Unfiltered VCF for pink salmon rapid adaptation

Introduced and invasive species make excellent natural experiments for
investigating rapid evolution. Here, we describe the effects of genetic
drift and rapid genetic adaptation in pink salmon (Oncorhynchus gorbuscha)
that were accidentally introduced to the Great Lakes via a single
introduction event 31-generations ago. Using whole-genome resequencing for
134 fish spanning five sample groups across the native and introduced
range, we estimate that the source population’s effective population size
was 146,886 at the time of introduction, whereas the founding population’s
effective population size was just 72—a 2040-fold decrease. As expected
with a severe founder event, we show reductions in genome-wide measures of
genetic diversity, specifically a 37.7% reduction in the number of SNPs
and an 8.2% reduction in observed heterozygosity. Despite this decline in
genetic diversity, we provide evidence for putative selection at 47 loci
across multiple chromosomes in the introduced populations, including
missense variants in genes associated with circadian rhythm, immunological
response, and maturation, which match expected or known phenotypic changes
in the Great Lakes. For one of these genes, we use a species-specific
agent-based model to rule out genetic drift and conclude our results
support a strong response to selection that occurred in a period gene
(per2) that plays a predominant role in determining an organism’s daily
clock, matching large day-length differences experienced by introduced
salmon during important phenological periods. Together, these results
inform how populations might evolve rapidly to new environments, even with
a small pool of standing genetic variation.