The molecular clock as a tool for understanding host-parasite evolution

Abstract

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 hostparasite interactions. Developments in models of molecular evolution and approaches to deriving temporal constraints from geological evidence will help overcome some of these issues. However, 1 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. IntroductionA timeline for events throughout geological history is required to address many questions in evolutionary biology, including establishing the sequence of key evolutionary transitions and assessing the role of environmental and evolutionary variables on the evolution of life (Rota-Stabelli et al., 2013;Betts et al., 2018;Morris et al., 2018;Silvestro et al., 2018). Due to the paucity of rocks from different time periods and environments, and the low fossilisation potential of many soft-bodied species, we cannot rely on the fossil record to establish this timeline very precisely (Benton et al., 2009; Parham et al., 2011;Holland, 2016). The genomes of living species provide an alternative source of evidence for inferring the sequence of events in deep time, although in themselves they provide no information about absolute time. Phylogenetic methods that enable us to leverage both sources of evidence simultaneously provide the most promising approach for generating a more precise timeline and a richer view of the past than either record can provide alone (Donoghue and Benton, 2007;Landis, 2017;Álvarez-Carretero et al., 2019).It is estimated that more than half of all living species are parasites (Windsor, 1998;Bass et al., 2015), that is, species that rely on a host organism for survival, at the expense of the other species.The ubiquity of the parasitic lifestyle and the often strong selection pressure imposed by parasites on their hosts (Hughes et al., 2012) indicate that parasites have played an important role in shaping the evolution of life, but the challenge in detecting many parasite species, both now and in the past, suggest that this role is not well understood (Dobson et al., 2008;De Baets and Littlewood, 2015). Estimating the time of origin of parasitism across different groups enables us to answer ...

Fossil Constraints on the Timescale of Parasitic Helminth Evolution

“…Some of the most commonly used examples for host or biogeographic constraints include those made for the monogenean group Polystomatidae (Verneau et al 2002(Verneau et al , 2009Badets et al 2011;Héritier et al 2015;Tinsley and Tinsley 2016). However, both approaches might involve circular reasoning (Kodandaramaiah 2011;Warnock and Engelstädter 2020). Fossil associations are among the only direct sources of evidence for the existence of particular lineages in the geological past (De Baets & Littlewood, 2015).…”