Data from: Phylogenetic inference and divergence dating of snakes using molecules, morphology and fossils: new insights into convergent evolution of feeding morphology and limb reduction

Bayesian divergence time analyses were used to simultaneously infer the phylogenetic relationships and date the major clades of snakes including several important fossils that have not previously been included in divergence dating analyses as terminal taxa. We also explored the effect of using fossilized birth–death (FBD) and uniform tree priors for divergence dating with terminal calibrations. Nonclock and relaxed clock analyses of the combined morphology and molecular data set supported previous molecular phylogenetic hypotheses for the major clades of snakes, including the paraphyly of the traditionally recognized Scolecophidia and Macrostomata. Tip-dating analyses using either a uniform tree prior or FBD prior that assume that all fossils are tips and that extant lineages are randomly sampled resulted in older ages than those inferred using a FBD prior assuming diversified sampling of extant lineages and those estimated by previous studies. We used Bayesian ancestral state reconstruction methods to map the evolution of the ability to consume large prey and the loss of limbs onto our inferred time-calibrated phylogeny. We found strong support for early evolution of the ability to consume large prey, indicating multiple independent losses of this ability. We also found strong support for retention of external hindlimbs until relatively late in snake evolution, indicating multiple independent losses of hindlimbs.

本研究采用贝叶斯分化时间分析（Bayesian divergence time analyses），同时推断蛇类主要演化支的系统发育关系并估算其分化时间，纳入了此前未被纳入分化定年分析的若干重要化石作为末端分类单元。本研究还探讨了在末端校准的分化定年分析中，使用化石出生-死亡（fossilized birth-death, FBD）模型与统一树先验的效果。基于形态学与分子学联合数据集的非分子钟及宽松分子钟分析，支持此前针对蛇类主要演化支的分子系统发育假说，其中包括传统分类单元中盲蛇下目（Scolecophidia）与大舌亚目（Macrostomata）为并系群的结论。采用统一树先验或FBD先验的末端定年分析——该类先验假设所有化石均为末端类群，且现生支系为随机采样——所得分化时间早于采用假设现生支系为多样化采样的FBD先验的分析结果，同时也早于此前相关研究的估算值。本研究借助贝叶斯祖先状态重建方法，将大型猎物捕食能力的演化历程与四肢丢失事件，映射至本研究推断得到的时间校准系统发育树。分析结果显示，大型猎物捕食能力起源于蛇类演化早期，且该能力曾多次独立丢失；同时，研究还为外后肢在蛇类演化中保留至相对较晚阶段提供了强有力的支持，表明后肢也曾多次独立丢失。