Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case

Abstract

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, 61 thousand base pairs) that includes nine complete primate genomes (3.4 million base pairs). 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 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.

Bayesian Estimation of Species Divergence Times Using Correlated Quantitative Characters

“…(4) is implemented in the computer program MCMCtree v4.9i, part of the PAML package (Yang, 2007). We have extended the package (dos Reis et al, 2018; https://github.com/dosreislab/mcmc3r) to help the user in preparing morphological alignments for analysis with MCMCtree, and in simulating continuous morphological data using different functions from the ape package (Paradis et al, 2004).…”

“…We use Bayes factors (BFs) to select among the three clock models for the morphological and molecular data sets. Marginal likelihoods for each model are calculated using the stepping-stone approach (Xie et al, 2011) as implemented in the package (dos Reis et al, 2018). The estimated marginal likelihoods are then used to calculate the BFs and posterior probabilities for each clock model.…”

A phylogenomic framework and timescale for comparative studies of tunicates

“…The selection of the clock model is often arbitrary and appears mostly dependent of the software choice, with an overwhelming majority of studies relying on the BEAST software [71] using an uncorrelated gamma (UGAM, also known as UCLN) model of clock relaxation. However, it has been shown that autocorrelated rate models, such as the autocorrelated log-normal model (LN), often provide a better fit with phylogenomic data [54,72,73]. Consequently, we compared the fit of both the UGAM and LN models to the fit of a strict molecular clock (CL) model for our dataset using cross-validation tests under the CAT-GTR+Γ 4 model.…”

The importance of scale in comparative microbiome research: New insights from the gut and glands of captive and wild lemurs

“…from Lepilemuridae. The species within these genera diverged over relatively similar evolutionary timescales (Dos Reis et al, ; Herrera & Dávalos, ). Today, they routinely live in sympatry across Madagascar's distinct habitats and display a diversity of feeding strategies (Figure ).…”