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：现存有鳞目（Squamata）类群包含超过9400种已知蜥蜴与蛇类，是陆生脊椎动物中多样性最高、最引人注目的辐射演化类群之一，但此前尚无研究采用大规模类群采样对该类群构建系统发育树。此类系统发育估算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）发布大规模系统发育估算结果。
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，单物种的序列长度最高可达12896个碱基对（平均长度为2497 bp），其中包含7个核基因座（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）。该系统发育树对近期基于分子数据（但类群采样规模有限）的有鳞目高阶系统发育估算结果提供了重要支持，而这些估算结果与此前基于形态学的分类假说存在显著差异。此外，本系统发育树还包含诸多与既往分子研究结果及传统分类学认知相悖的类群亲缘关系。
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极具价值的参考资源。同时，本研究针对有鳞目的科与亚科层级提出了修订后的分类系统，以使分类学体系更贴合新的系统发育假说。该分类系统在裸眼蜥科（Gymnophthalmidae）、石龙子科（Scincidae）蜥蜴，以及蚺科（Boidae）、游蛇科（Colubridae）和闪皮蛇科（Lamprophiidae）的蛇类中，纳入了全新、恢复以及经过修订的亚科类群。