Understanding if and when coevolution helps maintains genetic variation in hosts of a directly-transmissible pathogen is fundamental to quantifying the prevalence and impact of coevolution on disease epidemiology.Here, we extend our previous work on the maintenance of genetic variation in a classic matching-alleles coevolutionary model by exploring the effects of ecological and epidemiological feedbacks, where both allele frequencies and population sizes are allowed to vary over time. In general, we find that coevolution rarely maintains more host genetic variation than expected under neutral genetic drift alone. When and if coevolution maintains or depletes genetic variation relative to neutral drift is determined, predominantly, by two factors: the deterministic stability of the Red Queen allele frequency cycles and the frequency at which pathogen fixation occurs, as this results in directional selection and the depletion of genetic variation in the host. Compared to purely coevolutionary models with constant host and pathogen population sizes, ecological and epidemiological feedbacks stabilize Red Queen cycles deterministically, but population fluctuations in the pathogen increase the rate of pathogen fixation, especially in epidemiological models. Taken together our results illustrate the importance of considering the ecological and epidemiological context in which coevolution occurs when examining the impact of Red Queen cycles on genetic variation. eco-evolutionary feedbacks 15 variable. Our previous work has demonstrated that coevolution can, in turn, influence the epidemiological dynamics (MacPherson and Otto, 2018) and impact our ability to identify the genetic variation underlying the host and pathogen interactions .These potentially important impacts of coevolution on our understanding of infectious diseases are only relevant, however, if we are likely to find genetic variation segregating in both host and pathogen. As 20 first suggested by Haldane (1949), antagonistic coevolution between hosts and their parasites is thought to maintain genetic variation through negative frequency-dependent selection. For example, in the matchingalleles model (MAM), parasites are better at infecting hosts that carry a "matching" genotype; natural selection will thus favour host and parasite genotypes that are rare in the interacting species. Despite resembling negative frequency-dependent selection within a species, which does help to maintain genetic 25 variation (Takahata and Nei, 1990), our recent work showed that coevolution between a host and free-living pathogen does not maintain genetic variation relative to an equivalent model of neutral genetic drift when the host and pathogen population sizes are forced to remain constant (MacPherson et al., 2020). This previous chapter, however, ignored population dynamics that frequently accompany coevolutionary models, such as the SIR model Penman et al., 2013).
30In this chapter, we investigate the loss of genetic variation in a stochastic co-evolutionary model in which t...