DOI: 10.5061/dryad.4b8gthtb2
title: Mixed-stock analysis using Rapture genotyping to evaluate stock-specific exploitation of a walleye population despite weak genetic structure

description: Mixed-stock analyses using genetic markers have informed fisheries
 management in cases where strong genetic differentiation occurs among
 local spawning populations, yet many fisheries are supported by multiple
 spawning stocks that are weakly differentiated. Freshwater fisheries
 exemplify this problem, with many harvested populations supported by
 multiple stocks of young evolutionary age and that are isolated across
 small spatial scales. As a result, attempts to conduct genetic mixed-stock
 analyses of inland fisheries have often been unsuccessful. Advances in
 genomic sequencing now offer the ability to discriminate among populations
 with weak population structure, by providing the necessary resolution to
 conduct mixed-stock assignment among previously indistinguishable stocks.
 We demonstrate the use of genomic data to conduct a mixed-stock analysis
 of Lake Erie's commercial and recreational walleye (Sander vitreus)
 fisheries and estimate the relative harvest of weakly differentiated
 stocks. We used RAD-capture (Rapture) to sequence and genotype individuals
 at 12,081  loci that had been previously determined to be capable
 of discriminating between western and eastern basin stocks (mean pairwise
 FST = 0.001) with 95% reassignment accuracy. An outcome not possible in
 the past with microsatellite markers. Genetic assignment of 1,075 fish
 harvested from recreational and commercial fisheries in the eastern basin
 indicated that western basin stocks supported the majority of the harvest
 during peak harvest (July – September). Composition of harvest changed
 seasonally, with eastern basin fish comprising much of the early season
 harvest (May – June). Clear spatial structure in stock-specific harvest
 existed; more easterly sites contained more individuals of east basin
 origin than did westerly sites. Our study provides important stock
 contribution estimates for Lake Erie fishery management and demonstrates
 the power of genomic data to facilitate mixed-stock analysis in exploited
 fish populations with weak population structure or limited existing
 genetic resources.
description: All of these fish were collected by Lake Erie management
 agencies, includes the: Ohio Department of Natural Resources, New York
 Department of Environmental Conservation, and Ontario Ministry of Natural
 Resources. Fin clips were preserved in 95% ethanol until DNA extraction
 using Qiagen DNEasy 96 kits. Individuals for baseline analysis were
 sampled by by electrofishing or gillnets over known spawning locations
 during spawning seasons 2012 - 2017. Individuals of unkwon origin (labeled
 in VCF viles as "MS") were were sampled during the spring,
 summer, and fall of the 2016-2018 fishing seasons. For both commercial and
 recreational fishery samples, anglers and fishers reported the grid
 location of their harvest on a map provided by creel agents at boat
 ramps/docks. The and total length (nearest 1 mm) of all sampled
 individuals was also recorded. Rapture libraties were
 prepared using <i>SbfI</i> enzyme and the standard library
 preparation approach outlined in Ali et al. (2016) and detailed in Ackiss
 et al. (2020). Samples were sequenced using paired-end 150 BP sequencing
 on an Illumina HiSeq4000 at NovoGene (Sacramento, CA). Loci were then
 assembled <i>de novo</i> in STACKS v. 2.0 (Catchen et al.
 2011; 2013) and a catalog of all putative loci was created in
 <i>cstacks</i> from data of all 96 individuals. Samples were
 demultiplexed using <i>process_radtags</i> (-e sbfI -i gzfastq
 -c -q -r --filter_illumina –bestrad), assembled <i>de novo</i>
 in <i>ustacks</i> (--disable-gapped, -m3, -M 3, -H,
 --max_locus_stacks 4, --model_type bounded, --bound_high 0.05), matched in
 <i>sstacks</i> (--disable gapped), converted to bam files
 using <i>tsv2bam</i>, and genotyped in
 <i>gstacks</i>. Finally, genotypes were called for all single
 nucleotide polymorphisms (SNPs) with a minor allele count greater than 3
 (--mac 3) genotyped in 80% of all individuals (-R 0.8).
description: To retrieve the exact loci included in the Rapture panel the
 STACKS 2 catalog files can be used to generate identical SNP IDs as
 original research (included). However, data can be treated as a standard
 RAD-sequencing project and analyzed<em> de
 novo. </em>Additional metadata can be found on Geome.