10.5061/DRYAD.C020Q
dos Reis, Mario
University College London
Gunnell, Gregg F.
Duke University
Barba-Montoya, Jose
University College London
Wilkins, Alex
The Ohio State University
Duke University
Yang, Ziheng
University College London
Yoder, Anne D.
Duke University
Data from: Using phylogenomic data to explore the effects of relaxed
clocks and calibration strategies on divergence time estimation: primates
as a test case
Dryad
dataset
2018
relaxed clock
Catarrhini
Anthropoidea
Bayes factors
Primates
bayesian analysis
Platyrrhini
Late Cretaceous
Strepsirrhini
Haplorrhini
2018-01-09T17:52:16Z
2018-01-09T17:52:16Z
en
https://doi.org/10.1093/sysbio/syy001
12984230 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.pdf