Data from: Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating

Background Bayesian relaxed-clock dating has significantly influenced our understanding of the timeline of plant evolution. This approach requires the use of priors on the branching process, yet little is known about their impact on divergence time estimates. We investigated the effect of branching priors using the iconic cycads. We conducted phylogenetic estimations for 237 cycad species using three genes and two calibration strategies incorporating up to six fossil constraints to (i) test the impact of two different branching process priors on age estimates, (ii) assess which branching prior better fits the data, (iii) investigate branching prior impacts on diversification analyses, and (iv) provide insights into the diversification history of cycads. Results Using Bayes factors, we compared divergence time estimates and the inferred dynamics of diversification when using Yule versus birth-death priors. Bayes factors were calculated with marginal likelihood estimated with stepping-stone sampling. We found striking differences in age estimates and diversification dynamics depending on prior choice. Dating with the Yule prior suggested that extant cycad genera diversified in the Paleogene and with two diversification rate shifts. In contrast, dating with the birth-death prior yielded Neogene diversifications, and four rate shifts, one for each of the four richest genera. Nonetheless, dating with the two priors provided similar age estimates for the divergence of cycads from Ginkgo (Carboniferous) and their crown age (Permian). Of these, Bayes factors clearly supported the birth-death prior. Conclusions These results suggest the choice of the branching process prior can have a drastic influence on our understanding of evolutionary radiations. Therefore, all dating analyses must involve a model selection process using Bayes factors to select between a Yule or birth-death prior, in particular on ancient clades with a potential pattern of high extinction. We also provide new insights into the history of cycad diversification because we found (i) periods of extinction along the long branches of the genera consistent with fossil data, and (ii) high diversification rates within the Miocene genus radiations.背景 贝叶斯宽松分子钟定年法（Bayesian relaxed-clock dating）极大地推动了我们对植物演化时间线的认知。该方法需要为分支过程设定先验分布，但目前对这些先验对分歧时间估计的影响尚不明晰。我们以标志性的苏铁类（cycads）为研究对象，探究分支过程先验的作用效应。我们针对237个苏铁物种开展系统发育估计，采用3个基因标记与2种校准策略（最多纳入6项化石约束），旨在达成四个研究目标：(i) 检验两种不同分支过程先验对分歧时间估计的影响；(ii) 评估哪种分支先验更适配当前数据集；(iii) 探究分支先验对多样化分析的影响；(iv) 为苏铁类的多样化历史提供新的科学认知。 结果 借助贝叶斯因子（Bayes factors），我们比较了使用尤勒先验（Yule prior）与生灭先验（birth-death prior）时的分歧时间估计结果与推断得到的多样化动态。贝叶斯因子通过阶梯采样法（stepping-stone sampling）估计的边际似然值计算得到。我们发现，先验选择的差异会导致分歧时间估计与多样化动态出现显著差异。采用尤勒先验进行定年分析显示，现存苏铁类各属在古近纪发生多样化，并伴随两次多样化速率转移事件。与之相反，使用生灭先验的定年结果则表明苏铁类在新近纪发生多样化，且存在四次速率转移事件，对应物种丰富度最高的四个属各一次。不过，两种先验得到的苏铁与银杏属（Ginkgo）的分歧时间（石炭纪）以及苏铁类的冠群年龄（二叠纪）结果相近。其中，贝叶斯因子明确支持生灭先验。 结论 本研究结果表明，分支过程先验的选择会极大地影响我们对进化辐射的认知。因此，所有定年分析均应采用贝叶斯因子开展模型选择，以在尤勒先验与生灭先验之间做出最优抉择，针对存在高灭绝潜在模式的古老支系类群尤为如此。此外，我们的研究为苏铁类的多样化历史提供了新的科学认知：我们发现(1) 沿苏铁类各属长分支存在的灭绝时期与化石记录相符；(2) 中新世（Miocene）时期的属级辐射事件伴随较高的多样化速率。