Phylogenomic analyses reveal novel relationships among snake families

Snakes are a diverse and important group of vertebrates. However, relationships among the major groups of snakes have remained highly uncertain, with recent studies hypothesizing very different (and typically weakly supported) relationships. Here, we address family-level snake relationships with new phylogenomic data from 3,776 nuclear loci from ultraconserved elements (1.34 million aligned base pairs, 52% missing data overall) sampled from 29 snake species that together represent almost all families, a dataset ∼100 times larger than used in previous studies. We found relatively strong support from species-tree analyses (NJst) for most relationships, including three largely novel clades: (1) a clade uniting the boas, pythons and their relatives, (2) a clade placing cylindrophiids and uropeltids with this clade, and (3) a clade uniting bolyeriids (Round Island boas) with pythonids and their relatives (xenopeltids and loxocemids). Relationships among families of advanced snakes (caenophidians) were also strongly supported. The results show the potential for phylogenomic analyses to resolve difficult groups, but also show a surprising sensitivity of the analyses to the inclusion or exclusion of outgroups.

蛇类是一类物种多样性丰富、生态功能重要的脊椎动物类群。然而，蛇类主要类群间的系统发育关系长期以来始终存在极大不确定性，近年多项研究提出的演化关系假说差异显著，且多数支持度偏低。本研究基于超保守元件（ultraconserved elements）的3776个核基因座获取的系统基因组学新数据，对蛇类的科间系统发育关系开展解析：本次采样涵盖了几乎所有蛇类科的29个物种，所获比对序列总长134万个碱基对，整体缺失数据占比52%，数据集规模较既往研究提升约100倍。物种树分析（NJst）结果显示，绝大多数类群关系得到了较强的统计支持，其中包含三个全新的主要演化支：（1）整合蚺科、蟒科及其近缘类群的演化支；（2）将筒蛇科（cylindrophiids）与盾尾蛇科（uropeltids）归入该演化支的类群；（3）将雷蛇科（bolyeriids，即罗德里格斯岛蚺）与蟒科及其近缘类群（闪皮蛇科xenopeltids、林蚺科loxocemids）合并为独立演化支。高级蛇类（新蛇亚目Caenophidia）各科间的系统发育关系同样得到了较强支持。本研究结果既展现了系统基因组学分析在解析疑难类群演化关系上的巨大潜力，同时也揭示出相关分析对外类群的包含与排除存在出人意料的敏感性。