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.

灵长类长期以来均为分化时间估计（divergence time estimation）相关系统发育方法（phylogenetic methods）研发的经典测试案例。尽管已有大量相关研究，但相对于白垩纪-古近纪（K-Pg）界线的冠群灵长类（crown Primates）起源时间，以及主要冠群类群的分化时间节点，学界至今仍存在争议。我们在此分析了一套包含372个类群（367个灵长类与5个外类群（outgroups），共340万对比对碱基对（aligned base pairs））的数据集，该数据集涵盖9个灵长类基因组。我们系统探究了化石校准（fossil calibrations）的不同解读方案与分子钟模型（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，尤其对系统发育树中的古老节点作用更为明显。值得注意的是，分子速率模型的选择——自相关速率模型（auto-correlated rates model）与独立分布速率模型（independently distributed rates model）——对年代估计结果的影响尤为突出：独立分布速率模型会为系统发育的深层节点给出显著更古老的年代估计值。我们在MCMCTree软件中实现了结合高斯求积（Gaussian quadrature）的热力学积分（thermodynamic integration）方法，并利用该方法计算不同钟模型的贝叶斯因子（Bayes factors）。贝叶斯模型选择（Bayesian model selection）结果表明，自相关速率模型对本次灵长类数据集的拟合效果显著更优，因此我们认为该模型下的年代估计结果更为可靠。我们还发现，对于系统发育中的8个核心节点，年代估计的不确定性已接近由化石不确定性所限定的理论上限。这意味着，通过收集更多分子序列数据来优化这些年代估计结果的可能性极低。所有分析均表明，灵长类的起源时间紧邻K-Pg界线，要么处于白垩纪，要么跨越该界线延伸至古近纪。