Data from: Total-Evidence Dating under the Fossilized Birth-Death Process

Bayesian total-evidence dating involves the simultaneous analysis of morphological data from the fossil record and morphological and sequence data from recent organisms, and it accommodates the uncertainty in the placement of fossils while dating the phylogenetic tree. Due to the flexibility of the Bayesian approach, total-evidence dating can also incorporate additional sources of information. Here, we take advantage of this and expand the analysis to include information about fossilization and sampling processes. Our work is based on the recently described fossilized birth-death (FBD) process, which has been used to model speciation, extinction and fossilization rates that can vary over time in a piecewise manner. So far, sampling of extant and fossil taxa has been assumed to be either complete or uniformly at random, an assumption which is only valid for a minority of datasets. We therefore extend the FBD process to accommodate diversified sampling of extant taxa, which is standard practice in studies of higher-level taxa. We verify the implementation using simulations and apply it to the early radiation of Hymenoptera (wasps, ants and bees). Previous total-evidence dating analyses of this dataset were based on a simple uniform tree prior and dated the initial radiation of extant Hymenoptera to the late Carboniferous (309 Ma). The analyses using the FBD prior under diversified sampling, however, date the radiation to the Triassic and Permian (252 Ma), slightly older than the age of the oldest hymenopteran fossils. By exploring a variety of FBD model assumptions, we show that it is mainly the accommodation of diversified sampling that causes the push towards more recent divergence times. Accounting for diversified sampling thus has the potential to close the long-discussed gap between rocks and clocks. We conclude that the explicit modeling of fossilization and sampling processes can improve divergence time estimates, but only if all important model aspects, including sampling biases, are adequately addressed.贝叶斯全证据定年（Bayesian total-evidence dating）指同时分析化石记录中的形态学数据，以及现生生物的形态学与序列数据，可在对系统发育树进行定年的同时，容纳化石放置位置的不确定性。由于贝叶斯方法具备灵活性，全证据定年还可整合其他来源的信息。本研究利用这一优势，将分析拓展至纳入化石形成与采样过程的相关信息。本研究基于近年提出的化石出生-死亡（fossilized birth-death, FBD）过程展开，该模型已被用于构建可随时间呈分段式变化的物种形成、灭绝及化石形成速率模型。迄今为止，现生与化石类群的采样通常被假定为完全采样或均匀随机采样，但这类假设仅适用于少数数据集。因此，本研究对FBD过程进行拓展，以适配现生类群的差异化采样——这是高级类群研究中的标准范式。本研究通过模拟验证了该实现方案，并将其应用于膜翅目（Hymenoptera，涵盖胡蜂、蚂蚁与蜂类）的早期辐射演化分析。此前针对该数据集的全证据定年分析基于简单的均匀树先验，将现生膜翅目的初始辐射时间定年至石炭纪晚期（309 Ma）。但采用差异化采样下的FBD先验的分析结果，将该辐射事件定年至二叠纪与三叠纪之交（252 Ma），略早于已知最古老膜翅目化石的年代。通过探索多种FBD模型假设，本研究证实，正是差异化采样的适配性使得分歧时间的估算结果向更近的时间点偏移。因此，纳入差异化采样的考量，有望填补长期以来学界热议的岩石与分子钟之间的差距。本研究得出结论：对化石形成与采样过程进行显式建模，可提升分歧时间的估算精度，但前提是需充分涵盖模型的所有关键维度，包括采样偏差在内。