American Crow SNPs and microsatellite data

Infectious diseases can cause steep declines in wildlife populations,
leading to changes in genetic diversity that may affect the susceptibility
of individuals to infection and the overall resilience of populations to
pathogen outbreaks. Here, we examine evidence for a genetic bottleneck in
a population of American crows (Corvus brachyrhynchos) before and after
the emergence of West Nile virus (WNV). More than 50% of marked birds in
this population were lost over the two-year period of the epizootic,
representing a 10-fold increase in adult mortality. Using analyses of SNPs
and microsatellite markers, we tested for evidence of a genetic bottleneck
and compared levels of inbreeding and immigration in the pre- and post-WNV
populations. Counter to expectations, genetic diversity (allelic diversity
and the number of new alleles) increased after WNV emergence. This was
likely due to increases in immigration, as the estimated membership
coefficients were lower in the post-WNV population. Simultaneously,
however, the frequency of inbreeding appeared to increase: mean inbreeding
coefficients were higher among SNP markers, and
heterozygosity-heterozygosity correlations were stronger among
microsatellite markers, in the post-WNV population. These results indicate
that loss of genetic diversity at the population level is not an
inevitable consequence of a population decline, particularly in the
presence of gene flow. The changes observed in post-WNV crows could have
very different implications for their response to future pathogen risks,
potentially making the population as a whole more resilient to a changing
pathogen community, while increasing the frequency of inbred individuals
with elevated susceptibility to disease.