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（>9400个已知蜥蜴与蛇类物种）是陆生脊椎动物中多样性最为突出、最具辨识度的演化辐射类群之一，但此前尚无研究采用大规模类群采样来重建该类群的系统发育关系。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。本研究首次为有鳞目（Squamata）提供了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，覆盖了当前所有已正式确认的科与亚科。分析数据来源于12个基因的序列信息，单个物种的序列长度最高可达12896碱基对（平均长度为2497碱基对），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）。该系统发育树为近期基于分子数据（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撑，此类估算结果与此前基于形态学的演化假说存在显著差异。此外，本研究得到的系统发育关系中，诸多分支关系既不同于既往分子研究结果，也与传统分类学认知相悖。
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，将为未来的比较进化研究提供宝贵的研究资源。同时，我们针对有鳞目提出了科与亚科层面的修订分类方案，以使分类学体系与新的系统发育假说更相一致。该分类方案在裸眼蜥科（Gymnophthalmidae）、石龙子科（Scincidae）蜥蜴，以及蚺科（Boidae）、游蛇科（Colubridae）和闪皮蛇科（Lamprophiidae）的蛇类类群中，纳入了新命名、重新恢复以及经过修正的亚科类群。