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

Background: The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to clarify their taxonomy. Here, we present the first large-scale phylogenetic estimate for Squamata. Results: The estimated phylogeny contains 4161 species representing all currently recognized families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy. Conclusions: We present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for future comparative studies. We also present a revised classification of squamates at the family and subfamily level to bring the taxonomy more in line with the new phylogenetic hypothesis. This classification includes new, resurrected, and modified subfamilies within gymnophthalmid and scincid lizards and boid, colubrid, and lamprophiid snakes.背景：现存有鳞类（已知蜥蜴与蛇类物种超9400种）是陆生脊椎动物中多样性最高、最具辨识度的演化辐射类群之一，但此前尚未有研究采用大规模类群采样对该类群重建系统发育树。此类系统发育估计对于比较进化研究以及厘清其分类学体系均具有极高价值。本研究首次针对有鳞目（Squamata）开展大规模系统发育估计。 结果：本次构建的系统发育树涵盖4161个物种，覆盖当前所有已被认可的科与亚科。分析基于12个基因的序列数据，单物种序列长度最高可达12896碱基对（bp，平均为2497 bp），其中包含7个核基因位点（BDNF、c-mos、NT3、PDC、R35、RAG-1及RAG-2）以及5个线粒体基因（12S、16S、细胞色素b、ND2及ND4）。该树为近年来基于分子数据（但类群采样规模有限）的有鳞目高阶系统发育估计提供了重要支持，此类分子估计结果与此前基于形态学的分类假说差异显著。同时，本次构建的系统发育树包含诸多与以往分子估计及传统分类学均不一致的类群关系。 结论：本研究构建了全新的大规模有鳞爬行动物系统发育树，可为未来的比较进化研究提供宝贵资源。同时，我们还修订了有鳞类在科及亚科层级的分类体系，使其与新的系统发育假说更为契合。该分类体系在裸眼蜥科（Gymnophthalmidae）、石龙子科（Scincidae）的蜥蜴以及蚺科（Boidae）、游蛇科（Colubridae）和闪皮蛇科（Lamprophiidae）的蛇类中，纳入了新设立、恢复有效及经修订的亚科。