Molecular‐clock methods for estimating evolutionary rates and timescales

Abstract

The molecular clock presents a means of estimating evolutionary rates and timescales using genetic data. These estimates can lead to important insights into evolutionary processes and mechanisms, as well as providing a framework for further biological analyses. To deal with rate variation among genes and among lineages, a diverse range of molecular-clock methods have been developed. These methods have been implemented in various software packages and differ in their statistical properties, ability to handle different models of rate variation, capacity to incorporate various forms of calibrating information and tractability for analysing large data sets. Choosing a suitable molecular-clock model can be a challenging exercise, but a number of model-selection techniques are available. In this review, we describe the different forms of evolutionary rate heterogeneity and explain how they can be accommodated in molecular-clock analyses. We provide an outline of the various clock methods and models that are available, including the strict clock, local clocks, discrete clocks and relaxed clocks. Techniques for calibration and clock-model selection are also described, along with methods for handling multilocus data sets. We conclude our review with some comments about the future of molecular clocks.

Comprehensive Genome Scale Phylogenetic Study Provides New Insights on the Global Expansion of Chikungunya Virus

“…Phylogenetic estimations, including the MCC tree, substitution rates, and tMRCAs, were performed based on the complete and subdivided data sets for each lineage, with the results summarized in Table 3 Ϫ4 to 7.38 ϫ 10 Ϫ4 substitutions/site/year for reemerged, although the latter had a larger 95% HPD value than the former. Correspondingly, the large rate variation between the African and IOL subsets in the ECSA lineage made estimation of the tMRCA and divergence time less reliable using the total data set under the uncorrelated relaxed clock (lognormal) model, where evolutionary rates along each branch are assumed to be clustered around a mean (35). The most recent common ancestor of the ECSA lineage was dated to 1932 to 1951 or 1948 to 1953 based on the total data set according to the Bayesian Skyline or Skyride demographic model, respectively.…”

Infectious Disease Dynamics Inferred from Genetic Data via Sequential Monte Carlo

“…In our approach, this corresponds to constructing each edge length of PðtÞ as a stochastic process on the corresponding edge of T ðtÞ. Various forms of such processes have been assumed in the literature (Lepage et al 2007;Ho and Duchne 2014), but not all of these are compatible with a mechanistic approach. In particular, a mechanistic molecular clock must be defined at all times and must have non-negative increments.…”

Puzzling rocks and complicated clocks: how to optimize molecular dating approaches in historical phytogeography

“…(2) Increasing variety of molecular clock models: Various molecular clock models, such as local molecular clocks (Li & Tanimura, 1987;Yoder & Yang, 2000), random local molecular clocks (Drummond & Suchard, 2010;Bellot & Renner, 2014), and especially relaxed molecular clock methods (Sanderson, 2002;Thorne & Kishino, 2002;Drummond et al, 2006;Drummond & Rambaut, 2007;Rannala & Yang, 2007;Yang, 2007), have been developed to accommodate divergence rate variation among lineages (Renner, 2005;Brown & Yang, 2010;Ho & Duchene, 2014). (3) Better strategies to integrate fossil ages: There have been advances in how fossil calibration information is integrated into phylogenetic trees, such as using a multiple calibration points strategy (Soltis et al, 2002), 'node dating' methods (e.g.…”

“…Molecular dating approaches are constantly being updated (Ho, 2014;Ho & Duchene, 2014) and recent developments in Bayesian dating methods, for example, 'total evidence' (Ronquist et al, 2012a) and 'fossilized birth-death' (Heath et al, 2014) methods, may lead to further improvements in the accuracy of dating lineage diversification. In comparison to the traditional Bayesian methods of 'node dating' within a molecular phylogeny (e.g.…”