Data from: Harvest-associated size reductions and genomic changes within two generations in wild walleye populations

The extent and rate of harvest-induced genetic changes in natural
populations may impact population productivity, recovery and persistence.
While there is substantial evidence for phenotypic changes in harvested
fishes, knowledge of genetic change in the wild remains limited, as
phenotypic and genetic data are seldom considered in tandem, and the
number of generations needed for genetic changes to occur is not well
understood. We quantified changes in size-at-age, sex-specific changes in
body size, and genomic metrics in three harvested walleye (Sander vitreus)
populations and a fourth reference population with low harvest levels over
a 15-year period in Mistassini Lake, Quebec. We also collected Indigenous
knowledge (IK) surrounding concerns about these populations over time.
Using ~9000 SNPs, genomic metrics included changes in population
structure, neutral genomic diversity, effective population size and
signatures of selection. Indigenous knowledge revealed concerns about
overall reductions in body size and number of fish caught. Smaller body
size, smaller size-at-age, changing population structure (population
differentiation within one river and homogenization between two others),
and signatures of selection between historical and contemporary samples
reflected coupled phenotypic and genomic change in the three harvested
populations in both sexes, while no change occurred in the reference
population. Sex-specific analyses revealed differences in both body size
and genomic metrics but were inconclusive about whether one sex was
disproportionately affected. Our results suggest that harvest-induced
genetic changes may arise within 1-2.5 generations in long-lived wild
fishes, demonstrating the need to investigate concerns about
harvest-induced evolution quickly once they have been raised.