A Multipurpose Microhaplotype Panel for Genetic Analysis of California Chinook Salmon
ABSTRACT Genetic methods have become an essential component of ecological investigation and conservation planning for fish and wildlife. Among these methods is the use of genetic marker data to identify individuals to populations, or stocks, of origin. More recently, methods that involve genetic ped...
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Wiley
2025-05-01
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| Series: | Evolutionary Applications |
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| Online Access: | https://doi.org/10.1111/eva.70110 |
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| author | Eric C. Anderson Anthony J. Clemento Matthew A. Campbell Devon E. Pearse Anne K. Beulke Cassie Columbus Ellen Campbell Neil F. Thompson John Carlos Garza |
| author_facet | Eric C. Anderson Anthony J. Clemento Matthew A. Campbell Devon E. Pearse Anne K. Beulke Cassie Columbus Ellen Campbell Neil F. Thompson John Carlos Garza |
| author_sort | Eric C. Anderson |
| collection | DOAJ |
| description | ABSTRACT Genetic methods have become an essential component of ecological investigation and conservation planning for fish and wildlife. Among these methods is the use of genetic marker data to identify individuals to populations, or stocks, of origin. More recently, methods that involve genetic pedigree reconstruction to identify relationships between individuals within populations have also become common. We present here a novel set of multiallelic microhaplotype genetic markers for Chinook salmon, which provide excellent resolution for population discrimination and relationship identification from a rapidly and economically assayed panel of markers. We show how this set of genetic markers assayed by sequencing 204 amplicons, in tandem with a reference dataset of 1636 individual samples from 17 populations, provides definitive power to identify all known lineages of Chinook salmon in California. The inclusion of genetic loci that have known associations with phenotype and that were identified as outliers in examination of whole‐genome sequence data allows resolution of stocks that are not highly genetically differentiated but are phenotypically distinct and managed as such. This same set of multiallelic genetic markers has ample variation to accurately identify parent‐offspring and full‐sibling pairs in all California populations, including the genetically depauperate winter‐run lineage. Validation of this marker panel in coastal salmon populations not previously studied with modern genetic methods also reveals novel biological insights, including the presence of a single copy of a haplotype for a phenotype that has not been documented in that part of the species range, and a clear signal of mixed ancestry for a salmon population that is on the geographic margins of the primary evolutionary lineages present in California. |
| format | Article |
| id | doaj-art-754d3db5b9704270a88fe43db48b9bc7 |
| institution | OA Journals |
| issn | 1752-4571 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Wiley |
| record_format | Article |
| series | Evolutionary Applications |
| spelling | doaj-art-754d3db5b9704270a88fe43db48b9bc72025-08-20T02:29:04ZengWileyEvolutionary Applications1752-45712025-05-01185n/an/a10.1111/eva.70110A Multipurpose Microhaplotype Panel for Genetic Analysis of California Chinook SalmonEric C. Anderson0Anthony J. Clemento1Matthew A. Campbell2Devon E. Pearse3Anne K. Beulke4Cassie Columbus5Ellen Campbell6Neil F. Thompson7John Carlos Garza8Southwest Fisheries Science Center National Marine Fisheries Service, NOAA Santa Cruz California USASouthwest Fisheries Science Center National Marine Fisheries Service, NOAA Santa Cruz California USASouthwest Fisheries Science Center National Marine Fisheries Service, NOAA Santa Cruz California USASouthwest Fisheries Science Center National Marine Fisheries Service, NOAA Santa Cruz California USASouthwest Fisheries Science Center National Marine Fisheries Service, NOAA Santa Cruz California USASouthwest Fisheries Science Center National Marine Fisheries Service, NOAA Santa Cruz California USASouthwest Fisheries Science Center National Marine Fisheries Service, NOAA Santa Cruz California USASouthwest Fisheries Science Center National Marine Fisheries Service, NOAA Santa Cruz California USASouthwest Fisheries Science Center National Marine Fisheries Service, NOAA Santa Cruz California USAABSTRACT Genetic methods have become an essential component of ecological investigation and conservation planning for fish and wildlife. Among these methods is the use of genetic marker data to identify individuals to populations, or stocks, of origin. More recently, methods that involve genetic pedigree reconstruction to identify relationships between individuals within populations have also become common. We present here a novel set of multiallelic microhaplotype genetic markers for Chinook salmon, which provide excellent resolution for population discrimination and relationship identification from a rapidly and economically assayed panel of markers. We show how this set of genetic markers assayed by sequencing 204 amplicons, in tandem with a reference dataset of 1636 individual samples from 17 populations, provides definitive power to identify all known lineages of Chinook salmon in California. The inclusion of genetic loci that have known associations with phenotype and that were identified as outliers in examination of whole‐genome sequence data allows resolution of stocks that are not highly genetically differentiated but are phenotypically distinct and managed as such. This same set of multiallelic genetic markers has ample variation to accurately identify parent‐offspring and full‐sibling pairs in all California populations, including the genetically depauperate winter‐run lineage. Validation of this marker panel in coastal salmon populations not previously studied with modern genetic methods also reveals novel biological insights, including the presence of a single copy of a haplotype for a phenotype that has not been documented in that part of the species range, and a clear signal of mixed ancestry for a salmon population that is on the geographic margins of the primary evolutionary lineages present in California.https://doi.org/10.1111/eva.70110amplicon sequencinggenetic stock identficationparentage‐based taggingpopulation assignment |
| spellingShingle | Eric C. Anderson Anthony J. Clemento Matthew A. Campbell Devon E. Pearse Anne K. Beulke Cassie Columbus Ellen Campbell Neil F. Thompson John Carlos Garza A Multipurpose Microhaplotype Panel for Genetic Analysis of California Chinook Salmon Evolutionary Applications amplicon sequencing genetic stock identfication parentage‐based tagging population assignment |
| title | A Multipurpose Microhaplotype Panel for Genetic Analysis of California Chinook Salmon |
| title_full | A Multipurpose Microhaplotype Panel for Genetic Analysis of California Chinook Salmon |
| title_fullStr | A Multipurpose Microhaplotype Panel for Genetic Analysis of California Chinook Salmon |
| title_full_unstemmed | A Multipurpose Microhaplotype Panel for Genetic Analysis of California Chinook Salmon |
| title_short | A Multipurpose Microhaplotype Panel for Genetic Analysis of California Chinook Salmon |
| title_sort | multipurpose microhaplotype panel for genetic analysis of california chinook salmon |
| topic | amplicon sequencing genetic stock identfication parentage‐based tagging population assignment |
| url | https://doi.org/10.1111/eva.70110 |
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