RAD‐Seq Refines Previous Estimates of Genetic Structure in Lake Erie Walleye

Abstract

Delineating population structure helps fishery managers to maintain a diverse “portfolio” of local spawning populations (stocks), as well as facilitate stock‐specific management. In Lake Erie, commercial and recreational fisheries for Walleye Sander vitreus exploit numerous local spawning populations, which cannot be easily differentiated using traditional genetic data (e.g., microsatellites). Here, we used genomic information (12,264 polymorphic loci) generated using restriction site‐associated DNA sequencing to investigate stock structure in Lake Erie Walleye. We found low genetic divergence (genetic differentiation index FST = 0.0006–0.0019) among the four Lake Erie western basin stocks examined, which resulted in low classification accuracies for individual samples (40–60%). However, more structure existed between western and eastern Lake Erie basin stocks (FST = 0.0042–0.0064), resulting in greater than 95% classification accuracy of samples to a lake basin. Thus, our success in using genomics to identify stock structure varied with spatial scale. Based on our results, we offer suggestions to improve the efficacy of this new genetic tool for refining stock structure and eventually determining relative stock contributions in Lake Erie Walleye and other Great Lakes populations.

Mixed-stock analysis in the age of genomics: Rapture genotyping enables evaluation of stock-specific exploitation in a freshwater fish population with weak genetic structure

“…The reporting groups are (1) West/Central Basin: Maumee River, Sandusky River, Detroit River, the Ohio reef complex, Ohio Grand River; (2) East Basin: Shorehaven, Bournes Beach, Van Buren Bay, Cattaraugus Creek, Lackawanna Shore; and (3) Ontario Grand River. Reassignment accuracy was determined using either 0.5 or 1 proportion of training loci (gray and white bars, respectively) and a support-vector machine algorithm (Chen et al 2020), with training samples for each grouping consisting of 0.5, 0.7, or 0.9 proportion of the collected individuals (chosen randomly). The remainder of individuals (0.5, 0.3, or 0.1) was used as the test (holdout) data set to determine reassignment accuracy.…”

“…Loci for our Rapture panel were identified by conducting a preliminary RAD-sequencing on 96 walleye (Table 1). These individuals were sampled on known spawning grounds during the peak spawning season and were and therefore presumed to have originated from that site (Chen et al 2020). All of these fish were collected by Lake Erie management agencies, including: Ohio Department of Natural Resources, New York Department of Environmental Conservation, and Ontario Ministry of Natural Resources and Forestry.…”

“…Genomic tools represent an affordable solution for understanding stock-specific dynamics with a recent study using thousands of single nucleotide polymorphisms (SNPs) genotyped with RAD-seq suggesting that high-accuracy reassignment of walleye to basin of origin is possible using genomic tools (Chen et al 2020). Here, we developed a Rapture panel containing thousands of genetic markers to conduct a mixed-stock analysis of walleye harvest in Lake Erie’s eastern basin.…”

SNP analyses highlight a unique, imperiled southern walleye (Sander vitreus) in the Mobile River Basin

“…However, finer-scale demarcations of walleye populations across the upper northern regions (Northwest Lake Plains, Great Lakes watershed, and North Atlantic coastal) are not recovered. Future work could develop SNP resources for characterizing fine-scale population structure through GBS sequencing of all five major walleye lineages or by using existing GBS data generated from other northern walleye populations (Allen et al 2018;Chen et al 2019).…”

Genetic Diversity and Population Differentiation of Kashgarian Loach (Triplophysa yarkandensis) in Xinjiang Tarim River Basin

“…Over the past years, restriction site-associated DNA sequencing (RAD-seq) has become a powerful and widely-used technique in conservation biology studies, especially for the species without a reference genome [ 10 , 11 , 12 ]. Unlike microsatellites and mitochondrial genes (e.g., cytb , coi , d-loop), more than thousands of SNPs at genomic level could substantially improve the capacity to unravel genetic diversity and divergence in species with both strong and weak population structure [ 13 ].…”