DOI: 10.5061/dryad.c020q
title: Data from: Using phylogenomic data to explore the effects of relaxed clocks and calibration strategies on divergence time estimation: primates as a test case

description: 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.
description: 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.pdf