Rachel Warnock, Jan Engelstädter

The molecular clock in combination with evidence from the geological record can be applied to infer the timing and dynamics of evolutionary events. This has enormous potential to shed light on the complex and often evasive evolution of parasites. Here, we provide an overview of molecular clock methodology and recent advances that increase the potential for the study of host-parasite coevolutionary dynamics, with a focus on Bayesian approaches to divergence time estimation. We highlight the challenges in applying these methods to the study of parasites, including the nature of parasite genomes, the incompleteness of the rock and fossil records, and the complexity of host-parasite interactions. Developments in models of molecular evolution and approaches to deriving temporal constraints from geological evidence will help overcome some of these issues. However, we also describe a case study in which the timescale of host-parasite coevolution cannot easily be inferred using existing methods – that of the alpha-proteobacteria Wolbachia. We conclude by providing a prospective on future methodological developments and data collection that will facilitate in understanding the role of parasitism in deep time.