Neutral genomic signatures of host-parasite coevolution

Abstract Background Coevolution is a selective process of reciprocal adaptation in hosts and parasites or in mutualistic symbionts. Classic population genetics theory predicts the signatures of selection at the interacting loci of both species, but not the neutral genome-wide polymorphism patterns. To bridge this gap, we build an eco-evolutionary model, where neutral genomic changes over time are driven by a single selected locus in hosts and parasites via a simple biallelic gene-for-gene or matching-allele interaction. This coevolutionary process may lead to cyclic changes in the sizes of the interacting populations. Results We investigate if and when these changes can be observed in the site frequency spectrum of neutral polymorphisms from host and parasite full genome data. We show that changes of the host population size are too smooth to be observable in its polymorphism pattern over the course of time. Conversely, the parasite population may undergo a series of strong bottlenecks occurring on a slower relative time scale, which may lead to observable changes in a time series sample. We also extend our results to cases with 1) several parasites per host accelerating relative time, and 2) multiple parasite generations per host generation slowing down rescaled time. Conclusions Our results show that time series sampling of host and parasite populations with full genome data are crucial to understand if and how coevolution occurs. This model provides therefore a framework to interpret and draw inference from genome-wide polymorphism data of interacting species