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Scientific Report

2012 Annual Report: Genetic Assessment of Columbia River Stocks


This project combines four inter-related studies from the Fish & Wildlife Program Accords that address these current and future objectives: 1) discover and evaluate SNP markers in salmon and steelhead and other anadromous fishes; 2) expand and create genetic baselines for multiple species including Chinook salmon, steelhead (O. mykiss), sockeye salmon and kokanee (O. nerka), and coho salmon; 3) implement Genetic Stock Identification (GSI) programs for mainstem Chinook salmon and steelhead fisheries and 4) GSI of fish passing Bonneville Dam (steelhead, sockeye, and Chinook salmon). In the third year of this project, SNP discovery and evaluation goals (Objective 1) were achieved with two completed projects on O. mykiss and one project on Pacific lamprey which identified SNP markers using restriction associated DNA sequence (RAD-seq) technology. For genetic baseline expansion (Objective 2), the Chinook salmon and steelhead GSI baselines continue to expand using a total of 192 SNP markers for each species which includes a 96-SNP panel optimized for parentage based tagging (PBT) and a 96-SNP panel optimized for GSI. In addition, a 96-SNP baseline for O. nerka has become available for assigning individuals to the three major Columbia River sockeye stocks. We have now compiled genotypes from 192 SNP markers in 79 Chinook salmon collections, 192 SNP markers in 145 steelhead collections, and 96 SNP markers in 22 O. nerka collections from the Columbia River Basin. Results from population genetics analyses suggest SNPs are a class of markers that perform well for distinguishing populations, and these baselines will be useful for estimating stock composition in GSI applications. Results also identified loci in all three species that may be candidate markers and showed selective divergence across the study collections. The third year of the project included two broad applications of GSI; namely, stock composition of Chinook salmon and steelhead fisheries (Objective 3), and stock composition of Chinook and sockeye salmon and steelhead passing Bonneville Dam (Objective 4). Chinook salmon and steelhead fishery applications of GSI were integrated with the new genetic technology of parentage based tagging (PBT). The challenge imposed by long histories of exogenous stock transfers from specific hatchery programs often prevents effective application of GSI in assigning hatchery fish. However, as the role of PBT is expanding to tag all hatchery fish, the role of GSI is smaller but still essential for filling in information gaps that remain after PBT has been used to identify hatchery-origin fish. Objective 3 addressed a recent concern of fishery managers related to an expansion of the Chinook salmon sport fishing boundary around the mouth of the Wind R. A comparison of stock composition among spring Chinook salmon samples from below Bonneville Dam in the sport and commercial fishery, non-lethal interrogation at the dam, and above the dam in the tribal ceremonial fishery in Zone 6, demonstrated that the Wind R. sport fishery continues to primarily target its intended stock despite the boundary change. Spring-run Chinook salmon from these sources in the 2012 were primarily composed of two adipose-clipped stocks: Rapid River Hatchery/Clearwater R. and Upper Columbia R. (i.e., Carson stock). PBT-assignments made it possible to further discriminate fish by their hatchery-of-origin (ten total hatcheries represented), which is a vast improvement over the GSI assignments that would have mostly been to the Rapid River Hatchery/Clearwater R. stock (a very broadly distributed reporting group). A third spring-run stock, Willamette R., was found primarily in harvests taken closer to the mouth of the Columbia R. For fall-run Chinook salmon fisheries, we tested accuracy of the Chinook salmon baseline using known-origin mixture samples based on coded wire tags and observed greater than 90% reporting group concordance for the three main fall-run stocks. We demonstrated that we could in fact use PBT to assign a steelhead caught at high-seas in Alaskan waters to Snake River hatchery parents, which may warrant a more thorough examination of high-seas harvest of Snake River steelhead in the future. Stock composition of unclipped steelhead harvested in the tribal fishery in zone 6 was a quarter hatchery-origin fish from the Snake R. For Objective 4, fish were sampled as they migrated past Bonneville Dam. We used a combination of GSI and PBT to estimate run-timing distributions and abundance of hatchery and wild Chinook salmon and steelhead stocks in 2012. Our results indicate there were seven hatchery stocks and seven wild stocks of spring-run Chinook salmon estimated to have greater than 2,000 fish pass Bonneville Dam in 2012. It may interest fisheries managers to know that the run-timing of these stocks contributed to the total abundance of Chinook salmon that pass through the Columbia River mainstem in two management periods, spring and summer. In fact, we observed more than 4,000 natural-origin and 8,000 hatchery-origin fish from spring-run Chinook salmon reporting groups (mostly Snake R. origin) that are estimated to return during the summer management period (June 16 – July 31). There were some consistent run-timing results with those from previous analyses, e.g. Salmon R. and Klickitat R. spring-run Chinook salmon have relatively late runs compared to other spring stocks. There were seven wild steelhead and five hatchery steelhead stocks with an estimated abundance greater than 1000 fish passing Bonneville Dam in 2012. We described three run-timing categories which were most distinctive among hatchery stocks and included an early Skamania summer-run (and Yakima R.), an intermediate run-timing category that contains most wild and hatchery steelhead stocks, and a late run-timing category that arrives after August 25th and includes South Fork Clearwater R., and upper Clearwater R. Three sockeye populations were estimated with the following abundances and median run-timing dates: Okanogan (415,500, Jul. 3rd), Wenatchee (98,900, Jun. 27th), and Redfish Lake (500, Jul 25th). Examination of stock composition of PIT-tagged sockeye that were never detected at their terminal dam revealed differential survivorship of these stocks, with Redfish Lake and Wenatchee sockeye salmon having lower survivorship relative to the Okanogan stock.



Hess, J.E., N.R. Campbell, A.P. Matala, and S.R. Narum. 2014. 2012 Annual Report: Genetic Assessment of Columbia River Stocks. U.S. Dept. of Energy Bonneville Power Administration Report Project #2008-907-00.


Apr 1st, 2014

Report No.


Media Type

CRITFC Technical Report

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