Molecular-clock models for estimating evolutionary rates and timescales

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. In order to deal with rate variation among genes and among lineages, a diverse range of molecular-clock models have been developed. These models have been implemented in various software packages and differ in their statistical properties, ability to handle different forms of rate variation, capacity to incorporate calibrations, and tractability for analysing large data sets. Choosing a suitable molecular-clock method 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 accommodated in molecular-clock analyses. We provide an outline of the various clock models that are available, including the strict clock, multi-rate clocks (including local 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.