Genomic Baselines for Muskellunge in West Virginia: Implications for Stocking and Conservation
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. Study Area
2.3. DNA Extraction, Library Preparation, and Sequencing
2.4. Processing of Generated ddRAD Sequences
2.5. Population Structuring and Genomic Diversity
3. Results
3.1. Dataset Generation
3.2. Population Structuring and Strain Identification
3.3. Genomic Diversity
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Locus | Scaffold/Accession | BP | West Virginia | New York |
---|---|---|---|---|
871013 | JACXGI010036579.1 | 3233 | GCACACGCGCACAC | GCACACGCACACAC |
735725 | JACXGI010016854.1 | 8685 | GTCCTTTCTGAGCAGG | GTCCTTTCTGCGCAGG |
507110 | JACXGI010007232.1 | 10,652 | GGGGGAATTCAAACTC | GGGGGAATTCGAACTC |
540715 | JACXGI010008188.1 | 245 | AATGTCGGCATGTGTT | AATGTCGGCGTGTGTT |
582779 | JACXGI010009543.1 | 1068 | CAGTCACGCCTCAGTT | CAGTCACGCCCCAGTT |
747854 | JACXGI010017737.1 | 4800 | ACAGACACTCCTGCTC | ACAGACACTGCTGCTC |
439545 | JACXGI010005572.1 | 17,457 | TATTGCCCATTTGATAG | TATTGCCCATTCGATAG |
70328 | JACXGI010000404.1 | 116,957 | CATCTGTGGCGAGACC | CATCTGTGGGGAGACC |
393496 | JACXGI010004619.1 | 7201 | GACATTTCATTGCAGA | GACATTTCAGTGCAGA |
557283 | JACXGI010008711.1 | 3345 | GGCTGCTTTGGAAAC | GGCTGCTTTTGAAAC |
Population | P | P loci | Private | Π (SE) | HO (SE) | HE (SE) | HWE | FIS (SE) | Ɵ | Tajima | Ne (95% CI) |
---|---|---|---|---|---|---|---|---|---|---|---|
Buckhannon River (5) | 0.900 | 0.129 | 2 | 0.153 (0.004) | 0.155 (0.004) | 0.137 (0.003) | 11 (0.35%) | −0.003 (0.004) | 0.154 | −0.002 | ∞ |
East Lynn Lake (24) | 0.900 | 0.226 | 5 | 0.152 (0.003) | 0.128 (0.003) | 0.148 (0.003) | 310 (9.85%) | 0.098 (0.022) | 0.185 | −0.036 | 16.1 (15.9–16.2) |
Kimsey Run Lake (5) | 0.900 | 0.143 | 0 | 0.157 (0.003) | 0.128 (0.003) | 0.140 (0.003) | 38 (1.20%) | 0.066 (0.008) | 0.185 | −0.038 | ∞ |
Little Kanawha River (11) | 0.894 | 0.171 | 47 | 0.159 (0.003) | 0.103 (0.003) | 0.151 (0.003) | 267 (8.48%) | 0.172 (0.014) | 0.188 | −0.038 | 93.5 (83.6–105.8) |
Middle Island Creek (52) | 0.903 | 0.240 | 22 | 0.143 (0.003) | 0.129 (0.003) | 0.142 (0.003) | 390 (12.39%) | 0.082 (0.038) | 0.165 | −0.024 | 132.7 (72.7–79.6) |
Monongahela River (17) | 0.892 | 0.214 | 7 | 0.163 (0.003) | 0.142 (0.003) | 0.158 (0.003) | 228 (7.24%) | 0.078 (0.017) | 0.194 | −0.034 | 72.3 (69.6–75.2) |
North Bend Lake (65) | 0.902 | 0.247 | 33 | 0.145 (0.003) | 0.138 (0.004) | 0.144 (0.003) | 347 (11.02%) | 0.052 (0.050) | 0.162 | −0.019 | 61.6 (61.2–62.1) |
Sandy Creek (5) | 0.916 | 0.114 | 0 | 0.132 (0.003) | 0.112 (0.003) | 0.117 (0.003) | 19 (0.60%) | 0.044 (0.009) | 0.153 | −0.029 | ∞ |
Stonewall Jackson Lake (22) | 0.883 | 0.235 | 10 | 0.174 (0.003) | 0.167 (0.003) | 0.170 (0.003) | 154 (4.89%) | 0.033 (0.017) | 0.185 | −0.014 | 20.1 (19.9–20.3) |
Population | P | P loci | Private | Π (SE) | HO (SE) | HE (SE) | HWE | FIS (SE) | Ɵ | Tajima | Ne (95% CI) |
---|---|---|---|---|---|---|---|---|---|---|---|
East Lynn Lake (17) | 0.888 | 0.085 | 2 | 0.167 (0.003) | 0.147 (0.003) | 0.162 (0.003) | 249 (8.08%) | 0.080 (0.018) | 0.196 | −0.033 | 32.6 (32.0–33.3) |
Little Kanawha River (11) | 0.869 | 0.080 | 74 | 0.194 (0.003) | 0.124 (0.003) | 0.184 (0.003) | 303 (9.83%) | 0.207 (0.014) | 0.224 | −0.040 | 67.9 (63.1–73.4) |
Middle Island Creek (52) | 0.880 | 0.110 | 51 | 0.177 (0.003) | 0.158 (0.003) | 0.175 (0.003) | 489 (15.86%) | 0.102 (0.041) | 0.194 | −0.019 | 120.6 (119.0–122.3) |
North Bend Lake (62) | 0.879 | 0.113 | 78 | 0.179 (0.003) | 0.172 (0.003) | 0.177 (0.003) | 411 (13.33%) | 0.060 (0.051) | 0.191 | −0.015 | 58.0 (57.6–58.4) |
Sandy Creek (5) | 0.894 | 0.055 | 0 | 0.163 (0.004) | 0.139 (0.004) | 0.145 (0.003) | 24 (0.78%) | 0.054 (0.009) | 0.188 | −0.034 | ∞ |
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Johnson, A.; Taylor, N.; Welsh, A. Genomic Baselines for Muskellunge in West Virginia: Implications for Stocking and Conservation. Hydrobiology 2025, 4, 7. https://doi.org/10.3390/hydrobiology4010007
Johnson A, Taylor N, Welsh A. Genomic Baselines for Muskellunge in West Virginia: Implications for Stocking and Conservation. Hydrobiology. 2025; 4(1):7. https://doi.org/10.3390/hydrobiology4010007
Chicago/Turabian StyleJohnson, Andrew, Nate Taylor, and Amy Welsh. 2025. "Genomic Baselines for Muskellunge in West Virginia: Implications for Stocking and Conservation" Hydrobiology 4, no. 1: 7. https://doi.org/10.3390/hydrobiology4010007
APA StyleJohnson, A., Taylor, N., & Welsh, A. (2025). Genomic Baselines for Muskellunge in West Virginia: Implications for Stocking and Conservation. Hydrobiology, 4(1), 7. https://doi.org/10.3390/hydrobiology4010007