Data from: 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.蛇类是一类多样性丰富且兼具重要生态价值的脊椎动物类群。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，近期多项研究提出的亲缘关系假说差异显著，且多数置信度较低。本研究利用新获取的系统基因组数据，针对蛇类的科间系统发育关系展开解析：该数据来源于29个覆盖几乎所有蛇类科的物种的3776个超保守元件（ultraconserved elements）核基因座，比对序列总长达134万碱基对，整体缺失数据占比为52%，数据集规模较以往研究提升了约100倍。通过物种树分析（NJst），我们获得了多数类群关系的较强置信支持，其中包含三个全新的主要支系：(1) 涵盖蚺科、蟒科及其近缘类群的支系；(2) 将筒蛇科（cylindrophiids）与盾尾蛇科（uropeltids）归入上述支系的类群；(3) 将雷蛇科（bolyeriids，即圆岛蚺）与蟒科类群及其近缘类群（闪皮蛇科xenopeltids和中美蚺科loxocemids）整合为一支的支系。高等蛇类（新蛇类，caenophidians）各科间的亲缘关系同样得到了强有力的置信支持。本研究结果既展现了系统基因组分析在解析疑难类群系统发育关系上的应用潜力，同时也揭示了分析结果对外群的纳入或排除存在出人意料的敏感性。