Patterns of genomic variation in Coho salmon following reintroduction to the interior Columbia River

• Published in: Ecology and evolution Vol. 7; no. 23; pp. 10350 - 10360
• Main Authors: Campbell, Nathan R., Kamphaus, Cory, Murdoch, Keely, Narum, Shawn R.
• Format: Journal Article
• Language: English
• Published: England John Wiley & Sons, Inc 01-12-2017; Wiley Blackwell (John Wiley & Sons); John Wiley and Sons Inc
• Subjects: Coho salmon; Damsites; Deoxyribonucleic acid; DNA; DNA sequencing; Fish; genetic adaptation; Genetic diversity; genetic monitoring; Genetic structure; Hydroelectric dams; Hydroelectric power; Migration; Oncorhynchus kisutch; Original Research; RAD sequencing; Reintroduction; Reproductive isolation; Rivers; Salmon; Single-nucleotide polymorphism; Columbia River; genetic monitoring; Coho salmon; reintroduction; RAD sequencing; genetic adaptation
• ISSN: 2045-7758; 2045-7758
• DOI: 10.1002/ece3.3492

Coho salmon were extirpated in the mid‐20th century from the interior reaches of the Columbia River but were reintroduced with relatively abundant source stocks from the lower Columbia River near the Pacific coast. Reintroduction of Coho salmon to the interior Columbia River (Wenatchee River) using lower river stocks placed selective pressures on the new colonizers due to substantial differences with their original habitat such as migration distance and navigation of six additional hydropower dams. We used restriction site‐associated DNA sequencing (RAD‐seq) to genotype 5,392 SNPs in reintroduced Coho salmon in the Wenatchee River over four generations to test for signals of temporal structure and adaptive variation. Temporal genetic structure among the three broodlines of reintroduced fish was evident among the initial return years (2000, 2001, and 2002) and their descendants, which indicated levels of reproductive isolation among broodlines. Signals of adaptive variation were detected from multiple outlier tests and identified candidate genes for further study. This study illustrated that genetic variation and structure of reintroduced populations are likely to reflect source stocks for multiple generations but may shift over time once established in nature.
The manuscript describes genetic monitoring by way of RAD (restriction site DNA) sequencing of Coho salmon over a 12‐year period following their reintroduction to the Wenatchee River (a middle Columbia River tributary). Considerably increased freshwater migration distance between the newly established population and their source population created a unique opportunity to evaluate patterns of population level genetic adaptation in response to long‐distance migration. Changes in SNP allele frequencies over the course of four generations were used to identify loci potentially under adaptive selection in response to increased migration distance.