A mixed relaxed clock model

• Published in: Philosophical transactions of the Royal Society of London. Series B. Biological sciences Vol. 371; no. 1699; p. 20150132
• Main Authors: Lartillot, Nicolas, Phillips, Matthew J., Ronquist, Fredrik
• Format: Journal Article
• Language: English
• Published: England The Royal Society 19-07-2016; Royal Society, The
• Subjects: Animals; Bayes Theorem; Bayesian Inference; Diversity of life; Evolution, Molecular; Fossils - anatomy & histology; Life Sciences; Livets mångfald; Mammals - genetics; Molecular Dating; Monte Carlo; Phylogeny; Relaxed Molecular Clock; Time Factors; molecular dating; Monte Carlo; Bayesian inference; relaxed molecular clock
• ISSN: 0962-8436; 1471-2970; 1471-2970
• DOI: 10.1098/rstb.2015.0132

Over recent years, several alternative relaxed clock models have been proposed in the context of Bayesian dating. These models fall in two distinct categories: uncorrelated and autocorrelated across branches. The choice between these two classes of relaxed clocks is still an open question. More fundamentally, the true process of rate variation may have both long-term trends and short-term fluctuations, suggesting that more sophisticated clock models unfolding over multiple time scales should ultimately be developed. Here, a mixed relaxed clock model is introduced, which can be mechanistically interpreted as a rate variation process undergoing short-term fluctuations on the top of Brownian long-term trends. Statistically, this mixed clock represents an alternative solution to the problem of choosing between autocorrelated and uncorrelated relaxed clocks, by proposing instead to combine their respective merits. Fitting this model on a dataset of 105 placental mammals, using both node-dating and tip-dating approaches, suggests that the two pure clocks, Brownian and white noise, are rejected in favour of a mixed model with approximately equal contributions for its uncorrelated and autocorrelated components. The tip-dating analysis is particularly sensitive to the choice of the relaxed clock model. In this context, the classical pure Brownian relaxed clock appears to be overly rigid, leading to biases in divergence time estimation. By contrast, the use of a mixed clock leads to more recent and more reasonable estimates for the crown ages of placental orders and superorders. Altogether, the mixed clock introduced here represents a first step towards empirically more adequate models of the patterns of rate variation across phylogenetic trees.
This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.