Sequencing data from SBFI Rapture panel sequencing of walleye captured in the recreational fishery in the eastern basin of Lake Erie. (Part 2 of 2).</p><p>Using RAD capture (Rapture), we sequenced and genotyped individuals at 12,081 loci that had been previously determined to be capable of discriminating between western and eastern basin stocks with 95 percent reassignment accuracy, which was not possible in the past with microsatellite markers. The baseline assessment of 395 walleye from 11 spawning stocks identified three reporting groups and refined previous assessments of gene flow among walleye stocks. Genetic assignment of 1,075 walleye harvested in eastern Lake Eries recreational and commercial fisheries indicated that western basin stocks constituted the majority of harvest during the peak walleye fishing season (July to September), whereas eastern basin individuals comprised much of the early season harvest (May to June). Clear spatial structure in harvest composition existed. Catches in more easterly sites contained more individuals of eastern basin origin than did more westerly sites. Our study provides important stock contribution estimates for Lake Erie fishery management and demonstrates the utility of genomic data to facilitate mixed-stock analysis in exploited fish populations having weak population structure or limited existing genetic resources.