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ARS Home » Northeast Area » Orono, Maine » National Cold Water Marine Aquaculture Center » Research » Publications at this Location » Publication #416415
Research Project: Genetic Improvement of North American Atlantic Salmon and the Eastern Oyster for Aquaculture Production

Location: National Cold Water Marine Aquaculture Center

Title: Genetic resources to inform bull trout (Salvelinus confluentus) passage and conservation in the Snake River

Author
item HARGROVE, JOHN - University Of Maine
item Delomas, Thomas
item CAMPBELL, MATTHEW - Idaho Department Of Fish & Game
item HOWELL, PHILIP - Us Forest Service (FS)
item HARRIS, AUDREY - University Of Maine
item WILKINSON, RICHARD - University Of Maine

Submitted to: Conservation Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/3/2024
Publication Date: 10/15/2025
Citation: Hargrove, J.S., Delomas, T.A., Campbell, M.R., Howell, P.J., Harris, A.C., Wilkinson, R. 2025. Genetic resources to inform bull trout (Salvelinus confluentus) passage and conservation in the Snake River. Conservation Genetics. 26: 33-47. https://doi.org/10.1007/s10592-024-01649-z.
DOI: https://doi.org/10.1007/s10592-024-01649-z

Interpretive Summary: For management of natural-origin and aquaculture populations, it is often necessary to know the genetic origin of individuals. Bull trout in the Snake River originate from multiple populations, but individuals from each population are not always physically separate outside of the spawning season. To better inform research and management, we developed a genetic stock identification baseline that gives highly accurate individual assignments (> 99% accuracy at the reporting unit level). We demonstrated usage of this baseline by inferring the population of origin of migratory individuals captured downstream of Hells Canyon Dam. The genetic stock identification baseline will allow improved management of bull trout.

Technical Abstract: Barriers to upstream migration such as dams limit dispersal of fish in lotic systems, including the federally protected bull trout (Salvelinus confluentus). The Hells Canyon Dam on the Snake River currently prevents upstream passage of migratory bull trout into tributary systems in Idaho and Oregon, USA. Viability modeling previously identified the influx of a small number of migrant bull trout (1-6 spawning females annually) as the most important variable for increasing population persistence in the headwater resident bull trout populations above Hells Canyon Dam. Migratory bull trout that overwinter in the Snake River below Hells Canyon Dam could potentially serve as a source of migrants via upstream passage; however, the origin of these fish and their genetic relationship to populations above Hells Canyon Dam is unknown. Furthermore, contemporary details on the genetic status of populations above Hells Canyon Dam, including levels of genetic diversity, are limited. To address these knowledge gaps, we genotyped bull trout from Idaho and Oregon to describe levels of genetic diversity and differentiation among populations and develop a genetic baseline to identify the source populations of migratory bull trout from below Hells Canyon Dam. Bull trout above Hells Canyon Dam displayed variable, but generally modest, levels of genetic diversity and were genetically more similar to bull trout from the Imnaha River basin than other downstream reporting units. An assessment of genetic baseline performance via self-assignment tests and mixture simulations and found stock assignments were highly accurate and minimally biased. Genetic stock identification assigned 97% of the migratory bull trout captured below Hells Canyon Dam to the Imnaha River basin which supports one of the most abundant and viable populations in Oregon. Moving forward, the bull trout genetic resources described here can serve as a baseline for future monitoring and conservation efforts in the transboundary waters of Oregon and Idaho.