Abstract Bayesian molecular dating is widely used to study evolutionary timescales. This procedure usually involves phylogenetic analysis of nucleotide sequence data, with fossil-based calibrations applied as age constraints on internal nodes of the tree. An alternative approach is tip-dating, which explicitly includes fossil data in the analysis. This can be done, for example, through the joint analysis of molecular data from present-day taxa and morphological data from both extant and fossil taxa. In the context of tip-dating, an important development has been the fossilized birth–death process, which allows non-contemporaneous tips and sampled ancestors while providing a model of lineage diversification for the prior on the tree topology and internal node times. However, tip-dating with fossils faces a number of considerable challenges, especially, those associated with fossil sampling and evolutionary models for morphological characters. We conducted a simulation study to evaluate the performance of tip-dating using the fossilized birth–death model. We simulated fossil occurrences and the evolution of nucleotide sequences and morphological characters under a wide range of conditions. Our analyses of these data show that the number and the maximum age of fossil occurrences have a greater influence than the degree of among-lineage rate variation or the number of morphological characters on estimates of node times and the tree topology. Tip-dating with the fossilized birth–death model generally performs well in recovering the relationships among extant taxa but has difficulties in correctly placing fossil taxa in the tree and identifying the number of sampled ancestors. The method yields accurate estimates of the ages of the root and crown group, although the precision of these estimates varies with the probability of fossil occurrence. The exclusion of morphological characters results in a slight overestimation of node times, whereas the exclusion of nucleotide sequences has a negative impact on inference of the tree topology. Our results provide an overview of the performance of tip-dating using the fossilized birth–death model, which will inform further development of the method and its application to key questions in evolutionary biology.

中文翻译：

---

在僵化的生死过程下基于模拟的提示约会评估

摘要 贝叶斯分子测年被广泛用于研究进化时间尺度。该过程通常涉及核苷酸序列数据的系统发育分析，将基于化石的校准应用为树内部节点的年龄限制。另一种方法是提示约会，它在分析中明确包含化石数据。例如，这可以通过对现代分类群的分子数据和现存和化石分类群的形态数据进行联合分析来实现。在尖端约会的背景下，一个重要的发展是化石的生死过程，它允许非同时期的尖端和采样的祖先，同时为树拓扑和内部节点时间的先验提供谱系多样化模型。然而，用化石确定年代面临着许多相当大的挑战，特别是与化石采样和形态特征进化模型相关的那些。我们进行了一项模拟研究，以使用化石生死模型来评估提示约会的性能。我们模拟了各种条件下的化石发生以及核苷酸序列和形态特征的演变。我们对这些数据的分析表明，化石出现的数量和最大年龄对节点时间和树形拓扑结构的估计比谱系间变化的程度或形态特征的数量有更大的影响。使用化石生死模型进行提示约会通常在恢复现存分类群之间的关系方面表现良好，但在将化石分类群正确放置在树中并识别采样祖先的数量方面存在困难。该方法可以准确估计根和冠群的年龄，尽管这些估计的精度随化石出现的概率而变化。形态特征的排除导致节点时间的轻微高估，而核苷酸序列的排除对树拓扑的推断具有负面影响。我们的研究结果概述了使用化石生死模型进行尖端约会的性能，这将为该方法的进一步发展及其在进化生物学中的关键问题中的应用提供信息。而排除核苷酸序列对树拓扑的推断有负面影响。我们的研究结果概述了使用化石生死模型进行尖端约会的性能，这将为该方法的进一步发展及其在进化生物学中的关键问题中的应用提供信息。而排除核苷酸序列对树拓扑的推断有负面影响。我们的研究结果概述了使用化石生死模型进行尖端约会的性能，这将为该方法的进一步发展及其在进化生物学中的关键问题中的应用提供信息。