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.Supplementary Material for "Using phylogenomic data to explore the effects of relaxed clocks and calibration strategies on divergence time estimation: primates as a test case"This is the Supplementary Material for "Using phylogenomic data to explore the effects of relaxed clocks and calibration strategies on divergence time estimation: primates as a test case" published in Systematic Biology. This is a zip file containing all the data used to obtain Bayesian estimates of divergence times for primates. It includes all the nucleotide alignments for the primate species analysed, the timetrees estimated using the data, trees with fossil calibrations, and a spreadsheet with posterior estimates of divergence times and mean rates.primates.zipSupplementary Figure 1Calibration vs. prior densities for strategies A and B. The dotted lines represent the calibration density, while the shaded (grey) histograms represent the effective prior obtained from MCMC sampling. Numbers in brackets indicate the 95% prior CI. Note that the priors for three Cauchy-based calibrations in strategy B (Primates, Anthropoidea and Human-Gorilla) have heavy tails that extend substantially back in time.SupFig1.pd