Data from: Using phylogenomic data to explore the effects of relaxed clocks and calibration strategies on divergence time estimation: primates as a test case

Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the K-Pg boundary and the timing of diversification of the main crown groups remain controversial. Here we analysed a dataset of 372 taxa (367 Primates and 5 outgroups, 3.4 million aligned base pairs) that includes nine primate genomes. We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates. We find that even small differences in the construction of fossil calibrations can have a noticeable impact on estimated divergence times, especially for the oldest nodes in the tree. Notably, choice of molecular rate model (auto-correlated or independently distributed rates) has an especially strong effect on estimated times, with the independent rates model producing considerably more ancient age estimates for the deeper nodes in the phylogeny. We implement thermodynamic integration, combined with Gaussian quadrature, in the program MCMCTree, and use it to calculate Bayes factors for clock models. Bayesian model selection indicates that the auto-correlated rates model fits the primate data substantially better, and we conclude that time estimates under this model should be preferred. We show that for eight core nodes in the phylogeny, uncertainty in time estimates is close to the theoretical limit imposed by fossil uncertainties. Thus, these estimates are unlikely to be improved by collecting additional molecular sequence data. All analyses place the origin of Primates close to the K-Pg boundary, either in the Cretaceous or straddling the boundary into the Palaeogene.灵长类长期以来一直是分化时间估计相关系统发育方法开发的测试模型。然而，尽管已有大量相关研究，冠群灵长目（crown Primates）的起源时间相对于白垩纪-古近纪界线（K-Pg boundary）的位置，以及主要冠群类群的分化时间，至今仍存在争议。本研究分析了一套包含372个类群的数据集（其中367个为灵长类，5个为外类群，共包含340万对比对碱基对），并纳入了9个灵长类基因组数据。我们系统探究了化石校准（fossil calibrations）的不同解读方式与分子钟模型（molecular clock models）对灵长类分化时间估计结果的影响。研究发现，即便化石校准构建过程中的细微差异，也会对估计的分化时间产生显著影响，尤其是对于系统发育树中最古老的节点。值得注意的是，分子速率模型的选择（自相关速率模型或独立分布速率模型）对分化时间估计的影响尤为突出：独立分布速率模型会为系统发育中更深层的节点给出显著更古老的年代估计。我们在MCMCTree软件中集成了结合高斯求积（Gaussian quadrature）的热力学积分（thermodynamic integration）方法，并利用该方法计算了不同钟模型的贝叶斯因子（Bayes factors）。贝叶斯模型选择结果显示，自相关速率模型对灵长类数据的拟合效果显著更优，因此我们认为基于该模型的时间估计结果更为可靠。我们还发现，对于系统发育中的8个核心节点，其时间估计的不确定性接近由化石不确定性所限定的理论极限。这意味着，即便收集更多的分子序列数据，也难以进一步提升这些节点的时间估计精度。所有分析结果均表明，灵长目的起源时间紧邻白垩纪-古近纪界线，要么处于白垩纪，要么跨越该界线延伸至古近纪。