Semester

Spring

Date of Graduation

2025

Document Type

Dissertation

Degree Type

PhD

College

Davis College of Agriculture, Natural Resources and Design

Department

Wildlife and Fisheries Resources

Committee Chair

Amy Welsh

Committee Member

Carol Arantes

Committee Member

Craig Barrett

Committee Member

Dustin Smith

Committee Member

Katherine Zipfel

Abstract

Situated in the Appalachian Mountains, one of the oldest mountain ranges on Earth, West Virginia waters boast rich ichthyofauna including native sportfish species walleye (Sander vitreus), largemouth bass (Micropterus nigricans), and muskellunge (Esox masquinongy). These three species are all native to the contemporary Ohio River watershed and play a major recreational and ecological role in local fisheries. Ecologically, all three species are apex predators and play a key role in ecosystems by directly influencing local fish assemblages. As dominant apex predators all three species are highly sought after in recreational fisheries with largemouth bass being the most targeted freshwater fish among anglers in the United States, and muskellunge earning the nickname “fish of 10,000 casts” due its elusiveness to angler harvest. Genetic investigations of these sportfish species in West Virginia are limited, with only a handful of previous studies available. Noting a lack of genetic insight into these valuable sportfish species, the West Virginia Division of Natural Resources (WVDNR) employed significant sampling of sportfish populations throughout the state to establish state-wide genomic baselines to direct future management directives. Using a genotype-by-sequencing double digest restriction-site associated DNA sequencing protocol, a total of 642 sportfish samples from over 25 populations across the state were sequenced to identify genetically distinct populations, elucidate the impact of stocking non-native ancestry into native populations, quantify genomic diversity, and establish a genetic baseline foundation for each of the three species that can be incorporated into future management directives. Sub-objectives were also investigated for largemouth bass and walleye. Due to angler interest in creating a trophy fishery, Florida bass (Micropterus salmoides) presence and prevalence throughout the state was investigated using a 16 single nucleotide polymorphism (SNP) panel that was previously found to be fixed between Florida bass and northern largemouth bass to identify potential candidate populations. A total of 856 largemouth bass from 31 populations across the state were genotyped, along with known Florida bass and putative F1 hybrids to validate the panel.

Marker-assisted restoration of native walleye has previously used two microsatellite loci found to be correlative with diagnostic mitochondrial haplotypes of the native Eastern Highlands strain and introduced Great Lake strain. Difficulty with the two loci that displayed questionable diagnostic capability resulted in the need to change protocols and utilize diagnostic SNPs. Walleye of known Great Lakes and Eastern Highlands strain origins were sequenced and 57 fixed SNPs between the two strains were identified, resulting in a currently employed 2 SNP protocol being developed. The resulting panel’s diagnostic capability was compared to the microsatellite protocol, verified in diagnostic capability by comparing the 2 SNP protocol strain assignment to assignment using 42 diagnostic SNPs, and strain assignment of 1,532 walleye from 17 sampling locations across the state was assessed to determine the prevalence of the Eastern Highlands strain. The 2 SNP panel was found to be far superior to the microsatellite panel, which was only able to identify 58% of native Eastern Highlands strain broodstock in a 2-year period. The 2 SNP panel was also found to be highly effective in ancestry assignment, with almost 90% of 181 previously native walleye displaying > 80% probability of being pure Eastern Highlands strain ancestry. Among sampled populations, the Kanawha and New rivers both displayed the highest prevalence of the Eastern Highlands strain with the Ohio River showing a higher introgression of the Great Lakes strain in comparison. Along these lines, genomic investigations found that the Kanawha and New rivers were more genetically similar to each other than to Ohio River populations. Eastern Highlands walleye from the Kanawha and New rivers populations displayed an ancestry absent from Eastern Highlands Ohio River individuals, indicating a divergence from historic a baseline due to introgression of the Great Lakes strain in the Ohio River that has also been observed in previous research. Inbreeding coefficients (FIS) were observed to be highest upstream in the Kanawha Falls and New River populations, indicating potential management intervention is needed to alleviate this observed inbreeding via stocking of non-related Eastern Highlands strain individuals to mitigate further potential inbreeding. Summersville Lake also had the highest frequency of the minor allele of two SNPs found to be potentially undergoing selection, indicating potential lentic and riverine habitat selection within the Eastern Highlands strain. Management of walleye should include the continued use of broodstock screening, alleviation of potential inbreeding in the New River and Kanawha Falls populations and emphasis on conservation of the Kanawha River and New River to prevent divergence observed in the Ohio River. Additionally, given concerns over angler movement of fish into native watersheds, stocking of Florida Bass and their hybrids should likely be avoided in other watersheds of West Virginia.

With the combined use of the 16 SNP panel and sequencing of known Florida bass and putative F1 hybrids, no presence of Florida bass ancestry was found in any West Virginia largemouth bass populations. A total of four genetic ancestries were found in sampled populations, with the dominant Ohio River strain ancestry being found in every population. Two of the three genetically distinct ancestries observed occurred in non-native introduced largemouth bass populations indicating these ancestries and the one discovered in the native East Lynn Lake population are a result of stocking and not natural sub-structuring of the Ohio River strain. Stocking Florida bass into the Ohio River watershed would pose a threat to native genetic diversity and is not recommended based on current results. However, if a trophy Florida bass fishery is to be established, stocking of Florida bass into introduced non-native largemouth bass reservoirs could be potentially utilized that would both conserve native genetic diversity and satisfy recreational angling opportunity.

Muskellunge populations that had been previously stocked with muskellunge of New York origin including Stonewall Jackson Lake, East Lynn Lake, Kimsey Run Lake, and the Monongahela and Buckhannon rivers all displayed introgression of the New York strain. Individuals of native origin in these populations were more similar to each other and most differentiated from native populations that show no New York strain presence, indicating a genetic shift in native muskellunge in these populations. A genetically distinct population was found in the Little Kanawha River system, including North Bend Lake, a dammed reservoir of an upstream tributary North Fork Hughes River, indicating movement of muskellunge within the Little Kanawha River system. The Little Kanawha River system ancestry also displayed the highest genomic diversity metrics and highest inbreeding coefficients, highlighting the need to further research on this unique population through the use of telemetry studies to elucidate movement of muskellunge throughout the system and identifying distinct spawning sites.

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