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.