Data from: Phylogenomic analyses of more than 4,000 nuclear loci resolve the origin of snakes among lizard families

Squamate reptiles (lizards and snakes) are the most diverse group of terrestrial vertebrates, with >10,000 species. Despite considerable effort to resolve relationships among major squamates clades, some branches have remained difficult. Among the most vexing has been the placement of snakes among lizard families, with most studies yielding only weak support for the position of snakes. Furthermore, the placement of iguanian lizards has remained controversial. Here we used targeted sequence capture to obtain data from 4178 nuclear loci from ultraconserved elements (UCEs) from 32 squamate taxa (and 5 outgroups) including representatives of all major squamate groups. Using both concatenated and species-tree methods, we recover strong support for a sister relationship between iguanian and anguimorph lizards, with snakes strongly supported as the sister group of these two clades. These analyses strongly resolve the difficult placement of snakes within squamates and show overwhelming support for the contentious position of iguanians. More generally, we provide a strongly supported hypothesis of higher-level relationships in the most species-rich tetrapod clade using coalescent-based species-tree methods and ~100 times more loci than previous estimates.

有鳞目爬行动物（Squamate reptiles）是陆地脊椎动物中多样性最高的类群，现存物种数量超过10000种。尽管学界已付出诸多努力以厘清有鳞目主要演化支间的系统发育关系，但部分分支的归属仍难以确定。其中最棘手的问题之一，便是蛇类在蜥蜴类群中的系统发育位置，多数相关研究仅能为蛇类的定位提供微弱支持。此外，鬣蜥类蜥蜴的分类位置也始终存在争议。本研究通过靶向序列捕获技术，从32个有鳞目类群（外加5个外类群）的超保守元件（ultraconserved elements, UCEs）中获取了4178个核基因位点的数据，涵盖了所有主要有鳞目类群的代表物种。本研究同时采用串联法与物种树分析方法，结果强烈支持鬣蜥类与蛇蜥类蜥蜴构成姐妹群关系，且蛇类作为这两个类群的姐妹群得到了显著支持。本分析不仅成功解决了蛇类在有鳞目内系统发育位置这一长期难题，还为鬣蜥类存在争议的分类位置提供了压倒性的支持证据。更广泛而言，本研究基于溯祖法物种树分析方法，利用较以往研究多近百倍的基因位点数据，为这个物种最丰富的四足动物类群提供了得到强力支持的高阶系统发育关系假说。