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

Authors: ZHAO, HONGGANG - Auburn University; LEWIS, MATTHEW - Auburn University; SILLIMAN, KATHERINE - Auburn University; JOHNSON, SARAH - Auburn University; KRATINA, GARRET - Auburn University; RIDER, STEVE - Alabama Wildlife And Freshwater Fisheries; STEPIEN, CAROL - National Oceanic & Atmospheric Administration (NOAA); HALLERMAN, ERIC - Virginia Tech; Beck, Benjamin; Fuller, Adam; PEATMAN, ERIC - Auburn University

Submitted to: Canadian Journal of Fisheries and Aquatic Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/4/2020
Publication Date: 4/20/2020
Citation: Zhao, H., Lewis, M., Silliman, K., Johnson, S., Kratina, G., Rider, S.J., Stepien, C.A., Hallerman, E.M., Beck, B.H., Fuller, S.A., Peatman, E. 2020. SNP analyses highlight a unique, imperiled southern walleye (Sander vitreus) in the Mobile River Basin. Canadian Journal of Fisheries and Aquatic Sciences. 77(8):1366-1378. https://doi.org/10.1139/cjfas-2019-0351.
DOI: https://doi.org/10.1139/cjfas-2019-0351

Interpretive Summary: Walleye (Sander vitreus) is a freshwater species inhabiting a wide range of habitats across North America. Due to its economic importance and popularity as a sportfish, it has been widely introduced beyond its native range. Previous genetic studies have revealed a genetically distinct strain of walleye in Mobile River Basin drainages, but little is known about its genetic structure and how this southern strain relates to northern walleye populations. Another unresolved question is the hybridization status of walleye in Mobile River Basin following northern walleye introductions. In this study, we used a technique called genotyping-by-sequencing (GBS) and developed single nucleotide polymorphism (SNP) markers, a variation in a single base pair in a DNA sequence, data from 60 walleye individuals to determine the amount of genetic diversity and structure among northern and southern walleye populations. Genetic assessment with 2,782 SNPs confirmed a unique genomic pattern in the southern walleye group. We also found strong evidence for a historical declining population trend with reduced genetic diversity and effective population size in a southern walleye population spawning in Hatchet Creek, Alabama. Additionally, a SNP assay with 68 diagnostic markers was developed for rapid and accurate identification of genetic purity and classification of various (northern/southern) hybrid classes among walleye individuals. Utilizing this SNP assay, we genotyped an additional 545 walleye individuals across 23 populations and characterized broad-scale genetic structure, distinguishing three groups comprised of the Mobile River Basin, Great Lakes/upper Mississippi, and southern Ohio drainage populations. Using data generated through both GBS and SNP, we demonstrated that a suite of 68 SNPs could collectively classify advance-generation hybrids and enable us to identify a human-induced hybrid zone resulting from the previous introduction of northern walleye into the Black Warrior River. Our results highlight the need for further characterization and conservation management of southern walleye in Mobile River Basin, with our 68-SNP assay already being implemented in ongoing stream survey and captive breeding programs.

Technical Abstract: Walleye (Sander vitreus) is a freshwater species inhabiting a wide range of habitats across North America. Owing to its economic importance and popularity as a sportfish, this species has been widely introduced beyond its indigenous range. Previous genetic studies have revealed a genetically distinct strain of walleye in Mobile River Basin drainages, but little is known about its genetic structure and how this southern strain relates to northern walleye populations. Another unresolved question is the hybridization status of walleye in Mobile River Basin following northern walleye introductions. In this study, we used genotyping-by-sequencing (GBS) data from 60 walleye individuals to infer genetic diversity and structure among northern and southern (Mobile River Basin) walleye populations. Genetic assessment with 2,782 GBS SNPs confirmed a unique genomic pattern in southern walleye group (FST = 0.805 vs. northern Lake Erie walleye). We also found strong evidence for a historical declining population trend with reduced genetic diversity and effective population size in a southern walleye population spawning in Hatchet Creek, Alabama. Additionally, a SNP assay with 68 diagnostic markers was developed for rapid and accurate identification of genetic purity and classification of various (northern/southern) hybrid classes among walleye individuals. Utilizing this SNP assay, we genotyped an additional 545 walleye individuals across 23 populations and characterized broad-scale genetic structure, distinguishing three groups comprised of the Mobile River Basin, Great Lakes/upper Mississippi, and southern Ohio drainage populations. Using both GBS and SNP assay data, we demonstrated that a suite of 68 SNPs could collectively classify advance-generation hybrids and enable us to identify an anthropogenic hybrid zone resulting from the previous introduction of northern walleye into the Black Warrior River. Our results highlight the need for further characterization and conservation management of southern walleye in Mobile River Basin, with our 68-SNP assay already being implemented in ongoing stream survey and captive breeding programs.