At least two genetically distinct populations of walleye Sander vitreus reproduce in Lake Erie: one west-basinorigin population and one east-basin-origin population. Each year, some west-basin-origin walleyes migrate to the east basin and create a mixed-origin walleye population. Uncertainties associated with this migratory behavior make it difficult to describe the dynamics of the east-basin-origin population. We used mark-recapture analysis to estimate the dynamics of the east-basin-origin walleye population and to measure the contribution of west-basin-origin walleyes to the total walleye harvest in the east basin. Compared with the west-basin-origin walleyes, the east-basin-origin walleyes experienced lower fishing pressure, lower natural mortality, and a higher survival rate. On average, the west-basin-origin walleye migrants comprised about 90% of the annual harvest in the east basin. The number of the west-basin-origin walleyes migrating to the east basin was linearly related to their abundance. Walleyes showed a strong fidelity to their spawning sites. This study provided an approach to the assessment of population dynamics and the management of walleye fisheries in the east basin of Lake Erie.Lake Erie is the southernmost, warmest, and most productive of the five Laurentian Great Lakes (Hartman 1972). The lake consists of three distinct basins varying in depth, thermal regime, and productivity. The three basins are the shallow and warm west basin, the intermediate-depth and cool central basin, and the deep and cold east basin (Figure 1). The three basins are also distinguishable by their trophic states and local fish communities. Identification of these differences directly helped

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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 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 (pairwise FST < 0.01). 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 with 95% reassignment accuracy, which was 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 constituted the majority of individuals harvested during peak walleye fishing season (July – September). Composition of harvest changed seasonally, with eastern basin fish comprising much of the early season harvest (May – June). Clear spatial structure in harvest composition 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.

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