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2011 Annual Report: Genetic Assessment of Columbia River Stocks

Mar 31, 2012


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; 2) expand and create genetic baselines for multiple species including Chinook salmon, steelhead, sockeye salmon and kokanee (O. nerka), and coho salmon; 3) implement Genetic Stock Identification (GSI) programs for mainstem Chinook salmon fisheries and 4) GSI of fish passing Bonneville Dam (steelhead and Chinook). In the third year of this project, SNP discovery and evaluation goals (Objective 1) were achieved with evaluation of 245 available assays for Chinook salmon and the results were used to select two panels of 96 SNP markers. The Chinook salmon GSI baseline will be genotyped with the combined total of these 192 SNP markers which includes a 96-SNP panel optimized for parentage based tagging (PBT) and a 96-SNP panel optimized for GSI. In addition, 126 available assays for O. nerka were evaluated to choose a single panel of 96 SNPs for genetic applications. For genetic baseline expansion (Objective 2), we successfully genotyped 192 SNP markers in 40 Chinook salmon collections, 192 SNP markers in 129 steelhead collections, and 96 SNP markers in 14 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 indicated that some loci may be candidate markers and valuable for analyses based on selective divergence. The third year of the project included two broad applications of GSI; namely, stock composition of Chinook salmon fisheries (Objective 3), and stock composition of Chinook salmon and steelhead passing Bonneville Dam (Objective 4). Results of Objective 3 indicate that spring-run Chinook salmon harvested in the 2011 commercial, sport, and test fisheries were primarily composed of two adipose-clipped stocks: Rapid River Hatchery/Clearwater R. and Upper Columbia R. (i.e., Carson stock). These two Chinook salmon stocks were also the most strongly represented at Bonneville Dam and upstream in the ceremonial fishery during spring weeks. A third spring-run stock, Willamette R., was found primarily in harvests spanning the earlier spring weeks and locations closer to the mouth of the Columbia R. In a rare occurrence, the sport fishery continued into summer weeks in 2011, and during this time a 20% increase in the proportion of Salmon R. stocks was observed. For fall-run Chinook salmon fisheries, the commercial fishery below Bonneville Dam contained large proportions of west cascade fall-run and Spring Creek Group Tule stocks, as well as the following stocks (in descending order): Upper Columbia R. summer/fall, Deschutes R. fall, and Snake R. fall. The entire Zone 6 tribal Chinook fishery was heavily comprised of Upper Columbia R. summer/fall stock, but Region 01 (closest region to Bonneville Dam) of Zone 6 was the only location where the Spring Creek Group Tule stock can be found. The Snake R. stock exhibited an early peak in the fall in the upstream section of Zone 6. We tested accuracy of the Chinook salmon baseline using a combination of simulated data and known-origin mixture samples based on tagging methods (e.g. coded wire tags) and observed between 2%-14% improvement in reporting group accuracy relative to what had been achieved using half (96) of the 192 SNP loci in past years. The percentage of individuals correctly assigned to a particular reporting group using a Leave-one-out method was on average 86% and ranged from greater than 95% (west cascade spring- and fall-run and Yakima R. spring stocks) to a low of 61% (Snake R. fall-run stock). For Objective 4, fish were sampled as they migrated past Bonneville Dam. We used GSI to estimate run-timing distributions and abundance of the “major” stocks of wild and hatchery Chinook salmon in 2011 and steelhead over the period 2009 to 2011. Chinook salmon abundance estimates are listed in order of median day of peak run-timing as follows: Deschutes R. (May 9th, 18,000), Upper Columbia R. (May 10th, 111,000), Rapid R./Clearwater R. (May 11th, 96,000), John Day R. (May 12th, 16,000), and Yakima R. (May 13th, 24,000) spring-run stocks, followed by later run-timing stocks from the Middle Fork Salmon R. (May 30th, 3,000), South Fork Salmon R. (June 7th, 11,000), Klickitat R. (June 8th, 5,000), and Upper Salmon R. (June 11th, 15,000), and fall-run stocks of west cascade (Sep 8th, 3,000), Spring Cr. group tule (Sep 8th, 43,000), Upper Columbia R. summer/fall (Sep 9th, 339,000), Snake R. fall (Sep 11th, 33,000), and Deschutes R. fall (Sep. 13th, 101,000). Steelhead estimates are listed in order of median day of peak run-timing with wild and hatchery abundance separated by a semi-colon as follows: Skamania summer-run (Jul. 6th, <1,000; 7,000), Yakima R. (Jul. 22nd, 6,000; <1,000), Imnaha R. (Aug. 2nd, 5,000; 7,000), Upper Columbia R. (Aug. 3rd, 22,000; 51,000), middle Columbia R. (Aug. 4th, 48,000; 34,000), Klickitat R. (Aug. 5th, 3,000; <1,000), Grande Ronde R. (Aug. 5th, 19,000; 45,000), lower Columbia R. (Aug. 6th, 1,000; <1,000), lower Clearwater R. (Aug. 9th, 3,000; 2,000), Upper Salmon R. (Aug. 10th, 11,000; 93,000), lower/Little Salmon R. (Aug. 12th, 5,000; 12,000), Middle Fork Salmon R. (Aug. 17th, 5,000; <1,000), South Fork Salmon R. (Sep. 2nd, 2,000; <1,000), upper Clearwater R. (Sep. 7th, 6,000k; 3,000), and South Fork Clearwater R. (Sep. 11th, 9,000; 47,000). This study provided an opportunity to demonstrate the benefit of integrating the new genetic technology of parentage based tagging (PBT) into Chinook salmon and steelhead GSI applications. 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, now with the prospect of expanding PBT to mass mark all hatchery fish, GSI will soon be reserved for a smaller but essential role of filling in information gaps that remain after PBT has been used to identify hatchery-origin fish.



Hess, J.E., N.R. Campbell, A.P. Matala, and S.R. Narum. 2012. 2011 Annual report: genetic assessment of Columbia River stocks. U.S. Dept. of Energy Bonneville Power Administration Report Project 2008-907-00. Columbia River Inter-Tribal Fish Commission Technical Report 12-07, Portland, Oregon. 124p.



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CRITFC Technical Report