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 progenitor 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 bottleneck, 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 that a strong
response to selection 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.