Efficient population representation with more genetic markers increases performance of a steelhead (Oncorhynchus mykiss) genetic stock identification baseline
Abstract Genetic stock identification (GSI) is an important fisheries management tool to identify the origin of fish harvested in mixed stock fisheries. Periodic updates of genetic baselines can improve performance via the addition of unsampled or under‐sampled populations and the inclusion of more...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2024-02-01
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| Series: | Evolutionary Applications |
| Subjects: | |
| Online Access: | https://doi.org/10.1111/eva.13610 |
| _version_ | 1797294406049464320 |
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| author | John S. Hargrove Thomas A. Delomas John H. Powell Jon E. Hess Shawn R. Narum Matthew R. Campbell |
| author_facet | John S. Hargrove Thomas A. Delomas John H. Powell Jon E. Hess Shawn R. Narum Matthew R. Campbell |
| author_sort | John S. Hargrove |
| collection | DOAJ |
| description | Abstract Genetic stock identification (GSI) is an important fisheries management tool to identify the origin of fish harvested in mixed stock fisheries. Periodic updates of genetic baselines can improve performance via the addition of unsampled or under‐sampled populations and the inclusion of more informative markers. We used a combination of baselines to evaluate how population representation, marker number, and marker type affected the performance and accuracy of genetic stock assignments (self‐assignment, bias, and holdout group tests) for steelhead (Oncorhynchus mykiss) in the Snake River basin. First, we compared the performance of an existing genetic baseline with a newly developed one which had a reduced number of individuals from more populations using the same set of markers. Self‐assignment rates were significantly higher (p < 0.001; +5.4%) for the older, larger baseline, bias did not differ significantly between the two, but there was a significant improvement in performance for the new baseline in holdout results (p < 0.001; mean increase of 25.0%). Second, we compared the performance of the new baseline with increased numbers of genetic markers (~2x increase of single‐nucleotide polymorphisms; SNPs) for the same set of baseline individuals. In this comparison, results produced significantly higher rates of self‐assignment (p < 0.001; +9.7%) but neither bias nor leave‐one‐out were significantly affected. Third, we compared 334 SNPs versus opportunistically discovered microhaplotypes from the same amplicons for the new baseline, and showed the latter produced significantly higher rates of self‐assignment (p < 0.01; +2.6%), similar bias, but slightly lower holdout performance (−0.1%). Combined, we show the performance of genetic baselines can be improved via representative and efficient sampling, that increased marker number consistently improved performance over the original baseline, and that opportunistic discovery of microhaplotypes can lead to small improvements in GSI performance. |
| first_indexed | 2024-03-07T21:29:48Z |
| format | Article |
| id | doaj.art-77aa88483bcd4c5780911b5033ebac4c |
| institution | Directory Open Access Journal |
| issn | 1752-4571 |
| language | English |
| last_indexed | 2024-03-07T21:29:48Z |
| publishDate | 2024-02-01 |
| publisher | Wiley |
| record_format | Article |
| series | Evolutionary Applications |
| spelling | doaj.art-77aa88483bcd4c5780911b5033ebac4c2024-02-27T00:12:39ZengWileyEvolutionary Applications1752-45712024-02-01172n/an/a10.1111/eva.13610Efficient population representation with more genetic markers increases performance of a steelhead (Oncorhynchus mykiss) genetic stock identification baselineJohn S. Hargrove0Thomas A. Delomas1John H. Powell2Jon E. Hess3Shawn R. Narum4Matthew R. Campbell5Pacific States Marine Fisheries Commission Eagle Idaho USAU.S. Department of Agriculture Agricultural Research Service National Cold Water Marine Aquaculture Center Kingston Rhode Island USAIdaho Department of Fish and Game Eagle Idaho USAColumbia River Inter‐Tribal Fish Commission Portland Oregon USAColumbia River Inter‐Tribal Fish Commission Hagerman Idaho USAIdaho Department of Fish and Game Eagle Idaho USAAbstract Genetic stock identification (GSI) is an important fisheries management tool to identify the origin of fish harvested in mixed stock fisheries. Periodic updates of genetic baselines can improve performance via the addition of unsampled or under‐sampled populations and the inclusion of more informative markers. We used a combination of baselines to evaluate how population representation, marker number, and marker type affected the performance and accuracy of genetic stock assignments (self‐assignment, bias, and holdout group tests) for steelhead (Oncorhynchus mykiss) in the Snake River basin. First, we compared the performance of an existing genetic baseline with a newly developed one which had a reduced number of individuals from more populations using the same set of markers. Self‐assignment rates were significantly higher (p < 0.001; +5.4%) for the older, larger baseline, bias did not differ significantly between the two, but there was a significant improvement in performance for the new baseline in holdout results (p < 0.001; mean increase of 25.0%). Second, we compared the performance of the new baseline with increased numbers of genetic markers (~2x increase of single‐nucleotide polymorphisms; SNPs) for the same set of baseline individuals. In this comparison, results produced significantly higher rates of self‐assignment (p < 0.001; +9.7%) but neither bias nor leave‐one‐out were significantly affected. Third, we compared 334 SNPs versus opportunistically discovered microhaplotypes from the same amplicons for the new baseline, and showed the latter produced significantly higher rates of self‐assignment (p < 0.01; +2.6%), similar bias, but slightly lower holdout performance (−0.1%). Combined, we show the performance of genetic baselines can be improved via representative and efficient sampling, that increased marker number consistently improved performance over the original baseline, and that opportunistic discovery of microhaplotypes can lead to small improvements in GSI performance.https://doi.org/10.1111/eva.13610endangered species actmanagementmicrohaplotypesOncorhynchus mykisssingle‐nucleotide polymorphismsSnake River basin |
| spellingShingle | John S. Hargrove Thomas A. Delomas John H. Powell Jon E. Hess Shawn R. Narum Matthew R. Campbell Efficient population representation with more genetic markers increases performance of a steelhead (Oncorhynchus mykiss) genetic stock identification baseline Evolutionary Applications endangered species act management microhaplotypes Oncorhynchus mykiss single‐nucleotide polymorphisms Snake River basin |
| title | Efficient population representation with more genetic markers increases performance of a steelhead (Oncorhynchus mykiss) genetic stock identification baseline |
| title_full | Efficient population representation with more genetic markers increases performance of a steelhead (Oncorhynchus mykiss) genetic stock identification baseline |
| title_fullStr | Efficient population representation with more genetic markers increases performance of a steelhead (Oncorhynchus mykiss) genetic stock identification baseline |
| title_full_unstemmed | Efficient population representation with more genetic markers increases performance of a steelhead (Oncorhynchus mykiss) genetic stock identification baseline |
| title_short | Efficient population representation with more genetic markers increases performance of a steelhead (Oncorhynchus mykiss) genetic stock identification baseline |
| title_sort | efficient population representation with more genetic markers increases performance of a steelhead oncorhynchus mykiss genetic stock identification baseline |
| topic | endangered species act management microhaplotypes Oncorhynchus mykiss single‐nucleotide polymorphisms Snake River basin |
| url | https://doi.org/10.1111/eva.13610 |
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