Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.
Syst Biol. 2023 Aug 7;72(4):781-801. doi: 10.1093/sysbio/syad011.
Evolutionary timescales can be inferred by molecular-clock analyses of genetic data and fossil evidence. Bayesian phylogenetic methods such as tip dating provide a powerful framework for inferring evolutionary timescales, but the most widely used priors for tree topologies and node times often assume that present-day taxa have been sampled randomly or exhaustively. In practice, taxon sampling is often carried out so as to include representatives of major lineages, such as orders or families. We examined the impacts of different densities of diversified sampling on Bayesian tip dating on unresolved fossilized birth-death (FBD) trees, in which fossil taxa are topologically constrained but their exact placements are averaged out. We used synthetic data generated by simulations of nucleotide sequence evolution, fossil occurrences, and diversified taxon sampling. Our analyses under the diversified-sampling FBD process show that increasing taxon-sampling density does not necessarily improve divergence-time estimates. However, when informative priors were specified for the root age or when tree topologies were fixed to those used for simulation, the performance of tip dating on unresolved FBD trees maintains its accuracy and precision or improves with taxon-sampling density. By exploring three situations in which models are mismatched, we find that including all relevant fossils, without pruning off those that are incompatible with the diversified-sampling FBD process, can lead to underestimation of divergence times. Our reanalysis of a eutherian mammal data set confirms some of the findings from our simulation study, and reveals the complexity of diversified taxon sampling in phylogenomic data sets. In highlighting the interplay of taxon-sampling density and other factors, the results of our study have practical implications for using Bayesian tip dating to infer evolutionary timescales across the Tree of Life. [Bayesian tip dating; eutherian mammals; fossilized birth-death process; phylogenomics; taxon sampling.].
进化时间尺度可以通过遗传数据分析和化石证据的分子钟分析来推断。贝叶斯系统发育方法（如尖峰定年）为推断进化时间尺度提供了一个强大的框架，但最广泛使用的树拓扑和节点时间的先验假设通常是假定现代分类群是随机或详尽采样的。实际上，分类群采样通常是为了包括主要谱系的代表，如目或科。我们研究了不同多样化采样密度对未解决的化石出生-死亡（FBD）树的贝叶斯尖峰定年的影响，其中化石分类群在拓扑上受到限制，但它们的确切位置被平均化。我们使用核苷酸序列进化、化石出现和多样化分类群采样的模拟生成的合成数据。我们在多样化采样 FBD 过程下的分析表明，增加分类群采样密度不一定能提高分歧时间估计值。然而，当为根年龄指定有用的先验或当树拓扑固定为模拟中使用的拓扑时，未解决的 FBD 树上的尖峰定年的性能保持其准确性和精度，或随着分类群采样密度的提高而提高。通过探索模型不匹配的三种情况，我们发现包括所有相关的化石，而不修剪与多样化采样 FBD 过程不兼容的化石，可能会导致分歧时间的低估。我们对真兽类哺乳动物数据集的重新分析证实了我们模拟研究的部分发现，并揭示了系统基因组数据集多样化分类群采样的复杂性。通过强调分类群采样密度和其他因素的相互作用，本研究的结果对使用贝叶斯尖峰定年推断整个生命之树的进化时间尺度具有实际意义。[贝叶斯尖峰定年；真兽类哺乳动物；化石出生-死亡过程；系统基因组学；分类群采样。]
