Kris A Christensen, Anne-Marie Flores, Dionne Sakhrani, Carlo A Biagi, Robert H Devlin, Ben J G Sutherland, Ruth E Withler, Eric B Rondeau, Ben F Koop
{"title":"通过基因组重测序揭示菲沙河太平洋鲑鱼的进化史和当代种群结构。","authors":"Kris A Christensen, Anne-Marie Flores, Dionne Sakhrani, Carlo A Biagi, Robert H Devlin, Ben J G Sutherland, Ruth E Withler, Eric B Rondeau, Ben F Koop","doi":"10.1093/g3journal/jkae169","DOIUrl":null,"url":null,"abstract":"<p><p>The Fraser River once supported massive salmon returns. However, over the last century, the largest returns have consistently been less than half of the recorded historical maximum. There is substantial interest from surrounding communities and governments to increase salmon returns for both human use and functional ecosystems. To generate resources for this endeavor, we resequenced genomes of Chinook (Oncorhynchus tshawytscha), coho (Oncorhynchus kisutch), and sockeye salmon (Oncorhynchus nerka) from the Fraser River at moderate coverage (∼16×). A total of 954 resequenced genomes were analyzed, with 681 collected specifically for this study from tissues sampled between 1997 and 2021. An additional 273 were collected from previous studies. At the species level, Chinook salmon appeared to have 1.6-2.1× more SNPs than coho or sockeye salmon, respectively. This difference may be attributable to large historical declines of coho and sockeye salmon. At the population level, 3 Fraser River genetic groups were identified for each species using principal component and admixture analyses. These were consistent with previous research and supports the continued use of these groups in conservation and management efforts. Environmental factors and a migration barrier were identified as major factors influencing the boundaries of these genetic groups. Additionally, 20 potentially adaptive loci were identified among the genetic groups. This information may be valuable in new management and conservation efforts. Furthermore, the resequenced genomes are an important resource for contemporary genomics research on Fraser River salmon and have been made publicly available.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1000,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457079/pdf/","citationCount":"0","resultStr":"{\"title\":\"Revealing the evolutionary history and contemporary population structure of Pacific salmon in the Fraser River through genome resequencing.\",\"authors\":\"Kris A Christensen, Anne-Marie Flores, Dionne Sakhrani, Carlo A Biagi, Robert H Devlin, Ben J G Sutherland, Ruth E Withler, Eric B Rondeau, Ben F Koop\",\"doi\":\"10.1093/g3journal/jkae169\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The Fraser River once supported massive salmon returns. However, over the last century, the largest returns have consistently been less than half of the recorded historical maximum. There is substantial interest from surrounding communities and governments to increase salmon returns for both human use and functional ecosystems. To generate resources for this endeavor, we resequenced genomes of Chinook (Oncorhynchus tshawytscha), coho (Oncorhynchus kisutch), and sockeye salmon (Oncorhynchus nerka) from the Fraser River at moderate coverage (∼16×). A total of 954 resequenced genomes were analyzed, with 681 collected specifically for this study from tissues sampled between 1997 and 2021. An additional 273 were collected from previous studies. At the species level, Chinook salmon appeared to have 1.6-2.1× more SNPs than coho or sockeye salmon, respectively. This difference may be attributable to large historical declines of coho and sockeye salmon. At the population level, 3 Fraser River genetic groups were identified for each species using principal component and admixture analyses. These were consistent with previous research and supports the continued use of these groups in conservation and management efforts. Environmental factors and a migration barrier were identified as major factors influencing the boundaries of these genetic groups. Additionally, 20 potentially adaptive loci were identified among the genetic groups. This information may be valuable in new management and conservation efforts. 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Revealing the evolutionary history and contemporary population structure of Pacific salmon in the Fraser River through genome resequencing.
The Fraser River once supported massive salmon returns. However, over the last century, the largest returns have consistently been less than half of the recorded historical maximum. There is substantial interest from surrounding communities and governments to increase salmon returns for both human use and functional ecosystems. To generate resources for this endeavor, we resequenced genomes of Chinook (Oncorhynchus tshawytscha), coho (Oncorhynchus kisutch), and sockeye salmon (Oncorhynchus nerka) from the Fraser River at moderate coverage (∼16×). A total of 954 resequenced genomes were analyzed, with 681 collected specifically for this study from tissues sampled between 1997 and 2021. An additional 273 were collected from previous studies. At the species level, Chinook salmon appeared to have 1.6-2.1× more SNPs than coho or sockeye salmon, respectively. This difference may be attributable to large historical declines of coho and sockeye salmon. At the population level, 3 Fraser River genetic groups were identified for each species using principal component and admixture analyses. These were consistent with previous research and supports the continued use of these groups in conservation and management efforts. Environmental factors and a migration barrier were identified as major factors influencing the boundaries of these genetic groups. Additionally, 20 potentially adaptive loci were identified among the genetic groups. This information may be valuable in new management and conservation efforts. Furthermore, the resequenced genomes are an important resource for contemporary genomics research on Fraser River salmon and have been made publicly available.
期刊介绍:
G3: Genes, Genomes, Genetics provides a forum for the publication of high‐quality foundational research, particularly research that generates useful genetic and genomic information such as genome maps, single gene studies, genome‐wide association and QTL studies, as well as genome reports, mutant screens, and advances in methods and technology. The Editorial Board of G3 believes that rapid dissemination of these data is the necessary foundation for analysis that leads to mechanistic insights.
G3, published by the Genetics Society of America, meets the critical and growing need of the genetics community for rapid review and publication of important results in all areas of genetics. G3 offers the opportunity to publish the puzzling finding or to present unpublished results that may not have been submitted for review and publication due to a perceived lack of a potential high-impact finding. G3 has earned the DOAJ Seal, which is a mark of certification for open access journals, awarded by DOAJ to journals that achieve a high level of openness, adhere to Best Practice and high publishing standards.