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.

研究背景 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。该方法需要使用分支过程先验，但目前对其在分化时间估算中的影响尚不清楚。本研究以标志性的苏铁类（cycads）为研究对象，探究分支过程先验的影响效应。我们针对237个苏铁物种开展系统发育估算，采用3个基因标记与2种校准策略（最多纳入六项化石约束条件），旨在达成四大研究目标：其一，检验两种不同分支过程先验对定年估算结果的影响；其二，评估哪种分支先验更适配数据集；其三，探究分支先验对多样化分析的影响；其四，为苏铁类的多样化演化历史提供新的科学认知。

研究结果 本研究借助贝叶斯因子（Bayes factors），对比了使用尤尔先验（Yule prior）与出生-死亡先验（birth-death prior）时的分化时间估算结果，以及推断得到的多样化动态。贝叶斯因子通过步进石采样法（stepping-stone sampling）估算得到的边际似然值计算得出。研究发现，定年估算结果与多样化动态会因先验选择的不同而呈现显著差异。采用尤尔先验进行定年分析时，结果显示现生苏铁属类群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，采用出生-死亡先验时则得出苏铁类在新近纪发生多样化，且存在四次速率转移事件，分别对应物种丰富度最高的四个属。尽管如此，两种先验下得到的苏铁类与银杏类（Ginkgo）的分化时间（石炭纪）以及苏铁类的冠群年龄（二叠纪）估算结果均较为相近。其中，贝叶斯因子明确支持出生-死亡先验模型。

研究结论 本研究结果表明，分支过程先验的选择会极大影响我们对演化辐射事件的认知。因此，所有定年分析均需借助贝叶斯因子开展模型选择，以在尤尔先验与出生-死亡先验中做出最优选择，针对存在潜在高灭绝模式的古老支系类群尤为如此。此外，本研究还为苏铁类的多样化历史提供了新的科学认知：我们发现，其一，苏铁属类群长分支上的灭绝时段与化石记录相符；其二，中新世时期的属级辐射事件伴随较高的多样化速率。