Data from: Bayesian total-evidence dating reveals the recent crown radiation of penguins

The total-evidence approach to divergence-time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilisation process and can produce estimates that lead to erroneous conclusions. We address this shortcoming by providing a total-evidence method implemented in a Bayesian framework. This approach uses a mechanistic tree prior to describe the underlying diversification process that generated the tree of extant and fossil taxa. Previous attempts to apply the total-evidence approach have used tree priors that do not account for the possibility that fossil samples may be direct ancestors of other samples, that is, ancestors of fossil or extant species or of clades. The fossilised birth-death process explicitly models the diversification, fossilisation, and sampling processes and naturally allows for sampled ancestors. This model was recently applied to estimate divergence times based on molecular data and fossil occurrence dates. We incorporate the fossilised birth-death model and a model of morphological trait evolution into a Bayesian total-evidence approach to dating species phylogenies. We apply this method to extant and fossil penguins and show that the modern penguins radiated much more recently than has been previously estimated, with the basal divergence in the crown clade occurring at ~12.7 Ma and most splits leading to extant species occurring in the last 2 million years. Our results demonstrate that including stem-fossil diversity can greatly improve the estimates of the divergence times of crown taxa. The method is available in BEAST2 (version 2.4) software www.beast2.org with packages SA (version at least 1.1.4) and morph-models (version at least 1.0.4) installed.分歧时间定年的总证据法（total-evidence approach）利用现生物种与化石物种的分子、形态学数据，在单一统一的分析框架内推断系统发育关系、物种分歧时间与宏观演化参数。当前该方法的基于模型实现方案，缺少用于描述物种分化与化石形成过程的适配树模型，可能生成引发错误结论的估算结果。本研究针对这一缺陷，提出了一种在贝叶斯框架（Bayesian framework）下实现的总证据法。该方法采用机制性树先验（mechanistic tree prior），对生成现生与化石类群系统发育树的底层分化过程进行描述。此前应用总证据法的相关研究均采用了未考虑如下情形的树先验：化石样本可能成为其他样本的直接祖先，即化石物种、现生物种或演化支（clades）的直接祖先。化石出生-死亡过程（fossilised birth-death process）可显式对物种分化、化石形成与采样过程进行建模，并天然支持采样祖先（sampled ancestors）的存在。该模型近期已被应用于基于分子数据与化石产出年代的分歧时间估算研究。本研究将化石出生-死亡模型与形态性状演化模型整合至贝叶斯总证据法中，用于物种系统发育的定年分析。本研究将该方法应用于现生与化石企鹅类群，结果显示现代企鹅的辐射演化时间远晚于此前估算：冠群演化支（crown clade）的基底分化发生于约12.7 Ma，而绝大多数指向现生物种的分化事件均发生于近200万年以内。本研究结果表明，纳入茎部化石（stem-fossil）多样性可显著提升冠群类群分歧时间的估算精度。该方法已在BEAST2（版本2.4）软件中实现，可通过官网www.beast2.org获取，使用时需安装SA包（版本不低于1.1.4）与morph-models包（版本不低于1.0.4）。