DOI: 10.5061/dryad.5tb2rbp1z
title: Data from: Harvest-associated size reductions and genomic changes within two generations in wild walleye populations

description: 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.
description: Walleye were captured via angling using the same lures and a
 combination of boats and shore fishing, from the same locations within
 rivers, for both historical and contemporary sampling (Table 1). From each
 walleye, we collected total and fork length (TL ± 1 mm), wet mass (± 50
 g), sex (M, F, U (unknown, either spawned out or premature)) and a tissue
 sample for genetics; otoliths were collected from a random subsample.
 Opercular bones but not otoliths were collected for aging for historic
 samples (Table 1), and this was done before this study, for Dupont et al.
 (2007); 2015 and 2017 otoliths were aged at the Wisconsin Cooperative
 Fishery Unit, US Geological Service, University of Wisconsin, Stevens
 Point, USA. Otoliths were aged by two experienced readers; if they
 disagreed on an age they examined the structure together to agree upon one
 for that structure. No walleye were aged using both opercular bones and
 otoliths. DNA was extracted using a modified Qiagen
 blood and tissue kit protocol (Qiagen Inc., Valencia, CA) (see Table 1 for
 sample sizes) and was sequenced using individual-based
 genotyping-by-sequencing (GBS). Libraries for Ion Proton GBS were
 prepared using the procedure described by Masher et al.
 (2013) at IBIS, Université Laval, Québec,
 Canada, with modifications described in Abed et al. (2018).
 Single-nucleotide polymorphisms (SNPs) were determined from
 raw sequence reads using the<i> stacks</i> pipeline v1.45
 (Catchen<i> et al.</i> 2013), and <i>de novo</i>
 sequence alignment. 
description: For genomic data: r12d files were made with a
 population map specifying each population and year separately, and
 includes outlier loci. r12g files were made with a
 population map specifying Icon-Perch as a single population, and exclude
 outlier loci. For body size data:
 The all data file was used for body size modeling, while only the
 age data was used for the bayesian size-at-age models.