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 fossilization 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 fossilized birth–death (FBD) process explicitly models the diversification, fossilization, 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 FBD 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∼12.7 Ma and most splits leading to extant species occurring in the last 2 myr. 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. [Birth–death process; calibration; divergence times; MCMC; phylogenetics.]

用于分歧时间定年的全证据法（total-evidence approach），通过整合现生与化石物种的分子及形态学数据，在单一统一的分析框架内完成系统发育关系、物种分歧时间与宏观演化参数的推断。当前该方法的基于模型实现方案，缺乏适配于描述物种分化与化石形成过程的树模型，所得估计结果可能引发错误的推论。为此，我们提出一种基于贝叶斯框架的全证据法，以弥补这一不足。该方法采用机制性树先验，对生成现生与化石类群系统发育树的底层分化过程进行刻画。既往应用全证据法的研究，所使用的树先验未考虑化石样本可作为其他样本（即化石或现生物种、演化支的直接祖先）的可能性。化石出生-死亡过程（fossilized birth–death, FBD）可显式建模物种分化、化石形成与采样过程，天然支持采样祖先的存在。近期已有研究将该模型应用于基于分子数据与化石出现时间的分歧时间估计工作。我们将FBD模型与形态性状演化模型整合至贝叶斯全证据法中，用于物种系统发育的定年分析。我们将该方法应用于现生与化石企鹅类群的分析，结果显示现代企鹅的辐射演化时间远晚于此前的估计：冠群的基部分化发生于约12.7 Ma，绝大多数现生物种的分化事件均发生于近2 myr内。本研究结果表明，纳入茎部化石类群的多样性信息，可显著提升冠群物种分歧时间的估计精度。本方法可通过BEAST2（版本2.4）软件实现，相关网址为www.beast2.org，需安装SA（版本≥1.1.4）与morph-models（版本≥1.0.4）插件包。[出生-死亡过程；校准；分歧时间；马尔可夫链蒙特卡洛（Markov Chain Monte Carlo, MCMC）；系统发育学]