Genomic Baselines for Muskellunge in West Virginia: Implications for Stocking and Conservation

Muskellunge (Esox masquinongy) are a recreationally and ecologically important apex predator found throughout North America. In West Virginia, the genetic structuring and diversity of native muskellunge is poorly understood. The supplementary stocking of non-native muskellunge has further complicated the issue, as the introgression of non-native alleles and prevalence of non-native muskellunge post stocking remains unclear as well. Using ddRAD sequencing, several datasets were generated to investigate the population structure and genomic diversity of muskellunge in West Virginia. Populations stocked with New York-strain muskellunge exhibited significant introgression, with genetic composition diverging from unstocked native West Virginia populations. However, one population showed greater genetic similarity to native and unstocked populations despite New York-strain prevalence, suggesting resilience against genetic alteration. Fixed SNPs between the New York and West Virginia strains were identified that can be used for broodstock screening and the enhancement of native populations. A genetically distinct population was identified in the Little Kanawha River system, with this population having the highest levels of genomic diversity among native populations as well as a high number of private alleles. However, elevated inbreeding coefficients highlight potential conservation concerns for this unique population. This study establishes a genomic baseline for muskellunge in West Virginia and underscores the importance of preserving native genomic diversity while balancing the demands of recreational fishing programs.