Hunting alters diversity and selective pressure on the virus
Altered transmission dynamics at a population level were associated with changes in viral evolution and diversity in the treatment region. The increased number of transmission events in the no-hunting period was supported by the strong phylogenetic clustering (isolates with less phylogenetic diversity than expected by chance) detected relative to the hunting period (Fig. 3a). The link between reduced hunting pressure and increased transmission events was further supported as we did not find similar phylogenetic clustering in the stable region or hunting period (Fig. 3a). Moreover, our transmission tree results and previous phylogenetic reconstruction (Fountain-Jones et al. 2019) found little evidence for new lineages arriving during the no-hunting period in the treatment region (Fig. 1a). We further interrogated viral diversity patterns across time using skygrowth demographic analyses (Volz & Didelot 2018). Viral genetic diversity rapidly accrued at the end of the no-hunting period (~2009) before markedly declining after ~2011 when hunting was reinstated (Fig. 3b), closely mirroring male population size estimates (R2 = 0.8, p = 0.010, Fig 3c). Female population size was not significantly correlated to viral population growth rate (R2 = 0.190, p = 0.630, Fig. 3d) adding further evidence for the enhanced role of male interactions in transmission dynamics when hunting mortality was reduced. While we have no data on puma behavior across time, it is possible that the hunting-induced increase in male density increased competition for mates and thus aggressive interactions (Logan & Sweanor 2001). No such increase in FIVpco diversity and growth rate was detected in the stable population (Fig. S7b/c).
Within the treatment region, the increase in viral diversity was underpinned by greater effects of both purifying and diversifying selection acting on individuals infected during the no-hunting period compared to the hunting period (p = 0.01, likelihood ratio = 6.31). Purifying selection, potentially as a signature of rapid transmission events (e.g., 22 ), was dominant in both periods (97.25% sites ω < 1), as is often the case in error-prone RNA viruses, but stronger in the non-hunting period (ω2 nh = 0, ω2h = 0.1). In contrast, there was no shift in evolutionary pressure in the same periods in the stable population (p = 0.5, likelihood ratio = 0.43). While impacting a smaller proportion of the loci overall (2.79% loci ω > 1), there was strong diversifying selection in the no-hunting period as well (ω3 nh = 21.46, ω3h = 2.8). We identified five FIVpco loci under diversifying selection using the MEME routine in both regions (cutoff: p ≤ 0.1). Two of these loci were only found in isolates in males and, based on our transmission models, likely infected by FIVpco in the no-hunting period. There was no signature of diversifying or purifying selection in the envelope gene (env ), which was surprising given that env is generally under greater evolutionary pressure as it is responsible for the virus binding to the host cells (Kenyon & Lever 2011). All loci under diversifying selection were detected in the FIVpol integrase region. Putting these lines of evidence together, we not only detected population-level impacts of demographic changes due to cessation of hunting on viral mutation, but also at the individual scale with stronger evolutionary pressure on viruses infecting males. Increased evolutionary pressure on the virus may increase the probability of a new FIVpco phenotype occurring in this population. Systematic shifts in evolutionary pressure are known to occur when viruses switch hosts (e.g., Tamuri et al. 2009; Forniet al. 2017); however here we show that selective constraints on a virus can be altered in response to host demographic changes caused by wildlife hunting. We stress that FIVpco is largely apathogenic in puma and therefore our findings demonstrate the types of changes in pathogen transmission dynamics that can be caused by hunting induced changes in wildlife populations.