Revealing the evolutionary history and contemporary population structure of Pacific salmon in the Fraser River through genome resequencing.

IF 2.1 3区 生物学 Q3 GENETICS & HEREDITY
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
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Abstract

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.

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。
弗雷泽河曾经支持过大量鲑鱼的回归。然而,在过去的一个世纪里,最大的回游量一直不到历史最高记录的一半。周边社区和政府对增加鲑鱼回游量有着浓厚的兴趣,这既是为了人类使用,也是为了功能性生态系统。为了为这一努力创造资源,我们以中等覆盖率(∼16 倍)对菲沙河的大鳞鲑(Oncorhynchus tshawytscha)、小鳞鲑(O. kisutch)和红鲑(O. nerka)的基因组进行了重新测序。共分析了 954 个重新测序的基因组,其中 681 个是专门为本研究从 1997 年至 2021 年期间采样的组织中收集的。另有 273 个基因组是从以前的研究中收集的。在物种水平上,大鳞大麻哈鱼的 SNP 似乎分别比库克大麻哈鱼或红大麻哈鱼多 1.6-2.1 倍。这种差异可能是由于历史上库克鲑和红鲑的大量减少造成的。在种群水平上,利用主成分和掺杂分析为每个物种确定了三个弗雷泽河遗传组群,这与之前的研究一致,并支持在保护和管理工作中继续使用这些组群。环境因素和迁移障碍被认为是影响这些基因组边界的主要因素。此外,在这些基因群中还发现了 20 个潜在的适应性位点。这些信息可能对新的管理和保护工作很有价值。此外,重新测序的基因组是当代弗雷泽河鲑鱼基因组学研究的重要资源,并已公开发表。
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来源期刊
G3: Genes|Genomes|Genetics
G3: Genes|Genomes|Genetics GENETICS & HEREDITY-
CiteScore
5.10
自引率
3.80%
发文量
305
审稿时长
3-8 weeks
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.
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