BACKGROUND
squamate reptiles  are among the most diverse radiations of terrestrial vertebrates.
squamata includes more than  <dig> species as of december  <dig>  <cit> .
the rate of new species descriptions shows no signs of slowing, with a record  <dig> new species described in  <dig>  <cit> , greater than the highest yearly rates of the 18th and 19th centuries .
squamates are presently found on every continent except antarctica, and in the indian and pacific oceans, and span many diverse ecologies and body forms, from limbless burrowers to arboreal gliders .
squamates are key study organisms in numerous fields, from evolution, ecology, and behavior  <cit>  to medicine  <cit>  and applied physics  <cit> .
they have also been the focus of many pioneering studies using phylogenies to address questions about trait evolution .
phylogenies are now recognized as being integral to all comparative studies of squamate biology .
however, hypotheses about squamate phylogeny have changed radically in recent years  <cit> , especially when comparing trees generated from morphological  <cit>  and molecular data  <cit> .
furthermore, despite extensive work on squamate phylogeny at all taxonomic levels, a large-scale phylogeny  has never been attempted using morphological or molecular data.
squamate phylogenetics has changed radically in the last  <dig> years, revealing major conflicts between the results of morphological and molecular analyses  <cit> .
early estimates of squamate phylogeny  <cit>  and recent studies based on morphological data  <cit>  consistently supported a basal division between iguania , and scleroglossa, which comprises all other squamates .
within scleroglossa, many phylogenetic analyses of morphological data have also supported a clade containing limb-reduced taxa, including various combinations of snakes, dibamids, amphisbaenians, and  limb-reduced skinks and anguids  <cit> , though some of these authors also acknowledged that this clade was likely erroneous.
in contrast, recent molecular analyses have estimated very different relationships.
novel arrangements include placement of dibamids and gekkotans near the root of the squamate tree, a sister-group relationship between amphisbaenians and lacertids, and a clade  uniting iguania with snakes and anguimorphs within scleroglossa  <cit> .
these molecular results  suggest that some estimates of squamate phylogeny based on morphology may have been misled, especially by convergence associated with adaptations to burrowing  <cit> .
however, there have also been disagreements among molecular studies, such as placement of dibamids relative to gekkotans and other squamates, and relationships among snakes, iguanians, and anguimorphs .
analyses of higher-level squamate relationships based on molecular data have so far included relatively few  species, and none have included representatives from all described families and subfamilies  <cit> .
this limited taxon sampling makes existing molecular phylogenies difficult to use for broad-scale comparative studies, with some exceptions based on supertrees  <cit> .
in addition, limited taxon sampling is potentially a serious issue for phylogenetic accuracy  <cit> .
thus, an analysis with extensive taxon sampling is critically important to test hypotheses based on molecular datasets with more limited sampling, and to provide a framework for comparative analyses.
despite the lack of a large-scale phylogeny across squamates, recent molecular studies have produced phylogenetic estimates for many of the major groups of squamates, including iguanian lizards  <cit> , higher-level snake groups  <cit> , typhlopoid snakes  <cit> , colubroid snakes  <cit> , booid snakes  <cit> , scincid lizards  <cit> , gekkotan lizards  <cit> , teiioid lizards  <cit> , lacertid lizards  <cit> , and amphisbaenians  <cit> .
these studies have done an outstanding job of clarifying the phylogeny and taxonomy of these groups, but many were limited in some ways by the number of characters and taxa that they sampled .
here, we present a phylogenetic estimate for squamata based on combining much of the existing sequence data for squamate reptiles, using the increasingly well-established supermatrix approach  <cit> .
we present a new phylogenetic estimate including  <dig> squamate species.
the dataset includes up to  <dig> bp per species from  <dig> genes .
we include species from all currently described families and subfamilies.
in terms of species sampled, this is  <dig> times larger than any previous phylogeny for any one squamate group  <cit> ,  <dig> times larger than the largest supertree estimate  <cit> , and  <dig> times larger than the largest molecular study of higher-level squamate relationships  <cit> .
while we did not sequence any new taxa specifically for this project, much of the data in the combined matrix were generated in our labs or from our previous collaborative projects  <cit> , <cit> , including thousands of gene sequences from hundreds of species .
the supermatrix approach can provide a relatively comprehensive phylogeny, and uncover novel relationships not seen in any of the separate analyses in which the data were generated.
such novel relationships can be revealed via three primary mechanisms.
first, different studies may have each sampled different species from a given group for the same genes, and combining these data may reveal novel relationships not apparent in the separate analyses.
second, different studies may have used different genetic markers for the same taxa, and combining these markers can dramatically increase character sampling, potentially revealing new relationships and providing stronger support for previous hypotheses.
third, even for clades that were previously studied using complete taxon sampling and multiple loci, novel relationships may be revealed by including these lineages with other related groups in a large-scale phylogeny.
the estimated tree and branch-lengths should be useful for comparative studies of squamate biology.
however, this phylogeny is based on a supermatrix with extensive missing data .
some authors have suggested that matrices with missing cells may yield misleading estimates of topology, support, and branch lengths  <cit> .
nevertheless, most empirical and simulation studies have not found this to be the case, at least for topology and support  <cit> .
though fewer studies have examined the effects of missing data on branch lengths  <cit> , these also suggest that missing data do not strongly impact estimates.
here, we test whether branch lengths for terminal taxa are related to their completeness.
in general, our results corroborate those of many recent molecular studies with regard to higher-level relationships, species-level relationships, and the monophyly, composition, and relationships of most families, subfamilies, and genera.
however, our results differ from previous estimates for some groups, and reveal  numerous problems in the existing classification of squamates.
we therefore provide a conservative, updated classification of extant squamates at the family and subfamily level based on the new phylogeny, while highlighting problematic taxonomy at the genus level, without making changes.
the generic composition of all families and subfamilies under our revised taxonomy are provided in appendix i.
we note dozens of problems in the genus-level taxonomy suggested by our tree, but we acknowledge in advance that we do not provide a comprehensive review of the previous literature dealing with all these taxonomic issues .
similarly, we do not attempt to fix these genus-level problems here, as most will require more extensive taxon  sampling to adequately resolve.
throughout the paper, we address only extant squamates.
squamata also includes numerous extinct species classified in both extant and extinct families, subfamilies, and genera.
relationships and classification of extinct squamates based on morphological data from fossils have been addressed by numerous authors .
a classification based only on living taxa may create some problems for classifying fossil taxa, but these can be addressed in future studies that integrate molecular and fossil data  <cit> .
RESULTS
supermatrix phylogeny
we generated the final tree  using maximum likelihood  in raxmlv <dig> .
<dig>  support was assessed using the non-parametric shimodaira-hasegawa-like  implementation of the approximate likelihood-ratio test .
the tree and data matrix are available in nexus format in datadryad repository  <dig> /dryad.82h0m and as additional file 1: data file s <dig>  a skeletal representation of the tree  is shown in figure  <dig>  the full species-level phylogeny  is shown in figures  <dig>   <dig>   <dig>   <dig>   <dig>   <dig>   <dig>   <dig>   <dig>   <dig>   <dig>   <dig>   <dig>   <dig>   <dig>   <dig>   <dig>   <dig>   <dig>   <dig>   <dig>   <dig>   <dig>   <dig>   <dig>   <dig>   <dig>  the analysis yields a generally well-supported phylogenetic estimate for squamates .
there is no relationship between proportional completeness  and branch length  for terminal taxa, strongly suggesting that the estimated branch lengths are not consistently biased by missing data.
higher-level relationships
our tree  is broadly congruent with most previous molecular studies of higher-level squamate phylogeny using both nuclear data and combined nuclear and mitochondrial data , providing important confirmation of previous molecular studies based on more limited taxon sampling.
specifically we support :  the placement of dibamids and gekkotans near the base of the tree ;  a sister-group relationship between scincoidea  and a clade  containing the rest of the squamates excluding dibamids and gekkotans;  lacertoidea , and  a clade  containing anguimorphs , iguanians , and snakes  as the sister taxon to lacertoidea.
these relationships are strongly supported in general , but differ sharply from most trees based on morphological data  <cit> .
nevertheless, many clades found in previous morphological taxonomies and phylogenies are also present in this tree in some form, including amphisbaenia, anguimorpha, gekkota, iguania, lacertoidea , scincoidea, serpentes, and many families and subfamilies.
in contrast, the relationships among these groups differ strongly between molecular analyses  <cit>  and morphological analyses  <cit> .
our results demonstrate that this incongruence is not explained by limited taxon sampling in the molecular data sets.
in fact, our species-level sampling is far more extensive than in any morphological analyses , by an order of magnitude.
we find that the basal squamate relationships are strongly supported in our tree.
the family dibamidae is the sister group to all other squamates, and gekkota is the sister group to all squamates excluding dibamidae , as in some previous studies .
other recent molecular analyses have also placed dibamidae near the squamate root, but differed in placing it as either the sister taxon to all squamates excluding gekkota  <cit> , or the sister- group of gekkota  <cit> .
our results also corroborate that the new world genus anelytropsis is nested within the old world genus dibamus <cit> , but the associated branches are weakly supported .
gekkota
within gekkota, we corroborate both earlier morphological  <cit>  and recent molecular estimates  <cit>  in supporting a clade containing the australian radiation of "diplodactylid" geckos  and the snakelike pygopodids .
as in previous studies  <cit> , carphodactylidae is the weakly supported sister group to pygopodidae, and this clade is the sister group of diplodactylidae .
we recover clades within the former gekkonidae that correspond to the strongly supported families eublepharidae, sphaerodactylidae, phyllodactylidae, and gekkonidae as in previous studies, and similar relationships among these groups  <cit> .
within gekkota, we find evidence for non-monophyly of many genera.
many relationships among the new caledonian diplodactylids are weakly supported , and there is apparent non-monophyly of the genera rhacodactylus, bavayia, and eurydactylodes with respect to each other and oedodera, dierogekko, paniegekko, correlophus, and mniarogekko <cit> .
in the australian diplodactylids, strophurus taenicauda is strongly supported as belonging to a clade that is only distantly related to the other sampled strophurus species .
the two species of the north african sphaerodactylid genus saurodactylus are divided between the two major sphaerodactylid clades , but the associated branches are weakly supported.
the south american phyllodactylid genus homonota is strongly supported as being paraphyletic with respect to phyllodactylus .
a number of gekkonid genera  also appear to be non-monophyletic, including the asian genera cnemaspis , lepidodactylus , gekko , luperosaurus , mediodactylus , and bunopus , and the african afrogecko , afroedura , chondrodactylus , and pachydactylus .
many of these taxonomic problems in gekkotan families have been identified in previous studies , and extensive changes will likely be required to fix them.
scincoidea
we strongly support  the monophyly of scincoidea , as in other recent studies  <cit> .
all four families are strongly supported .
a similar clade is also recognized in morphological phylogenies  <cit> , though without xantusiidae in some  <cit> .
within the new world family xantusiidae, we corroborate previous analyses  <cit>  that found strong support for a sister-group relationship between xantusia and lepidophyma, excluding cricosaura .
these relationships support the subfamily cricosaurinae for cricosaura <cit> .
we also recognize xantusiinae for the north american genus xantusia and lepidophyminae for the central american genus lepidophyma <cit> .
within the african and madagascan family gerrhosauridae , the genus gerrhosaurus is weakly supported as being paraphyletic with respect to the clade comprising tetradactylus + cordylosaurus, with g. major placed as the sister group to all other gerrhosaurids.
within cordylidae , we use the generic taxonomy from a recent phylogenetic analysis and re-classification based on multiple nuclear and mitochondrial genes  <cit> .
this classification broke up the non-monophyletic cordylus <cit>  into several smaller genera, and we corroborate the non-monophyly of the former cordylus and support the monophyly of the newly recognized genera .
we support the distinctiveness of platysaurus  and recognition of the subfamily platysaurinae  <cit> .
we strong support  for the monophyly of scincidae  as in previous studies .
we strongly support the basal placement of the monophyletic subfamily acontiinae , as found in some previous studies  but not others .
similar to earlier studies, we find that the subfamily scincinae  is non-monophyletic, as feylininae is nested within scincinae .
based on these results, synonymizing feylininae with scincinae produces a monophyletic scincinae , which is then sister to a monophyletic lygosominae  with 94% shl support .
this yields a new classification in which all three subfamilies  are strongly supported.
importantly, these definitions approxi\mate the traditional content of the three subfamilies  <cit> , except for recognition of feylininae.
we note that a recent revision of the new world genus mabuya introduced a nontraditional family-level classification for scincidae  <cit> .
these authors divided scincidae into seven families: acontiidae, egerniidae, eugongylidae, lygosomidae, mabuyidae, scincidae and sphenomorphidae.
however, there was no phylogenetic need for considering these clades as families, since the family scincidae is clearly monophyletic, based on our results and others .
thus, their new taxonomy changes the long-standing definition of scincidae unnecessarily .
furthermore, these changes were done without defining the full content  of any of these families other than scincidae  and acontiidae .
most importantly, the new taxonomy proposed by these authors  <cit>  is at odds with the phylogeny estimated here, with respect to the familial and subfamilial classification of > <dig> skink species .
for instance, sphenomorphus stellatus is found in a strongly supported clade containing lygosoma , which is separate from the other clade  containing the other sampled sphenomorphus species .
an additional problem is that egernia, lygosoma, and sphenomorphus are the type genera of egerniidae, lygosomidae, and sphenomorphidae, but are paraphyletic as currently defined , leading to further uncertainty in the content and definition of these putative families.
furthermore, mabuyidae apparently refers to the clade  containing chioninia, dasia, mabuya, trachylepis, with each of these genera placed in its own subfamily .
however, several other genera are strongly placed in this group, such as eumecia, eutropis, lankaskincus, and ristella .
these other genera cannot be readily fit into these subfamilial groups , and trachylepis is paraphyletic with respect to eumecia, chioninia, and mabuya .
also, we find that emoia is divided between clades containing lygosoma  and eugongylus , and many of these relationships have strong support .
finally, ateuchosaurus is apparently not accounted for in their classification, and here is weakly placed as the sister-group to a clade comprising their sphenomorphidae, egerniidae, mabuyidae, and lygosomidae .
these authors  <cit>  argued that a more heavily subdivided classification for skinks may be desirable for facilitating future taxonomic revisions and species descriptions.
however, this classification seems likely to only exacerbate existing taxonomic problems .
here, we retain the previous definition of mabuya , and we support the traditional definitions of scincidae, acontiinae, scincinae , and lygosominae .
the other taxonomic issues in scincidae identified here and elsewhere should be resolved in future studies.
our phylogeny provides a framework in which these analyses can take place , which we think may be more useful than a classification lacking clear taxon definitions.
of the  <dig> scincid genera  <cit> , we can assign the  <dig> sampled in our tree to one of the three subfamilies in our classification .
we place  <dig> of the remaining genera into one of the three subfamilies based on previous classifications , with ateuchosaurus as incertae sedis in scincidae.
below, we review the non-monophyletic genera in our tree.
many of these problems have been reported by previous authors  <cit> , and for brevity we do not distinguish between cases reported in previous studies, and potentially new instances found here.
within acontiinae, we find that the two genera are both monophyletic .
within scincinae, many genera are now strongly monophyletic , but some problems remain .
the genera scincus and scincopus are strongly supported as being nested inside of the remaining eumeces.
among malagasy scincines , pseudacontias is nested inside madascincus, and the genera androngo, pygomeles, and voeltzkowia are all nested in amphiglossus .
we also find numerous taxonomic problems within lygosomines .
species of sphenomorphus are widely dispersed among other lygosomine genera.
the genus tropidophorus is paraphyletic with respect to a clade containing many other genera .
the sampled species of asymblepharus are only distantly related to each other, including one species  nested inside of scincella .
the genus lipinia is polyphyletic, with one species  strongly placed as the sister taxon to isopachys, and with two other species  placed in a well-supported clade that also includes papuascincus .
among australian skinks, the genus eulamprus is polyphyletic with respect to nangura, calyptotis, gnypetoscincus, coggeria, coeranoscincus, ophioscincus, saiphos, anomalopus, eremiascincus, hemiergis, glaphyromorphus, notoscincus, ctenotus, and lerista, and most of the relevant nodes are strongly supported .
the genera coeranoscincus and ophioscincus are polyphyletic with respect to each other and to saiphos and coggeria .
the genus glaphyromorphus is paraphyletic with respect to a clade of eulamprus .
the genus egernia is paraphyletic with respect to bellatorias  and lissolepis, although many of the relevant nodes are not strongly supported .
the genera cyclodomorphus and tiliqua are paraphyletic with respect to each other .
among other lygosomines, trachylepis is non-monophyletic  <cit> , with two species  that fall outside the strongly supported clade containing the other species .
the latter clade is weakly supported as the sister group to a clade containing chioninia, eumecia, and mabuya.
in mabuya, a few species  have unorthodox placements within a monophyletic mabuya, potentially due to uncertain taxonomic assignment of specimens by previous authors  <cit> .
the genus lygosoma is paraphyletic with respect to lepidothyris and mochlus, and many of the relevant nodes are strongly supported .
among new caledonian skinks, the genus lioscincus is polyphyletic with respect to marmorosphax, celatiscincus, and tropidoscincus, and both lioscincus and tropidoscincus are paraphyletic with respect to, kanakysaurus, lacertoides, phoboscincus, sigaloseps, tropidoscincus, graciliscincus, simiscincus, and caledoniscincus, with strong support for most relevant nodes .
the genera emoia and bassiana are massively polyphyletic and divided across multiple lygosomine clades .
the genus lygisaurus appears to be nested inside of carlia, although many of the relevant branches are only weakly supported .
lacertoidea
within lacertoidea , we corroborate recent molecular analyses  and morphology-based phylogenies and classifications  in supporting the clade including the new world families gymnophthalmidae and teiidae .
within a weakly supported teiidae , the subfamilies tupinambinae and teiinae are each strongly supported as monophyletic, as in previous studies  <cit> .
in tupinambinae, callopistes is the sister group to a clade containing tupinambis, dracaena, and crocodilurus.
the clade dracaena + crocodilurus is nested within tupinambis, and the associated clades have strong support .
we find that the teiine genera ameiva and cnemidophorus are non-monophyletic , interdigitating with each other and the monophyletic genera aspidoscelis, dicrodon , and kentropyx, as in previous phylogenies  <cit> .
a recent study  <cit>  proposed a re-classification of the family teiidae based on analysis of  <dig> morphological characters for  <dig> terminal species .
those authors erected several new genera and subfamilies in an attempt to deal with the apparent non-monophyly of currently recognized taxa in their tree.
however, in our tree, some of these new taxa conflict strongly with the phylogeny or are rendered unnecessary.
first, they recognize callopistinae as a distinct subfamily for callopistes, arguing that failure to do so would produce a taxonomy inconsistent with teiid phylogeny.
however, we find strong support for callopistes in its traditional placement as part of tupinambinae , and this change is thus not needed based on our results.
the genus ameiva is paraphyletic under traditional definitions  <cit> .
in our tree, their conception of ameiva is also non-monophyletic, with species found in three distinct clades .
we also find non-monophyly of many of their species groups within ameiva, including the ameiva, bifrontata, dorsalis, and erythrocephala groups .
their genera aurivela  and contomastyx  are strongly supported as sister taxa in our tree, and are nested within ameiva in their erythrocephala species group, along with dicrodon .
on the positive side, many of the genera they recognize are monophyletic and are not nested in other genera in our tree, including their ameivula , aspidoscelis , cnemidophorus , holcosus , kentropyx , salvator , and teius .
we did not sample ameiva edracantha .
given our results, major taxonomic rearrangements within teiidae seem problematic at present, especially with the extensive paraphyly of many traditional and re-defined teiid genera, the lack of strong resolution of many of these relationships based on molecular and morphological data, and incomplete taxon sampling in all studies so far.
thus, we provisionally retain the traditional taxonomy of teiidae, pending additional data and analyses.
however, we note that ameiva, cnemidophorus, and tupinambis are clearly non-monophyletic based on both our results and those of recent authors  <cit> , and will require taxonomic changes in the future.
we anticipate that many of these newly proposed genera  <cit>  will be useful in such revisions.
we find strong support  for monophyly of gymnophthalmidae .
within gymnophthalmidae, we find strong support for the monophyly of the previously recognized subfamilies  <cit> , with the exception of cercosaurinae .
previous researchers considered the genus bachia a distinct tribe  within cercosaurinae, based on a poorly supported sister-group relationship with the tribe cercosaurini  <cit> .
here, we find a moderately well supported relationship  between bachia and gymnophthalminae + rhachisaurinae, and we find that this clade is only distantly related to other cercosaurinae.
therefore, we restrict cercosaurinae to the tribe cercosaurini, and elevate the tribe bachiini  <cit>  to the subfamily level.
the subfamily bachiinae contains only the genus bachia , identical in content to the previously recognized tribe  <cit> .
within cercosaurinae, we find that the genus petracola is nested within proctoporus .
in ecpleopinae, leposoma is divided into two clades, separated by anotosaura, colobosauroides, and arthrosaura , and many of the relevant nodes are very strongly supported.
these issues should be addressed in future studies.
our results show strong support for a clade uniting lacertidae and amphisbaenia , as in many previous studies  <cit> .
we also find strong support for monophyly of amphisbaenians , in contrast to some molecular analyses  <cit> .
relationships among amphisbaenian families are generally strongly supported and similar to those in earlier molecular studies , including the placement of the new world family rhineuridae as sister group to all other amphisbaenians  <cit> .
the family cadeidae is placed as the sister-group to amphisbaenidae + trogonophiidae  with weak support, but has been placed with blanidae in previous studies, with strong support but less- extensive taxon sampling  <cit> .
we find strong support for monophyly of the old world family lacertidae .
within lacertidae, branch support for the monophyly of most genera and for the subfamilies gallotiinae and lacertinae is very high .
however, we find that relationships among many genera are poorly supported, as in previous studies  <cit> .
our results  also indicate that several lacertid genera are non-monophyletic with strong support for the associated nodes, including algyroides , ichnotropis , meroles , nucras , and pedioplanis .
higher-level phylogeny of toxicofera
we find strong support  for monophyly of toxicofera , and moderate support for a sister-group relationship between iguania and anguimorpha .
relationships among anguimorpha, iguania, and serpentes were weakly supported in some bayesian and likelihood analyses  <cit> , but strongly supported in others  <cit> .
we further corroborate previous studies in also placing anguimorpha with iguania  <cit> .
in contrast, some other studies have placed anguimorphs with snakes as the sister group to iguanians  <cit> .
anguimorpha
our hypothesis for family-level anguimorphan relationships  is generally similar to that of other recent studies  <cit> , and is strongly supported.
our results differ from some analyses based only on morphology, which place anguidae near the base of anguimorpha  <cit> .
here, shinisauridae is strongly supported as the sister taxon to a well-supported clade of varanidae + lanthanotidae .
varanid relationships are similar to previous estimates .
xenosauridae is here strongly supported as the sister-group to a strongly supported clade containing helodermatidae and the strongly supported anniellidae + anguidae clade .
however, previous molecular analyses have placed helodermatidae as the sister to xenosauridae + , typically with strong support  <cit> .
within anguidae , our phylogeny indicates non-monophyly of genera within every subfamily, including diploglossinae , anguinae , and gerrhonotinae .
some of these problems were not reported previously , due to incomplete taxon sampling in previous studies  <cit> , but relationships within gerrhonotinae are under detailed investigation by other researchers, so these issues are likely to be resolved in the near future.
iguania
we find strong support  for the monophyly of iguania .
this clade is strongly supported by nuclear data  <cit> , but an apparent episode of convergent molecular evolution in several mitochondrial genes has seemingly misled some analyses of mtdna, leading to weak support for iguania  <cit> , or even separation of the acrodonts and pleurodonts  <cit>  in previous studies.
within iguania , we find strong support  for a sister-group relationship between chamaeleonidae and agamidae , and for a clade of mostly new world families .
we find strong support for the monophyly of chamaeleonidae and the subfamily chamaeleoninae, and weak support for the paraphyly of brookesiinae .
the sampled species of the brookesia nasus group appear as the sister group to all other chamaeleonids  as found by some previous authors  <cit> , though other studies have recovered a monophyletic brookesia <cit> .
within chamaeleoninae , we find strong support for the monophyly of most genera and species-level relationships.
however, we find strong support for the non-monophyly of calumma, with some species strongly placed with chamaeleo, others strongly placed with rieppeleon, and a third set weakly placed with nadzikambia + rhampoleon.
while non-monophly of calumma has also been found in previous studies  <cit> , a recent study strongly supports monophyly of brookesia and weakly supports monophyly of calumma <cit> .
monophyly of agamidae is strongly supported , contrary to some previous estimates  <cit> .
most relationships among agamid subfamilies and genera are strongly supported , and largely congruent with earlier studies  <cit> .
there are some differences with earlier studies.
for example, previous studies based on 29– <dig> loci  <cit>  placed hydrosaurinae as sister to amphibolurinae +  with strong support, whereas we place hydrosaurinae as the sister-group to amphibolurinae with weak support.
other authors  <cit>  placed leiolepiedinae with uromastycinae, but we  place uromastycinae as the sister group to all other agamids.
our phylogeny indicates several taxonomic problems within amphibolurine agamids .
the genera moloch and chelosania render hypsilurus paraphyletic, although the support for the relevant clades is weak.
the species lophognathus gilberti is placed in a strongly supported clade with chlamydosaurus and amphibolurus, a clade that is not closely related to the other lophognathus.
many of these taxonomic problems were also noted by previous authors  <cit> .
within agamine agamids , most relationships are well supported and monophyly of all sampled genera is strongly supported.
in contrast, within draconine agamids , many intergeneric relationships are weakly supported, and some genera are non-monophyletic , including gonocephalus  and japalura .
recent authors suggested dividing laudakia into three genera  based on a non-phylogenetic analysis of morphology  <cit> .
here, laudakia  is strongly supported as monophyletic , and this change is not necessitated by the phylogeny.
similarly, based on genetic and morphological data, recent authors  <cit>  suggested resurrecting the genus saara for the basal clade of uromastyx .
however, uromastyx  is strongly supported as monophyletic in our results  and in those of the recent revision  <cit> , and this change is not needed.
we therefore retain laudakia and uromastyx as previously defined, to preserve taxonomic stability in these groups  <cit> .
we note that recent studies have also begun to revise species limits in other groups such as trapelus <cit> , and taxa such as t. pallidus  may represent populations within other species.
within pleurodonta we generally confirm the monophyly and composition of the clades that were ranked as families  within the group  based on previous molecular studies  <cit>  and earlier morphological analyses  <cit> .
one important exception is the previously recognized polychrotidae.
our results confirm that anolis and polychrus are not sister taxa , as also found in some previous molecular studies  <cit> , but not others  <cit> .
our results provide strong support for non-monophyly of polychrotidae, placing polychrus with hoplocercidae  and anolis with corytophanidae .
recent analyses placing anolis with polychrus showed only weak support for this relationship  <cit> , despite many loci .
we support continued recognition of dactyloidae for anolis and polychrotidae for polychrus <cit> , based on a limited number of loci but extensive taxon sampling.
we note that these families are still monophlyetic, even if they prove to be sister taxa.
interestingly, our results for relationships among pleurodont families differ from most previous studies, and are surprisingly well-supported in some cases by shl values .
in previous studies, many relationships among pleurodont families were poorly supported by bayesian posterior probabilities and by parsimony and likelihood bootstrap values, though typically sampling fewer taxa or characters  <cit> .
studies including  <dig> nuclear loci found strong concatenated bayesian support for many relationships but weak support from ml bootstrap analyses for many of the same relationships  <cit> .
the latter pattern  was also found in an analysis including those same  <dig> loci and mitochondrial data for > <dig> species  <cit> .
we also find a mixture of strongly and weakly supported clades, but with many relationships that are incongruent with these previous studies.
first, we find that tropiduridae is weakly supported as the sister group to all other pleurodonts , followed successively  by iguanidae, leiocephalidae, crotaphytidae + phrynosomatidae, polychrotidae + hoplocercidae, and corytophanidae + dactyloidae.
the relatively strong support for the clades crotaphytidae + phrynosomatidae , polychrotidae + hoplocercidae , and corytophanidae + dactyloidae  is largely unprecedented in previous studies .
as in many previous analyses, deeper relationships among the families remain weakly supported.
we also find a strongly supported clade containing liolaemidae, opluridae, and leiosauridae , with opluridae + leiosauridae also strongly supported .
both clades have also been found in previous studies  <cit> , including studies based on  <dig> or more nuclear loci  <cit> .
we note that previous studies have shown strong support for some pleurodont relationships , only to be strongly overturned with additional data  <cit> .
therefore, the relationships found here should be taken with some caution , with the possible exception of the recurring clade of liolaemidae + .
all pleurodont families are strongly supported as monophyletic .
within the pleurodont families, our results generally support the current generic-level taxonomy .
however, there are some exceptions.
within tropiduridae , tropidurus is paraphyletic with respect to eurolophosaurus, strobilurus, uracentron, and plica.
within opluridae , the monotypic genus chalarodon renders oplurus paraphyletic.
two leiosaurid genera are also problematic .
in enyaliinae, anisolepis is paraphyletic with respect to urostrophus, and this clade is nested within enyalius.
in leiosaurinae, pristidactylus is rendered paraphyletic by leiosaurus and diplolaemus .
within dactyloidae, a recent study re-introduced a more subdivided classification of anoles  <cit> , an issue that has been debated extensively in the past  <cit> .
our results support the monophyly of all the genera recognized by recent authors  <cit> , including anolis, audantia, chamaelinorops, dactyloa, deiroptyx, norops, and xiphosurus .
however, since anolis is monophyletic as traditionally defined, we retain that definition here  for continuity with the recent literature  <cit> .
serpentes
relationships among the major serpent groups  are generally similar to other recent studies  <cit> .
we find that the blindsnakes, scolecophidia  are not monophyletic, as in previous studies  <cit> .
similar to some previous studies  <cit> , our data weakly place anomalepididae as the sister taxon to all snakes, and the scolecophidian families gerrhopilidae, leptotyphlopidae, typhlopidae, and xenotyphlopidae as the sister-group to all other snakes excluding anomalepididae .
previous studies have also placed anomalepididae as the sister-group to all non-scolecophidian snakes  <cit> , in some cases with strong support  <cit> .
although it might appear that recent analyses of scolecophidian relationships  <cit>  support monophyly of scolecophidia , the tree including non-snake outgroups from that study shows weak support for placing anomalepidids with alethinophidians, as in other studies  <cit> .
we follow recent authors  <cit>  in recognizing xenotyphlopidae  and gerrhopilidae  as distinct families .
leptotyphlopidae is strongly supported as the sister group of a clade comprising gerrhopilidae, xenotyphlopidae, and typhlopidae .
as in previous studies  <cit> , we find strong support for non-monophyly of several typhlopid genera .
there are also undescribed taxa  of uncertain placement within this group .
the systematics of typhlopoid snakes will thus require extensive revision in the future, with additional taxon and character sampling.
within alethinophidia , aniliidae is strongly supported  as the sister taxon of tropidophiidae , and all other alethinophidians form a strongly supported sister group to this clade .
the enigmatic family xenophidiidae is weakly placed as the sister-group to all alethinophidians exclusive of anilioidea .
the family bolyeriidae is weakly placed as the sister-group to pythons, boas, and relatives , which are strongly supported .
relationships in this group are generally consistent with other recent molecular studies  <cit> .
relationships among other alethinophidians are a mixture of strongly and weakly supported nodes .
we find strong support  for a clade containing anomochilidae + cylindrophiidae + uropeltidae.
this clade of three families is strongly supported  as the sister taxon to xenopeltidae + .
together, these six families form a strongly supported clade  that is weakly supported as the sister group to the strongly supported clade of boidae + calabariidae.
within the clade of anomochilidae, cylindrophiidae, and uropeltidae , we weakly place anomochilus as the sister group to cylindrophiidae  <cit> , in contrast to previous studies which placed anomochilus within cylindrophis <cit> .
however, support for monophyly of cylindrophis excluding anomochilus is weak .
as in previous studies  <cit> , we find several taxonomic problems within uropeltidae .
specifically, rhinophis and uropeltis are paraphyletic with respect to each other and to pseudotyphlops.
the problematic taxa are primarily sri lankan  <cit> , and forthcoming analyses will address these issues.
within pythonidae , the genus python is the sister group to all other genera.
some species that were traditionally referred to as python  are instead sister to an australasian clade consisting of antaresia, apodora, aspidites, bothrochilus, leiopython, liasis, and morelia .
these taxa  have been referred to as broghammerus, a name originating from an act of "taxonomic vandalism"  in a non-peer reviewed organ without data or analyses  <cit> .
however, this name was, perhaps inadvertently, subsequently used by researchers in peer-reviewed work  <cit>  and has entered into somewhat widespread usage  <cit> .
this name should be ignored and replaced with a suitable substitute.
within the australasian clade , morelia is paraphyletic with respect to all other genera, and liasis is non-monophyletic with respect to apodora, although many of the relevant relationships are weakly supported.
within boidae , our results and those of other recent studies  <cit>  have converged on estimated relationships that are generally similar to each other but which differ from traditional taxonomy  <cit> .
however, the classification has yet to be modified to reflect this, and we rectify this situation here.
we find that calabariidae is nested within boidae  <cit> , but this is poorly supported, and contrary to most previous studies  <cit> .
while calabaria has been classified as an erycine boid in the past, this placement is strongly rejected here and in other studies  <cit> .
if the current placement of calabaria is supported in the future, it would require recognition as the subfamily calabariinae in boidae.
the malagasy boine genera acrantophis and sanzinia are placed as the sister taxa to a weakly-supported clade containing calabariidae and a strongly supported clade  comprising the currently recognized subfamilies erycinae, ungaliophiinae, and other boines .
regardless of the position of calabariidae, this placement of malagasy boines renders boinae paraphyletic.
we therefore resurrect the subfamily sanziniinae  <cit>  for acrantophis and sanzinia.
this subfamily could be recognized as a distinct family if future studies also support placement of this clade as distinct from other boidae + calabariidae.
the genera lichanura and charina are currently classified as erycines  <cit> , but are strongly supported as the sister group to ungaliophiinae, as in previous studies  <cit> .
we expand ungaliophiinae to include these two genera , rather than erect a new subfamily for these taxa.
the subfamily ungaliophiinae is placed as the sister group to a well-supported clade  containing the rest of the traditionally recognized erycinae and boinae.
we restrict erycinae to the old world genus eryx.
the genus candoia  from oceania and new guinea  <cit> , is placed as the sister taxon to a moderately supported clade  consisting of erycinae  and the remaining genera of boinae .
to solve the non-monophyly of boinae with respect to erycinae , we place candoia in a new subfamily .
boinae then comprises the four neotropical genera that have traditionally been classified in this group .
we acknowledge that non-monophyly of boinae could be resolved in other ways .
however, our taxonomy maintains the traditionally used subfamilies boinae, erycinae, and ungaliophiinae, modifies them to reflect the phylogeny, and recognizes the phylogenetically distinct boine clades as separate subfamilies .
within boinae, eunectes renders epicrates paraphyletic, but this is not strongly supported .
our results for advanced snakes  are generally similar to those of other recent studies  <cit> , and will only be briefly described.
however, in contrast to most recent studies  <cit> , acrochordidae is here strongly placed  as the sister group to xenodermatidae.
this clade is then the sister group to the remaining colubroidea, which form a strongly supported clade .
this relationship has been found in some previous studies  <cit> , and was hypothesized by early authors  <cit> .
further evidence will be required to resolve this conclusively.
analyses based on concatenation of 20– <dig> loci do not support this grouping  <cit> , though preliminary species-tree analyses of > <dig> loci do .
relationships in pareatidae are similar to recent studies  <cit> , and the group is strongly placed as the sister taxon to colubroids excluding xenodermatids , as in most recent analyses .
the family viperidae is the sister group to all colubroids excluding xenodermatids and pareatids , as in other recent studies.
the family viperidae is strongly supported , as is the subfamily viperinae, and the sister-group relationship between azemiopinae and crotalinae .
our results generally support the existing generic-level taxonomy within viperinae .
however, we recover a strongly supported clade within viperinae consisting of daboia russelii, d. palaestinae, macrovipera mauritanica, and m. deserti , as in previous studies  <cit> .
we corroborate previous suggestions that these taxa be included in daboia <cit> , though this has not been widely adopted  <cit> .
the other macrovipera species  remain in that genus .
within crotalinae , a number of genera appear to be non-monophyletic.
the species trimeresurus gracilis is strongly supported as the sister taxon to ovophis okinavensis and distantly related to other trimeresurus, whereas the other ovophis are strongly placed as the sister group to protobothrops.
a well-supported clade  containing atropoides picadoi, cerrophidion, and porthidium renders atropoides paraphyletic .
the species bothrops pictus, considered incertae sedis in previous studies  <cit> , is here strongly supported as the sister taxon to a clade containing rhinocerophis, bothropoides, bothriopsis, and bothrops .
most of these relationships are strongly supported.
viperidae is strongly placed  as the sister taxon to a well-supported clade  containing colubridae, elapidae, homalopsidae, and lamprophiidae .
monophyly of homalopsidae is also strongly supported .
within homalopsidae, non-monophyly of the genus enhydris is strongly supported , and it should likely be split into multiple genera.
homalopsidae is weakly supported  as the sister group of elapidae + lamprophiidae .
this same relationship was also weakly supported by previous analyses  <cit> , but other studies have found strong support for placing homalopsidae as the sister group of a strongly supported clade including elapidae, lamprophiidae, and colubridae  <cit> , including data from > <dig> loci .
support for the monophyly of lamprophiidae is strong , and most of its subfamilies are well-supported  <cit>  including atractaspidinae, aparallactinae, lamprophiinae, prosymninae , pseudaspidinae, psammophiinae, and pseudoxyrhophiinae .
in lamprophiidae, most genera are monophyletic based on our sampling .
however, within aparallactinae, xenocalamus is strongly placed within amblyodipsas, and in atractaspidinae, homoroselaps is weakly placed in atractaspis.
in lamprophiinae, lamprophis is paraphyletic with respect to lycodonomorphus but support for the relevant clades is weak.
the enigmatic genera buhoma from africa and psammodynastes from asia were both previously considered incertae sedis within lamprophiidae  <cit> .
here they are weakly placed as sister taxa, and more importantly, they form a strongly supported clade with the african genus pseudaspis .
therefore, we expand pseudaspidinae to include these two genera.
the genus micrelaps  is weakly placed as the sister taxon to lamprophiidae + elapidae.
along with oxyrhabdium  and montaspis <cit> , this genus is treated as incertae sedis in our classification .
if future studies strongly support these relationships, they may require a new family for micrelaps and possibly a new subfamily for oxyrhabdium, though placement of these taxa has been highly variable in previous studies  <cit> .
monophyly of elapidae is strongly supported , and calliophis melanurus is strongly supported as the sister group to all other elapids .
within elapidae , relationships are generally concordant with previous taxonomy, with some exceptions.
the genera toxicocalamus, simoselaps, and echiopsis are all divided across multiple clades, with strong support for many of the relevant branches.
a recent study  <cit>  has provided a generic re-classification of the sea snakes  to resolve the extensive paraphyly of genera found in previous studies .
our results support this classification.
monophyly of colubridae and most of its subfamilies  are strongly supported .
however, relationships among many of these subfamilies are weakly supported , as in most previous studies  <cit> .
the subfamilies calamariinae and pseudoxenodontinae are strongly supported as sister taxa, and weakly placed as the sister-group to the rest of colubridae .
there is a weakly supported clade  comprising natricinae + , but the clade uniting the new world dipsadinae with the asian genus thermophis is strongly supported .
here, we place thermophis  in dipsadinae , making it the first and only asian member of this otherwise exclusively new world subfamily.
however, despite the strong support for its placement here, placement of this taxon has been variable in previous analyses  <cit> , and we acknowledge that future analyses may support recognition of a distinct subfamily .
the clade of natricinae and dipsadinae is weakly supported as the sister group  to a clade containing sibynophiinae  <cit>  + .
the subfamily colubrinae is weakly supported; we find that the colubrine genera ahaetulla, chrysopelea, and dendrelaphis form a strongly supported clade that is weakly placed as the sister group to the rest of colubrinae, which form a strongly supported clade .
this clade was also placed with grayiinae or sibynophiinae in many preliminary analyses, rendering colubrinae paraphyletic.
this group of three genera has been strongly supported in the past, and only weakly placed with colubrinae  <cit> .
it is possible that future analyses will reveal that the clade of ahaetulla, chrysopelea, and dendrelaphis is placed elsewhere in colubridae with strong support, and thus merit recognition as a distinct subfamily .
a notable feature of this clade is the presence of gliding flight in most species of chrysopelea, less-developed non-flight jumping with similar locomotor origins in dendrelaphis, and homologous glide-related traits in ahaetulla <cit> .
numerous colubroid genera are not included in our tree and are not clearly placed in subfamilies based on previous morphological evidence.
in our classification, these genera are also considered incertae sedis within colubridae, including blythia, cyclocorus, elapoidis, gongylosoma, helophis, myersophis, oreocalamus, poecilopholis, rhabdops, and tetralepis, as in previous classifications  <cit> .
our phylogeny reveals numerous taxonomic problems within colubrinae .
the genus boiga is paraphyletic with respect to crotaphopeltis, dipsadoboa, telescopus, toxicodryas, and dasypeltis, with strong support .
the genus philothamnus is paraphyletic with respect to hapsidophrys .
the genus coluber is split between old world and new world clades .
the species hierophis spinalis is sister to eirenis to the exclusion of the other hierophis species .
the genus dryocalamus is nested within lycodon .
the species chironius carinatus and c. quadricarinatus are weakly placed in a clade of neotropical colubrines only distantly related to the other chironius species .
the genus drymobius renders dendrophidion paraphyletic .
the monotypic genus rhynchophis renders the two species of rhadinophis paraphyletic .
the genus coronella is rendered paraphyletic  by oocatochus with weak support .
finally, the genus rhinechis is nested within zamenis .
we find numerous non-monophyletic genera within natricinae , as in previous studies  <cit> .
these non-monophyletic genera include the asian genera amphiesma, atretium, and xenocrophis.
among new world genera, we find regina to be non-monophyletic with respect to most other genera, as in previous phylogenetic studies .
also, as in previous studies , we find that adelophis <cit>  is nested deep within thamnophis <cit> .
finally, within a weakly supported dipsadinae , we find non-monophyly of numerous genera, as in many earlier studies .
these problems of non-monophyly include leptodeira , geophis , atractus , sibynomorphus , dipsas , taeniophallus , and echinanthera .
recent revisions have begun to tackle these problems  <cit> , but additional taxon and character sampling will be crucial to resolve relationships and taxonomy.
discussion
in this study, we provide a phylogenetic estimate for  <dig> species of squamates based on molecular data from up to  <dig> genes per species, combining much of the relevant data used in previous molecular phylogenetic analyses.
this tree provides a framework for future evolutionary studies, spanning from the species level to relationships among families, utilizing a common set of branch lengths.
these estimated branch lengths are critically important for most phylogenetic comparative methods.
to further facilitate use of this phylogeny in comparative studies, we provide the newick version of this tree  in datadryad repository  <dig> /dryad.82h0m and additional file 1: data file s <dig>  our results also suggest that the branch lengths in this tree should not generally be compromised by missing data for some genes in some taxa.
our results also reveal many problems in squamate classification at nearly all phylogenetic levels.
we make several changes to higher-level taxonomy based on this phylogeny, including changes to the traditionally recognized subfamilies of boid snakes , lamprophiid snakes , colubrid snakes , and gymnophthalmid lizards  and scincid lizards .
in appendix i, we list the generic content of all families and subfamilies.
we also find dozens of problems at the genus level, many of which have been identified previously, and which we defer the resolution of to future studies.
our results also highlight potential problems in recent proposals to modify the classification of scincid  <cit>  and teiid lizards  <cit> .
in addition to synthesizing existing molecular data for squamate phylogeny, our analyses also reveal several apparently novel findings .
given space constraints, we cannot detail every deviation from previous phylogenetic hypotheses .
nevertheless, we focus on three sets of examples.
first, we find some relatively novel, strongly-supported relationships at the family level.
these include the placement of helodermatidae  and the placement of xenodermatidae as the sister taxon to acrochordidae , in contrast to most recent analyses of anguimorphs and snakes .
we also find some novel, strongly supported relationships among pleurodont families, but we acknowledge that these may be overturned in future studies.
the second example is the higher-level relationships within scincidae, the largest family of lizards  <cit> .
no previous studies examining higher-level relationships within the group included more than ~ <dig> species  <cit> .
in this study, we sample  <dig> skink species , and our phylogeny provides a unique resolution of higher-level skink relationships.
some previous researchers  <cit>  placed acontiines as the sister group to all other skinks, but suggested that scincines and lygosomines were paraphyletic with respect to each other .
in contrast, others  <cit>  suggested that acontiines, feyliniines, and lygosomines were all nested inside scincines , although many clades were only weakly supported.
here , we find that acontiines are the sister group to a strongly supported clade consisting of a monophyletic scincinae and a monophyletic lygosominae .
third, our phylogeny reveals numerous genera that appear to be non-monophyletic, with many of these cases having strong support for the associated nodes.
our examples include genera in many families, including dibamids, diplodactylids, gekkonids, phyllodactylids, gerrhosaurids, scincids, teiids, gymnophthalmids, lacertids, anguids, chamaeleonids, agamids, tropidurids, oplurids, leiosaurids, typhlopids, pythonids, uropeltids, boids, viperids, lamprophiids, elapids, and colubrids .
although many problems noted here were found in previous studies, some seem to be new, such as placement of crocodilurus and draceana within tupinambis  and coloptychon within gerrhonotus .
our study also offers an important test of higher-level squamate relationships using a very different sampling strategy than that used in most previous analyses.
squamates have traditionally been divided into two clades based on morphology, iguania and scleroglossa .
despite considerable disagreement among morphology-based hypotheses, this basic division is supported by nearly all phylogenetic analyses based on morphological data  <cit> .
in contrast, our results and those of most previous molecular analyses strongly support placement of iguanians with anguimorphs and snakes  <cit> .
the causes of this conflict remain unclear, but may be related to morphological traits associated with different feeding strategies of iguanian and  scleroglossan squamates  <cit> .
additionally, analyses of morphology often place dibamids, amphisbaenians, snakes, and  some scincids and anguids in a single clade  <cit> .
our analyses do not support such a clade , nor do other analyses of molecular data alone  <cit> , or analyses of combined molecular and morphological data  <cit> .
instead, these morphological results seem to be explained by convergence associated with burrowing .
overall, molecular datasets have shown overwhelmingly strong support for placement of dibamids and gekkonids at the base of the tree, amphisbaenians with lacertoids, and iguanians with snakes and anguimorphs  <cit> .
these results have now been corroborated with up to  <dig> genes  for  <dig> taxa  <cit> ,  <dig> genes  for  <dig> taxa  <cit> , and  <dig> genes  for  <dig> taxa  <cit> .
we now support this basic topology with  <dig> species sampled for up to  <dig> genes each .
nevertheless, despite the overall strong support for most of the tree , certain clades remain poorly supported .
a potential criticism of the supermatrix approach used here is that this weak support may occur due to missing data.
however, previous studies of  <dig> datasets have shown explicitly that there is typically little relationship between branch support for terminal taxa and the amount of missing data  <cit> .
instead, these patterns of weak support are more likely to reflect short underlying branch lengths  <cit> , and may be difficult to resolve even with more complete taxonomic and genomic sampling.
indeed, as noted above, many of the weakly supported nodes in our phylogeny are also weakly supported in analyses with little missing data  and large numbers of genes , such as the relationships of many pleurodont lizard families and colubroid snake families and subfamilies.
we acknowledge that the differences between our results and previous studies  do not necessarily mean that our results are right and those of previous studies are wrong.
in some cases, we provide strong support for novel relationships when previous, conflicting studies showed only weak support .
in other cases, our results disagree with other studies for clades that were strongly supported .
in the best-case scenario, these conflicts may be resolved because our results are correct, possibly reflecting the beneficial effects of adding taxa and the associated subdivision of long branches  <cit> .
furthermore, in many cases, we are including more genes than used in previous studies of particular clades, increasing sampling of characters and loci.
this should generally reduce spurious results caused by sampling few characters and by incongruence between gene and species trees.
however, other explanations for incongruence between our results and previous studies are also possible.
adding taxa can potentially lead to incorrect results in some cases , such as when a long terminal branch is added that further subdivides a short internal branch.
in other cases, conflicts with our results might reflect the impact of our sampling fewer nuclear genes and a correspondingly increased influence of mitochondrial data.
mitochondrial genes have relatively fast evolutionary rates , and their phylogenetic resolution for a particular node may also reflect introgression or incomplete lineage sorting rather than the species phylogeny .
many taxa in the matrix are represented only by mitochondrial data, and highly variable mitochondrial genes might also overcome the influence of less variable nuclear genes in combined analyses .
such cases might explain some strongly supported conflicts between our results and those based on multiple nuclear loci.
another possibility is that some cases may represent failure to find the optimal tree .
we acknowledge that there are many reasons why our results may differ from previous studies, and the ultimate test of these novel findings will be corroboration in future studies that include more taxa and characters.
this analysis also corroborates several recent studies suggesting that the supermatrix approach is a powerful strategy for large-scale phylogenetic inference  <cit> .
for example, even though each species had 81% missing data on average, we found that most species were placed in the families and genera expected based on previous taxonomy, often with very strong support.
furthermore, we found that incompleteness of terminal taxa is not related to branch lengths , suggesting that missing data are not significantly biasing branch-length estimates .
also, the ml models we used have been shown to be robust to missing data in large, sparse supermatrices  <cit> .
even though we did find some subfamilies and genera to be non-monophyletic, similar relationships were often found in previous studies based on data matrices with only limited missing data .
we suggest that further resolution of the squamate tree will be greatly facilitated if researchers deliberately sample mitochondrial genes and nuclear genes that include the set of genes used here and in recent phylogenomic studies , to increase overlap between genes and taxa, and decrease missing data.
with over  <dig> species remaining to be included and only  <dig> genes sampled, our study is far from the last word on squamate phylogeny.
we note that new data can easily be added to this matrix, in terms of both new taxa and new genes.
increased sampling of other nuclear genes is likely to be advantageous as well.
next-generation sequencing strategies and phylogenomic methods should help resolve difficult nodes  <cit> , as should application of species-tree methods  <cit> .
species-tree analyses of  <dig> nuclear loci support many of these same clades across squamates  <cit> , and data from > <dig> nuclear loci reinforces many of the relationships found here among the colubroid snake subfamilies .
in addition, it would be useful to incorporate fossil taxa in future studies  <cit> , utilizing the large morphological datasets that are now available  <cit> .
despite these areas for future studies, the present tree provides a framework for researchers analyzing patterns of squamate evolution at both lower and higher taxonomic levels , and for building a more complete picture of squamate phylogeny.
CONCLUSIONS
in this study, we provide a phylogenetic estimate for  <dig> squamate species, based on a supermatrix approach.
our results provide important confirmation for previous studies based on more limited taxon sampling, and reveal new relationships at the level of families, genera, and species.
we also provide a phylogenetic framework for future comparative studies, with a large-scale tree including a common set of estimated branch lengths.
finally, we provide a revised classification for squamates based on this tree, including changes in the higher-level taxonomy of gymnophthalmid and scincid lizards and boid, colubrid, and lamprophiid snakes.

 squamate reptiles are among the most diverse radiations of terrestrial vertebrates. squamata includes more than species as of december. the rate of new species descriptions shows no signs of slowing, with a record new species described in, greater than the highest yearly rates of the 18th and 19th centuries. squamates are presently found on every continent except antarctica, and in the indian and pacific oceans, and span many diverse ecologies and body forms, from limbless burrowers to arboreal gliders. squamates are key study organisms in numerous fields, from evolution, ecology, and behavior to medicine and applied physics. they have also been the focus of many pioneering studies using phylogenies to address questions about trait evolution. phylogenies are now recognized as being integral to all comparative studies of squamate biology. however, hypotheses about squamate phylogeny have changed radically in recent years, especially when comparing trees generated from morphological and molecular data. furthermore, despite extensive work on squamate phylogeny at all taxonomic levels, a large-scale phylogeny has never been attempted using morphological or molecular data. squamate phylogenetics has changed radically in the last years, revealing major conflicts between the results of morphological and molecular analyses. early estimates of squamate phylogeny and recent studies based on morphological data consistently supported a basal division between iguania, and scleroglossa, which comprises all other squamates. within scleroglossa, many phylogenetic analyses of morphological data have also supported a clade containing limb-reduced taxa, including various combinations of snakes, dibamids, amphisbaenians, and limb-reduced skinks and anguids, though some of these authors also acknowledged that this clade was likely erroneous. in contrast, recent molecular analyses have estimated very different relationships. novel arrangements include placement of dibamids and gekkotans near the root of the squamate tree, a sister-group relationship between amphisbaenians and lacertids, and a clade uniting iguania with snakes and anguimorphs within scleroglossa. these molecular results suggest that some estimates of squamate phylogeny based on morphology may have been misled, especially by convergence associated with adaptations to burrowing. however, there have also been disagreements among molecular studies, such as placement of dibamids relative to gekkotans and other squamates, and relationships among snakes, iguanians, and anguimorphs. analyses of higher-level squamate relationships based on molecular data have so far included relatively few species, and none have included representatives from all described families and subfamilies. this limited taxon sampling makes existing molecular phylogenies difficult to use for broad-scale comparative studies, with some exceptions based on supertrees. in addition, limited taxon sampling is potentially a serious issue for phylogenetic accuracy. thus, an analysis with extensive taxon sampling is critically important to test hypotheses based on molecular datasets with more limited sampling, and to provide a framework for comparative analyses. despite the lack of a large-scale phylogeny across squamates, recent molecular studies have produced phylogenetic estimates for many of the major groups of squamates, including iguanian lizards, higher-level snake groups, typhlopoid snakes, colubroid snakes, booid snakes, scincid lizards, gekkotan lizards, teiioid lizards, lacertid lizards, and amphisbaenians. these studies have done an outstanding job of clarifying the phylogeny and taxonomy of these groups, but many were limited in some ways by the number of characters and taxa that they sampled. here, we present a phylogenetic estimate for squamata based on combining much of the existing sequence data for squamate reptiles, using the increasingly well-established supermatrix approach. we present a new phylogenetic estimate including squamate species. the dataset includes up to bp per species from genes. we include species from all currently described families and subfamilies. in terms of species sampled, this is times larger than any previous phylogeny for any one squamate group, times larger than the largest supertree estimate, and times larger than the largest molecular study of higher-level squamate relationships. while we did not sequence any new taxa specifically for this project, much of the data in the combined matrix were generated in our labs or from our previous collaborative projects,, including thousands of gene sequences from hundreds of species. the supermatrix approach can provide a relatively comprehensive phylogeny, and uncover novel relationships not seen in any of the separate analyses in which the data were generated. such novel relationships can be revealed via three primary mechanisms. first, different studies may have each sampled different species from a given group for the same genes, and combining these data may reveal novel relationships not apparent in the separate analyses. second, different studies may have used different genetic markers for the same taxa, and combining these markers can dramatically increase character sampling, potentially revealing new relationships and providing stronger support for previous hypotheses. third, even for clades that were previously studied using complete taxon sampling and multiple loci, novel relationships may be revealed by including these lineages with other related groups in a large-scale phylogeny. the estimated tree and branch-lengths should be useful for comparative studies of squamate biology. however, this phylogeny is based on a supermatrix with extensive missing data. some authors have suggested that matrices with missing cells may yield misleading estimates of topology, support, and branch lengths. nevertheless, most empirical and simulation studies have not found this to be the case, at least for topology and support. though fewer studies have examined the effects of missing data on branch lengths, these also suggest that missing data do not strongly impact estimates. here, we test whether branch lengths for terminal taxa are related to their completeness. in general, our results corroborate those of many recent molecular studies with regard to higher-level relationships, species-level relationships, and the monophyly, composition, and relationships of most families, subfamilies, and genera. however, our results differ from previous estimates for some groups, and reveal numerous problems in the existing classification of squamates. we therefore provide a conservative, updated classification of extant squamates at the family and subfamily level based on the new phylogeny, while highlighting problematic taxonomy at the genus level, without making changes. the generic composition of all families and subfamilies under our revised taxonomy are provided in appendix i. we note dozens of problems in the genus-level taxonomy suggested by our tree, but we acknowledge in advance that we do not provide a comprehensive review of the previous literature dealing with all these taxonomic issues. similarly, we do not attempt to fix these genus-level problems here, as most will require more extensive taxon sampling to adequately resolve. throughout the paper, we address only extant squamates. squamata also includes numerous extinct species classified in both extant and extinct families, subfamilies, and genera. relationships and classification of extinct squamates based on morphological data from fossils have been addressed by numerous authors. a classification based only on living taxa may create some problems for classifying fossil taxa, but these can be addressed in future studies that integrate molecular and fossil data.  supermatrix phylogeny we generated the final tree using maximum likelihood in raxmlv. support was assessed using the non-parametric shimodaira-hasegawa-like implementation of the approximate likelihood-ratio test. the tree and data matrix are available in nexus format in datadryad repository /dryad.82h0m and as additional file 1: data file s a skeletal representation of the tree is shown in figure  the full species-level phylogeny is shown in figures  the analysis yields a generally well-supported phylogenetic estimate for squamates. there is no relationship between proportional completeness and branch length for terminal taxa, strongly suggesting that the estimated branch lengths are not consistently biased by missing data. higher-level relationships our tree is broadly congruent with most previous molecular studies of higher-level squamate phylogeny using both nuclear data and combined nuclear and mitochondrial data, providing important confirmation of previous molecular studies based on more limited taxon sampling. specifically we support: the placement of dibamids and gekkotans near the base of the tree; a sister-group relationship between scincoidea and a clade containing the rest of the squamates excluding dibamids and gekkotans; lacertoidea, and a clade containing anguimorphs, iguanians, and snakes as the sister taxon to lacertoidea. these relationships are strongly supported in general, but differ sharply from most trees based on morphological data. nevertheless, many clades found in previous morphological taxonomies and phylogenies are also present in this tree in some form, including amphisbaenia, anguimorpha, gekkota, iguania, lacertoidea, scincoidea, serpentes, and many families and subfamilies. in contrast, the relationships among these groups differ strongly between molecular analyses and morphological analyses. our results demonstrate that this incongruence is not explained by limited taxon sampling in the molecular data sets. in fact, our species-level sampling is far more extensive than in any morphological analyses, by an order of magnitude. we find that the basal squamate relationships are strongly supported in our tree. the family dibamidae is the sister group to all other squamates, and gekkota is the sister group to all squamates excluding dibamidae, as in some previous studies. other recent molecular analyses have also placed dibamidae near the squamate root, but differed in placing it as either the sister taxon to all squamates excluding gekkota, or the sister- group of gekkota. our results also corroborate that the new world genus anelytropsis is nested within the old world genus dibamus, but the associated branches are weakly supported. gekkota within gekkota, we corroborate both earlier morphological and recent molecular estimates in supporting a clade containing the australian radiation of "diplodactylid" geckos and the snakelike pygopodids. as in previous studies, carphodactylidae is the weakly supported sister group to pygopodidae, and this clade is the sister group of diplodactylidae. we recover clades within the former gekkonidae that correspond to the strongly supported families eublepharidae, sphaerodactylidae, phyllodactylidae, and gekkonidae as in previous studies, and similar relationships among these groups. within gekkota, we find evidence for non-monophyly of many genera. many relationships among the new caledonian diplodactylids are weakly supported, and there is apparent non-monophyly of the genera rhacodactylus, bavayia, and eurydactylodes with respect to each other and oedodera, dierogekko, paniegekko, correlophus, and mniarogekko. in the australian diplodactylids, strophurus taenicauda is strongly supported as belonging to a clade that is only distantly related to the other sampled strophurus species. the two species of the north african sphaerodactylid genus saurodactylus are divided between the two major sphaerodactylid clades, but the associated branches are weakly supported. the south american phyllodactylid genus homonota is strongly supported as being paraphyletic with respect to phyllodactylus. a number of gekkonid genera also appear to be non-monophyletic, including the asian genera cnemaspis, lepidodactylus, gekko, luperosaurus, mediodactylus, and bunopus, and the african afrogecko, afroedura, chondrodactylus, and pachydactylus. many of these taxonomic problems in gekkotan families have been identified in previous studies, and extensive changes will likely be required to fix them. scincoidea we strongly support the monophyly of scincoidea, as in other recent studies. all four families are strongly supported. a similar clade is also recognized in morphological phylogenies, though without xantusiidae in some. within the new world family xantusiidae, we corroborate previous analyses that found strong support for a sister-group relationship between xantusia and lepidophyma, excluding cricosaura. these relationships support the subfamily cricosaurinae for cricosaura. we also recognize xantusiinae for the north american genus xantusia and lepidophyminae for the central american genus lepidophyma. within the african and madagascan family gerrhosauridae, the genus gerrhosaurus is weakly supported as being paraphyletic with respect to the clade comprising tetradactylus + cordylosaurus, with g. major placed as the sister group to all other gerrhosaurids. within cordylidae, we use the generic taxonomy from a recent phylogenetic analysis and re-classification based on multiple nuclear and mitochondrial genes. this classification broke up the non-monophyletic cordylus into several smaller genera, and we corroborate the non-monophyly of the former cordylus and support the monophyly of the newly recognized genera. we support the distinctiveness of platysaurus and recognition of the subfamily platysaurinae. we strong support for the monophyly of scincidae as in previous studies. we strongly support the basal placement of the monophyletic subfamily acontiinae, as found in some previous studies but not others. similar to earlier studies, we find that the subfamily scincinae is non-monophyletic, as feylininae is nested within scincinae. based on these results, synonymizing feylininae with scincinae produces a monophyletic scincinae, which is then sister to a monophyletic lygosominae with 94% shl support. this yields a new classification in which all three subfamilies are strongly supported. importantly, these definitions approxi\mate the traditional content of the three subfamilies, except for recognition of feylininae. we note that a recent revision of the new world genus mabuya introduced a nontraditional family-level classification for scincidae. these authors divided scincidae into seven families: acontiidae, egerniidae, eugongylidae, lygosomidae, mabuyidae, scincidae and sphenomorphidae. however, there was no phylogenetic need for considering these clades as families, since the family scincidae is clearly monophyletic, based on our results and others. thus, their new taxonomy changes the long-standing definition of scincidae unnecessarily. furthermore, these changes were done without defining the full content of any of these families other than scincidae and acontiidae. most importantly, the new taxonomy proposed by these authors is at odds with the phylogeny estimated here, with respect to the familial and subfamilial classification of > skink species. for instance, sphenomorphus stellatus is found in a strongly supported clade containing lygosoma, which is separate from the other clade containing the other sampled sphenomorphus species. an additional problem is that egernia, lygosoma, and sphenomorphus are the type genera of egerniidae, lygosomidae, and sphenomorphidae, but are paraphyletic as currently defined, leading to further uncertainty in the content and definition of these putative families. furthermore, mabuyidae apparently refers to the clade containing chioninia, dasia, mabuya, trachylepis, with each of these genera placed in its own subfamily. however, several other genera are strongly placed in this group, such as eumecia, eutropis, lankaskincus, and ristella. these other genera cannot be readily fit into these subfamilial groups, and trachylepis is paraphyletic with respect to eumecia, chioninia, and mabuya. also, we find that emoia is divided between clades containing lygosoma and eugongylus, and many of these relationships have strong support. finally, ateuchosaurus is apparently not accounted for in their classification, and here is weakly placed as the sister-group to a clade comprising their sphenomorphidae, egerniidae, mabuyidae, and lygosomidae. these authors argued that a more heavily subdivided classification for skinks may be desirable for facilitating future taxonomic revisions and species descriptions. however, this classification seems likely to only exacerbate existing taxonomic problems. here, we retain the previous definition of mabuya, and we support the traditional definitions of scincidae, acontiinae, scincinae, and lygosominae. the other taxonomic issues in scincidae identified here and elsewhere should be resolved in future studies. our phylogeny provides a framework in which these analyses can take place, which we think may be more useful than a classification lacking clear taxon definitions. of the scincid genera, we can assign the sampled in our tree to one of the three subfamilies in our classification. we place of the remaining genera into one of the three subfamilies based on previous classifications, with ateuchosaurus as incertae sedis in scincidae. below, we review the non-monophyletic genera in our tree. many of these problems have been reported by previous authors, and for brevity we do not distinguish between cases reported in previous studies, and potentially new instances found here. within acontiinae, we find that the two genera are both monophyletic. within scincinae, many genera are now strongly monophyletic, but some problems remain. the genera scincus and scincopus are strongly supported as being nested inside of the remaining eumeces. among malagasy scincines, pseudacontias is nested inside madascincus, and the genera androngo, pygomeles, and voeltzkowia are all nested in amphiglossus. we also find numerous taxonomic problems within lygosomines. species of sphenomorphus are widely dispersed among other lygosomine genera. the genus tropidophorus is paraphyletic with respect to a clade containing many other genera. the sampled species of asymblepharus are only distantly related to each other, including one species nested inside of scincella. the genus lipinia is polyphyletic, with one species strongly placed as the sister taxon to isopachys, and with two other species placed in a well-supported clade that also includes papuascincus. among australian skinks, the genus eulamprus is polyphyletic with respect to nangura, calyptotis, gnypetoscincus, coggeria, coeranoscincus, ophioscincus, saiphos, anomalopus, eremiascincus, hemiergis, glaphyromorphus, notoscincus, ctenotus, and lerista, and most of the relevant nodes are strongly supported. the genera coeranoscincus and ophioscincus are polyphyletic with respect to each other and to saiphos and coggeria. the genus glaphyromorphus is paraphyletic with respect to a clade of eulamprus. the genus egernia is paraphyletic with respect to bellatorias and lissolepis, although many of the relevant nodes are not strongly supported. the genera cyclodomorphus and tiliqua are paraphyletic with respect to each other. among other lygosomines, trachylepis is non-monophyletic, with two species that fall outside the strongly supported clade containing the other species. the latter clade is weakly supported as the sister group to a clade containing chioninia, eumecia, and mabuya. in mabuya, a few species have unorthodox placements within a monophyletic mabuya, potentially due to uncertain taxonomic assignment of specimens by previous authors. the genus lygosoma is paraphyletic with respect to lepidothyris and mochlus, and many of the relevant nodes are strongly supported. among new caledonian skinks, the genus lioscincus is polyphyletic with respect to marmorosphax, celatiscincus, and tropidoscincus, and both lioscincus and tropidoscincus are paraphyletic with respect to, kanakysaurus, lacertoides, phoboscincus, sigaloseps, tropidoscincus, graciliscincus, simiscincus, and caledoniscincus, with strong support for most relevant nodes. the genera emoia and bassiana are massively polyphyletic and divided across multiple lygosomine clades. the genus lygisaurus appears to be nested inside of carlia, although many of the relevant branches are only weakly supported. lacertoidea within lacertoidea, we corroborate recent molecular analyses and morphology-based phylogenies and classifications in supporting the clade including the new world families gymnophthalmidae and teiidae. within a weakly supported teiidae, the subfamilies tupinambinae and teiinae are each strongly supported as monophyletic, as in previous studies. in tupinambinae, callopistes is the sister group to a clade containing tupinambis, dracaena, and crocodilurus. the clade dracaena + crocodilurus is nested within tupinambis, and the associated clades have strong support. we find that the teiine genera ameiva and cnemidophorus are non-monophyletic, interdigitating with each other and the monophyletic genera aspidoscelis, dicrodon, and kentropyx, as in previous phylogenies. a recent study proposed a re-classification of the family teiidae based on analysis of morphological characters for terminal species. those authors erected several new genera and subfamilies in an attempt to deal with the apparent non-monophyly of currently recognized taxa in their tree. however, in our tree, some of these new taxa conflict strongly with the phylogeny or are rendered unnecessary. first, they recognize callopistinae as a distinct subfamily for callopistes, arguing that failure to do so would produce a taxonomy inconsistent with teiid phylogeny. however, we find strong support for callopistes in its traditional placement as part of tupinambinae, and this change is thus not needed based on our results. the genus ameiva is paraphyletic under traditional definitions. in our tree, their conception of ameiva is also non-monophyletic, with species found in three distinct clades. we also find non-monophyly of many of their species groups within ameiva, including the ameiva, bifrontata, dorsalis, and erythrocephala groups. their genera aurivela and contomastyx are strongly supported as sister taxa in our tree, and are nested within ameiva in their erythrocephala species group, along with dicrodon. on the positive side, many of the genera they recognize are monophyletic and are not nested in other genera in our tree, including their ameivula, aspidoscelis, cnemidophorus, holcosus, kentropyx, salvator, and teius. we did not sample ameiva edracantha. given our results, major taxonomic rearrangements within teiidae seem problematic at present, especially with the extensive paraphyly of many traditional and re-defined teiid genera, the lack of strong resolution of many of these relationships based on molecular and morphological data, and incomplete taxon sampling in all studies so far. thus, we provisionally retain the traditional taxonomy of teiidae, pending additional data and analyses. however, we note that ameiva, cnemidophorus, and tupinambis are clearly non-monophyletic based on both our results and those of recent authors, and will require taxonomic changes in the future. we anticipate that many of these newly proposed genera will be useful in such revisions. we find strong support for monophyly of gymnophthalmidae. within gymnophthalmidae, we find strong support for the monophyly of the previously recognized subfamilies, with the exception of cercosaurinae. previous researchers considered the genus bachia a distinct tribe within cercosaurinae, based on a poorly supported sister-group relationship with the tribe cercosaurini. here, we find a moderately well supported relationship between bachia and gymnophthalminae + rhachisaurinae, and we find that this clade is only distantly related to other cercosaurinae. therefore, we restrict cercosaurinae to the tribe cercosaurini, and elevate the tribe bachiini to the subfamily level. the subfamily bachiinae contains only the genus bachia, identical in content to the previously recognized tribe. within cercosaurinae, we find that the genus petracola is nested within proctoporus. in ecpleopinae, leposoma is divided into two clades, separated by anotosaura, colobosauroides, and arthrosaura, and many of the relevant nodes are very strongly supported. these issues should be addressed in future studies. our results show strong support for a clade uniting lacertidae and amphisbaenia, as in many previous studies. we also find strong support for monophyly of amphisbaenians, in contrast to some molecular analyses. relationships among amphisbaenian families are generally strongly supported and similar to those in earlier molecular studies, including the placement of the new world family rhineuridae as sister group to all other amphisbaenians. the family cadeidae is placed as the sister-group to amphisbaenidae + trogonophiidae with weak support, but has been placed with blanidae in previous studies, with strong support but less- extensive taxon sampling. we find strong support for monophyly of the old world family lacertidae. within lacertidae, branch support for the monophyly of most genera and for the subfamilies gallotiinae and lacertinae is very high. however, we find that relationships among many genera are poorly supported, as in previous studies. our results also indicate that several lacertid genera are non-monophyletic with strong support for the associated nodes, including algyroides, ichnotropis, meroles, nucras, and pedioplanis. higher-level phylogeny of toxicofera we find strong support for monophyly of toxicofera, and moderate support for a sister-group relationship between iguania and anguimorpha. relationships among anguimorpha, iguania, and serpentes were weakly supported in some bayesian and likelihood analyses, but strongly supported in others. we further corroborate previous studies in also placing anguimorpha with iguania. in contrast, some other studies have placed anguimorphs with snakes as the sister group to iguanians. anguimorpha our hypothesis for family-level anguimorphan relationships is generally similar to that of other recent studies, and is strongly supported. our results differ from some analyses based only on morphology, which place anguidae near the base of anguimorpha. here, shinisauridae is strongly supported as the sister taxon to a well-supported clade of varanidae + lanthanotidae. varanid relationships are similar to previous estimates. xenosauridae is here strongly supported as the sister-group to a strongly supported clade containing helodermatidae and the strongly supported anniellidae + anguidae clade. however, previous molecular analyses have placed helodermatidae as the sister to xenosauridae +, typically with strong support. within anguidae, our phylogeny indicates non-monophyly of genera within every subfamily, including diploglossinae, anguinae, and gerrhonotinae. some of these problems were not reported previously, due to incomplete taxon sampling in previous studies, but relationships within gerrhonotinae are under detailed investigation by other researchers, so these issues are likely to be resolved in the near future. iguania we find strong support for the monophyly of iguania. this clade is strongly supported by nuclear data, but an apparent episode of convergent molecular evolution in several mitochondrial genes has seemingly misled some analyses of mtdna, leading to weak support for iguania, or even separation of the acrodonts and pleurodonts in previous studies. within iguania, we find strong support for a sister-group relationship between chamaeleonidae and agamidae, and for a clade of mostly new world families. we find strong support for the monophyly of chamaeleonidae and the subfamily chamaeleoninae, and weak support for the paraphyly of brookesiinae. the sampled species of the brookesia nasus group appear as the sister group to all other chamaeleonids as found by some previous authors, though other studies have recovered a monophyletic brookesia. within chamaeleoninae, we find strong support for the monophyly of most genera and species-level relationships. however, we find strong support for the non-monophyly of calumma, with some species strongly placed with chamaeleo, others strongly placed with rieppeleon, and a third set weakly placed with nadzikambia + rhampoleon. while non-monophly of calumma has also been found in previous studies, a recent study strongly supports monophyly of brookesia and weakly supports monophyly of calumma. monophyly of agamidae is strongly supported, contrary to some previous estimates. most relationships among agamid subfamilies and genera are strongly supported, and largely congruent with earlier studies. there are some differences with earlier studies. for example, previous studies based on 29– loci placed hydrosaurinae as sister to amphibolurinae + with strong support, whereas we place hydrosaurinae as the sister-group to amphibolurinae with weak support. other authors placed leiolepiedinae with uromastycinae, but we place uromastycinae as the sister group to all other agamids. our phylogeny indicates several taxonomic problems within amphibolurine agamids. the genera moloch and chelosania render hypsilurus paraphyletic, although the support for the relevant clades is weak. the species lophognathus gilberti is placed in a strongly supported clade with chlamydosaurus and amphibolurus, a clade that is not closely related to the other lophognathus. many of these taxonomic problems were also noted by previous authors. within agamine agamids, most relationships are well supported and monophyly of all sampled genera is strongly supported. in contrast, within draconine agamids, many intergeneric relationships are weakly supported, and some genera are non-monophyletic, including gonocephalus and japalura. recent authors suggested dividing laudakia into three genera based on a non-phylogenetic analysis of morphology. here, laudakia is strongly supported as monophyletic, and this change is not necessitated by the phylogeny. similarly, based on genetic and morphological data, recent authors suggested resurrecting the genus saara for the basal clade of uromastyx. however, uromastyx is strongly supported as monophyletic in our results and in those of the recent revision, and this change is not needed. we therefore retain laudakia and uromastyx as previously defined, to preserve taxonomic stability in these groups. we note that recent studies have also begun to revise species limits in other groups such as trapelus, and taxa such as t. pallidus may represent populations within other species. within pleurodonta we generally confirm the monophyly and composition of the clades that were ranked as families within the group based on previous molecular studies and earlier morphological analyses. one important exception is the previously recognized polychrotidae. our results confirm that anolis and polychrus are not sister taxa, as also found in some previous molecular studies, but not others. our results provide strong support for non-monophyly of polychrotidae, placing polychrus with hoplocercidae and anolis with corytophanidae. recent analyses placing anolis with polychrus showed only weak support for this relationship, despite many loci. we support continued recognition of dactyloidae for anolis and polychrotidae for polychrus, based on a limited number of loci but extensive taxon sampling. we note that these families are still monophlyetic, even if they prove to be sister taxa. interestingly, our results for relationships among pleurodont families differ from most previous studies, and are surprisingly well-supported in some cases by shl values. in previous studies, many relationships among pleurodont families were poorly supported by bayesian posterior probabilities and by parsimony and likelihood bootstrap values, though typically sampling fewer taxa or characters. studies including nuclear loci found strong concatenated bayesian support for many relationships but weak support from ml bootstrap analyses for many of the same relationships. the latter pattern was also found in an analysis including those same loci and mitochondrial data for > species. we also find a mixture of strongly and weakly supported clades, but with many relationships that are incongruent with these previous studies. first, we find that tropiduridae is weakly supported as the sister group to all other pleurodonts, followed successively by iguanidae, leiocephalidae, crotaphytidae + phrynosomatidae, polychrotidae + hoplocercidae, and corytophanidae + dactyloidae. the relatively strong support for the clades crotaphytidae + phrynosomatidae, polychrotidae + hoplocercidae, and corytophanidae + dactyloidae is largely unprecedented in previous studies. as in many previous analyses, deeper relationships among the families remain weakly supported. we also find a strongly supported clade containing liolaemidae, opluridae, and leiosauridae, with opluridae + leiosauridae also strongly supported. both clades have also been found in previous studies, including studies based on or more nuclear loci. we note that previous studies have shown strong support for some pleurodont relationships, only to be strongly overturned with additional data. therefore, the relationships found here should be taken with some caution, with the possible exception of the recurring clade of liolaemidae +. all pleurodont families are strongly supported as monophyletic. within the pleurodont families, our results generally support the current generic-level taxonomy. however, there are some exceptions. within tropiduridae, tropidurus is paraphyletic with respect to eurolophosaurus, strobilurus, uracentron, and plica. within opluridae, the monotypic genus chalarodon renders oplurus paraphyletic. two leiosaurid genera are also problematic. in enyaliinae, anisolepis is paraphyletic with respect to urostrophus, and this clade is nested within enyalius. in leiosaurinae, pristidactylus is rendered paraphyletic by leiosaurus and diplolaemus. within dactyloidae, a recent study re-introduced a more subdivided classification of anoles, an issue that has been debated extensively in the past. our results support the monophyly of all the genera recognized by recent authors, including anolis, audantia, chamaelinorops, dactyloa, deiroptyx, norops, and xiphosurus. however, since anolis is monophyletic as traditionally defined, we retain that definition here for continuity with the recent literature. serpentes relationships among the major serpent groups are generally similar to other recent studies. we find that the blindsnakes, scolecophidia are not monophyletic, as in previous studies. similar to some previous studies, our data weakly place anomalepididae as the sister taxon to all snakes, and the scolecophidian families gerrhopilidae, leptotyphlopidae, typhlopidae, and xenotyphlopidae as the sister-group to all other snakes excluding anomalepididae. previous studies have also placed anomalepididae as the sister-group to all non-scolecophidian snakes, in some cases with strong support. although it might appear that recent analyses of scolecophidian relationships support monophyly of scolecophidia, the tree including non-snake outgroups from that study shows weak support for placing anomalepidids with alethinophidians, as in other studies. we follow recent authors in recognizing xenotyphlopidae and gerrhopilidae as distinct families. leptotyphlopidae is strongly supported as the sister group of a clade comprising gerrhopilidae, xenotyphlopidae, and typhlopidae. as in previous studies, we find strong support for non-monophyly of several typhlopid genera. there are also undescribed taxa of uncertain placement within this group. the systematics of typhlopoid snakes will thus require extensive revision in the future, with additional taxon and character sampling. within alethinophidia, aniliidae is strongly supported as the sister taxon of tropidophiidae, and all other alethinophidians form a strongly supported sister group to this clade. the enigmatic family xenophidiidae is weakly placed as the sister-group to all alethinophidians exclusive of anilioidea. the family bolyeriidae is weakly placed as the sister-group to pythons, boas, and relatives, which are strongly supported. relationships in this group are generally consistent with other recent molecular studies. relationships among other alethinophidians are a mixture of strongly and weakly supported nodes. we find strong support for a clade containing anomochilidae + cylindrophiidae + uropeltidae. this clade of three families is strongly supported as the sister taxon to xenopeltidae +. together, these six families form a strongly supported clade that is weakly supported as the sister group to the strongly supported clade of boidae + calabariidae. within the clade of anomochilidae, cylindrophiidae, and uropeltidae, we weakly place anomochilus as the sister group to cylindrophiidae, in contrast to previous studies which placed anomochilus within cylindrophis. however, support for monophyly of cylindrophis excluding anomochilus is weak. as in previous studies, we find several taxonomic problems within uropeltidae. specifically, rhinophis and uropeltis are paraphyletic with respect to each other and to pseudotyphlops. the problematic taxa are primarily sri lankan, and forthcoming analyses will address these issues. within pythonidae, the genus python is the sister group to all other genera. some species that were traditionally referred to as python are instead sister to an australasian clade consisting of antaresia, apodora, aspidites, bothrochilus, leiopython, liasis, and morelia. these taxa have been referred to as broghammerus, a name originating from an act of "taxonomic vandalism" in a non-peer reviewed organ without data or analyses. however, this name was, perhaps inadvertently, subsequently used by researchers in peer-reviewed work and has entered into somewhat widespread usage. this name should be ignored and replaced with a suitable substitute. within the australasian clade, morelia is paraphyletic with respect to all other genera, and liasis is non-monophyletic with respect to apodora, although many of the relevant relationships are weakly supported. within boidae, our results and those of other recent studies have converged on estimated relationships that are generally similar to each other but which differ from traditional taxonomy. however, the classification has yet to be modified to reflect this, and we rectify this situation here. we find that calabariidae is nested within boidae, but this is poorly supported, and contrary to most previous studies. while calabaria has been classified as an erycine boid in the past, this placement is strongly rejected here and in other studies. if the current placement of calabaria is supported in the future, it would require recognition as the subfamily calabariinae in boidae. the malagasy boine genera acrantophis and sanzinia are placed as the sister taxa to a weakly-supported clade containing calabariidae and a strongly supported clade comprising the currently recognized subfamilies erycinae, ungaliophiinae, and other boines. regardless of the position of calabariidae, this placement of malagasy boines renders boinae paraphyletic. we therefore resurrect the subfamily sanziniinae for acrantophis and sanzinia. this subfamily could be recognized as a distinct family if future studies also support placement of this clade as distinct from other boidae + calabariidae. the genera lichanura and charina are currently classified as erycines, but are strongly supported as the sister group to ungaliophiinae, as in previous studies. we expand ungaliophiinae to include these two genera, rather than erect a new subfamily for these taxa. the subfamily ungaliophiinae is placed as the sister group to a well-supported clade containing the rest of the traditionally recognized erycinae and boinae. we restrict erycinae to the old world genus eryx. the genus candoia from oceania and new guinea, is placed as the sister taxon to a moderately supported clade consisting of erycinae and the remaining genera of boinae. to solve the non-monophyly of boinae with respect to erycinae, we place candoia in a new subfamily. boinae then comprises the four neotropical genera that have traditionally been classified in this group. we acknowledge that non-monophyly of boinae could be resolved in other ways. however, our taxonomy maintains the traditionally used subfamilies boinae, erycinae, and ungaliophiinae, modifies them to reflect the phylogeny, and recognizes the phylogenetically distinct boine clades as separate subfamilies. within boinae, eunectes renders epicrates paraphyletic, but this is not strongly supported. our results for advanced snakes are generally similar to those of other recent studies, and will only be briefly described. however, in contrast to most recent studies, acrochordidae is here strongly placed as the sister group to xenodermatidae. this clade is then the sister group to the remaining colubroidea, which form a strongly supported clade. this relationship has been found in some previous studies, and was hypothesized by early authors. further evidence will be required to resolve this conclusively. analyses based on concatenation of 20– loci do not support this grouping, though preliminary species-tree analyses of > loci do. relationships in pareatidae are similar to recent studies, and the group is strongly placed as the sister taxon to colubroids excluding xenodermatids, as in most recent analyses. the family viperidae is the sister group to all colubroids excluding xenodermatids and pareatids, as in other recent studies. the family viperidae is strongly supported, as is the subfamily viperinae, and the sister-group relationship between azemiopinae and crotalinae. our results generally support the existing generic-level taxonomy within viperinae. however, we recover a strongly supported clade within viperinae consisting of daboia russelii, d. palaestinae, macrovipera mauritanica, and m. deserti, as in previous studies. we corroborate previous suggestions that these taxa be included in daboia, though this has not been widely adopted. the other macrovipera species remain in that genus. within crotalinae, a number of genera appear to be non-monophyletic. the species trimeresurus gracilis is strongly supported as the sister taxon to ovophis okinavensis and distantly related to other trimeresurus, whereas the other ovophis are strongly placed as the sister group to protobothrops. a well-supported clade containing atropoides picadoi, cerrophidion, and porthidium renders atropoides paraphyletic. the species bothrops pictus, considered incertae sedis in previous studies, is here strongly supported as the sister taxon to a clade containing rhinocerophis, bothropoides, bothriopsis, and bothrops. most of these relationships are strongly supported. viperidae is strongly placed as the sister taxon to a well-supported clade containing colubridae, elapidae, homalopsidae, and lamprophiidae. monophyly of homalopsidae is also strongly supported. within homalopsidae, non-monophyly of the genus enhydris is strongly supported, and it should likely be split into multiple genera. homalopsidae is weakly supported as the sister group of elapidae + lamprophiidae. this same relationship was also weakly supported by previous analyses, but other studies have found strong support for placing homalopsidae as the sister group of a strongly supported clade including elapidae, lamprophiidae, and colubridae, including data from > loci. support for the monophyly of lamprophiidae is strong, and most of its subfamilies are well-supported including atractaspidinae, aparallactinae, lamprophiinae, prosymninae, pseudaspidinae, psammophiinae, and pseudoxyrhophiinae. in lamprophiidae, most genera are monophyletic based on our sampling. however, within aparallactinae, xenocalamus is strongly placed within amblyodipsas, and in atractaspidinae, homoroselaps is weakly placed in atractaspis. in lamprophiinae, lamprophis is paraphyletic with respect to lycodonomorphus but support for the relevant clades is weak. the enigmatic genera buhoma from africa and psammodynastes from asia were both previously considered incertae sedis within lamprophiidae. here they are weakly placed as sister taxa, and more importantly, they form a strongly supported clade with the african genus pseudaspis. therefore, we expand pseudaspidinae to include these two genera. the genus micrelaps is weakly placed as the sister taxon to lamprophiidae + elapidae. along with oxyrhabdium and montaspis, this genus is treated as incertae sedis in our classification. if future studies strongly support these relationships, they may require a new family for micrelaps and possibly a new subfamily for oxyrhabdium, though placement of these taxa has been highly variable in previous studies. monophyly of elapidae is strongly supported, and calliophis melanurus is strongly supported as the sister group to all other elapids. within elapidae, relationships are generally concordant with previous taxonomy, with some exceptions. the genera toxicocalamus, simoselaps, and echiopsis are all divided across multiple clades, with strong support for many of the relevant branches. a recent study has provided a generic re-classification of the sea snakes to resolve the extensive paraphyly of genera found in previous studies. our results support this classification. monophyly of colubridae and most of its subfamilies are strongly supported. however, relationships among many of these subfamilies are weakly supported, as in most previous studies. the subfamilies calamariinae and pseudoxenodontinae are strongly supported as sister taxa, and weakly placed as the sister-group to the rest of colubridae. there is a weakly supported clade comprising natricinae +, but the clade uniting the new world dipsadinae with the asian genus thermophis is strongly supported. here, we place thermophis in dipsadinae, making it the first and only asian member of this otherwise exclusively new world subfamily. however, despite the strong support for its placement here, placement of this taxon has been variable in previous analyses, and we acknowledge that future analyses may support recognition of a distinct subfamily. the clade of natricinae and dipsadinae is weakly supported as the sister group to a clade containing sibynophiinae +. the subfamily colubrinae is weakly supported; we find that the colubrine genera ahaetulla, chrysopelea, and dendrelaphis form a strongly supported clade that is weakly placed as the sister group to the rest of colubrinae, which form a strongly supported clade. this clade was also placed with grayiinae or sibynophiinae in many preliminary analyses, rendering colubrinae paraphyletic. this group of three genera has been strongly supported in the past, and only weakly placed with colubrinae. it is possible that future analyses will reveal that the clade of ahaetulla, chrysopelea, and dendrelaphis is placed elsewhere in colubridae with strong support, and thus merit recognition as a distinct subfamily. a notable feature of this clade is the presence of gliding flight in most species of chrysopelea, less-developed non-flight jumping with similar locomotor origins in dendrelaphis, and homologous glide-related traits in ahaetulla. numerous colubroid genera are not included in our tree and are not clearly placed in subfamilies based on previous morphological evidence. in our classification, these genera are also considered incertae sedis within colubridae, including blythia, cyclocorus, elapoidis, gongylosoma, helophis, myersophis, oreocalamus, poecilopholis, rhabdops, and tetralepis, as in previous classifications. our phylogeny reveals numerous taxonomic problems within colubrinae. the genus boiga is paraphyletic with respect to crotaphopeltis, dipsadoboa, telescopus, toxicodryas, and dasypeltis, with strong support. the genus philothamnus is paraphyletic with respect to hapsidophrys. the genus coluber is split between old world and new world clades. the species hierophis spinalis is sister to eirenis to the exclusion of the other hierophis species. the genus dryocalamus is nested within lycodon. the species chironius carinatus and c. quadricarinatus are weakly placed in a clade of neotropical colubrines only distantly related to the other chironius species. the genus drymobius renders dendrophidion paraphyletic. the monotypic genus rhynchophis renders the two species of rhadinophis paraphyletic. the genus coronella is rendered paraphyletic by oocatochus with weak support. finally, the genus rhinechis is nested within zamenis. we find numerous non-monophyletic genera within natricinae, as in previous studies. these non-monophyletic genera include the asian genera amphiesma, atretium, and xenocrophis. among new world genera, we find regina to be non-monophyletic with respect to most other genera, as in previous phylogenetic studies. also, as in previous studies, we find that adelophis is nested deep within thamnophis. finally, within a weakly supported dipsadinae, we find non-monophyly of numerous genera, as in many earlier studies. these problems of non-monophyly include leptodeira, geophis, atractus, sibynomorphus, dipsas, taeniophallus, and echinanthera. recent revisions have begun to tackle these problems, but additional taxon and character sampling will be crucial to resolve relationships and taxonomy. discussion in this study, we provide a phylogenetic estimate for species of squamates based on molecular data from up to genes per species, combining much of the relevant data used in previous molecular phylogenetic analyses. this tree provides a framework for future evolutionary studies, spanning from the species level to relationships among families, utilizing a common set of branch lengths. these estimated branch lengths are critically important for most phylogenetic comparative methods. to further facilitate use of this phylogeny in comparative studies, we provide the newick version of this tree in datadryad repository /dryad.82h0m and additional file 1: data file s our results also suggest that the branch lengths in this tree should not generally be compromised by missing data for some genes in some taxa. our results also reveal many problems in squamate classification at nearly all phylogenetic levels. we make several changes to higher-level taxonomy based on this phylogeny, including changes to the traditionally recognized subfamilies of boid snakes, lamprophiid snakes, colubrid snakes, and gymnophthalmid lizards and scincid lizards. in appendix i, we list the generic content of all families and subfamilies. we also find dozens of problems at the genus level, many of which have been identified previously, and which we defer the resolution of to future studies. our results also highlight potential problems in recent proposals to modify the classification of scincid and teiid lizards. in addition to synthesizing existing molecular data for squamate phylogeny, our analyses also reveal several apparently novel findings. given space constraints, we cannot detail every deviation from previous phylogenetic hypotheses. nevertheless, we focus on three sets of examples. first, we find some relatively novel, strongly-supported relationships at the family level. these include the placement of helodermatidae and the placement of xenodermatidae as the sister taxon to acrochordidae, in contrast to most recent analyses of anguimorphs and snakes. we also find some novel, strongly supported relationships among pleurodont families, but we acknowledge that these may be overturned in future studies. the second example is the higher-level relationships within scincidae, the largest family of lizards. no previous studies examining higher-level relationships within the group included more than ~ species. in this study, we sample skink species, and our phylogeny provides a unique resolution of higher-level skink relationships. some previous researchers placed acontiines as the sister group to all other skinks, but suggested that scincines and lygosomines were paraphyletic with respect to each other. in contrast, others suggested that acontiines, feyliniines, and lygosomines were all nested inside scincines, although many clades were only weakly supported. here, we find that acontiines are the sister group to a strongly supported clade consisting of a monophyletic scincinae and a monophyletic lygosominae. third, our phylogeny reveals numerous genera that appear to be non-monophyletic, with many of these cases having strong support for the associated nodes. our examples include genera in many families, including dibamids, diplodactylids, gekkonids, phyllodactylids, gerrhosaurids, scincids, teiids, gymnophthalmids, lacertids, anguids, chamaeleonids, agamids, tropidurids, oplurids, leiosaurids, typhlopids, pythonids, uropeltids, boids, viperids, lamprophiids, elapids, and colubrids. although many problems noted here were found in previous studies, some seem to be new, such as placement of crocodilurus and draceana within tupinambis and coloptychon within gerrhonotus. our study also offers an important test of higher-level squamate relationships using a very different sampling strategy than that used in most previous analyses. squamates have traditionally been divided into two clades based on morphology, iguania and scleroglossa. despite considerable disagreement among morphology-based hypotheses, this basic division is supported by nearly all phylogenetic analyses based on morphological data. in contrast, our results and those of most previous molecular analyses strongly support placement of iguanians with anguimorphs and snakes. the causes of this conflict remain unclear, but may be related to morphological traits associated with different feeding strategies of iguanian and scleroglossan squamates. additionally, analyses of morphology often place dibamids, amphisbaenians, snakes, and some scincids and anguids in a single clade. our analyses do not support such a clade, nor do other analyses of molecular data alone, or analyses of combined molecular and morphological data. instead, these morphological results seem to be explained by convergence associated with burrowing. overall, molecular datasets have shown overwhelmingly strong support for placement of dibamids and gekkonids at the base of the tree, amphisbaenians with lacertoids, and iguanians with snakes and anguimorphs. these results have now been corroborated with up to genes for taxa, genes for taxa, and genes for taxa. we now support this basic topology with species sampled for up to genes each. nevertheless, despite the overall strong support for most of the tree, certain clades remain poorly supported. a potential criticism of the supermatrix approach used here is that this weak support may occur due to missing data. however, previous studies of datasets have shown explicitly that there is typically little relationship between branch support for terminal taxa and the amount of missing data. instead, these patterns of weak support are more likely to reflect short underlying branch lengths, and may be difficult to resolve even with more complete taxonomic and genomic sampling. indeed, as noted above, many of the weakly supported nodes in our phylogeny are also weakly supported in analyses with little missing data and large numbers of genes, such as the relationships of many pleurodont lizard families and colubroid snake families and subfamilies. we acknowledge that the differences between our results and previous studies do not necessarily mean that our results are right and those of previous studies are wrong. in some cases, we provide strong support for novel relationships when previous, conflicting studies showed only weak support. in other cases, our results disagree with other studies for clades that were strongly supported. in the best-case scenario, these conflicts may be resolved because our results are correct, possibly reflecting the beneficial effects of adding taxa and the associated subdivision of long branches. furthermore, in many cases, we are including more genes than used in previous studies of particular clades, increasing sampling of characters and loci. this should generally reduce spurious results caused by sampling few characters and by incongruence between gene and species trees. however, other explanations for incongruence between our results and previous studies are also possible. adding taxa can potentially lead to incorrect results in some cases, such as when a long terminal branch is added that further subdivides a short internal branch. in other cases, conflicts with our results might reflect the impact of our sampling fewer nuclear genes and a correspondingly increased influence of mitochondrial data. mitochondrial genes have relatively fast evolutionary rates, and their phylogenetic resolution for a particular node may also reflect introgression or incomplete lineage sorting rather than the species phylogeny. many taxa in the matrix are represented only by mitochondrial data, and highly variable mitochondrial genes might also overcome the influence of less variable nuclear genes in combined analyses. such cases might explain some strongly supported conflicts between our results and those based on multiple nuclear loci. another possibility is that some cases may represent failure to find the optimal tree. we acknowledge that there are many reasons why our results may differ from previous studies, and the ultimate test of these novel findings will be corroboration in future studies that include more taxa and characters. this analysis also corroborates several recent studies suggesting that the supermatrix approach is a powerful strategy for large-scale phylogenetic inference. for example, even though each species had 81% missing data on average, we found that most species were placed in the families and genera expected based on previous taxonomy, often with very strong support. furthermore, we found that incompleteness of terminal taxa is not related to branch lengths, suggesting that missing data are not significantly biasing branch-length estimates. also, the ml models we used have been shown to be robust to missing data in large, sparse supermatrices. even though we did find some subfamilies and genera to be non-monophyletic, similar relationships were often found in previous studies based on data matrices with only limited missing data. we suggest that further resolution of the squamate tree will be greatly facilitated if researchers deliberately sample mitochondrial genes and nuclear genes that include the set of genes used here and in recent phylogenomic studies, to increase overlap between genes and taxa, and decrease missing data. with over species remaining to be included and only genes sampled, our study is far from the last word on squamate phylogeny. we note that new data can easily be added to this matrix, in terms of both new taxa and new genes. increased sampling of other nuclear genes is likely to be advantageous as well. next-generation sequencing strategies and phylogenomic methods should help resolve difficult nodes, as should application of species-tree methods. species-tree analyses of nuclear loci support many of these same clades across squamates, and data from > nuclear loci reinforces many of the relationships found here among the colubroid snake subfamilies. in addition, it would be useful to incorporate fossil taxa in future studies, utilizing the large morphological datasets that are now available. despite these areas for future studies, the present tree provides a framework for researchers analyzing patterns of squamate evolution at both lower and higher taxonomic levels, and for building a more complete picture of squamate phylogeny.  in this study, we provide a phylogenetic estimate for squamate species, based on a supermatrix approach. our results provide important confirmation for previous studies based on more limited taxon sampling, and reveal new relationships at the level of families, genera, and species. we also provide a phylogenetic framework for future comparative studies, with a large-scale tree including a common set of estimated branch lengths. finally, we provide a revised classification for squamates based on this tree, including changes in the higher-level taxonomy of gymnophthalmid and scincid lizards and boid, colubrid, and lamprophiid snakes. 
this classification includes new, resurrected, and modified subfamilies within gymnophthalmid and scincid lizards, and boid, colubrid, and lamprophiid snakes. we present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for future comparative studies. the tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy. the extant squamates are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. the tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data, estimates that are very different from previous morphology-based hypotheses. the analysis is based on up to base pairs of sequence data per species from genes, including seven nuclear loci, and five mitochondrial genes.
 the extant squamates are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. such an estimate is invaluable for comparative evolutionary studies, and to address their classification. here, we present the first large-scale phylogenetic estimate for squamata.  the estimated phylogeny contains species, representing all currently recognized families and subfamilies. the analysis is based on up to base pairs of sequence data per species from genes, including seven nuclear loci, and five mitochondrial genes. the tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data, estimates that are very different from previous morphology-based hypotheses. the tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy.  we present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for future comparative studies. we also present a revised classification of squamates at the family and subfamily level to bring the taxonomy more in line with the new phylogenetic hypothesis. this classification includes new, resurrected, and modified subfamilies within gymnophthalmid and scincid lizards, and boid, colubrid, and lamprophiid snakes. amphisbaenialacertilialikelihood support measuresmissing dataserpentessquamataphylogeneticsreptiliasupermatricessystematics 