Genetic monitoring tools provide critical information, improve management for salmon and steelhead

The Council's Fish and Wildlife Program has been instrumental in developing genetic approaches to monitoring fish stocks in the basin and improving the effectiveness and efficiency of tagging technology more generally.

At its October meeting, the Council heard updates, successes, and ideas for future improvements from some of the scientists working to advance these genetic monitoring tools, including Matt Campbell, Fisheries Genetics Program Coordinator with the Idaho Department of Fish and Game (IDFG), and Dr. Shawn Narum and Dr. Jon Hess with the Columbia River Inter-Tribal Fish Commission (CRITFC).

Fish and Wildlife Committee Chair and Idaho member Ed Schriever joined representatives from CRITFC, the University of Idaho, the offices of Idaho Senator Risch and Senator Crapo, and IDFG to celebrate the 20th anniversary of the fish genetics lab in Hagerman, Idaho.

Campbell began by explaining some of the basics of the genetic tools. Parentage-based tagging (PBT) is an approach that works best for hatchery fish. It involves taking a genetic sample from all fish spawned at a hatchery to build a large genetic database. Researchers can use that database to figure out the parents of a particular fish when it is later caught and sampled, which can then be used to determine age and hatchery of origin. This way, scientists can permanently tag thousands of offspring per set of parents.

Genetic stock identification (GSI) is focused on wild fish. Since it is much harder to sample wild fish, researchers created more general genetic stock profiles. When wild fish are able to be sampled- at Bonneville Dam, for example- they can be traced back to one of these genetic stocks.

The genetic monitoring project has contributed to a comprehensive, coordinated approach to monitoring and managing Snake River stocks and helped improve accuracy in multiple ways. For example, parentage-based tagging has helped more accurately estimate the number of natural origin fish returning. Not all hatchery fish have their adipose fin clipped (a common way of indicating hatchery origin) or other form of marking. Because of that, prior to the widespread use of genetic tools, it was much harder to tell if a fish with an intact adipose fin was a natural origin fish or an unmarked hatchery fish. Last year, parentage-based tagging identified about 19% of those adipose-intact returns as hatchery origin. "These corrected counts matter," Campbell said, "Because they feed into status and viability assessments."

Parentage-based tagging was also used to make more accurate estimates of hatchery abundance by stock, which has led to an increase in harvest share and additional fishing time in multiple locations. Campbell gave the example of the Rapid River fishery in Idaho, where the harvest share of Chinook salmon increased from 850 to 1,625 fish in 2025, a 91% increase, and from 683 to 1,049 fish in 2026, a 53% increase.

Campbell also introduced the idea of "grandparentage-based tagging". One thing that managers want to know is how many offspring were produced by hatchery fish that spawn in the wild. New research shows that parentage-based tagging can be extended to identify the grandparents of a sampled fish, and thus determine if one parent was a hatchery fish. A recent study published by Campbell and others demonstrated that this approach works, even on the very large scale of the Snake River Basin. One way this is already being applied is through testing for hatchery fish in core habitat areas set aside for Snake River ESA-listed wild steelhead and Chinook salmon.

"Importantly, there was little evidence of wild-born adults with hatchery grandparents detected in wild spawning areas," Campbell said.

An inside view of the CRITFC Mobile Genetics Lab. The mobile lab has meant that scientists can collect and process samples much more quickly and provide close to real-time results to fish and wildlife managers.

Using the PBT and GSI techniques, scientists have been able to report estimates of abundance and timing at Bonneville Dam for specific stocks of Chinook, steelhead, and sockeye about every two weeks. A desire for even faster results to facilitate management decisions led to a first-of-its kind mobile genetics lab with the ability to turn around samples in sometimes less than a day. This has been particularly useful for the region during times when listed or priority species are migrating through the system.

"Bonneville Dam is one of these critical locations in this genetic monitoring program because it's the first dam that these fish encounter where not only are we able to get counts of fish as they're passing Bonneville Dam based off the fish windows and counts, but we try to get a representative sample of fish as they're passing that adult fish facility," said Dr. Narum.

Dr. Jon Hess gave more examples of how the genetic tools have been applied in the region, starting with spring Chinook at Bonneville Dam. It's an important monitoring point, with a mix of ESA-listed and hatchery populations. The use of in-season GSI has meant that managers can receive almost real-time reports on which kind and how many fish are passing the dam, which allows them to make harvest decisions. The PBT testing of the hatchery-origin fish means that each hatchery can receive custom reports about the fish that originated there. And the amount of data that has been collected over the years means that scientists can use samples collected early in the season to predict how that stock will do over the course of the season with enough precision to make management decisions.

Lamprey collected as part of the translocation program in a holding pool at Bonneville Hatchery (Photo credit: Council staff)

Another example was Pacific lamprey, a culturally and ecologically important species. "The tribes have been using translocation and artificial propagation as two of the major tools for boosting numbers in the basin," said Hess. "Before genetic analysis, there was no way to really track the success of these larvae or the adults back to these programs." PBT can help researchers track offspring back to their translocation release groups or hatchery parents. Analyzing sibling relationships (called 'sibship') can identify family groups and survival. Combined, this allows researchers to track the lamprey over time and throughout life stages. This research has demonstrated that translocation leads to more juvenile fish in the targeted tributaries.

"I remember in 2008 when we were talking about this stuff as proof of concept," said Idaho Council member and Fish & Wildlife Committee Chair Ed Schriever. "What a ways we've come, beyond proving the concept to using it effectively in the management arena."