Data from: Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria)

Dated phylogenies of fossil taxa allow palaeobiologists to estimate the timing of major divergences and placement of extinct lineages, and to test macroevolutionary hypotheses. Recently developed Bayesian ‘tip-dating’ methods simultaneously infer and date the branching relationships among fossil taxa, and infer putative ancestral relationships. Using a previously published dataset for extinct theropod dinosaurs, we contrast the dated relationships inferred by several tip-dating approaches and evaluate potential downstream effects on phylogenetic comparative methods. We also compare tip-dating analyses to maximum-parsimony trees time-scaled via alternative a posteriori approaches including via the probabilistic cal3 method. Among tip-dating analyses, we find opposing but strongly-supported relationships, despite similarity in inferred ancestors. Overall, tip-dating methods infer divergence dates often millions (or tens of millions) of years older than the earliest stratigraphic appearance of that clade. Model-comparison analyses of the pattern of body-size evolution found that the support for evolutionary mode can vary across and between tree-samples from cal3 and tip-dating approaches. These differences suggest that model and software choice in dating analyses can have a substantial impact on the dated phylogenies obtained and broader evolutionary inferences.

化石类群的定年系统发育树（dated phylogenies）可助力古生物学家估算主要分化事件的发生时序、明确已灭绝支系的系统发育位置，并检验宏进化假说（macroevolutionary hypotheses）。近年发展出的贝叶斯末端定年法（Bayesian tip-dating）可同时推断化石类群间的分支关系并为其定年，同时推测推定的祖先关系。
本研究利用一套已公开的灭绝兽脚类恐龙（theropod dinosaurs）数据集，对比多种末端定年法推断得到的定年系统发育关系，并评估其对系统发育比较方法（phylogenetic comparative methods）可能产生的后续影响。此外，本研究还将末端定年分析结果，与通过不同后验（a posteriori）方法（包括概率性cal3方法（cal3 method））完成时间校准的最大简约树（maximum-parsimony trees）进行了对比。
在末端定年分析中，尽管不同方法推断得到的祖先关系较为相似，但我们发现其得到的系统发育关系存在对立冲突，且均具有极高的统计支持度。总体而言，末端定年法推断出的类群分化时间，通常比该演化支（clade）最早的地层化石出现时间早数百万乃至数千万年。
针对体型演化模式的模型比较分析显示，基于cal3方法与末端定年法得到的树样本，其对演化模式（evolutionary mode）的支持度存在组内与组间差异。上述差异表明，在定年分析中选用的模型与软件，会对最终得到的定年系统发育树及更广泛的进化推论产生显著影响。