaena barbouri

Amphisbaena anaemariae

Amphisbaena silvestrii

Amphisbaena leeseri

Amphisbaena angustifrons

Amphisbaena darwini

Amphisbaena munoai

Amphisbaena kingiiAmphisbaena cuiabana

Amphisbaena hastata

Amphisbaena infraorbitale

Amphisbaena microcephalum

Amphisbaena polystegum

Amphisbaena anomala

Amphisbaena bolivica

Amphisbaena camura

Amphisbaena alba

Amphisbaena vermicularis

Amphisbaena roberti

Amphisbaena kraoh

Amphisbaena saxosa

Amphisbaena ignatiana

Amphisbaena leali

Amphisbaena innocens

Amphisbaena hyporissor

Amphisbaena mertensii

Amphisbaena cunhai

Amphisbaena fuliginosa

Amphisbaena brasiliana

Monopeltis capensis

Geocalamus acutus

Chirindia swynnertoni

Cynisca leucura

Trogonophis wiegmanni

Diplometopon zarudnyi

Cadea blanoides

Blanus tingitanus

Blanus mettetali

Blanus cinereus

Blanus strauchi

Bipes canaliculatus

Bipes biporus

Bipes tridactylus

Rhineura floridana

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


Darevskia derjuginiDarevskia caucasica

Darevskia daghestanicaDarevskia mixta

Darevskia clarkorumDarevskia armeniaca

Darevskia bendimahiensisDarevskia sapphirina

Darevskia uzzelliDarevskia raddei

Darevskia rostombekoviDarevskia saxicola

Darevskia brauneriDarevskia lindholmi

Darevskia alpinaDarevskia chlorogaster

Darevskia praticolaDarevskia valentini

Darevskia portschinskiiDarevskia rudis

Darevskia parvulaIranolacerta zagrosicaIranolacerta brandtii

Algyroides fitzingeriAlgyroides marchi

Dinarolacerta montenegrinaDinarolacerta mosorensis

Algyroides nigropunctatusAlgyroides moreoticus

Anatololacerta danfordiAnatololacerta oertzeni

Anatololacerta anatolicaParvilacerta parva

Parvilacerta fraasiiIberolacerta aranicaIberolacerta bonnali

Iberolacerta aurelioiIberolacerta horvathi

Iberolacerta monticolaIberolacerta cyreni

Iberolacerta galaniApathya cappadocica

Archaeolacerta bedriagaeHellenolacerta graecaDalmatolacerta oxycephala

Podarcis carbonelliPodarcis bocagei

Podarcis hispanicusPodarcis vaucheri

Podarcis liolepisPodarcis peloponnesiacusPodarcis erhardii

Podarcis raffoneaePodarcis lilfordi

Podarcis pityusensisPodarcis siculus

Podarcis muralisPodarcis tiliguerta

Podarcis filfolensisPodarcis gaigeae

Podarcis milensisPodarcis tauricus

Podarcis melisellensisScelarcis perspicillata

Teira dugesiiLacerta pamphylicaLacerta trilineata

Lacerta mediaLacerta agilis

Lacerta schreiberiLacerta strigata

Lacerta bilineataLacerta viridis

Timon tangitanusTimon lepidusTimon pater

Timon princepsTakydromus stejnegeriTakydromus septentrionalisTakydromus toyamaiTakydromus wolteriTakydromus formosanus

Takydromus hsuehshanensisTakydromus amurensis

Takydromus sylvaticusTakydromus dorsalis

Takydromus intermediusTakydromus sauteri

Takydromus smaragdinusTakydromus tachydromoides

Takydromus sexlineatusTakydromus kuehnei

Zootoca viviparaPhoenicolacerta cyanisparsa

Phoenicolacerta laevisPhoenicolacerta kulzeri

Acanthodactylus schreiberiAcanthodactylus boskianus

Acanthodactylus opheodurusAcanthodactylus gongrorhynchatus

Acanthodactylus masiraeAcanthodactylus cantoris

Acanthodactylus schmidtiAcanthodactylus longipes

Acanthodactylus scutellatusAcanthodactylus aureus

Acanthodactylus maculatusAcanthodactylus pardalis

Acanthodactylus beershebensisAcanthodactylus busacki

Acanthodactylus erythrurusAcanthodactylus blanci

Acanthodactylus tristramiAcanthodactylus orientalisOphisops elegans

Ophisops occidentalisMesalina rubropunctata

Mesalina brevirostrisMesalina adramitana

Mesalina balfouriMesalina guttulata

Mesalina bahaeldiniMesalina olivieri

Mesalina simoniOmanosaura jayakariOmanosaura cyanura

Congolacerta vauereselliEremias grammica

Eremias pleskeiEremias multiocellata

Eremias przewalskiiEremias arguta

Eremias nigrolateralisEremias persica

Eremias montanusEremias velox

Eremias vermiculataEremias argus

Eremias brenchleyiAdolfus jacksoni

Adolfus alleniAdolfus africanus

Gastropholis prasinaGastropholis vittata

Holaspis guentheriHolaspis laevis

Pedioplanis gaerdesiPedioplanis inornata

Pedioplanis rubensPedioplanis undata

Pedioplanis husabensisPedioplanis namaquensis

Pedioplanis brevicepsPedioplanis burchelli

Pedioplanis laticepsNucras tessellata

Pedioplanis lineoocellataMeroles cuneirostrisMeroles micropholidotus

Meroles ctenodactylusMeroles anchietaeIchnotropis squamulosa

Meroles suborbitalisMeroles knoxii

Meroles reticulatusIchnotropis capensis

Tropidosaura gularisAustralolacerta australis

Heliobolus spekiiHeliobolus lugubris

Pseuderemias smithiiPhilochortus spinalis

Latastia longicaudataNucras lalandii

Poromera fordiiAtlantolacerta andreanskyiGallotia bravoana

Gallotia simonyiGallotia intermedia

Gallotia caesarisGallotia galloti

Gallotia atlanticaGallotia stehlini

Psammodromus blanciPsammodromus algirus

Psammodromus hispanicus

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


Varanus baritjiVaranus acanthurus

Varanus storriVaranus primordius

Varanus kingorumVaranus bushiVaranus gilleni

Varanus caudolineatusVaranus eremius

Varanus brevicaudaVaranus semiremex

Varanus mitchelliVaranus timorensis

Varanus scalarisVaranus glauerti

Varanus tristisVaranus pilbarensis

Varanus glebopalmaVaranus komodoensis

Varanus variusVaranus salvadoriiVaranus gouldiiVaranus panoptes

Varanus rosenbergiVaranus giganteus

Varanus spenceriVaranus mertensi

Varanus bengalensisVaranus flavescens

Varanus dumeriliiVaranus rudicollis

Varanus salvatorVaranus marmoratus

Varanus finschiVaranus doreanusVaranus yuwonoiVaranus jobiensis

Varanus caerulivirensVaranus cerambonensisVaranus melinusVaranus indicus

Varanus rainerguentheriVaranus prasinusVaranus macraeiVaranus boehmei

Varanus beccariiVaranus keithhornei

Varanus olivaceusVaranus yemenensis

Varanus albigularisVaranus exanthematicusVaranus niloticus

Varanus griseusLanthanotus borneensis

Shinisaurus crocodilurusAbronia auritaAbronia campbelliAbronia anzuetoiAbronia matudai

Abronia fimbriataAbronia lythrochilaAbronia ornelasi

Abronia frostiAbronia graminea

Abronia oaxacaeAbronia chiszari

Mesaspis gadoviiMesaspis moreletiiBarisia rudicollis

Barisia herreraeBarisia imbricataBarisia levicollis

Abronia mixtecaGerrhonotus infernalisGerrhonotus liocephalusColoptychon rhombifer

Gerrhonotus parvusElgaria multicarinataElgaria panamintinaElgaria paucicarinataElgaria kingii

Elgaria coeruleaDopasia harti

Dopasia gracilisOphisaurus attenuatus

Anguis fragilisPseudopus apodus

Ophisaurus koellikeriOphisaurus ventralis

Celestus haetianusCelestus agasepsoides

Ophiodes striatusDiploglossus pleii

Diploglossus bilobatusCelestus enneagrammus

Anniella geronimensisAnniella pulchra

Heloderma horridumHeloderma suspectum

Xenosaurus grandisXenosaurus platyceps

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


Trioceros sternfeldiTrioceros rudis

Trioceros elliotiTrioceros hoehneliiTrioceros schubotzi

Trioceros narraiocaTrioceros jacksonii

Trioceros bitaeniatusTrioceros fuelleborni

Trioceros goetzeiTrioceros tempeli

Trioceros werneriTrioceros deremensis

Trioceros melleriTrioceros johnstoni

Trioceros oweniTrioceros pfefferiTrioceros quadricornisTrioceros wiedersheimi

Trioceros cristatusTrioceros montiumTrioceros feae

Trioceros balebicornutusTrioceros harennae

Trioceros affinisChamaeleo arabicus

Chamaeleo calyptratusChamaeleo zeylanicus

Chamaeleo chamaeleonChamaeleo calcaricarensChamaeleo africanus

Chamaeleo monachusChamaeleo senegalensis

Chamaeleo roperiChamaeleo dilepis

Chamaeleo quilensisChamaeleo gracilis

Chamaeleo necasiChamaeleo laevigatus

Chamaeleo namaquensisCalumma globifer

Calumma parsoniiCalumma oshaughnessyi

Calumma capuroniRhampholeon chapmanorum

Rhampholeon platycepsRhampholeon nchisiensis

Rhampholeon beraducciiRhampholeon boulengeriRhampholeon acuminatus

Rhampholeon uluguruensisRhampholeon moyeri

Rhampholeon marshalliRhampholeon viridis

Rhampholeon spinosusRhampholeon temporalis

Rhampholeon spectrumNadzikambia mlanjensis

Calumma nasutumCalumma boettgeri

Calumma fallaxCalumma gallus

Calumma maltheCalumma guibei

Calumma hilleniusiCalumma tsaratananense

Calumma brevicorneCalumma crypticum

Calumma cucullatumRieppeleon brevicaudatus

Rieppeleon brachyurusRieppeleon kerstenii

Calumma gastrotaeniaCalumma furcifer

Bradypodion ventraleBradypodion karrooicumBradypodion taeniabronchum

Bradypodion gutturaleBradypodion atromontanum

Bradypodion occidentaleBradypodion setaroi

Bradypodion nemoraleBradypodion dracomontanumBradypodion transvaalense

Bradypodion thamnobatesBradypodion melanocephalum

Bradypodion cafferBradypodion damaranumBradypodion pumilum

Kinyongia fischeriKinyongia vosseleri

Kinyongia multituberculataKinyongia matschiei

Kinyongia boehmeiKinyongia tavetana

Kinyongia uthmoelleriKinyongia carpenteri

Kinyongia xenorhinaKinyongia excubitor

Kinyongia adolfifridericiKinyongia tenue

Kinyongia oxyrhinaFurcifer antimenaFurcifer labordi

Furcifer lateralisFurcifer belalandaensis

Furcifer verrucosusFurcifer oustaleti

Furcifer angeliFurcifer pardalis

Furcifer polleniFurcifer cephalolepis

Furcifer campaniFurcifer petteri

Furcifer willsiiFurcifer minor

Furcifer bifidusFurcifer balteatus

Brookesia lineataBrookesia betschiBrookesia thieliBrookesia vadoni

Brookesia ebenauiBrookesia antakaranaBrookesia ambreensis

Brookesia stumpffiBrookesia griveaudi

Brookesia valerieaeBrookesia superciliaris

Brookesia therezieniBrookesia bonsiBrookesia brygooi

Brookesia decaryiBrookesia perarmata

Brookesia peyrierasiBrookesia karchei

Brookesia tuberculataBrookesia minima

Brookesia exarmataBrookesia dentata

Brookesia nasusBrookesia lolontany

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


Pseudocalotes flavigulaPseudocalotes brevipes

Pseudocalotes kakhienensisJapalura splendida

Japalura flavicepsOtocryptis wiegmanniSitana ponticeriana

Acanthosaura lepidogasterAcanthosaura capraAcanthosaura armataAcanthosaura crucigera

Salea horsfieldiiCalotes htunwiniCalotes calotes

Calotes irawadiCalotes versicolor

Calotes liolepisCalotes nigrilabris

Calotes ceylonensisCalotes liocephalusCalotes emma

Calotes chincolliumCalotes mystaceus

Ceratophora erdeleniCeratophora stoddartii

Ceratophora karuCeratophora aspera

Cophotis ceylanicaCophotis dumbara

Lyriocephalus scutatusGonocephalus kuhliiGonocephalus chamaeleontinus

Gonocephalus grandisBronchocela cristatella

Coryphophylax subcristatusAphaniotis fusca

Gonocephalus robinsoniiJapalura polygonata

Phoxophrys nigrilabrisDraco ornatusDraco palawanensisDraco spilopterus

Draco cornutusDraco guentheri

Draco quadrasiDraco cyanopterusDraco reticulatusDraco boschmai

Draco timorensisDraco volans

Draco bimaculatusDraco rhytismaDraco bourouniensis

Draco beccariiDraco biaroDraco caerulhians

Draco spilonotusDraco obscurusDraco taeniopterus

Draco blanfordiiDraco indochinensisDraco haematopogon

Draco melanopogonDraco quinquefasciatus

Draco mindanensisDraco maximus

Draco cristatellusDraco fimbriatus

Draco maculatusDraco lineatus

Draco dussumieriPtyctolaemus collicristatus

Ptyctolaemus gularisJapalura tricarinata

Japalura variegataMantheyus phuwuanensis

Agama paragamaAgama planiceps

Agama finchiAgama agama

Agama doriaeAgama sankaranicaAgama mwanzae

Agama kaimosaeAgama lionotus

Agama rueppelliAgama caudospinosa

Agama aculeataAgama armata

Agama hispidaAgama atraAgama anchietae

Agama weidholziAgama gracilimembris

Agama insularisAgama boulengeri

Agama castroviejoiAgama impalearis

Agama bouetiAgama spinosa

Trapelus savigniiTrapelus flavimaculatus

Trapelus pallidusTrapelus ruderatus

Trapelus agilisTrapelus mutabilisTrapelus sanguinolentus

Bufoniceps laungwalaensisXenagama taylori

Acanthocercus atricollisPseudotrapelus sinaitus

Phrynocephalus guttatusPhrynocephalus albolineatus

Phrynocephalus melanurusPhrynocephalus przewalskiiPhrynocephalus versicolorPhrynocephalus raddei

Phrynocephalus mystaceusPhrynocephalus helioscopus

Phrynocephalus axillarisPhrynocephalus lidskiiPhrynocephalus vlangalii

Phrynocephalus putjataiPhrynocephalus theobaldiPhrynocephalus forsythiiPhrynocephalus interscapularis

Phrynocephalus scutellatusLaudakia erythrogasterLaudakia caucasia

Laudakia microlepisLaudakia stoliczkana

Laudakia himalayanaLaudakia lehmanni

Laudakia nuptaLaudakia tuberculataLaudakia sacra

Laudakia stellio

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Diporiphora lalliaeDiporiphora arnhemica

Diporiphora albilabrisDiporiphora bennettii

Diporiphora nobbiDiporiphora australis

Diporiphora amphiboluroidesDiporiphora valensDiporiphora pindanDiporiphora bilineataDiporiphora magnaDiporiphora reginae

Diporiphora winneckeiDiporiphora linga

Diporiphora superbaPogona vitticepsPogona minorPogona minimaPogona henrylawsoni

Pogona nullarborPogona barbata

Rankinia diemensisTympanocryptis lineataTympanocryptis pinguicollaTympanocryptis cephalusTympanocryptis tetraporophoraTympanocryptis intima

Tympanocryptis uniformisAmphibolurus norrisiAmphibolurus muricatus

Lophognathus gilbertiChlamydosaurus kingii

Lophognathus longirostrisLophognathus temporalis

Ctenophorus femoralisCtenophorus fordiCtenophorus maculatusCtenophorus pictusCtenophorus mckenzieiCtenophorus scutulatus

Ctenophorus isolepisCtenophorus ornatus

Ctenophorus caudicinctusCtenophorus fionni

Ctenophorus decresiiCtenophorus vadnappaCtenophorus tjantjalka

Ctenophorus rufescensCtenophorus reticulatusCtenophorus nuchalis

Ctenophorus cristatusCtenophorus salinarum

Ctenophorus gibbaCtenophorus clayi

Ctenophorus adelaidensisCtenophorus maculosus

Intellagama lesueuriiHypsilurus bruijniiHypsilurus nigrigularis

Hypsilurus papuensisHypsilurus modestus

Chelosania brunneaMoloch horridus

Hypsilurus dilophusHypsilurus boydii

Hypsilurus spinipesPhysignathus cocincinus

Hydrosaurus amboinensisLeiolepis guentherpetersiLeiolepis guttataLeiolepis reevesiiLeiolepis belliana

Uromastyx yemenensisUromastyx bentiUromastyx ocellata

Uromastyx ornataUromastyx leptieniUromastyx aegyptia

Uromastyx thomasiUromastyx disparUromastyx acanthinuraUromastyx geyri

Uromastyx macfadyeniUromastyx princepsUromastyx asmussi

Uromastyx loricataUromastyx hardwickii

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


Ctenosaura oaxacanaCtenosaura quinquecarinataCtenosaura flavidorsalisCtenosaura palearis

Ctenosaura bakeriCtenosaura oedirhinaCtenosaura melanosterna

Ctenosaura pectinataCtenosaura acanthuraCtenosaura hemilophaCtenosaura similis

Conolophus pallidusConolophus subcristatusAmblyrhynchus cristatus

Cyclura cychluraCyclura nubila

Cyclura rileyiCyclura colleiCyclura carinataCyclura ricordiCyclura cornuta

Cyclura pinguisSauromalus variusSauromalus hispidusSauromalus klauberiSauromalus aterIguana delicatissima

Iguana iguanaBrachylophus vitiensisBrachylophus fasciatus

Dipsosaurus dorsalisTropidurus torquatusTropidurus hispidus

Tropidurus oreadicusTropidurus insulanus

Tropidurus erythrocephalusTropidurus mucujensis

Tropidurus etheridgeiTropidurus cocorobensis

Tropidurus itambereTropidurus psammonastes

Tropidurus montanusTropidurus hygomi

Eurolophosaurus nanuzaeEurolophosaurus amathites

Eurolophosaurus divaricatusTropidurus spinulosus

Tropidurus callathelysPlica plica

Plica lumariaPlica umbra

Strobilurus torquatusTropidurus bogerti

Uracentron flavicepsUranoscodon superciliosus

Microlophus duncanensisMicrolophus albemarlensisMicrolophus pacificusMicrolophus grayii

Microlophus delanonisMicrolophus stolzmanni

Microlophus habeliiMicrolophus bivittatus

Microlophus occipitalisMicrolophus koepckeorum

Microlophus yaneziMicrolophus theresioidesMicrolophus atacamensis

Microlophus quadrivittatusMicrolophus peruvianus

Microlophus tigrisMicrolophus heterolepis

Microlophus theresiaeMicrolophus thoracicus

Stenocercus stigmosusStenocercus melanopygus

Stenocercus latebrosusStenocercus orientalis

Stenocercus ornatissimusStenocercus chrysopygus

Stenocercus cupreusStenocercus boettgeriStenocercus empetrusStenocercus eunetopsisStenocercus imitator

Stenocercus variusStenocercus torquatus

Stenocercus crassicaudatusStenocercus marmoratus

Stenocercus humeralisStenocercus angel

Stenocercus guentheriStenocercus festae

Stenocercus chotaStenocercus rhodomelasStenocercus anguliferStenocercus iridescens

Stenocercus puyangoStenocercus percultusStenocercus ornatus

Stenocercus caducusStenocercus limitaris

Stenocercus doellojuradoiStenocercus azureusStenocercus roseiventris

Stenocercus ochoaiStenocercus formosus

Stenocercus apurimacusStenocercus scapularis

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


Sceloporus adleriSceloporus stejnegeriSceloporus formosusSceloporus subpictusSceloporus cryptus

Sceloporus lundelliSceloporus malachiticusSceloporus smaragdinus

Sceloporus taeniocnemisSceloporus spinosusSceloporus edwardtaylori

Sceloporus horridusSceloporus cautusSceloporus undulatus

Sceloporus consobrinusSceloporus woodiSceloporus virgatus

Sceloporus occidentalisSceloporus olivaceus

Sceloporus clarkiiSceloporus cyanogenysSceloporus serriferSceloporus ornatus

Sceloporus minorSceloporus dugesii

Sceloporus poinsettiiSceloporus macdougalli

Sceloporus mucronatusSceloporus bulleri

Sceloporus torquatusSceloporus jarrovii

Sceloporus insignisSceloporus megalepidurus

Sceloporus goldmaniSceloporus samcolemani

Sceloporus chaneyiSceloporus slevini

Sceloporus scalarisSceloporus bicanthalis

Sceloporus aeneusSceloporus heterolepis

Sceloporus palaciosiSceloporus grammicus

Sceloporus melanorhinusSceloporus hunsakeriSceloporus orcuttiSceloporus lickiSceloporus lineatulus

Sceloporus zosteromusSceloporus magister

Sceloporus arenicolusSceloporus graciosusSceloporus vandenburgianus

Sceloporus ochoterenaeSceloporus jalapae

Sceloporus maculosusSceloporus gadoviae

Sceloporus nelsoniSceloporus pyrocephalus

Sceloporus merriamiSceloporus siniferus

Sceloporus squamosusSceloporus carinatus

Sceloporus utiformisSceloporus angustus

Sceloporus grandaevusSceloporus cozumelae

Sceloporus smithiSceloporus variabilis

Sceloporus teapensisSceloporus chrysostictus

Sceloporus couchiiSceloporus parvus

Urosaurus auriculatusUrosaurus clarionensisUrosaurus ornatus

Urosaurus graciosusUrosaurus nigricaudusUrosaurus lahtelaiUrosaurus bicarinatus

Urosaurus gadoviUta stejnegeri

Uta stansburianaUta palmeriUta squamataPetrosaurus thalassinusPetrosaurus repens

Petrosaurus mearnsiPhrynosoma hernandesi

Phrynosoma douglassiiPhrynosoma ditmarsiPhrynosoma orbiculare

Phrynosoma modestumPhrynosoma taurusPhrynosoma braconnieri

Phrynosoma asioPhrynosoma wigginsiPhrynosoma cerroense

Phrynosoma blainvilliiPhrynosoma coronatum

Phrynosoma platyrhinosPhrynosoma mcalliiPhrynosoma solare

Phrynosoma cornutumHolbrookia maculataHolbrookia propinquaHolbrookia lacerata

Cophosaurus texanusCallisaurus draconoides

Uma notataUma inornataUma scoparia

Uma paraphygasUma exsul

Crotaphytus collarisCrotaphytus nebriusCrotaphytus bicinctores

Crotaphytus grismeriCrotaphytus insularis

Crotaphytus vestigiumCrotaphytus reticulatus

Crotaphytus antiquusGambelia copeiiGambelia sila

Gambelia wislizeniiLeiocephalus barahonensisLeiocephalus schreibersii

Leiocephalus personatusLeiocephalus psammodromus

Leiocephalus ravicepsLeiocephalus carinatus

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Liolaemus lavillaiLiolaemus ornatusLiolaemus calchaquiLiolaemus albicepsLiolaemus irregularis

Liolaemus crepuscularisLiolaemus abaucanLiolaemus espinozai

Liolaemus quilmesLiolaemus koslowskyi

Liolaemus laurentiLiolaemus darwiniiLiolaemus grosseorum

Liolaemus olongastaLiolaemus chacoensis

Liolaemus uspallatensisLiolaemus hermannuneziLiolaemus xanthoviridisLiolaemus fitzingerii

Liolaemus chehuachekenkLiolaemus morenoiLiolaemus canqueli

Liolaemus melanopsLiolaemus donosobarrosiLiolaemus cuyanus

Liolaemus telsenLiolaemus inacayali

Liolaemus boulengeriLiolaemus rothi

Liolaemus wiegmanniiLiolaemus azarai

Liolaemus scapularisLiolaemus multimaculatusLiolaemus riojanusLiolaemus salinicola

Liolaemus lutzaeLiolaemus occipitalis

Liolaemus pseudoanomalusLiolaemus andinus

Liolaemus multicolorLiolaemus molinaiLiolaemus dorbignyiLiolaemus huacahuasicusLiolaemus fabianiLiolaemus audituvelatus

Liolaemus ruibaliLiolaemus vallecurensisLiolaemus famatinae

Liolaemus orientalisLiolaemus stolzmanni

Liolaemus archeforusLiolaemus tristisLiolaemus zullyaeLiolaemus scolaroi

Liolaemus sarmientoiLiolaemus gallardoi

Liolaemus kingiiLiolaemus escarchadosiLiolaemus tari

Liolaemus bagualiLiolaemus somuncurae

Liolaemus uptoniLiolaemus magellanicus

Liolaemus kolenghLiolaemus silvanaeLiolaemus lineomaculatus

Liolaemus hatcheriLiolaemus saxatilis

Liolaemus gracilisLiolaemus robertmertensiLiolaemus ramirezae

Liolaemus yanalcuLiolaemus walkeriLiolaemus puna

Liolaemus chaltinLiolaemus bitaeniatus

Liolaemus pagaburoiLiolaemus bibronii

Liolaemus hernaniLiolaemus pictusLiolaemus cyanogaster

Liolaemus chiliensisLiolaemus schroederi

Liolaemus gravenhorstiiLiolaemus belliiLiolaemus coeruleusLiolaemus elongatus

Liolaemus kriegiLiolaemus leopardinus

Liolaemus ceiiLiolaemus buergeriLiolaemus petrophilusLiolaemus umbriferLiolaemus capillitasLiolaemus heliodermis

Liolaemus dicktracyiLiolaemus thermarum

Liolaemus austromendocinusLiolaemus paulinaeLiolaemus plateiLiolaemus nigromaculatus

Liolaemus pseudolemniscatusLiolaemus zapallarensisLiolaemus atacamensis

Liolaemus fuscusLiolaemus nigroviridisLiolaemus nitidus

Liolaemus monticolaLiolaemus lemniscatus

Liolaemus tenuisPhymaturus antofagastensisPhymaturus mallimacciiPhymaturus punaePhymaturus palluma

Phymaturus dorsimaculatusPhymaturus patagonicusPhymaturus somuncurensis

Phymaturus indistinctusCtenoblepharys adspersa

Leiosaurus catamarcensisLeiosaurus paronae

Leiosaurus belliiPristidactylus torquatus

Diplolaemus darwiniiPristidactylus scapulatus

Urostrophus vautieriAnisolepis longicauda

Urostrophus gallardoiEnyalius leechii

Enyalius bilineatusOplurus fierinensis

Oplurus grandidieriOplurus saxicola

Oplurus quadrimaculatusOplurus cuvieri

Oplurus cyclurusChalarodon madagascariensis

Enyalioides praestabilisEnyalioides microlepisEnyalioides palpebralis

Enyalioides oshaughnessyiEnyalioides heterolepis

Enyalioides laticepsMorunasaurus annularis

Hoplocercus spinosusPolychrus marmoratus

Polychrus femoralisPolychrus acutirostris

Polychrus gutturosus

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Enyaliinae

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


Anolis smaragdinusAnolis allisoniAnolis maynardi

Anolis brunneusAnolis longiceps

Anolis porcatusAnolis carolinensisAnolis isolepisAnolis oporinus

Anolis argillaceusAnolis centralis

Anolis pumilusAnolis loysiana

Anolis guazumaAnolis garridoi

Anolis angusticepsAnolis paternusAnolis alayoniAnolis sheplaniAnolis placidus

Anolis alutaceusAnolis inexpectatus

Anolis vanidicusAnolis alfaroi

Anolis macilentusAnolis cupeyalensisAnolis cyanopleurusAnolis rejectus

Anolis clivicolaAnolis lucius

Anolis whitemaniAnolis cybotes

Anolis armouriAnolis shreveiAnolis haetianusAnolis longitibialis

Anolis strahmiAnolis marcanoi

Anolis barahonaeAnolis baleatus

Anolis ricordiAnolis eugenegrahami

Anolis christopheiAnolis cuvieri

Anolis guamuhayaAnolis chamaeleonides

Anolis porcusAnolis barbatus

Anolis argenteolusAnolis alumina

Anolis semilineatusAnolis olssoni

Anolis barbouriAnolis insolitus

Anolis fowleriAnolis etheridgei

Anolis equestrisAnolis luteogularis

Anolis baracoaeAnolis nobleiAnolis smallwoodi

Anolis alinigerAnolis singularisAnolis chlorocyanusAnolis coelestinus

Anolis hendersoniAnolis dolichocephalus

Anolis bahorucoensisAnolis darlingtoni

Anolis monticolaAnolis occultus

Anolis vermiculatusAnolis bartschi

Anolis maculigulaAnolis casildae

Anolis frenatusAnolis princeps

Anolis chocorumAnolis fraseri

Anolis danieliAnolis insignisAnolis microtus

Anolis agassiziAnolis neblininusAnolis calimae

Anolis anatolorosAnolis jacare

Anolis tigrinusAnolis transversalisAnolis punctatus

Anolis inderenaeAnolis vanzoliniiAnolis heterodermusAnolis nicefori

Anolis euskalerriariAnolis gemmosusAnolis aequatorialisAnolis ventrimaculatusAnolis chlorisAnolis festae

Anolis peraccaeAnolis huilaeAnolis fitchi

Anolis extremusAnolis roquet

Anolis aeneusAnolis richardii

Anolis trinitatisAnolis griseus

Anolis bonairensisAnolis luciae

Anolis boettgeriBasiliscus basiliscus

Basiliscus plumifronsBasiliscus vittatus

Basiliscus galeritusCorytophanes cristatus

Corytophanes percarinatusLaemanctus longipes

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Anolis trachydermaAnolis poecilopusAnolis tropidogaster

Anolis lionotusAnolis oxylophus

Anolis zeusAnolis limifrons

Anolis lemurinusAnolis bicaorum

Anolis carpenteriAnolis ocelloscapularisAnolis tropidonotus

Anolis capitoAnolis polylepis

Anolis cupreusAnolis fuscoauratusAnolis kemptoniAnolis altae

Anolis humilisAnolis pachypus

Anolis sericeusAnolis isthmicus

Anolis intermediusAnolis laeviventris

Anolis ortoniiAnolis quercorum

Anolis aquaticusAnolis woodiAnolis biporcatus

Anolis bitectusAnolis uniformisAnolis polyrhachis

Anolis sminthusAnolis crassulusAnolis utilensisAnolis purpurgularis

Anolis loveridgeiAnolis chrysolepis

Anolis bombicepsAnolis nitens

Anolis meridionalisAnolis lineatus

Anolis oncaAnolis annectens

Anolis auratusAnolis grahamiAnolis conspersus

Anolis garmaniAnolis opalinusAnolis valencienni

Anolis reconditusAnolis lineatopus

Anolis bremeriAnolis quadriocellifer

Anolis sagreiAnolis ophiolepis

Anolis mestreiAnolis homolechisAnolis jubar

Anolis confususAnolis guafe

Anolis ahliAnolis allogus

Anolis rubribarbarisAnolis imias

Anolis cristatellusAnolis desechensis

Anolis ernestwilliamsiAnolis scriptus

Anolis cookiAnolis monensis

Anolis krugiAnolis pulchellus

Anolis gundlachiAnolis poncensis

Anolis evermanniAnolis stratulusAnolis acutus

Anolis caudalisAnolis marron

Anolis brevirostrisAnolis websteriAnolis distichus

Anolis marmoratusAnolis sabanusAnolis nubilus

Anolis lividusAnolis ferreus

Anolis terraealtaeAnolis oculatus

Anolis gingivinusAnolis bimaculatus

Anolis leachiiAnolis pogus

Anolis wattsi

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


Austrotyphlops pilbarensisAustrotyphlops hamatus

Austrotyphlops endoterusAustrotyphlops australisAustrotyphlops waitiiAustrotyphlops splendidusAustrotyphlops pinguisRamphotyphlops bicolor

Austrotyphlops ligatusAustrotyphlops ganei

Austrotyphlops troglodytesAustrotyphlops kimberleyensis

Austrotyphlops ammodytesAustrotyphlops unguirostris

Austrotyphlops leptosomusAustrotyphlops longissimus

Austrotyphlops grypusAustrotyphlops bituberculatus

Austrotyphlops guentheriAustrotyphlops howi

Austrotyphlops diversusRamphotyphlops polygrammicusAcutotyphlops kunuaensis

Acutotyphlops subocularisRamphotyphlops acuticaudus

Ramphotyphlops lineatusTyphlopidae sp. (Sri Lanka)

Ramphotyphlops braminusTyphlops pammeces

Ramphotyphlops albicepsTyphlops ruber

Typhlops luzonensisTyphlops arenarius

Typhlops vermicularisAfrotyphlops punctatus

Afrotyphlops congestusAfrotyphlops lineolatus

Afrotyphlops bibroniiAfrotyphlops fornasinii

Megatyphlops schlegeliiAfrotyphlops angolensis

Typhlops elegansLetheobia obtusa

Letheobia newtoniLetheobia feae

Rhinotyphlops lalandeiTyphlops catapontusTyphlops richardiTyphlops platycephalusTyphlops hypomethesTyphlops granti

Typhlops dominicanusTyphlops monastusTyphlops notorachiusTyphlops anousiusTyphlops anchaurusTyphlops contorhinusTyphlops aratorTyphlops caymanensis

Typhlops agoralionisTyphlops sylleptor

Typhlops jamaicensisTyphlops capitulatus

Typhlops rostellatusTyphlops sulcatus

Typhlops titanopsTyphlops schwartzi

Typhlops lumbricalisTyphlops eperopeus

Typhlops syntherusTyphlops hectusTyphlops pusillus

Typhlops biminiensisTyphlops reticulatus

Typhlops brongersmianusXenotyphlops grandidieri

Gerrhopilus mirusGerrhopilus hedraeusLeptotyphlops scutifrons

Leptotyphlops distantiLeptotyphlops conjunctusLeptotyphlops sylvicolus

Leptotyphlops nigricansLeptotyphlops nigroterminus

Namibiana occidentalisMyriopholis adleri

Myriopholis macrorhynchaMyriopholis blanfordi

Myriopholis bouetiMyriopholis rouxestevae

Myriopholis algeriensisMyriopholis longicauda

Mitophis leptipileptusMitophis pyrites

Mitophis asbolepisTetracheilostoma breuili

Tetracheilostoma carlaeRena humilisRena dulcis

Trilepida macrolepisEpictia columbiEpictia goudotii

Epictia albifronsSiagonodon septemstriatus

Tricheilostoma bicolorTyphlophis squamosus

Liotyphlops albirostris

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GerrhopilidaeXenotyphlopidae

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


Antaresia childreniAntaresia stimsoniAntaresia perthensisAntaresia maculosaMorelia bredliMorelia spilota

Morelia carinataMorelia viridisBothrochilus boaLeiopython albertisii

Liasis fuscusLiasis mackloti

Apodora papuanaLiasis olivaceus

Aspidites melanocephalusAspidites ramsayi

Morelia amethistinaMorelia boeleniMorelia oenpelliensisBroghammerus timoriensisBroghammerus reticulatus

Python molurusPython sebaePython curtusPython regius

Python brongersmaiLoxocemus bicolor

Xenopeltis unicolorRhinophis blythiiRhinophis homolepisPseudotyphlops philippinusRhinophis oxyrhynchus

Rhinophis philippinusRhinophis dorsimaculatus

Rhinophis drummondhayiUropeltis phillipsiUropeltis melanogaster

Rhinophis travancoricusUropeltis ceylanicus

Uropeltis liuraBrachyophidium rhodogaster

Melanophidium punctatumCylindrophis ruffus

Cylindrophis maculatusAnomochilus leonardi

Epicrates striatusEpicrates exsulEpicrates chrysogasterEpicrates subflavus

Epicrates fordiEpicrates monensisEpicrates inornatus

Epicrates anguliferEunectes notaeusEunectes murinus

Epicrates cenchriaCorallus annulatus

Corallus caninusCorallus hortulanusBoa constrictorEryx tataricusEryx miliaris

Eryx elegansEryx jaculusEryx johnii

Eryx conicusEryx colubrinus

Eryx jayakariCandoia bibroni

Candoia carinataCandoia aspera

Lichanura trivirgataCharina bottae

Ungaliophis continentalisExiliboa placata

Calabaria reinhardtiiAcrantophis dumeriliAcrantophis madagascariensisSanzinia madagascariensisCasarea dussumieriXenophidion schaeferiTropidophis melanurusTropidophis feicki

Tropidophis haetianusTropidophis greenwayi

Tropidophis wrightiTropidophis pardalis

Trachyboa boulengeriTrachyboa gularis

Anilius scytale

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Tropidophiidae

XenophidiidaeBolyeriidae

Boidae

AnomochilidaeCylindrophiidae

Uropeltidae

XenopeltidaeLoxocemidae

Pythonidae

CalabariidaeSanziniinae

Ungaliophiinae

Candoiinae

Erycinae

Boinae

TU-AA

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


Bitis rubida

Bitis cornuta

Bitis atropos

Bitis xeropaga

Bitis caudalis

Bitis peringueyi

Bitis gabonica

Bitis nasicornisBitis arietans

Bitis worthingtoni

Atheris desaixi

Atheris nitschei

Atheris squamigera

Atheris hispida

Atheris chlorechis

Atheris barbouri

Atheris ceratophora

Echis pyramidum

Echis leucogaster

Echis coloratus

Echis omanensis

Echis jogeri

Echis ocellatus

Echis carinatus

Causus defilippii

Causus rhombeatus

Causus resimus

Cerastes gasperettii

Cerastes cerastes

Cerastes vipera

Proatheris superciliaris

Vipera lotievi

Vipera renardi

Vipera dinniki

Vipera ursinii

Vipera eriwanensis

Vipera kaznakovi

Vipera barani

Vipera berus

Vipera nikolskii

Vipera seoanei

Vipera aspis

Vipera latastei

Vipera ammodytes

Macrovipera mauritanica

Macrovipera deserti

Daboia russelii

Daboia palaestinae

Montivipera wagneri

Montivipera albizona

Montivipera bornmuelleri

Montivipera raddei

Montivipera xanthina

Macrovipera schweizeri

Macrovipera lebetina

Pseudocerastes fieldi

Pseudocerastes persicus

Eristicophis macmahoni

Pareas nuchalis

Pareas carinatus

Pareas hamptoni

Pareas macularius

Pareas margaritophorus

Pareas formosensis

Pareas boulengeri

Pareas monticola

Aplopeltura boa

Asthenodipsas vertebralis

Achalinus rufescens

Achalinus meiguensis

Xenodermus javanicus

Stoliczkia borneensis

Acrochordus arafurae

Acrochordus granulatus

Acrochordus javanicus

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Crotalus adamanteusCrotalus tigris

Crotalus mitchelliiCrotalus viridis

Crotalus oreganusCrotalus scutulatusCrotalus tortugensis

Crotalus atroxCrotalus catalinensis

Crotalus ruberCrotalus totonacusCrotalus molossus

Crotalus basiliscusCrotalus simusCrotalus durissus

Crotalus horridusCrotalus willardi

Crotalus ravusCrotalus cerastesCrotalus polystictus

Crotalus enyoCrotalus aquilus

Crotalus lepidusCrotalus pusillus

Crotalus triseriatusCrotalus tancitarensis

Crotalus transversusCrotalus intermedius

Crotalus priceiSistrurus miliarius

Sistrurus catenatusAgkistrodon bilineatus

Agkistrodon tayloriAgkistrodon piscivorus

Agkistrodon contortrixBothriechis rowleyi

Bothriechis auriferBothriechis bicolor

Bothriechis thalassinusBothriechis marchi

Bothriechis lateralisBothriechis nigroviridis

Bothriechis schlegeliiLachesis mutaLachesis stenophrys

Mixcoatlus melanurusMixcoatlus barbouri

Ophryacus undulatusBothrops leucurus

Bothrops moojeniBothrops atrox

Bothrops colombiensisBothrops marajoensis

Bothrops asperBothrops lanceolatus

Bothrops caribbaeusBothrops punctatusBothrops jararacussu

Bothrops braziliBothriopsis bilineata

Bothriopsis taeniataBothriopsis chloromelasBothriopsis pulchra

Bothropoides alcatrazBothropoides insularis

Bothropoides jararacaBothropoides neuwiedi

Bothropoides diporusBothropoides erythromelas

Rhinocerophis itapetiningaeRhinocerophis alternatus

Rhinocerophis fonsecaiRhinocerophis cotiara

Rhinocerophis ammodytoidesBothrops pictus

Bothrocophias hyoproraBothrocophias microphthalmus

Bothrocophias campbelliPorthidium lansbergii

Porthidium porrasiPorthidium nasutum

Porthidium yucatanicumPorthidium dunni

Porthidium ophryomegasCerrophidion petlalcalensis

Cerrophidion tzotzilorumCerrophidion godmani

Atropoides picadoiAtropoides olmec

Atropoides nummiferAtropoides occiduus

Gloydius saxatilisGloydius intermedius

Gloydius shedaoensisGloydius halys

Gloydius strauchiGloydius blomhoffiiGloydius ussuriensis

Gloydius brevicaudusGloydius tsushimaensis

Trimeresurus gracilisOvophis okinavensis

Protobothrops tokarensisProtobothrops flavoviridis

Protobothrops mucrosquamatusProtobothrops elegans

Protobothrops jerdoniiProtobothrops xiangchengensis

Protobothrops cornutusProtobothrops mangshanensis

Protobothrops sieversorumProtobothrops kaulbacki

Ovophis tonkinensisOvophis zayuensisOvophis monticola

Trimeresurus purpureomaculatusTrimeresurus erythrurus

Trimeresurus cantoriTrimeresurus albolabris

Trimeresurus andersoniiTrimeresurus septentrionalis

Trimeresurus insularisTrimeresurus fasciatus

Trimeresurus macropsTrimeresurus venustus

Trimeresurus kanburiensisTrimeresurus vogeli

Trimeresurus stejnegeriTrimeresurus gumprechti

Trimeresurus yunnanensisTrimeresurus medoensis

Trimeresurus tibetanusTrimeresurus popeiorum

Trimeresurus sumatranusTrimeresurus schultzei

Trimeresurus flavomaculatusTrimeresurus malcolmiTrimeresurus hageni

Trimeresurus trigonocephalusTrimeresurus gramineus

Trimeresurus malabaricusTrimeresurus borneensis

Trimeresurus puniceusHypnale zara

Hypnale hypnaleHypnale nepa

Calloselasma rhodostomaDeinagkistrodon acutus

Tropidolaemus wagleriGarthius chaseni

Azemiops feae

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


Liophidium chabaudiLiophidium mayottensis

Liophidium torquatumLiophidium therezieni

Liophidium vaillantiLiophidium rhodogaster

Liopholidophis sexlineatusLiopholidophis dolicocercus

Liopholidophis dimorphusHeteroliodon occipitalis

Pseudoxyrhopus ambreensisThamnosophis lateralis

Thamnosophis stumpffiThamnosophis epistibes

Thamnosophis martaeThamnosophis infrasignatus

Dromicodryas bernieriDromicodryas quadrilineatus

Lycodryas granulicepsLycodryas pseudogranuliceps

Lycodryas inopinaeLycodryas sanctijohannis

Lycodryas citrinusLycodryas inornatus

Madagascarophis meridionalisMadagascarophis colubrinus

Ithycyphus oursiIthycyphus miniatus

Micropisthodon ochraceusLangaha madagascariensis

Leioheterodon modestusLeioheterodon madagascariensis

Leioheterodon geayiParastenophis betsileanus

Alluaudina bellyiCompsophis infralineatus

Compsophis laphystiusCompsophis albiventris

Compsophis boulengeriDitypophis vivaxDuberria lutrix

Duberria variegataAmplorhinus multimaculatus

Lycodonomorphus whytiiLycodonomorphus laevissimus

Lycodonomorphus rufulusLycodonomorphus inornatus

Lamprophis fiskiiLamprophis aurora

Lamprophis fuscusLamprophis guttatus

Boaedon olivaceusBoaedon fuliginosus

Boaedon lineatusBoaedon virgatus

Bothrophthalmus lineatusBothrophthalmus brunneus

Bothrolycus aterPseudoboodon lemniscatus

Gonionotophis capensisGonionotophis poensis

Gonionotophis brussauxiGonionotophis nyassae

Gonionotophis stenophthalmusInyoka swazicus

Hormonotus modestusLycophidion ornatum

Lycophidion capenseLycophidion laterale

Lycophidion nigromaculatumBuhoma depressiceps

Buhoma procteraePsammodynastes pictus

Psammodynastes pulverulentusPseudaspis cana

Pythonodipsas carinataAparallactus guentheri

Aparallactus capensisAparallactus werneriAparallactus modestus

Polemon acanthiasPolemon collaris

Polemon notatusAmblyodipsas dimidiata

Xenocalamus transvaalensisAmblyodipsas polylepis

Macrelaps microlepidotusAtractaspis corpulenta

Atractaspis micropholisAtractaspis bibronii

Atractaspis boulengeriAtractaspis microlepidota

Atractaspis irregularisHomoroselaps lacteus

Psammophis phillipsiPsammophis mossambicusPsammophis leopardinus

Psammophis sibilansPsammophis rukwae

Psammophis orientalisPsammophis sudanensis

Psammophis subtaeniatusPsammophis lineatusPsammophis biseriatus

Psammophis tanganicusPsammophis praeornatus

Psammophis punctulatusPsammophis schokari

Psammophis angolensisPsammophis notostictusPsammophis leightoniPsammophis jallae

Psammophis trigrammusPsammophis condanarus

Psammophis lineolatusPsammophis crucifer

Psammophylax tritaeniatusPsammophylax variabilis

Psammophylax rhombeatusPsammophylax acutus

Hemirhagerrhis hildebrandtiiHemirhagerrhis kelleri

Hemirhagerrhis viperinaDipsina multimaculata

Mimophis mahfalensisRhagerhis moilensis

Malpolon monspessulanusRhamphiophis rubropunctatus

Rhamphiophis oxyrhynchusProsymna meleagris

Prosymna greigertiProsymna janii

Prosymna visseriProsymna ruspolii

Oxyrhabdium leporinumMicrelaps bicoloratus

Cerberus rynchopsCerberus microlepis

Cerberus australisHomalopsis buccataEnhydris punctata

Fordonia leucobaliaGerarda prevostiana

Cantoria violaceaBitia hydroides

Enhydris bocourtiErpeton tentaculatum

Pseudoferania polylepisMyron richardsonii

Enhydris innominataEnhydris longicauda

Enhydris jagoriiEnhydris enhydris

Enhydris matannensisEnhydris plumbea

Enhydris chinensis

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


Hydrophis ornataHydrophis peronii

Hydrophis kingiiHydrophis macdowelli

Hydrophis schistosaHydrophis majorHydrophis czeblukovi

Hydrophis caerulescensHydrophis brooki

Hydrophis atricepsHydrophis stokesii

Hydrophis platuraHydrophis curtus

Hydrophis parvicepsHydrophis melanocephala

Hydrophis cyanocinctaHydrophis pacificaHydrophis semperi

Hydrophis spiralisHydrophis lapemoides

Hydrophis elegansHydrelaps darwiniensis

Ephalophis greyaeParahydrophis mertoni

Aipysurus laevisAipysurus fuscusAipysurus apraefrontalisAipysurus duboisii

Aipysurus eydouxiiEmydocephalus annulatus

Hemiaspis dameliiHemiaspis signata

Tropidechis carinatusNotechis scutatus

Echiopsis atricepsHoplocephalus bitorquatus

Austrelaps superbusAustrelaps labialis

Drysdalia coronoidesDrysdalia mastersii

Echiopsis curtaPseudonaja textilisPseudonaja modesta

Oxyuranus scutellatusOxyuranus microlepidotus

Denisonia devisiSimoselaps calonotus

Vermicella intermediaSuta spectabilis

Suta sutaSuta monachus

Suta fasciataRhinoplocephalus bicolor

Cryptophis nigrescensElapognathus coronata

Cacophis squamulosusPseudechis guttatus

Pseudechis papuanusPseudechis colletti

Pseudechis australisPseudechis butleri

Pseudechis porphyriacusAcanthophis antarcticusAcanthophis praelongus

Aspidomorphus muelleriAspidomorphus lineaticollis

Aspidomorphus schlegeliSimoselaps bertholdi

Simoselaps anomalusSimoselaps semifasciatus

Furina diademaFurina ornata

Toxicocalamus loriaeDemansia psammophis

Demansia papuensisDemansia vestigiata

Toxicocalamus preussiMicropechis ikaheka

Laticauda colubrinaLaticauda guineai

Laticauda saintgironsiLaticauda laticaudata

Bungarus candidusBungarus multicinctus

Bungarus nigerBungarus caeruleus

Bungarus ceylonicusBungarus sindanus

Bungarus fasciatusBungarus bungaroidesBungarus flavicepsElapsoidea sundevalliiElapsoidea semiannulata

Elapsoidea nigraNaja ashei

Naja nigricollisNaja mossambica

Naja katiensisNaja pallida

Naja nubiaeNaja haje

Naja annuliferaNaja nivea

Naja annulataNaja melanoleuca

Naja multifasciataNaja sumatranaNaja siamensis

Naja mandalayensisNaja naja

Naja atraNaja kaouthia

Hemachatus haemachatusAspidelaps scutatus

Walterinnesia aegyptiaDendroaspis polylepis

Dendroaspis angusticepsOphiophagus hannah

Hemibungarus calligasterMicrurus brasiliensisMicrurus frontalisMicrurus spixii

Micrurus ibibobocaMicrurus altirostris

Micrurus pyrrhocryptusMicrurus baliocoryphus

Micrurus decoratusMicrurus lemniscatusMicrurus hemprichii

Micrurus surinamensisMicrurus dissoleucus

Micrurus mipartitusMicrurus narduccii

Micrurus diastemaMicrurus fulvius

Micrurus psychesMicrurus albicinctus

Micrurus corallinusSinomicrurus macclellandi

Sinomicrurus kelloggiSinomicrurus japonicus

Micruroides euryxanthusMaticora bivirgata

Calliophis melanurus

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


Eirenis punctatolineatusEirenis barani

Eirenis collarisEirenis eiselti

Eirenis coronelloidesEirenis rothiiEirenis lineomaculatus

Eirenis thospitisEirenis medus

Eirenis levantinusEirenis decemlineatus

Eirenis persicusEirenis aurolineatus

Eirenis modestusHierophis spinalisHierophis gemonensis

Hierophis viridiflavusDolichophis caspius

Dolichophis schmidtiDolichophis jugularis

Platyceps florulentusPlatyceps collaris

Platyceps najadumPlatyceps ventromaculatus

Platyceps kareliniPlatyceps rogersi

Platyceps rhodorachisSpalerosophis diadema

Spalerosophis microlepisHemorrhois ravergieri

Hemorrhois nummiferHemorrhois algirus

Hemorrhois hippocrepisHemerophis socotrae

Macroprotodon abubakeriMacroprotodon cucullatus

Bamanophis dorriColuber zebrinus

Lytorhynchus diademaHapsidophrys principis

Hapsidophrys smaragdinaHapsidophrys lineatus

Philothamnus hoplogasterPhilothamnus natalensisPhilothamnus thomensis

Philothamnus girardiPhilothamnus angolensis

Philothamnus semivariegatusPhilothamnus nitidus

Philothamnus heterodermusPhilothamnus carinatus

Thelotornis capensisDispholidus typus

Thrasops jacksoniiCoelognathus flavolineatus

Coelognathus subradiatusCoelognathus erythrurus

Coelognathus helenaCoelognathus radiatus

Oligodon planicepsOligodon torquatus

Oligodon theobaldiOligodon cruentatus

Oligodon splendidusOligodon maculatus

Oligodon cinereusOligodon formosanus

Oligodon ocellatusOligodon chinensisOligodon taeniatusOligodon barroniOligodon cyclurus

Oligodon octolineatusOligodon taeniolatusOligodon sublineatus

Oligodon arnensisScaphiophis albopunctatus

Dasypeltis fasciataDasypeltis gansi

Dasypeltis sahelensisDasypeltis scabra

Dasypeltis atraDasypeltis confusa

Toxicodryas pulverulentaBoiga multomaculata

Boiga beddomeiBoiga ceylonensisBoiga trigonata

Boiga barnesiiBoiga cynodon

Boiga forsteniBoiga dendrophila

Boiga irregularisTelescopus fallax

Dipsadoboa unicolorCrotaphopeltis tornieri

Boiga kraepeliniDendrelaphis tristis

Dendrelaphis schokariDendrelaphis caudolineatus

Dendrelaphis caudolineolatusDendrelaphis bifrenalis

Chrysopelea paradisiChrysopelea ornata

Chrysopelea taprobanicaAhaetulla nasuta

Ahaetulla pulverulentaAhaetulla fronticincta

Grayia smithiiGrayia ornataGrayia tholloni

Sibynophis chinensisSibynophis collaris

Sibynophis triangularisSibynophis subpunctatus

Sibynophis bistrigatusScaphiodontophis annulatus

Pseudoxenodon karlschmidtiPseudoxenodon macrops

Pseudoxenodon bambusicolaPlagiopholis styani

Calamaria yunnanensisCalamaria pavimentata

Pseudorabdion oxycephalum

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


Lampropeltis californiaeLampropeltis splendidaLampropeltis holbrooki

Lampropeltis getulaLampropeltis nigraLampropeltis alterna

Lampropeltis extenuatumLampropeltis triangulumLampropeltis ruthveniLampropeltis mexicanaLampropeltis elapsoidesLampropeltis zonataLampropeltis pyromelana

Lampropeltis webbiLampropeltis calligaster

Cemophora coccineaPseudelaphe flavirufa

Arizona elegansRhinocheilus lecontei

Bogertophis rosaliaeBogertophis subocularis

Pantherophis bairdiPantherophis obsoletusPantherophis alleghaniensis

Pantherophis spiloidesPantherophis slowinskii

Pantherophis emoryiPantherophis guttatus

Pantherophis vulpinusPituophis cateniferPituophis ruthveniPituophis melanoleucus

Pituophis lineaticollisPituophis vertebralis

Pituophis deppeiSenticolis triaspis

Oocatochus rufodorsatusCoronella austriaca

Coronella girondicaElaphe sauromates

Elaphe quatuorlineataElaphe quadrivirgata

Elaphe schrenckiiElaphe climacophora

Elaphe dioneElaphe bimaculata

Elaphe carinataElaphe davidi

Zamenis situlaRhinechis scalaris

Zamenis lineatusZamenis longissimus

Zamenis persicusZamenis hohenackeri

Orthriophis cantorisOrthriophis moellendorffi

Orthriophis hodgsoniOrthriophis taeniurus

Oreocryptophis porphyraceusEuprepiophis mandarinus

Euprepiophis conspicillataArchelaphe bella

Lycodon aulicusLycodon zawi

Lycodon osmanhilliLycodon capucinus

Lycodon carinatusDryocalamus nympha

Lycodon semicarinatumLycodon rufozonatum

Lycodon paucifasciatusLycodon fasciatus

Lycodon laoensisLycodon ruhstrati

Rhadinophis frenatusRhynchophis boulengeri

Rhadinophis prasinusGonyosoma jansenii

Gonyosoma oxycephalumSympholis lippiens

Pseudoficimia frontalisGyalopion canum

Ficimia streckeriConopsis nasusConopsis biserialis

Sonora semiannulataChilomeniscus stramineus

Chionactis occipitalisStenorrhina freminvillei

Rhinobothryum lentiginosumMastigodryas bifossatus

Mastigodryas boddaertiMastigodryas melanolomus

Drymoluber braziliDrymoluber dichrous

Chironius multiventrisChironius laurenti

Chironius exoletusChironius monticola

Chironius bicarinatusChironius flavolineatus

Chironius grandisquamisChironius laevicollisChironius scurrulus

Chironius fuscusDrymarchon corais

Pseustes sulphureusSpilotes pullatus

Phyllorhynchus decurtatusTrimorphodon biscutatus

Drymobius rhombiferDendrophidion percarinatum

Dendrophidion dendrophisLeptophis ahaetulla

Chironius carinatusChironius quadricarinatus

Coluber flagellumColuber constrictor

Coluber taeniatusTantilla melanocephala

Salvadora mexicanaOpheodrys aestivusOpheodrys vernalisOxybelis aeneus

Oxybelis fulgidusPtyas mucosa

Ptyas korrosCyclophiops major

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


Thamnophis butleriThamnophis radixThamnophis brachystomaThamnophis elegansThamnophis gigasThamnophis atratusThamnophis couchii

Thamnophis ordinoidesThamnophis hammondii

Thamnophis marcianusThamnophis equesThamnophis cyrtopsis

Thamnophis chrysocephalusThamnophis fulvus

Thamnophis mendaxThamnophis sumichrasti

Thamnophis scaligerThamnophis godmaniThamnophis exsulThamnophis melanogaster

Thamnophis validaAdelophis foxi

Thamnophis rufipunctatusThamnophis proximusThamnophis sauritus

Thamnophis sirtalisNerodia sipedon

Nerodia fasciataNerodia harteriNerodia erythrogaster

Nerodia rhombiferNerodia taxispilota

Nerodia floridanaNerodia cyclopion

Tropidoclonion lineatumRegina grahami

Regina septemvittataRegina alleni

Regina rigidaSeminatrix pygaea

Storeria dekayiStoreria occipitomaculata

Virginia striatulaClonophis kirtlandii

Natrix tessellataNatrix natrix

Natrix mauraSinonatrix annularis

Sinonatrix percarinataSinonatrix aequifasciata

Opisthotropis cheniOpisthotropis latouchii

Opisthotropis lateralisOpisthotropis guangxiensis

Aspidura guentheriAspidura ceylonensis

Aspidura trachyproctaAspidura drummondhayi

Atretium yunnanensisXenochrophis asperrimus

Xenochrophis punctulatusAtretium schistosum

Xenochrophis piscatorXenochrophis flavipunctatusXenochrophis vittatus

Amphiesma stolatumRhabdophis nuchalis

Rhabdophis tigrinusRhabdophis subminiatus

Balanophis ceylonensisMacropisthodon rudis

Lycognathophis seychellensisAfronatrix anoscopus

Natriciteres olivaceaAmphiesma craspedogasterAmphiesma sauteri

Trachischium monticola

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


Sibynomorphus neuwiedi

Sibynomorphus ventrimaculatus

Dipsas albifrons

Dipsas articulata

Sibynomorphus turgidus

Sibynomorphus mikanii

Dipsas pratti

Dipsas variegata

Dipsas neivai

Dipsas catesbyi

Dipsas indica

Tropidodipsas sartorii

Sibon nebulatus

Ninia atrata

Atractus zebrinus

Atractus trihedrurus

Atractus reticulatus

Atractus badius

Atractus flammigerus

Atractus elaps

Atractus albuquerquei

Atractus schach

Atractus wagleri

Atractus zidoki

Geophis godmani

Geophis carinosus

Cryophis hallbergi

Tretanorhinus nigroluteus

Hydromorphus concolor

Adelphicos quadrivirgatum

Leptodeira rubricata

Leptodeira maculata

Leptodeira bakeri

Leptodeira annulata

Leptodeira septentrionalis

Leptodeira punctata

Leptodeira splendida

Leptodeira frenata

Leptodeira uribei

Imantodes cenchoa

Imantodes gemmistratus

Imantodes lentiferus

Imantodes inornatus

Leptodeira nigrofasciata

Tretanorhinus variabilis

Hypsiglena chlorophaea

Hypsiglena torquata

Hypsiglena ochrorhyncha

Hypsiglena affinis

Hypsiglena jani

Hypsiglena slevini

Trimetopon gracile

Pseudoleptodeira latifasciata

Rhadinaea fulvivittis

Rhadinaea flavilata

Coniophanes fissidens

Tantalophis discolor

Amastridium veliferum

Nothopsis rugosus

Farancia erytrogramma

Farancia abacura

Carphophis amoenus

Diadophis punctatus

Heterodon nasicus

Heterodon simus

Heterodon platirhinos

Contia tenuis

Thermophis baileyi

Thermophis zhaoermii

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Pseudoboa coronataPseudoboa nigra

Pseudoboa neuwiediiRhachidelus brazili

Boiruna maculataDrepanoides anomalus

Mussurana bicolorClelia clelia

Phimophis gueriniParaphimophis rusticus

Rodriguesophis iglesiasiOxyrhopus guibei

Oxyrhopus melanogenysOxyrhopus rhombifer

Oxyrhopus clathratusOxyrhopus trigeminus

Oxyrhopus formosusOxyrhopus petolarius

Siphlophis longicaudatusSiphlophis pulcher

Siphlophis compressusSiphlophis cervinus

Hydrodynastes gigasHydrodynastes bicinctus

Caaeteboia amaraliXenopholis scalarisXenopholis undulatus

Tropidodryas striaticepsTropidodryas serra

Thamnodynastes rutilusThamnodynastes strigatus

Thamnodynastes hypoconiaThamnodynastes laneiThamnodynastes pallidusTomodon dorsatus

Ptychophis flavovirgatusTachymenis peruviana

Pseudotomodon trigonatusCalamodontophis paucidens

Gomesophis brasiliensisHelicops angulatus

Helicops gomesiHelicops carinicaudus

Helicops hagmanniHelicops infrataeniatus

Pseudoeryx plicatilisHydrops triangularis

Manolepis putnamiApostolepis cearensisApostolepis sanctaeritae

Apostolepis flavotorquataApostolepis albicollaris

Apostolepis dimidiataApostolepis assimilis

Elapomorphus quinquelineatusPhalotris mertensi

Phalotris lativittatusPhalotris nasutusPhalotris lemniscatusTaeniophallus affinisEchinanthera undulataEchinanthera melanostigma

Taeniophallus nicagusTaeniophallus brevirostris

Sordellina punctataPhilodryas patagoniensis

Philodryas agassiziiPhilodryas aestiva

Philodryas psammophideaPhilodryas mattogrossensis

Philodryas georgeboulengeriPhilodryas argentea

Philodryas olfersiiPhilodryas viridissima

Philodryas nattereriPhilodryas baroni

Erythrolamprus aesculapiiErythrolamprus mimus

Eryrthrolamprus typhlusEryrthrolamprus pygmaea

Eryrthrolamprus brevicepsEryrthrolamprus reginae

Eryrthrolamprus miliarisEryrthrolamprus juliae

Eryrthrolamprus epinephelusEryrthrolamprus poecilogyrusEryrthrolamprus ceii

Eryrthrolamprus almadensisEryrthrolamprus jaegeri

Eryrthrolamprus atraventerXenodon pulcherXenodon matogrossensisXenodon semicinctusXenodon guentheri

Xenodon nattereriXenodon histricus

Xenodon dorbignyiXenodon neuwiedii

Xenodon werneriXenodon merremi

Xenodon severusLygophis meridionalis

Lygophis flavifrenatusLygophis paucidens

Lygophis lineatusLygophis elegantissimus

Lygophis anomalusUromacer frenatusUromacer oxyrhynchusUromacer catesbyi

Schwartzophis funereumSchwartzophis polylepis

Schwartzophis callilaemumAntillophis parvifrons

Hypsirhynchus feroxDarlingtonia haetiana

Ialtris dorsalisAlsophis rufiventrisAlsophis antiguaeAlsophis rijgersmaei

Alsophis antillensisBorikenophis portoricensisHaitiophis anomalusCaraiba andreae

Cubophis vudiiCubophis cantherigerus

Magliophis exiguumArrhyton dolichura

Arrhyton tanyplectumArrhyton procerum

Arrhyton landoiArrhyton vittatum

Arrhyton supernumArrhyton taeniatum

Pseudalsophis elegansPseudalsophis biserialis

Psomophis jobertiPsomophis genimaculatus

Psomophis obtususCrisantophis nevermanni

Conophis lineatus

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



need for considering these clades as families, since thefamily Scincidae is clearly monophyletic, based on our re-sults and others (see above). Thus, their new taxonomychanges the long-standing definition of Scincidae un-necessarily (see [113]). Furthermore, these changes weredone without defining the full content (beyond a typegenus) of any of these families other than Scincidae (theformer Scincinae + Feylininae) and Acontiidae (the formerAcontiinae).Most importantly, the new taxonomy proposed by these

authors [112] is at odds with the phylogeny estimatedhere, with respect to the familial and subfamilial classifica-tion of >1000 skink species (Figures 6, 7, 8, 9, 10). For in-stance, Sphenomorphus stellatus is found in a stronglysupported clade containing Lygosoma (presumablyLygosomidae; Figure 10), which is separate from the otherclade (presumably Sphenomorphidae) containing theother sampled Sphenomorphus species (Figure 7; note thatthese Sphenomorphus species are divided among severalsubclades within this latter clade). An additional problemis that Egernia, Lygosoma, and Sphenomorphus are thetype genera of Egerniidae, Lygosomidae, and Sphenomor-phidae, but are paraphyletic as currently defined (Figures 7,8, 9, 10), leading to further uncertainty in the content anddefinition 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 ownsubfamily (Chioniniinae, Dasiinae, Mabuyinae, andTrachylepidinae). However, several other genera arestrongly placed in this group, such as Eumecia, Eutropis,Lankaskincus, and Ristella (Figure 9). These other ge-nera cannot be readily fit into these subfamilial groups(i.e. they are not the sister group of any genera in thosesubfamilies), and Trachylepis is paraphyletic with respectto Eumecia, Chioninia, and Mabuya (Figure 9). Also, wefind that Emoia is divided between clades containingLygosoma (Lygosomidae) and Eugongylus (Eugongylidae),and many of these relationships have strong support(Figure 10). Finally, Ateuchosaurus is apparently notaccounted for in their classification, and here is weaklyplaced as the sister-group to a clade comprising theirSphenomorphidae, Egerniidae, Mabuyidae, and Lygoso-midae (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 forfacilitating future taxonomic revisions and species de-scriptions. However, this classification seems likely toonly exacerbate existing taxonomic problems (e.g. pla-cing congeneric species in different families without re-vising the genus-level taxonomy). Here, we retain theprevious definition of Mabuya (restricted to the NewWorld clade; sensu [114]), and we support the traditional

definitions of Scincidae, Acontiinae, Scincinae (but in-cluding Feylininae), and Lygosominae (Figures 6, 7, 8, 9,10; note that we leave Ateuchosaurus as incertae sedis).The other taxonomic issues in Scincidae identified hereand elsewhere should be resolved in future studies. Ourphylogeny provides a framework in which these analysescan take place (i.e. identifying major subclades withinskinks), which we think may be more useful than a classi-fication 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 ourclassification (Acontiinae, Lygosominae, and Scincinae;Appendix I). We place 19 of the remaining genera intoone of the three subfamilies based on previous classifica-tions (e.g. [110]), with Ateuchosaurus as incertae sedis inScincidae. Below, we review the non-monophyletic generain our tree. Many of these problems have been reportedby previous authors [51,111,115-118], and for brevity wedo not distinguish between cases reported in previousstudies, and potentially new instances found here.Within Acontiinae, we find that the two genera are

both monophyletic (Figure 6). Within Scincinae, manygenera are now strongly monophyletic (thanks in part tothe dismantling of Eumeces; [49,50,119]), but some prob-lems remain (Figure 6). The genera Scincus and Scincopusare strongly supported as being nested inside of theremaining Eumeces. Among Malagasy scincines (see[49,120]), Pseudacontias is nested inside Madascincus,and the genera Androngo, Pygomeles, and Voeltzkowia areall nested in Amphiglossus (Figure 6).We also find numerous taxonomic problems within

lygosomines (Figures 7, 8, 9, 10). Species of Sphenomor-phus are widely dispersed among other lygosomine gen-era. The genus Tropidophorus is paraphyletic with respectto a clade containing many other genera (Figure 7). Thesampled species of Asymblepharus are only distantly re-lated to each other, including one species (A. sikimmensis)nested inside of Scincella (Figure 7). The genus Lipinia ispolyphyletic, with one species (L. vittigera) strongly placedas the sister taxon to Isopachys, and with two other species(L. pulchella and L. noctua) placed in a well-supportedclade 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, Gla-phyromorphus, Notoscincus, Ctenotus, and Lerista, andmost of the relevant nodes are strongly supported(Figure 8). The genera Coeranoscincus and Ophios-cincus are polyphyletic with respect to each other andto Saiphos and Coggeria (Figure 8). The genus Glaphy-romorphus is paraphyletic with respect to a clade ofEulamprus (Figure 8). The genus Egernia is paraphy-letic with respect to Bellatorias (which is paraphyletic


with respect to Egernia and Lissolepis) and Lissolepis,although many of the relevant nodes are not stronglysupported (Figure 9). The genera Cyclodomorphus andTiliqua 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 cladecontaining the other species (Figure 9). The latter clade isweakly supported as the sister group to a clade containingChioninia, Eumecia, and Mabuya. In Mabuya, a few spe-cies (M. altamazonica, M. bistriata, and M. nigropuncata)have unorthodox placements within a monophyleticMabuya, potentially due to uncertain taxonomic assign-ment of specimens by previous authors [51,122]. Thegenus Lygosoma is paraphyletic with respect to Lepido-thyris and Mochlus, and many of the relevant nodes arestrongly supported (Figure 10). Among New Caledonianskinks, the genus Lioscincus is polyphyletic with respectto Marmorosphax, Celatiscincus, and Tropidoscincus,and both Lioscincus and Tropidoscincus are paraphyleticwith respect to, Kanakysaurus, Lacertoides, Phoboscincus,Sigaloseps, Tropidoscincus, Graciliscincus, Simiscincus, andCaledoniscincus, with strong support for most relevantnodes (Figure 10). The genera Emoia and Bassiana aremassively polyphyletic and divided across multiplelygosomine clades (Figure 10). The genus Lygisaurus ap-pears to be nested inside of Carlia, although many of therelevant branches are only weakly supported (Figure 10).

LacertoideaWithin Lacertoidea (Figure 1), we corroborate recentmolecular analyses (e.g. [16,17,19,20]) and morphology-based phylogenies and classifications (e.g. [13,15]) insupporting the clade including the New World familiesGymnophthalmidae and Teiidae (Figure 11). Within aweakly supported Teiidae (Figure 11), the subfamiliesTupinambinae and Teiinae are each strongly supportedas monophyletic, as in previous studies [61]. In Tupi-nambinae, Callopistes is the sister group to a cladecontaining Tupinambis, Dracaena, and Crocodilurus.The clade Dracaena + Crocodilurus is nested withinTupinambis, and the associated clades have strong sup-port (Figure 11). We find that the teiine genera Ameivaand Cnemidophorus are non-monophyletic (Figure 11),interdigitating with each other and the monophyleticgenera 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 morphologicalcharacters for 101 terminal species (with ~150 species inthe family [1]). Those authors erected several new gen-era and subfamilies in an attempt to deal with the appar-ent non-monophyly of currently recognized taxa in their

tree. However, in our tree, some of these new taxa conflictstrongly with the phylogeny or are rendered unnecessary.First, they recognize Callopistinae as a distinct subfamilyfor Callopistes, arguing that failure to do so wouldproduce a taxonomy inconsistent with teiid phylogeny.However, we find strong support for Callopistes in itstraditional 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 defini-tions [62]. In our tree, their conception of Ameiva is alsonon-monophyletic, with species found in three distinctclades (Figure 11). We also find non-monophyly of manyof their species groups within Ameiva, including theameiva, bifrontata, dorsalis, and erythrocephala groups(Figure 11). Their genera Aurivela (Cnemidophorus longi-caudus) and Contomastyx (Cnemidophorus lacertoides)are strongly supported as sister taxa in our tree, and arenested within Ameiva in their erythrocephala speciesgroup, 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 ourtree, including their Ameivula (Cnemidophorus ocellifer),Aspidoscelis (unchanged from previous definitions),Cnemidophorus (excluding C. ocellifer, C. lacertoides, andC. longicaudus), Holcosus (Ameiva undulata, A. festiva, andA. quadrilineatus), Kentropyx (unchanged from previousdefinitions), Salvator (Tupinambis rufescens, T. duseni, andT. merianae), and Teius (unchanged from previous defini-tions). We did not sample Ameiva edracantha (theirMedopheos).Given our results, major taxonomic rearrangements

within Teiidae seem problematic at present, especiallywith the extensive paraphyly of many traditional and re-defined teiid genera, the lack of strong resolution of manyof these relationships based on molecular and morpho-logical data, and incomplete taxon sampling in all studiesso far. Thus, we provisionally retain the traditional tax-onomy of Teiidae, pending additional data and analyses.However, we note that Ameiva, Cnemidophorus, andTupinambis are clearly non-monophyletic based on bothour results and those of recent authors [123], and will re-quire taxonomic changes in the future. We anticipate thatmany of these newly proposed genera [123] will be usefulin such revisions.We find strong support (SHL = 98) for monophyly of

Gymnophthalmidae (Figure 11). Within Gymnophthal-midae, we find strong support for the monophyly of thepreviously recognized subfamilies [63,64,124], with the ex-ception of Cercosaurinae (Figure 11). Previous researchersconsidered 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 dis-tantly related to other Cercosaurinae. Therefore, we re-strict Cercosaurinae to the tribe Cercosaurini, and elevatethe tribe Bachiini [64] to the subfamily level. The subfa-mily Bachiinae contains only the genus Bachia (Figure 11),identical in content to the previously recognized tribe[64]. Within Cercosaurinae, we find that the genusPetracola is nested within Proctoporus (Figure 11). InEcpleopinae, Leposoma is divided into two clades, sepa-rated by Anotosaura, Colobosauroides, and Arthrosaura(Figure 11), and many of the relevant nodes are verystrongly supported. These issues should be addressed infuture studies.Our results show strong support for a clade uniting

Lacertidae and Amphisbaenia (Figure 1), as in many previ-ous studies [16-20,23]. We also find strong support formonophyly of amphisbaenians (SHL = 99), in contrastto some molecular analyses [19,20]. Relationshipsamong amphisbaenian families are generally stronglysupported and similar to those in earlier molecularstudies (Figure 12), including the placement of the NewWorld family Rhineuridae as sister group to all otheramphisbaenians [70,71,125]. The family Cadeidae is placedas the sister-group to Amphisbaenidae + Trogonophiidae(Figures 1 and Figure 12) with weak support, but has beenplaced with Blanidae in previous studies, with strong sup-port but less- extensive taxon sampling [125,126].We find strong support for monophyly of the Old World

family Lacertidae (Figure 13). Within Lacertidae, branchsupport for the monophyly of most genera and for the sub-families Gallotiinae and Lacertinae is very high (Figure 13).However, we find that relationships among many generaare poorly supported, as in previous studies [65,67,68]. Ourresults (Figure 13) also indicate that several lacertid generaare non-monophyletic with strong support for the associ-ated nodes, including Algyroides (paraphyletic with respectto Dinarolacerta), Ichnotropis (paraphyletic with respect toMeroles), Meroles (paraphyletic with respect to Ichno-tropis), Nucras (polyphyletic with respect to several genera,including Pedioplanis, Poromera, Latastia, Philocortus,Pseuderemias, and Heliobolus), and Pedioplanis (paraphy-letic with respect to Nucras).

Higher-level phylogeny of ToxicoferaWe find strong support (SHL = 96) for monophyly ofToxicofera (Anguimorpha, Iguania, and Serpentes;Figure 1), and moderate support for a sister-group re-lationship between Iguania and Anguimorpha (SHL =79). Relationships among Anguimorpha, Iguania, andSerpentes were weakly supported in some Bayesianand likelihood analyses [16-19], but strongly sup-ported in others [20]. We further corroborate previ-ous studies in also placing Anguimorpha with Iguania[16-20]. In contrast, some other studies have placed

anguimorphs with snakes as the sister group toiguanians [127,128].

AnguimorphaOur hypothesis for family-level anguimorphan relation-ships (Figures 1, 14) is generally similar to that of otherrecent studies [17,19,20,129], and is strongly supported.Our results differ from some analyses based only onmorphology, which place Anguidae near the base ofAnguimorpha [130]. Here, Shinisauridae is stronglysupported as the sister taxon to a well-supportedclade of Varanidae + Lanthanotidae (Figures 1, 14).Varanid relationships are similar to previous estimates(e.g. [131]). Xenosauridae is here strongly supportedas the sister-group to a strongly supported cladecontaining Helodermatidae and the strongly supportedAnniellidae + Anguidae clade (Figures 1, 14). However,previous molecular analyses have placed Helodermatidaeas 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, includ-ing Diploglossinae (Diploglossus and Celestus are stronglysupported as paraphyletic with respect to each other andto Ophiodes), Anguinae (Ophisaurus is strongly supportedas paraphyletic with respect to Anguis, Dopasia, andPseudopus), and Gerrhonotinae (Abronia and Mesaspisare non-monophyletic, and Coloptychon is nested insideGerrhonotus). Some of these problems were not reportedpreviously (e.g. Coloptychon, Abronia, and Mesaspis), dueto incomplete taxon sampling in previous studies[129,132,133], but relationships within Gerrhonotinae areunder detailed investigation by other researchers, so theseissues are likely to be resolved in the near future.

IguaniaWe find strong support (SHL = 100) for the monophylyof Iguania (Figure 1). This clade is strongly supported bynuclear data [16,17,19,20], but an apparent episode ofconvergent molecular evolution in several mitochondrialgenes has seemingly misled some analyses of mtDNA,leading to weak support for Iguania [134], or even separ-ation of the acrodonts and pleurodonts [17,135] in previ-ous studies. Within Iguania (Figure 1), we find strongsupport (SHL = 100) for a sister-group relationship be-tween Chamaeleonidae and Agamidae (Acrodonta), andfor a clade of mostly New World families (Pleurodonta;SHL = 100).We find strong support for the monophyly of Cha-

maeleonidae and the subfamily Chamaeleoninae, andweak support for the paraphyly of Brookesiinae (Figures 1,15). The sampled species of the Brookesia nasus group ap-pear as the sister group to all other chamaeleonids (thelatter clade weakly supported) as found by some previous


authors [136], though other studies have recovereda monophyletic Brookesia [137,138]. Within Chamae-leoninae (Figure 15), we find strong support for the mono-phyly of most genera and species-level relationships.However, we find strong support for the non-monophylyof Calumma, with some species strongly placed withChamaeleo, others strongly placed with Rieppeleon, and athird set weakly placed with Nadzikambia + Rhampoleon.While non-monophly of Calumma has also been found inprevious studies [138], a recent study strongly supportsmonophyly of Brookesia and weakly supports monophylyof Calumma [139].Monophyly of Agamidae is strongly supported

(Figure 16; SHL = 100), contrary to some previous esti-mates [15,31]. Most relationships among agamid subfam-ilies and genera are strongly supported (Figure 16), andlargely congruent with earlier studies [17,29,34,140].There are some differences with earlier studies. For ex-ample, previous studies based on 29–44 loci [20,29,34]placed Hydrosaurinae as sister to Amphibolurinae +(Agaminae + Draconinae) with strong support, whereaswe place Hydrosaurinae as the sister-group to Amphibo-lurinae with weak support. Other authors [140] placedLeiolepiedinae with Uromastycinae, but we (and mostother studies) place Uromastycinae as the sister group toall other agamids.Our phylogeny indicates several taxonomic problems

within amphibolurine agamids (Figure 16). The generaMoloch and Chelosania render Hypsilurus paraphyletic,although the support for the relevant clades is weak.The species Lophognathus gilberti is placed in a stronglysupported clade with Chlamydosaurus and Amphibolurus,a clade that is not closely related to the otherLophognathus. Many of these taxonomic problems werealso noted by previous authors [141].Within agamine agamids (Figure 16), most relation-

ships are well supported and monophyly of all sam-pled genera is strongly supported. In contrast, withindraconine agamids (Figure 16), many intergeneric rela-tionships are weakly supported, and some genera arenon-monophyletic (Figure 16; see also [142]), includingGonocephalus (G. robinsonii is only distantly related toother Gonocephalus) and Japalura (with species distri-buted among three distantly related clades, includingone 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) isstrongly supported as monophyletic (Figure 16), andthis change is not necessitated by the phylogeny. Simi-larly, based on genetic and morphological data, recentauthors [144] suggested resurrecting the genus Saara for

the basal clade of Uromastyx (U. asmussi, U. hardwickii,and U. loricata). However, Uromastyx (as previously de-fined) is strongly supported as monophyletic in our results(Figure 16) and in those of the recent revision [144], andthis change is not needed. We therefore retain Laudakiaand Uromastyx as previously defined, to preserve taxo-nomic stability in these groups [113]. We note that recentstudies have also begun to revise species limits in othergroups such as Trapelus [145], and taxa such as T.pallidus (Figure 16) may represent populations withinother species.Within Pleurodonta we generally confirm the mono-

phyly and composition of the clades that were ranked asfamilies (or subfamilies) within the group (e.g. Phry-nosomatidae, Opluridae, Leiosauridae, Leiocephalidae, andCorytophanidae; Figures 1, 17, 18, 19) based on previousmolecular studies [31,33,34] and earlier morphologicalanalyses [146,147].One important exception is the previously recognized

Polychrotidae. Our results confirm that Anolis andPolychrus are not sister taxa (Figures 1, 18, 19), as alsofound in some previous molecular studies [31,33,34], butnot others [20,29]. Our results provide strong supportfor non-monophyly of Polychrotidae, placing Polychruswith Hoplocercidae (SHL = 99) and Anolis withCorytophanidae (SHL = 99; the latter also found by[34]). Recent analyses placing Anolis with Polychrusshowed only weak support for this relationship [20,29],despite many loci (30–44). We support continued rec-ognition of Dactyloidae for Anolis and Polychrotidaefor Polychrus [34], based on a limited number of locibut extensive taxon sampling. We note that these fa-milies are still monophlyetic, even if they prove to be sistertaxa.Interestingly, our results for relationships among pleu-

rodont families differ from most previous studies, and aresurprisingly well-supported in some cases by SHL values(but see below). In previous studies, many relationshipsamong pleurodont families were poorly supported byBayesian posterior probabilities and by parsimony andlikelihood bootstrap values, though typically samplingfewer taxa or characters [17,31,33,148-151]. Studies in-cluding 29 nuclear loci found strong concatenated Bayes-ian support for many relationships but weak support fromML bootstrap analyses for many of the same relationships[34]. The latter pattern (typically weak ML support) wasalso found in an analysis including those same 29 loci andmitochondrial data for >150 species [29]. We also find amixture of strongly and weakly supported clades, but withmany relationships that are incongruent with these previ-ous studies. First, we find that Tropiduridae is weakly sup-ported as the sister group to all other pleurodonts (alsofound by [29]), followed successively (Figures 1, 17, 18, 19)by Iguanidae, Leiocephalidae, Crotaphytidae + Phrynoso-


matidae, Polychrotidae + Hoplocercidae, and Coryto-phanidae + Dactyloidae.The relatively strong support for the clades

Crotaphytidae + Phrynosomatidae (SHL = 87), Poly-chrotidae + Hoplocercidae (SHL = 99), and Coryto-phanidae + Dactyloidae (SHL = 99) is largelyunprecedented in previous studies (although Coryto-phanidae + Dactyloidae is strongly supported in someBayesian analyses [34]). As in many previous analyses,deeper relationships among the families remain weaklysupported. We also find a strongly supported cladecontaining Liolaemidae, Opluridae, and Leiosauridae(SHL = 95), with Opluridae + Leiosauridae also stronglysupported (SHL = 99). Both clades have also been foundin previous studies [149,151], including studies based on29 or more nuclear loci [20,29,34].We note that previous studies have shown strong sup-

port for some pleurodont relationships (e.g. basal place-ment of phrynosomatids; see [34]), only to be stronglyoverturned with additional data [20,29]. Therefore, the re-lationships found here should be taken with some caution(even if strongly supported), with the possible exceptionof the recurring clade of Liolaemidae + (Opluridae +Leiosauridae).All pleurodont families are strongly supported as mono-

phyletic (SHL > 85). Within the pleurodont families, ourresults generally support the current generic-level ta-xonomy (Figures 17, 18, 19). However, there are some ex-ceptions. Within Tropiduridae (Figure 17), Tropidurus isparaphyletic with respect to Eurolophosaurus, Strobilurus,Uracentron, and Plica. Within Opluridae (Figure 18), themonotypic genus Chalarodon renders Oplurus para-phyletic. Two leiosaurid genera are also problematic(Figure 18). In Enyaliinae, Anisolepis is paraphyletic withrespect to Urostrophus, and this clade is nested withinEnyalius. In Leiosaurinae, Pristidactylus is rendered para-phyletic by Leiosaurus and Diplolaemus (Figure 18).Within Dactyloidae, a recent study re-introduced a

more subdivided classification of anoles [152], an issuethat has been debated extensively in the past [153-156].Our results support the monophyly of all the genera rec-ognized by recent authors [152], including Anolis,Audantia, Chamaelinorops, Dactyloa, Deiroptyx, Norops,and Xiphosurus (see Figure 19). However, since Anolis ismonophyletic as traditionally defined, we retain that def-inition here (including the seven listed genera) for con-tinuity with the recent literature [113,157].

SerpentesRelationships 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, Sco-lecophidia (Figures 1, 20) are not monophyletic, as inprevious studies [19,20,36,44,159,160]. Similar to some

previous studies [44,159], our data weakly place Ano-malepididae as the sister taxon to all snakes, and thescolecophidian families Gerrhopilidae, Leptotyphlopidae,Typhlopidae, and Xenotyphlopidae as the sister-group toall other snakes excluding Anomalepididae (Figures 1, 20).Previous studies have also placed Anomalepididaeas the sister-group to all non-scolecophidian snakes[19,20,35,36,158,160], in some cases with strong sup-port [20]. Although it might appear that recent ana-lyses of scolecophidian relationships [38] supportmonophyly of Scolecophidia (e.g. Figure 1 of [38]), thetree including non-snake outgroups from that studyshows weak support for placing anomalepidids withalethinophidians, as in other studies [19,20,36,160].We follow recent authors [38] in recognizing Xeno-

typhlopidae (strongly placed as the sister taxon ofTyphlopidae) and Gerrhopilidae (strongly placed as thesister group of Xenotyphlopidae + Typhlopidae) as dis-tinct families (Figure 20). Leptotyphlopidae is stronglysupported as the sister group of a clade compri-sing Gerrhopilidae, Xenotyphlopidae, and Typhlopidae(Figure 20). As in previous studies [38,44], we find strongsupport for non-monophyly of several typhlopid genera(Afrotyphlops, Austrotyphlops, Ramphotyphlops, Letheo-bia, and Typhlops; Figure 20). There are also undescribedtaxa (e.g. Typhlopidae sp. from Sri Lanka; [44]) of uncer-tain placement within this group (Figure 20). The syste-matics of typhlopoid snakes will thus require extensiverevision in the future, with additional taxon and charactersampling.Within Alethinophidia (SHL = 100), Aniliidae is

strongly supported (SHL = 98) as the sister taxon ofTropidophiidae (together comprising Anilioidea), and allother alethinophidians form a strongly supported sistergroup to this clade (SHL = 97; Figures 1, 21). The enig-matic family Xenophidiidae is weakly placed as the sister-group to all alethinophidians exclusive of Anilioidea(Figures 1, 21). The family Bolyeriidae is weakly placedas the sister-group to pythons, boas, and relatives(Booidea), which are strongly supported (SHL = 88). Re-lationships in this group are generally consistent withother recent molecular studies [20,35-37,47,159].Relationships among other alethinophidians are a mix-

ture of strongly and weakly supported nodes (Figures 1,21). We find strong support (SHL = 100) for a cladecontaining Anomochilidae + Cylindrophiidae + Uro-peltidae. This clade of three families is strongly supported(SHL = 89) as the sister taxon to Xenopeltidae +(Loxocemidae + Pythonidae). Together, these six familiesform a strongly supported clade (SHL = 89; Figures 1, 21)that is weakly supported as the sister group to the stronglysupported clade of Boidae + Calabariidae. Within theclade of Anomochilidae, Cylindrophiidae, and Uropeltidae(Figure 21), we weakly place Anomochilus as the sister


group to Cylindrophiidae [44], in contrast to previousstudies which placed Anomochilus within Cylindrophis[161]. However, support for monophyly of Cylindrophisexcluding Anomochilus is weak (Figure 21). As in previousstudies [44,162], we find several taxonomic problemswithin Uropeltidae (Figure 21). Specifically, Rhinophis andUropeltis are paraphyletic with respect to each other andto Pseudotyphlops. The problematic taxa are primarily SriLankan [44], and forthcoming analyses will address theseissues.Within Pythonidae (Figure 21), the genus Python is

the sister group to all other genera. Some species thatwere traditionally referred to as Python (P. reticulatusand P. timoriensis) are instead sister to an Australasianclade consisting of Antaresia, Apodora, Aspidites,Bothrochilus, Leiopython, Liasis, and Morelia (Figure 21).These taxa (P. reticulatus and P. timoriensis) have beenreferred to as Broghammerus, a name originating froman act of "taxonomic vandalism" (i.e. an apparentlyintentional attempt to disrupt stable taxonomy) in anon-peer reviewed organ without data or analyses[163,164]. However, this name was, perhaps inadvert-ently, subsequently used by researchers in peer-reviewedwork [165] and has entered into somewhat widespreadusage [1]. This name should be ignored and replacedwith a suitable substitute. Within the Australasian clade(Figure 21), Morelia is paraphyletic with respect to allother genera, and Liasis is non-monophyletic with re-spect to Apodora, although many of the relevant rela-tionships are weakly supported.Within Boidae (Figure 21), our results and those of

other recent studies [20,36,47,48,150,166] have con-verged on estimated relationships that are generallysimilar to each other but which differ from traditionaltaxonomy [167]. However, the classification has yet tobe modified to reflect this, and we rectify this situationhere. We find that Calabariidae is nested within Boidae[150], but this is poorly supported, and contrary to mostprevious studies [47,48]. While Calabaria has been clas-sified as an erycine boid in the past, this placement isstrongly rejected here and in other studies [47,48]. If thecurrent placement of Calabaria is supported in thefuture, it would require recognition as the subfamilyCalabariinae in Boidae.The Malagasy boine genera Acrantophis and Sanzinia

are placed as the sister taxa to a weakly-supported cladecontaining Calabariidae and a strongly supported clade(SHL = 99) comprising the currently recognized sub-families Erycinae, Ungaliophiinae, and other boines(Figure 21). Regardless of the position of Calabariidae,this placement of Malagasy boines renders Boinae para-phyletic. We therefore resurrect the subfamily San-ziniinae [168] for Acrantophis and Sanzinia. Thissubfamily could be recognized as a distinct family if

future studies also support placement of this clade asdistinct from other Boidae + Calabariidae.The genera Lichanura and Charina are currently clas-

sified as erycines [1], but are strongly supported as thesister group to Ungaliophiinae, as in previous studies[20,36,47,166]. We expand Ungaliophiinae to includethese two genera (Figure 21), rather than erect a newsubfamily for these taxa. The subfamily Ungaliophiinaeis placed as the sister group to a well-supported clade(SHL = 87) containing the rest of the traditionally recog-nized Erycinae and Boinae. We restrict Erycinae to theOld World genus Eryx.The genus Candoia (Boinae) from Oceania and New

Guinea [1], is placed as the sister taxon to a moderatelysupported clade (SHL = 83) consisting of Erycinae (Eryx)and the remaining genera of Boinae (Boa, Corallus,Epicrates, and Eunectes). To solve the non-monophyly ofBoinae with respect to Erycinae (due to Candoia), weplace Candoia in a new subfamily (Candoiinae, subfam.nov.; see Appendix I). Boinae then comprises the fourNeotropical genera that have traditionally been classifiedin this group (Boa, Corallus, Epicrates, and Eunectes).We acknowledge that non-monophyly of Boinae couldbe resolved in other ways (e.g. expanding it to includeErycinae). However, our taxonomy maintains the trad-itionally used subfamilies Boinae, Erycinae, and Ungalio-phiinae, modifies them to reflect the phylogeny, andrecognizes the phylogenetically distinct boine clades asseparate subfamilies (Candoiinae, Sanziniinae). WithinBoinae, Eunectes renders Epicrates paraphyletic, but thisis not strongly supported (see also [48]).Our results for advanced snakes (Caenophidia) are gen-

erally similar to those of other recent studies [41,42,169],and will only be briefly described. However, in contrast tomost recent studies [20,36,41,42,81,159,160], Acrochor-didae is here strongly placed (SHL = 95) as the sistergroup to Xenodermatidae. This clade is then the sistergroup to the remaining Colubroidea, which form astrongly supported clade (SHL = 100; Figures 1, 22). Thisrelationship has been found in some previous studies[169,170], and was hypothesized by early authors [171].Further evidence will be required to resolve this conclu-sively. Analyses based on concatenation of 20–44 loci donot support this grouping [20,36], though preliminaryspecies-tree analyses of >400 loci do (Pyron et al., inprep.). Relationships in Pareatidae are similar to recentstudies [172], and the group is strongly placed as the sistertaxon 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 inother recent studies. The family Viperidae is strongly sup-ported (Figure 22), as is the subfamily Viperinae, and thesister-group relationship between Azemiopinae and Cro-


talinae (SHL = 100). Our results generally supportthe existing generic-level taxonomy within Viperinae(Figure 22). However, we recover a strongly supportedclade within Viperinae consisting of Daboia russelii, D.palaestinae, Macrovipera mauritanica, and M. deserti(Figure 22), as in previous studies [173]. We corroborateprevious suggestions that these taxa be included in Daboia[174], though this has not been widely adopted [1]. Theother Macrovipera species (including the type species) re-main in that genus (Figure 22).Within Crotalinae (Figure 22), a number of genera ap-

pear to be non-monophyletic. The species Trimeresurusgracilis is strongly supported as the sister taxon to Ovophisokinavensis and distantly related to other Trimeresurus,whereas the other Ovophis are strongly placed as the sistergroup to Protobothrops. A well-supported clade (SHL = 90)containing Atropoides picadoi, Cerrophidion, and Por-thidium renders Atropoides paraphyletic (see also [175]).The species Bothrops pictus, considered incertae sedis inprevious studies [176], is here strongly supported as thesister taxon to a clade containing Rhinocerophis, Bothro-poides, Bothriopsis, and Bothrops (Figure 22). Most of theserelationships are strongly supported.Viperidae is strongly placed (SHL = 95) as the sister

taxon to a well-supported clade (SHL = 100) containingColubridae, Elapidae, Homalopsidae, and Lamprophiidae(Figure 1). Monophyly of Homalopsidae is also stronglysupported (Figure 23). Within Homalopsidae, non-monophyly of the genus Enhydris is strongly supported(Figure 23), and it should likely be split into multiplegenera. Homalopsidae is weakly supported (SHL = 58) asthe sister group of Elapidae + Lamprophiidae (Figure 1).This same relationship was also weakly supported by pre-vious analyses [41,44], but other studies have foundstrong support for placing Homalopsidae as the sistergroup of a strongly supported clade including Elapidae,Lamprophiidae, and Colubridae [20,36], including datafrom >400 loci (Pyron et al., in prep.).Support for the monophyly of Lamprophiidae is

strong (but excluding Micrelaps; see below), and mostof its subfamilies are well-supported [40,41,177,178]including Atractaspidinae, Aparallactinae, Lamprophiinae,Prosymninae (weakly placed as the sister-group toOxyrhabdium), Pseudaspidinae, Psammophiinae, andPseudoxyrhophiinae (Figure 23). In Lamprophiidae,most genera are monophyletic based on our sam-pling (Figure 23). However, within Aparallactinae,Xenocalamus is strongly placed within Amblyodipsas,and in Atractaspidinae, Homoroselaps is weaklyplaced in Atractaspis. In Lamprophiinae, Lamprophisis paraphyletic with respect to Lycodonomorphus butsupport for the relevant clades is weak.The enigmatic genera Buhoma from Africa and Psam-

modynastes from Asia were both previously considered

incertae sedis within Lamprophiidae [41]. Here they areweakly placed as sister taxa, and more importantly, theyform a strongly supported clade with the African genusPseudaspis (Pseudaspidinae; SHL = 95; Figure 23). There-fore, we expand Pseudaspidinae to include these twogenera.The genus Micrelaps (putatively an aparallactine; [1])

is weakly placed as the sister taxon to Lamprophiidae +Elapidae. Along with Oxyrhabdium (see above) andMontaspis [40], this genus is treated as incertae sedis inour classification (Appendix I). If future studies stronglysupport these relationships, they may require a new fam-ily for Micrelaps and possibly a new subfamily forOxyrhabdium, though placement of these taxa has beenhighly variable in previous studies [40,41,44,81].Monophyly of Elapidae is strongly supported (Figure 24),

and Calliophis melanurus is strongly supported as the sis-ter group to all other elapids (see also [44]). WithinElapidae (Figure 24), relationships are generally concord-ant with previous taxonomy, with some exceptions. Thegenera Toxicocalamus, Simoselaps, and Echiopsis are alldivided across multiple clades, with strong support formany of the relevant branches. A recent study [46] hasprovided a generic re-classification of the sea snakes(Hydrophis group) to resolve the extensive paraphyly ofgenera found in previous studies (e.g. [179,180]). Our re-sults 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 thesesubfamilies are weakly supported (Figure 1), as in mostprevious studies [41,43,45,181]. The subfamilies Calama-riinae and Pseudoxenodontinae are strongly supportedas sister taxa, and weakly placed as the sister-group tothe rest of Colubridae (Figure 25). There is a weaklysupported clade (Figure 1) comprising Natricinae +(Dipsadinae + Thermophis), but the clade uniting the NewWorld Dipsadinae with the Asian genus Thermophis isstrongly supported (SHL = 100; Figure 28). Here, we placeThermophis (recently in Pseudoxenodontinae [41]) inDipsadinae (following [182]), making it the first and onlyAsian member of this otherwise exclusively New Worldsubfamily. However, despite the strong support for itsplacement here, placement of this taxon has been variablein previous analyses [41,182,183], and we acknowledgethat future analyses may support recognition of a distinctsubfamily (Thermophiinae).The clade of Natricinae and Dipsadinae is weakly sup-

ported as the sister group (Figures 1, 25, 26, 27, 28) to aclade containing Sibynophiinae [181] + (Colubrinae +Grayiinae). The subfamily Colubrinae is weakly sup-ported; we find that the colubrine genera Ahaetulla,Chrysopelea, and Dendrelaphis form a strongly sup-ported clade that is weakly placed as the sister group to


the rest of Colubrinae, which form a strongly supportedclade (Figure 25). This clade was also placed withGrayiinae or Sibynophiinae in many preliminary ana-lyses, rendering Colubrinae paraphyletic. This group ofthree genera has been strongly supported in the past,and only weakly placed with Colubrinae [41,44]. It ispossible that future analyses will reveal that the clade ofAhaetulla, Chrysopelea, and Dendrelaphis is placed else-where in Colubridae with strong support, and thus meritrecognition as a distinct subfamily (Ahaetuliinae). A not-able feature of this clade is the presence of gliding flightin most species of Chrysopelea, less-developed non-flight jumping with similar locomotor origins inDendrelaphis, and homologous glide-related traits inAhaetulla [184].Numerous colubroid genera are not included in our

tree and are not clearly placed in subfamilies based onprevious morphological evidence. In our classification,these genera are also considered incertae sedis withinColubridae, including Blythia, Cyclocorus, Elapoidis,Gongylosoma, Helophis, Myersophis, Oreocalamus, Poeci-lopholis, Rhabdops, and Tetralepis, as in previous classi-fications [1].Our phylogeny reveals numerous taxonomic problems

within Colubrinae (Figures 25, 26). The genus Boiga isparaphyletic with respect to Crotaphopeltis, Dipsadoboa,Telescopus, Toxicodryas, and Dasypeltis, with strongsupport (Figure 25). The genus Philothamnus is para-phyletic with respect to Hapsidophrys (Figure 25). Thegenus Coluber is split between Old World and NewWorld clades (Figures 25, 26). The species Hierophisspinalis is sister to Eirenis to the exclusion of the otherHierophis species (Figure 25). The genus Dryocalamus isnested within Lycodon (Figure 26). The species Chironiuscarinatus and C. quadricarinatus are weakly placed in aclade of Neotropical colubrines only distantly relatedto the other Chironius species (Figure 26). The ge-nus Drymobius renders Dendrophidion paraphyletic(Figure 26). The monotypic genus Rhynchophis rendersthe 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 generaAmphiesma, Atretium, and Xenocrophis. Among NewWorld genera, we find Regina to be non-monophyleticwith respect to most other genera, as in previous phylo-genetic studies (e.g. [41,186]). Also, as in previous studies(e.g. [41,187]), we find that Adelophis [188] is nested deepwithin 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 prob-lems of non-monophyly include Leptodeira (with respectto Imantodes), Geophis (with respect to Atractus),Atractus (with respect to Geophis), Sibynomorphus (withrespect to Dipsas), Dipsas (with respect to Sibynomor-phus), Taeniophallus (with respect to Echinanthera), andEchinanthera (with respect to Taeniophallus). Recent revi-sions have begun to tackle these problems [42,43,190], butadditional taxon and character sampling will be crucial toresolve relationships and taxonomy.

DiscussionIn this study, we provide a phylogenetic estimate for4161 species of squamates based on molecular data fromup to 12 genes per species, combining much of the re-levant data used in previous molecular phylogeneticanalyses. This tree provides a framework for future evo-lutionary studies, spanning from the species level to rela-tionships among families, utilizing a common set ofbranch lengths. These estimated branch lengths are crit-ically important for most phylogenetic comparativemethods. To further facilitate use of this phylogeny incomparative studies, we provide the Newick version ofthis tree (with estimated branch lengths) in DataDryadrepository 10.5061/dryad.82h0m and Additional file 1:Data File S1. Our results also suggest that the branchlengths in this tree should not generally be compromisedby missing data for some genes in some taxa.Our results also reveal many problems in squamate

classification at nearly all phylogenetic levels. We makeseveral changes to higher-level taxonomy based on thisphylogeny, including changes to the traditionally re-cognized subfamilies of boid snakes (i.e. resurrectingSanziniinae for the boine genera Acrantophis andSanzinia, erecting Candoiinae for the boine genusCandoia, and moving Lichanura and Charina fromErycinae to Ungaliophiinae), lamprophiid snakes (expan-sion of Pseudaspidinae to include the formerly incertaesedis genera Buhoma and Psammodynastes), colubridsnakes (expansion of Dipsadinae to include the Asianpseudoxenodontine genus Thermophis), and gymno-phthalmid lizards (recognition of Bachiinae for the tribeBachiini, containing Bachia) and scincid lizards (synony-mizing Feylininae with Scincinae to yield a total of threescincid subfamilies: Acontiinae, Lygosominae, andScincinae). In Appendix I, we list the generic content ofall families and subfamilies. We also find dozens of prob-lems at the genus level, many of which have been identi-fied previously, and which we defer the resolution of tofuture studies. Our results also highlight potential prob-lems in recent proposals to modify the classification ofscincid [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 detailevery deviation from previous phylogenetic hypotheses(especially pre-molecular studies). Nevertheless, wefocus on three sets of examples. First, we find some rela-tively novel, strongly-supported relationships at the fam-ily level. These include the placement of Helodermatidae(as sister to Xenosauridae, Anguidae, and Anniellidae)and the placement of Xenodermatidae as the sister taxonto Acrochordidae (rendering Colubroidea paraphyletic),in contrast to most recent analyses of anguimorphs andsnakes (see above). We also find some novel, stronglysupported relationships among pleurodont families, butwe acknowledge that these may be overturned in futurestudies.The second example is the higher-level relationships

within Scincidae, the largest family of lizards [1]. Noprevious studies examining higher-level relationshipswithin 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 aunique resolution of higher-level skink relationships.Some previous researchers [51] placed acontiines as thesister group to all other skinks, but suggested thatscincines and lygosomines were paraphyletic with respectto each other (with feyliniines placed with scincines). Incontrast, others [50] suggested that acontiines, feyliniines,and lygosomines were all nested inside scincines (but witheach of those three subfamilies as monophyletic), althoughmany clades were only weakly supported. Here (Figures 1,6, 7, 8, 9, 10), we find that acontiines are the sister groupto a strongly supported clade consisting of a monophyleticScincinae and a monophyletic Lygosominae (exceptingthe weakly supported placement of Ateuchosaurus andplacement of Feyliniinae in Scincinae).Third, our phylogeny reveals numerous genera that ap-

pear to be non-monophyletic, with many of these caseshaving strong support for the associated nodes. Our exam-ples include genera in many families, including dibamids,diplodactylids, gekkonids, phyllodactylids, gerrhosaurids,scincids, teiids, gymnophthalmids, lacertids, anguids, cha-maeleonids, agamids, tropidurids, oplurids, leiosaurids,typhlopids, pythonids, uropeltids, boids, viperids, lam-prophiids, elapids, and colubrids (see Results). Althoughmany problems noted here were found in previous studies,some seem to be new, such as placement of Crocodilurusand 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 samplingstrategy than that used in most previous analyses. Squa-mates 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 bynearly all phylogenetic analyses based on morphologicaldata [13-15,19,22,95,191]. In contrast, our results andthose of most previous molecular analyses strongly sup-port 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 withdifferent 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]. Ouranalyses do not support such a clade (Figure 1), nor doother analyses of molecular data alone [17-20], or ana-lyses of combined molecular and morphological data[19]. Instead, these morphological results seem to beexplained by convergence associated with burrowing(e.g. [19]). Overall, molecular datasets have shown over-whelmingly strong support for placement of dibamidsand gekkonids at the base of the tree, amphisbaenianswith lacertoids, and iguanians with snakes and angui-morphs [17-20,23]. These results have now been corro-borated 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 basictopology with 4161 species sampled for up to 12 geneseach (up to 12896 bp).Nevertheless, despite the overall strong support for most

of the tree (i.e. 70% of all nodes have SHL > 85), certainclades remain poorly supported (e.g. relationships amongmany pleurodont iguanian families; Figures 1, 17, 18, 19).A potential criticism of the supermatrix approach usedhere is that this weak support may occur due to missingdata. However, previous studies of 8 datasets have shownexplicitly that there is typically little relationship betweenbranch support for terminal taxa and the amount of miss-ing data [85]. Instead, these patterns of weak support aremore likely to reflect short underlying branch lengths[20,36,41], and may be difficult to resolve even with morecomplete taxonomic and genomic sampling. Indeed, asnoted above, many of the weakly supported nodes in ourphylogeny are also weakly supported in analyses with littlemissing data (<20%) and large numbers of genes (e.g. 44genes as in [20]), such as the relationships of manypleurodont lizard families and colubroid snake familiesand subfamilies.We acknowledge that the differences between our re-

sults and previous studies (noted above) do not necessarilymean that our results are right and those of previous stud-ies are wrong. In some cases, we provide strong supportfor novel relationships when previous, conflicting studiesshowed only weak support (as in scincids, see above). In


other cases, our results disagree with other studies forclades that were strongly supported (e.g. placement ofxenodermatids). In the best-case scenario, these conflictsmay be resolved because our results are correct, possiblyreflecting the beneficial effects of adding taxa and theassociated subdivision of long branches [25,26,28,87,192-194]. Furthermore, in many cases, we are includingmore genes than used in previous studies of particularclades, increasing sampling of characters and loci. Thisshould generally reduce spurious results caused by sam-pling few characters and by incongruence between geneand species trees.However, other explanations for incongruence between

our results and previous studies are also possible.Adding taxa can potentially lead to incorrect results insome cases (e.g. [195]), such as when a long terminalbranch is added that further subdivides a short internalbranch. In other cases, conflicts with our results mightreflect the impact of our sampling fewer nuclear genesand a correspondingly increased influence of mitochon-drial data. Mitochondrial genes have relatively fast evo-lutionary rates (potentially exacerbating the impacts oflong branches), and their phylogenetic resolution for aparticular node may also reflect introgression or incom-plete lineage sorting rather than the species phylogeny(review in [196]). Many taxa in the matrix are repre-sented only by mitochondrial data, and highly variablemitochondrial genes might also overcome the influenceof less variable nuclear genes in combined analyses(although this scenario does not seem to be common[196]). Such cases might explain some strongly sup-ported conflicts between our results and those based onmultiple nuclear loci. Another possibility is that somecases may represent failure to find the optimal tree(although we assume that these cases will likely showonly weak support). We acknowledge that there aremany reasons why our results may differ from previousstudies, and the ultimate test of these novel findings willbe corroboration in future studies that include moretaxa and characters.This analysis also corroborates several recent studies

suggesting that the supermatrix approach is a powerfulstrategy for large-scale phylogenetic inference [41,72,73,75,76,197]. For example, even though each specieshad 81% missing data on average, we found that mostspecies were placed in the families and genera expectedbased on previous taxonomy, often with very strong sup-port. Furthermore, we found that incompleteness of ter-minal taxa is not related to branch lengths (at least notterminal branch lengths), suggesting that missing dataare not significantly biasing branch-length estimates (seealso [84,86,87]). Also, the ML models we used have beenshown to be robust to missing data in large, sparsesupermatrices [84].

Even though we did find some subfamilies and generato be non-monophyletic, similar relationships were oftenfound in previous studies based on data matrices withonly limited missing data (e.g. non-monophyly of boidsnake subfamilies [47], lacertid and scincid lizard genera[67,111], and scolecophidian, dipsadine, and natricinesnake genera [38,43,186]). We suggest that further reso-lution of the squamate tree will be greatly facilitated ifresearchers deliberately sample mitochondrial genes andnuclear genes that include the set of genes used hereand in recent phylogenomic studies (e.g. [20]), to in-crease overlap between genes and taxa, and decreasemissing data.With over 5000 species remaining to be included and

only 12 genes sampled, our study is far from the lastword on squamate phylogeny. We note that new datacan easily be added to this matrix, in terms of both newtaxa and new genes. Increased sampling of other nucleargenes is likely to be advantageous as well. Next-generationsequencing strategies and phylogenomic methods shouldhelp resolve difficult nodes [16,20,36,198-200], as shouldapplication of species-tree methods [201,202]. Species-treeanalyses of 44 nuclear loci support many of these sameclades across squamates [20], and data from >400 nuclearloci reinforces many of the relationships found hereamong the colubroid snake subfamilies (Pyron et al., inprep.). In addition, it would be useful to incorporate fossiltaxa in future studies [15,19,22,86], utilizing the large mor-phological datasets that are now available [14,15]. Despitethese areas for future studies, the present tree providesa framework for researchers analyzing patterns of squa-mate evolution at both lower and higher taxonomiclevels (e.g. [10,11,203,204]), and for building a morecomplete picture of squamate phylogeny.

ConclusionsIn this study, we provide a phylogenetic estimate for4161 squamate species, based on a supermatrix ap-proach. Our results provide important confirmation forprevious studies based on more limited taxon sampling,and reveal new relationships at the level of families, gen-era, and species. We also provide a phylogenetic frame-work for future comparative studies, with a large-scaletree including a common set of estimated branchlengths. Finally, we provide a revised classification forsquamates based on this tree, including changes in thehigher-level taxonomy of gymnophthalmid and scincidlizards and boid, colubrid, and lamprophiid snakes.

MethodsInitial classificationOur initial squamate classification is based on the June2009 version of the Reptile Database [1] (http://www.reptile-database.org/), accessed in September of 2009

http://www.reptile-database.org/



when this research was begun. Minor modifications tothis scheme were made, primarily to update changes incolubroid snake taxonomy [41-44,205]. This initial taxo-nomic database consists of 8650 species (169 amp-hisbaenians, 5270 lizards, 3209 snakes, and 2 tuataras),against which the classification of species in the molecularsequence database was fixed. While modifications and up-dates (i.e. new species, revisions) have been made to squa-mate taxonomy subsequently, these are minor and shouldhave no impact on our phylogenetic results. This databaserepresents ~92% of the current estimated diversity ofsquamates (~9400 species as of December 2012).Throughout the paper, we refer to the updated version

of squamate taxonomy from the December 2012 updateof the Reptile Database [1], incorporating major, well-accepted changes from recent studies (summarized in[1]). However, for large, taxonomic groups that have re-cently been broken up for reasons other than resolvingparaphyly or matters of priority (e.g. in dactyloid andscincid lizards; see Results), we generally retain the older,more inclusive name in the interest of clarity, while pro-viding references to the recent revision. We attempt toalter existing classifications as little as possible (see also[113]). Therefore, we generally only make changes whenthere is strong support for non-monophyly of currentlyrecognized taxa and our proposed changes yield stronglysupported monophyletic groups. Similarly, we only erectnew taxa if they are strongly supported. Finally, althoughnumerous genera are identified as being non-monophyleticin our tree, we refrain from changing genus-level tax-onomy, given that our taxon sampling within many generais limited.

Molecular dataPreliminary literature searches were conducted to iden-tify candidate genes for which a substantial number ofsquamate species were sequenced and available onGenBank (with the sampled species spread across mul-tiple families), and which were demonstrably useful inprevious phylogenetic studies of squamates (see Intro-duction for references). Twelve genes were identified asmeeting these criteria: seven nuclear genes (brain-derivedneurotrophic factor [BDNF], oocyte maturation factor[c-mos], neurotrophin-3 [NT3], phosducin [PDC], Gprotein-coupled receptor 35 [R35], and recombination-activating genes 1 [RAG-1] and 2 [RAG-2]); and fivemitochondrial genes (12S/16S long and short subunitRNAs, cytochrome b [cyt-b], and nicotinamide adeninedehydrogenase subunits 2 [ND2] and 4 [ND4]). Thissampling of genes does not include all available markers.For example, we omitted several nuclear and mitochon-drial genes because they were available only for a limitedsubset of taxa. We also excluded tRNAs associated with

the protein-coding sequences, given their short lengthsand difficulty in alignment across the large time scalesconsidered here.To ensure maximal taxonomic coverage from the avail-

able data, searches were conducted on GenBank by family(stopping in October 2012), and the longest sequence forevery species was gathered. Sequences totaling less than250 bp for any species were not included. Only species inthe taxonomic database were included in the sequencematrix, which resulted in the exclusion of numerousnamed taxa of ambiguous status, a few taxa described veryrecently, and many sequences labeled 'sp.' Some recentlydescribed phylogeographic lineages were also omitted.Species and GenBank accession numbers are available inAdditional file 2: Table S1.With respect to the December 2012 update of the

Reptile Database [1], we sampled 52 of 183 amphisbae-nian species (28%) from 11 of 19 (58%) genera; 2847 of5799 lizard species (49%) from 448 of 499 genera (90%);and 1262 of 3434 snake species (39%) in 396 of 500 gen-era (80%). This yielded a total of 4161 species in 855genera in the final matrix, 44% of the 9416 known, ex-tant squamate species in 84% of 1018 genera [1]. Thespecies-level classification of squamates is in constantflux, and the numbers of species and genera changedeven as this paper was under review. The extant speciesof tuatara (Sphenodon punctatus) was included as a non-squamate outgroup taxon (see below). We acknowledgethat our sampling of outgroup taxa is not extensive.However, placement of Sphenodon as the sister group tosquamates is well-established by molecular analyses withextensive taxon sampling (e.g. [16,128,206]) and mor-phological data (e.g. [13]).Alignment for protein-coding sequences was relatively

straightforward. We converted them to amino acids, andthen used the translation alignment algorithm in theprogram Geneious v4.8.4 (GeneMatters Corp.), with thedefault cost matrix (Blosum62) and gap penalties(open=12, extension=3). Alignments were relativelyunambiguous after being trimmed for quality and max-imum coverage (i.e. ambiguous end regions were re-moved, and most sequences began and ended at thesame point).For the ribosomal RNA sequences (12S and 16S se-

quences), alignment was more challenging. Preliminaryglobal alignments using the algorithms MUSCLE [207]and CLUSTAL [208] under a variety of gap-cost parame-ters yielded low-quality results (i.e. alignments with largenumbers of gaps and little overlap of potentially hom-ologous characters). We subsequently employed a two-step strategy for these data. We first grouped sequencesby higher taxa (i.e. Amphisbaenia, Anguimorpha, Gek-kota, Iguania, Scincomorpha, and Serpentes, thoughthese are not all monophyletic as previously defined), for


which alignments were relatively straightforward underthe default MUSCLE parameters.These were then combined using the profile alignment

feature of MUSCLE, and the global alignment was sub-sequently updated using the "refine alignment" option.Minor adjustments were then made by eye, and ambigu-ously aligned end-regions were trimmed for maximumcoverage and quality. We did not include partitions forstems and loops for the ribosomal sequences, althoughthis has been shown to improve model fit in previoussquamate studies (e.g. [82]). Although it is possible toassign individual nucleotide positions to these partitions,this would have been challenging given the large numberof sequences, and the potential for stems and loops toshift across the many species and large time scalesinvolved.Each species was represented by a single terminal

taxon in the matrix. In many cases, sequences from mul-tiple individuals of the same species were combined, toallow us to combine data from different genes for thesame species. We acknowledge the possibility that insome cases this approach may cause us to combinegenes from different species in the same terminal taxon(e.g. due to changing taxonomy or incorrect identifica-tions). Additionally, many sequences are not fromvouchered specimens, and it is possible that misidenti-fied species are present on GenBank and in our matrix.However, most of our data came from lower-level phylo-genetic studies, in which the identification of species byprevious authors should be highly accurate. In addition,any such mistakes should be among closely related spe-cies, and lead to minimal phylogenetic distortion, as thegrossest errors are easily identified.Some species were removed after preliminary analyses,

due either to obvious sequencing errors (e.g. highBLAST homology with unrelated families or non-squamates, excessive ambiguities) or a lack of overlap ingenes sampled with other members of the same genus(leading to seemingly artificial paraphyly). We also ex-cluded species with identical sequences between taxaacross all genes, arbitrarily choosing the first taxon in al-phabetical 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 suspectplacement (e.g. in a clearly incorrect family), and weretypically represented in the matrix by short fragments ofsingle genes (e.g. an ND4 fragment from the enigmaticcolubroid 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 forcyt-b (48%, 1000 bp), 437 for NT3 (10%, 675 bp), 1860for ND2 (45%, 960 bp), 1556 for ND4 (37%, 696 bp), 393

for PDC (9%, 395 bp), 401 for R35 (10%, 768 bp), 1379for RAG-1 (33%, 2700 bp), and 471 for RAG2 (11%, 720bp). The total alignment consists of 12896 bp for 4162taxa (4161 squamates and 1 outgroup). The mean lengthis 2497 bp of sequence data present per species from3.75 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 (seebelow) 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 suggestthat these missing data are not generally problematic.First, a large body of empirical and theoretical studieshas shown that highly incomplete taxa can be accuratelyplaced in model-based phylogenetic analyses (and withhigh levels of branch support), especially if a large num-ber of characters have been sampled (recent reviews in[84,85]). Second, several recent empirical studies haveshown that the supermatrix approach (with extensivemissing data in some taxa) yields generally well-supported large-scale trees that are generally congruentwith previous taxonomies and phylogenetic estimates(e.g. [41,48,72,73,75,76,197]). Third, recent studies havealso shown that there is generally little relationship be-tween the amount of missing data in individual taxa andthe support for their placement on the tree [41,73,85].Finally, we note that some highly incomplete taxa wereunstable in their placement (“rogue taxa;" [75]), butthese were removed prior to the analysis of the finalmatrix (see above).Our sampling design should be especially robust to

the impacts of missing data for several reasons. Mostimportantly, most terminal taxon (species) had substan-tial data present (mean of 2497 bp per species) regard-less of the number of missing data cells. Simulations (seereviews in [84,85]) suggest that the amount of datapresent is a key parameter in determining the accuracywith which incomplete taxa are placed in phylogenies,not the amount of data absent. Additionally, severalgenes (e.g. 12S/16S, cyt-b, and c-mos) were shared bymany (>40%) of taxa. Thus, there was typically extensiveoverlap among the genes present for each taxon (as alsoindicated by the mean bp per species being much greaterthan the length of most genes). Limited overlap in genesampling among taxa could be highly problematic, irre-spective of the amount of missing data per se, but thisdoes 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 representmost (>80%) squamate families and subfamilies (e.g. [20]),providing a scaffold of well-sampled taxa spanning allmajor clades, as recommended by recent authors [84].


Phylogenetic analysesWe performed phylogenetic analyses of the 12-geneconcatenated matrix using Maximum Likelihood (ML).We assessed node support using the non-parametricShimodaira-Hasegawa-Like (SHL) implementation of theapproximate likelihood-ratio test (aLRT; [94]). This in-volved a two-stage strategy. We first performed initialML tree- inference using the program RAxML-Lightv1.0.7 [209], a modification of the original RAxML algo-rithm [210]. This program uses the GTRCAT strategyfor all genes and partitions, a high-speed approximationof the GTR+Γ model (general time-reversible withgamma-distribution of rate heterogeneity among sites).The GTR model is the only substitution model imple-mented in RAxML [210], and all other substitution modelsare simply special cases of the GTR model [211]. Previousanalyses suggest that GTR is generally the best-fittingmodel for these genes and that they should be partitionedby 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 searchesfrom 11 parsimony starting trees generated under the de-fault parsimony model in RAxMLv7.2.8. This number islikely to be sufficient when datasets contain many charac-ters that have strong phylogenetic signal (A. Stamatakis,pers. comm.). Additionally, the dataset was analyzed withthese settings (GTRCAT search from a randomized parsi-mony starting tree) numerous times (>20) as the finalmatrix was assembled and tested, representing hundredsof independent searches from random starting points. Allof the estimated trees from these various analyses showedhigh overall congruence with the final topology. The con-cordance between the preliminary and final results sug-gests that the tree was not strongly impacted by searchesstuck on local optima, and that it should be a good ap-proximation of the ML tree.We then performed a final topology optimization and

assessed support. We passed our best ML estimate ofthe phylogeny (based on GTRCAT) from RAxML-Lightto RAxMLv7.2.8, which does an additional search (usingthe GTRGAMMA model) to produce a nearest-neighborinterchange (NNI)-optimized estimate of the ML tree.This optimization is needed to calculate the SHL versionof the aLRT for estimating support values [94]. The SHL-aLRT strategy approximates a test of the null hypothesisthat the branch length subtending each node equals 0(i.e. that the node can be resolved, rather than estimatedas a polytomy) with a test of the more general null hy-pothesis that "the branch is incorrect" relative to the fournext suboptimal arrangements of that node relative to theNNI-optimal arrangement [94]. Based on initial analyses,generating sufficient ML bootstrap replicates for a tree ofthis size proved computationally intractable, so we rely onSHL values alone to assess support.

The SHL approach has at least two major advantagesover non-parametric bootstrapping for large ML trees:(i) values are apparently robust to many potential modelviolations and have the same properties as bootstrapproportions for all but the shortest branches [41,94,212],and (ii) values for short branches may be more accuratethan bootstrap proportions, as support is evaluatedbased on whole-alignment likelihoods, rather than thefrequency of re-sampled characters [94,213]. Additio-nally, the SHL approach is orders of magnitude fasterthan traditional bootstrapping [94,212,213], and it ap-pears to be similarly robust to matrices with extensivemissing data [41]. As in previous studies, we take a con-servative view, considering SHL values of 85 or greater(i.e. a 15% chance that a branch is "incorrect") as strongsupport [41,212,213].These analyses were performed on a 360-core SGI ICE

supercomputing system ("ANDY") at the High Perform-ance Computing Center at the City University of NewYork (CUNY). The final analysis was completed in 8.8days of computer time using 188 nodes of the CUNYsupercomputing cluster.Finally, we assessed the potential impact of missing data

on our branch-length estimates. We performed linear re-gression (in R) of the proportional completeness of eachterminal taxa (non-missing data in bp / maximum amountof non-missing data, 12896 bp) against the length of itsterminal branch. This test addresses whether incompletetaxa have branch-length estimates that are consistentlybiased in one direction (shorter vs. longer) relative tomore complete terminals. However, it does not directlytest whether branch length estimates are correct or not,nor how branch length estimates are impacted by re-placing non-missing data with missing data (see [87] forresults suggesting that such replacements have little effectin real data sets).

Appendix INote that we only provide here an account for the onesubfamily newly erected in this study. We do not provideaccounts for subfamilies with changes in content (Boinae,Erycinae, Dipsadinae, Pseudaspidinae, Scincinae, Unga-liophiinae), that have been resurrrected (Sanziniinae), orthat represent elevation of lower-ranked taxa (tribe Bachi-ini 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, andall its descendants. These species are morphologically dis-tinguished in part from other boid snakes by a flattened


rostrum leading to an angular snout [215] and a wide pre-maxillary 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 sis-ter taxon to a moderately supported clade consisting ofErycinae + Boinae (SHL = 83).

Proposed Generic Composition of Higher TaxaBelow, we list the familial and subfamilial assignment ofall squamate genera from the December, 2012 update ofthe Reptile Database [1], updated to reflect some recentchanges and the proposed subfamily level changes listedabove. As this classification includes numerous taxa notsampled in our tree, we deal with them conservatively.For traditionally recognized families and subfamilies thatwe found to be monophyletic, we include all taxa trad-itionally assigned to them. Taxa are denoted incertaesedis if they are of ambiguous familial or subfamilial as-signment due to uncertain placement in our tree, or dueto absence from our tree and lack of assignment by pre-vious authors. This classification includes 67 families and56 subfamilies, and accounts for >9400 squamate species in1018 genera [1]. Higher taxa are listed (more-or-less)phylogenetically (starting closest to the root; Figure 1), fa-milies are listed alphabetically within higher taxa, and sub-families and genera are listed alphabetically within families.

SquamataDibamidae (Anelytropsis, Dibamus)

GekkotaCarphodactylidae (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 (Aelurosca-labotes, Coleonyx, Eublepharis, Goniurosaurus, Hemithe-conyx, Holodactylus); Gekkonidae (Afroedura, Afrogecko,Agamura, Ailuronyx, Alsophylax, Asiocolotes, Blaeso-dactylus, Bunopus, Calodactylodes, Chondrodactylus,Christinus, Cnemaspis, Colopus, Crossobamon, Cryptactites,Cyrtodactylus, Cyrtopodion, Dixonius, Ebenavia, Elasmo-dactylus, Geckolepis, Gehyra, Gekko, Goggia, Hemidactylus,Hemiphyllodactylus, Heteronotia, Homopholis, Lepidoda-ctylus, Luperosaurus, Lygodactylus, Matoatoa, Mediodac-tylus, Nactus, Narudasia, Pachydactylus, Paragehyra,

Paroedura, Perochirus, Phelsuma, Pseudoceramodactylus,Pseudogekko, Ptenopus, Ptychozoon, Rhinogecko, Rhoptro-pella, Rhoptropus, Stenodactylus, Tropiocolotes, Urocotyledon,Uroplatus); Phyllodactylidae (Asaccus, Gymnodactylus,Haemodracon, Homonota, Phyllodactylus, Phyllopezus,Ptyodactylus, Tarentola, Thecadactylus); Pygopodidae(Aprasia, Delma, Lialis, Ophidiocephalus, Paradelma, Ple-tholax, Pygopus); Sphaerodactylidae (Aristelliger, Chato-gekko, Coleodactylus, Euleptes, Gonatodes, Lepidoblepharis,Pristurus, Pseudogonatodes, Quedenfeldtia, Saurodactylus,Sphaerodactylus, Teratoscincus)

ScincoideaCordylidae, Cordylinae (Chamaesaura, Cordylus, Hemi-cordylus, Karusasaurus, Namazonurus, Ninurta, Ouro-borus, Pseudocordylus, Smaug), Platysaurinae (Platysaurus);Gerrhosauridae, Gerrhosaurinae (Cordylosaurus, Gerrho-saurus, Tetradactylus), Zonosaurinae (Tracheloptychus,Zonosaurus); Scincidae, Acontiinae (Acontias, Typhlosau-rus), Lygosominae (Ablepharus, Afroablepharus, Anomalo-pus, Asymblepharus, Ateuchosaurus, Bartleia, Bassiana,Bellatorias, Caledoniscincus, Calyptotis, Carlia, Cautula,Celatiscincus, Chioninia, Coeranoscincus, Coggeria, Cophos-cincopus, Corucia, Cryptoblepharus, Ctenotus, Cyclodomor-phus, Dasia, Egernia, Emoia, Eremiascincus, Eroticoscincus,Eugongylus, Eulamprus, Eumecia, Eutropis, Fojia, Geo-myersia, 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, Marmo-rosphax, Menetia, Mochlus, Morethia, Nangura, Nanno-scincus, Niveoscincus, Notoscincus, Oligosoma, Ophioscincus,Otosaurus, Panaspis, Papuascincus, Parvoscincus, Phobosci-ncus, Pinoyscincus, Prasinohaema, Proablepharus, Pseude-moia, Ristella, Saiphos, Saproscincus, Scincella, Sigaloseps,Simiscincus, Sphenomorphus, Tachygyia, Tiliqua, Trachy-lepis, Tribolonotus, Tropidophorus, Tropidoscincus, Tytthos-cincus, Vietnascincus), Scincinae (Amphiglossus, Androngo,Barkudia, Brachymeles, Chabanaudia, Chalcides, Chalci-doseps, Eumeces, Eurylepis, Feylinia, Gongylomorphus,Hakaria, Janetaescincus, Jarujinia, Madascincus, Melano-seps, Mesoscincus, Nessia, Ophiomorus, Pamelaescincus,Paracontias, Plestiodon, Proscelotes, Pseudoacontias, Pygo-meles, 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); Gymnoph-thalmidae, Alopoglossinae (Alopoglossus, Ptychoglossus),Bachiinae (Bachia), Cercosaurinae (Anadia, Cercosaura,Echinosaura, Euspondylus, Macropholidus, Neusticurus,Opipeuter, Petracola, Pholidobolus, Placosoma, Pota-mites, Proctoporus, Riama, Riolama, Teuchocercus), Ec-pleopinae (Adercosaurus, Amapasaurus, Anotosaura,Arthrosaura, Colobosauroides, Dryadosaura, Ecpleopus,Kaieteurosaurus, Leposoma, Marinussaurus, Pantepuisaurus),Gymnophthalminae (Acratosaura, Alexandresaurus, Calyp-tommatus, Caparaonia, Colobodactylus, Colobosaura,Gymnophthalmus, Heterodactylus, Iphisa, Micrablepharus,Nothobachia, Procellosaurinus, Psilophthalmus, Scripto-saura, Stenolepis, Tretioscincus, Vanzosaura), Rhachisau-rinae (Rhachisaurus); Lacertidae, Gallotiinae (Gallotia,Psammodromus), Lacertinae (Acanthodactylus, Adolfus,Algyroides, Anatololacerta, Apathya, Archaeolacerta,Atlantolacerta, Australolacerta, Congolacerta, Dalmato-lacerta, Darevskia, Dinarolacerta, Eremias, Gastropholis,Heliobolus, Hellenolacerta, Holaspis, Iberolacerta, Ichno-tropis, Iranolacerta, Lacerta, Latastia, Meroles, Mesalina,Nucras, Omanosaura, Ophisops, Parvilacerta, Pedioplanis,Philochortus, Phoenicolacerta, Podarcis, Poromera, Pseude-remias, Scelarcis, Takydromus, Teira, Timon, Tropidosaura,Zootoca); Rhineuridae (Rhineura); Teiidae, Teiinae(Ameiva, Aspidoscelis, Cnemidophorus, Dicrodon, Ken-tropyx, Teius), Tupinambinae (Callopistes, Crocodilurus,Dracaena, Tupinambis); Trogonophiidae (Agamodon,Diplometopon, Pachycalamus,Trogonophis)

IguaniaAgamidae, 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, Ca-lotes, Ceratophora, Complicitus, Cophotis, Coryphophylax,Dendragama, Draco, Gonocephalus, Harpesaurus, Hypsica-lotes, Japalura, Lophocalotes, Lyriocephalus, Mantheyus,Oriocalotes, Otocryptis, Phoxophrys, Psammophilus,Pseudocalotes, Pseudocophotis, Ptyctolaemus, Salea, Sitana,Thaumatorhynchus), Hydrosaurinae (Hydrosaurus), Leiole-pidinae (Leiolepis), Uromastycinae (Uromastyx); Cha-maeleonidae, Brookesiinae (Brookesia), Chamaeleoninae(Archaius, Bradypodion, Calumma, Chamaeleo, Furcifer,Kinyongia, Nadzikambia, Rhampholeon, Rieppeleon, Trioceros);Corytophanidae (Basiliscus, Corytophanes, Laemanctus);Crotaphytidae (Crotaphytus, Gambelia); Dactyloidae (Ano-lis); 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)

AnguimorphaAnguidae, Anguinae (Anguis, Dopasia, Ophisaurus,Pseudopus), Diploglossinae (Celestus, Diploglossus,Ophiodes), Gerrhonotinae (Abronia, Barisia, Colo-ptychon, Elgaria, Gerrhonotus, Mesaspis); Anniellidae(Anniella); Helodermatidae (Heloderma); Lanthano-tidae (Lanthanotus); Shinisauridae (Shinisaurus);Varanidae (Varanus); Xenosauridae (Xenosaurus)

SerpentesAcrochordidae (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); Calaba-riidae (Calabaria); Colubridae incertae sedis (Blythia,Cyclocorus, Elapoidis, Gongylosoma, Helophis, Myersophis,Oreocalamus, Poecilopholis, Rhabdops, Tetralepis),Calamariinae (Calamaria, Calamorhabdium, Collor-habdium, Etheridgeum, Macrocalamus, Pseudorabdion,Rabdion), Colubrinae (Aeluroglena, Ahaetulla, Apros-doketophis, Archelaphe, Argyrogena, Arizona, Bamanophis,Bogertophis, Boiga, Cemophora, Chilomeniscus, Chionactis,Chironius, Chrysopelea, Coelognathus, Coluber, Colubroe-laps, Conopsis, Coronella, Crotaphopeltis, Cyclophiops,Dasypeltis, Dendrelaphis, Dendrophidion, Dipsadoboa,Dispholidus, Dolichophis, Drymarchon, Drymobius, Drymo-luber, Dryocalamus, Dryophiops, Eirenis, Elachistodon,Elaphe, Euprepiophis, Ficimia, Geagras, Gonyophis, Gonyo-soma, Gyalopion, Hapsidophrys, Hemerophis, Hemorrhois,Hierophis, Lampropeltis, Leptodrymus, Leptophis, Leptu-rophis, Limnophis, Liopeltis, Lycodon, Lytorhynchus, Macro-protodon, Mastigodryas, Meizodon, Oligodon, Oocatochus,Opheodrys, Oreocryptophis, Orthriophis, Oxybelis, Panthe-rophis, Philothamnus, Phyllorhynchus, Pituophis, Platyceps,Pseudelaphe, Pseudoficimia, Pseustes, Ptyas, Rhadinophis,Rhamnophis, Rhinechis, Rhinobothryum, Rhinocheilus, Rhy-nchocalamus, Rhynchophis, Salvadora, Scaphiophis, Scole-cophis, Senticolis, Simophis, Sonora, Spalerosophis, Spilotes,Stegonotus, Stenorrhina, Symphimus, Sympholis, Tantilla,Tantillita, Telescopus, Thelotornis, Thrasops, Toxicodryas,Trimorphodon, Xenelaphis, Xyelodontophis, Zamenis),


Dipsadinae (Adelphicos, Alsophis, Amastridium, Amnes-teophis, Antillophis, Apostolepis, Arrhyton, Atractus, Boiru-na, Borikenophis, Caaeteboia, Calamodontophis, Caraiba,Carphophis, Cercophis, Chapinophis, Chersodromus, Clelia,Coniophanes, Conophis, Contia, Coronelaps, Crisantophis,Cryophis, Cubophis, Darlingtonia, Diadophis, Diaphoro-lepis, Dipsas, Ditaxodon, Drepanoides, Echinanthera,Elapomorphus, Emmochliophis, Enuliophis, Enulius, Eryth-rolamprus, Farancia, Geophis, Gomesophis, Haitiophis,Helicops, Heterodon, Hydrodynastes, Hydromorphus, Hy-drops, Hypsiglena, Hypsirhynchus, Ialtris, Imantodes, Lepto-deira, Lioheterophis, Lygophis, Magliophis, Manolepis,Mussurana, Ninia, Nothopsis, Ocyophis, Omoadiphas, Oxy-rhopus, Paraphimophis, Phalotris, Philodryas, Phimophis,Plesiodipsas, Pliocercus, Pseudalsophis, Pseudoboa, Pseu-doeryx, Pseudoleptodeira, Pseudotomodon, Psomophis, Pty-chophis, Rhachidelus, Rhadinaea, Rhadinella, Rhadinophanes,Rodriguesophis, Saphenophis, Schwartzophis, Sibon, Sibyno-morphus, Siphlophis, Sordellina, Synophis, Tachymenis,Taeniophallus, Tantalophis, Thamnodynastes, Thermophis,Tomodon, Tretanorhinus, Trimetopon, Tropidodipsas, Tropi-dodryas, 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, Opistho-tropis, Parahelicops, Pararhabdophis, Paratapinophis,Regina, Rhabdophis, Seminatrix, Sinonatrix, Storeria,Thamnophis, Trachischium, Tropidoclonion, Tropidonophis,Virginia, Xenochrophis), Pseudoxenodontinae (Plagiopholis,Pseudoxenodon), Sibynophiinae (Scaphiodontophis, Siby-nophis); Cylindrophiidae (Cylindrophis); Elapidae (Acan-thophis, Aipysurus, Aspidelaps, Aspidomorphus, Austrelaps,Bungarus, Cacophis, Calliophis, Cryptophis, Demansia,Dendroaspis, Denisonia, Drysdalia, Echiopsis, Elapo-gnathus, Elapsoidea, Emydocephalus, Ephalophis, Furina,Hemachatus, Hemiaspis, Hemibungarus, Hoplocephalus,Hydrelaps, Hydrophis, Kolpophis, Laticauda, Loveridgelaps,Maticora, Micropechis, Micruroides, Micrurus, Naja,Notechis, Ogmodon, Ophiophagus, Oxyuranus, Parahy-drophis, Parapistocalamus, Parasuta, Pseudechis, Pseu-dohaje, Pseudolaticauda, Pseudonaja, Rhinoplocephalus,Salomonelaps, Simoselaps, Sinomicrurus, Suta, Thalas-sophis, Toxicocalamus, Tropidechis, Vermicella, Walterin-nesia); Gerrhopilidae (Gerrhopilus); Homalopsidae (Bitia,Brachyorrhos, Cantoria, Cerberus, Djokoiskandarus,Enhydris, Erpeton, Fordonia, Gerarda, Heurnia, Homa-lopsis, Myron, Pseudoferania); Lamprophiidae incertaesedis (Micrelaps, Montaspis, Oxyrhabdium), Aparallactinae(Amblyodipsas, Aparallactus, Brachyophis, Chilorhinophis,Elapotinus, Hypoptophis, Macrelaps, Polemon, Xenocala-mus), Atractaspidinae (Atractaspis, Homoroselaps), Lam-prophiinae (Boaedon, Bothrophthalmus, Chamaelycus,

Dendrolycus, Gonionotophis, Hormonotus, Inyoka, Lam-prophis, Lycodonomorphus, Lycophidion, Pseudoboodon),Prosymninae (Prosymna), Psammophiinae (Dipsina, Hemi-rhagerrhis, Malpolon, Mimophis, Psammophis, Psam-mophylax, Rhagerhis, Rhamphiophis), Pseudaspidinae(Buhoma, Psammodynastes, Pseudaspis, Pythonodipsas),Pseudoxyrhophiine (Alluaudina, Amplorhinus, Bothrolycus,Brygophis, Compsophis, Ditypophis, Dromicodryas, Duber-ria, Exallodontophis, Heteroliodon, Ithycyphus, Langaha,Leioheterodon, Liophidium, Liopholidophis, Lycodryas,Madagascarophis, Micropisthodon, Pararhadinaea, Paras-tenophis, 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, Tropido-phis); Typhlopidae (Acutotyphlops, Afrotyphlops, Aus-trotyphlops, Cyclotyphlops, Grypotyphlops, Letheobia,Megatyphlops, Ramphotyphlops, Rhinotyphlops, Typhlops);Uropeltidae (Brachyophidium, Melanophidium, Platyp-lectrurus, Plectrurus, Pseudotyphlops, Rhinophis,Teretrurus,Uropeltis); Viperidae, Azemiopinae (Azemiops), Crotalinae(Agkistrodon, Atropoides, Bothriechis, Bothriopsis, Bothro-cophias, Bothropoides, Bothrops, Calloselasma, Cerrophi-dion, Crotalus, Deinagkistrodon, Garthius, Gloydius,Hypnale, Lachesis, Mixcoatlus, Ophryacus, Ovophis, Porthi-dium, Protobothrops, Rhinocerophis, Sistrurus, Trimere-surus, Tropidolaemus), Viperinae (Atheris, Bitis, Causus,Cerastes, Daboia, Echis, Eristicophis, Macrovipera, Monta-theris, Montivipera, Proatheris, Pseudocerastes, Vipera);Xenodermatidae (Achalinus, Fimbrios, Stoliczkia, Xeno-dermus, Xylophis); Xenopeltidae (Xenopeltis); Xeno-phidiidae (Xenophidion); Xenotyphlopidae (Xenotyphlops)

Additional files

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

Additional file 2: Table S1. GenBank accession numbers for all taxaincluded in this analysis.

Competing interestsThe authors declare that they have no competing interests.

Authors' contributionsRAP and JJW conceived the study. RAP, FTB, and JJW conducted analysesand checked results. RAP, FTB, and JJW wrote the MS. All authors read andapproved the final manuscript.

AcknowledgementsWe thank the many researchers who made this study possible through theirdetailed studies of squamate phylogeny with a (mostly) shared set ofmolecular markers, and uploading their sequence data to GenBank. Wethank E. Paradis, J. Lombardo T. Guiher, R. Walsh, and P. Muzio for

http://www.biomedcentral.com/content/supplementary/1471-2148-13-93-S1.txt

http://www.biomedcentral.com/content/supplementary/1471-2148-13-93-S2.docx


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 thismanuscript. The research was supported in part by the U.S. National ScienceFoundation, including a Bioinformatics Postdoctoral grant to R.A.P.(DBI-0905765), an AToL grant to J.J.W. (EF-0334923), and grants to theCUNY HPCC (CNS-0958379 and CNS-0855217).

Author details1Department of Biological Sciences, The George Washington University,2023 G St. NW, Washington, DC 20052, USA. 2Department of Biology, TheGraduate School and University Center, The City University of New York, 3655th Ave., New York, NY 10016, USA. 3Department of Biology, The College ofStaten Island, The City University of New York, 2800 Victory Blvd., StatenIsland, NY 10314, USA. 4Department of Ecology and Evolutionary Biology,University of Arizona, Tucson, AZ 85721-0088, USA.

Received: 30 January 2013 Accepted: 19 March 2013Published: 29 April 2013

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doi:10.1186/1471-2148-13-93Cite this article as: Pyron et al.: A phylogeny and revised classification ofSquamata, including 4161 species of lizardsand snakes. BMC Evolutionary Biology 2013 13:93.

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