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.