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  • Genetic Monitoring of Interior Columbia River Chinook Salmon and Steelhead


Northwest Fisheries Science Center (NWFSC) Conservation Biology CB - Genetics and Evolution


Genetic effects of hatchery supplementation
Genetic Monitoring of Interior Columbia River Chinook Salmon and Steelhead
This project encompasses two long-term Bonneville Power Administration (BPA)-funded activities aimed at understanding how hatchery supplementation influences genetic variation and reproductive fitness within and among natural and hatchery salmon populations. Understanding the risks and benefits of these programs has been identified as a very high priority for the West Coast Region, and is listed as a specific requirement in multiple NMFS salmon recovery plans. This project is addressing this question with multiple approaches: 1) Genetic parentage analysis to estimate the reproductive success of individual fish in several interior Columbia River Chinook salmon and steelhead populations. These individual estimates are then used to evaluate the relative fitness of hatchery-origin and natural-origin spawners. By doing this over several generations, we can evaluate the relative contributions of genetic and environmental factors to differences in reproductive success between hatchery and natural fish. 2) Whole genome sequencing to directly evaluate the degree of genetic differentiation between groups of hatchery and natural fish, how this changes over time, and how this compares to differences among natural populations and ESUs. Our results are provided to the West Coast Regional office and other regional partners in the form of annual reports, peer-reviewed journal articles and direct meetings and personal interactions with regional staff

Research Themes

Recovery and rebuilding of marine and coastal species
The Pacific Northwest is home to several iconic endangered species, including Pacific salmon and killer whales, and several rockfish species. Mandates such as the Endangered Species Act, MagnusonStevens Act, and the Marine Mammal Protection Act, grant NOAA Fisheries the authority to manage the recovery of depleted species and stocks. The NWFSC contributes to species recovery through research, monitoring and analysis, providing NOAA managers and regional stakeholders the tools and information they need to craft effective regulations and develop sustainable plans for recovery.

Research Foci

Characterize the population biology of species, and develop and improve methods for predicting the status of populations
To evaluate species status and recovery, it is necessary to understand key aspects of the population biology of the species in question. This includes basic information on abundance, age structure, recruitment, spatial distribution, life history and how the species interacts with its ecosystem. For some recovering species, including most overfished groundfish stocks, many ESA-listed Pacific salmon stocks, and high profile species such as Southern Resident killer whales, this basic information is often reasonably well understood. For other recovering species, such as Pacific eulachon and some ESA-listed rockfish species, even basic information (e.g. stock abundance) is unknown. Even for well-studied species, key information on survival rates for critical life stages and how the environment affects these vital rates is lacking. Without basic information on species dynamics, achieving other goals such as quantifying relationships between human activities and species recovery or even knowing if species recovery goals are being met will not be successful. The NWFSC, in partnership with regional stakeholders, including states, tribes and industry, is conducting research to collect and monitor critical demographic information for recovering species.
Evaluate the effects of artificial propagation on recovery, rebuilding and sustainability of marine and anadromous species
Artificial propagation has the potential to provide benefits both to species recovery and to seafood sustainability. Artificial propagation also poses risks to wild species and ecosystems. In the past, the use of artificial propagation has been an important risk factor for several threatened and endangered species, particularly Pacific salmon. Assessing the effects of artificial propagation is complicated by the fact that programs vary widely in size, rearing practices, and goals. The NWFSC conducts critical research on the influence of artificial propagation on population dynamics, growth rate, ecology of infectious disease, and the evolutionary fitness of wild fish and other marine organisms. Results of this research are needed to support the recovery of fish populations and have been especially valuable in providing critical information for recent, larger scale habitat restoration activities such as the Elwha Dam removal. NWFSC will continue to conduct science that informs the discussion about whether to allow fish to recolonize naturally after barrier removal, or to supplement populations with hatchery fish and on the impacts of aquaculture on fishing pressure and practices, and on the surrounding environment and ecosystem.


Snake River
research area
artificial propagation
research technique
research focus
all salmonids


Monitoring and evaluating the genetic characteristics of supplemented salmon and steelhead
Annual report of activities and results from calendar year 2019.
Monitoring and evaluating the genetic characteristics of supplemented salmon and steelhead
Rollup report of BiOp-related activities from calendar year 2019.


Species Oncorhynchus mykiss
rainbow trout, steelhead trout, syeelhead trout
Species Oncorhynchus tshawytscha
Chinook salmon, king salmon, spring salmon


David Kuligowski
Donald Van Doornik
Eric Iwamoto
Ewann Berntson
Principal Investigator
Ewann Berntson
Principal Investigator
Jim Myers
Internal Collaborator
Kathleen Neely
Krista Nichols
Mike Ford
Principal Investigator
Paul Moran