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Modern fisheries management strives to balance opposing goals of protection for weak stocks and opportunity for harvesting healthy stocks. Test fisheries can aid management of anadromous fishes if they can forecast the strength and timing of an annual run with adequate time to allow fisheries planning. Integration of genetic stock identification (GSI) can further maximize utility of test fisheries by resolving run forecasts into weak‐ and healthy‐stock subcomponents. Using 5 years (2017–2022) of test fishery data, our study evaluated accuracy, resolution, and lead time of predictions for stock‐specific run timing and abundance of Columbia River spring Chinook salmon (Oncorhynchus tshawytscha). We determined if this test fishery (1) could use visual stock identification (VSI) to forecast at the coarse stock resolution (i.e., classification of "lower" vs. "upriver" stocks) upon which current management is based and (2) could be enhanced with GSI to forecast at higher stock resolution. VSI accurately identified coarse stocks (83.3% GSI concordance), and estimated a proxy for abundance (catch per unit effort, CPUE) of the upriver stock in the test fishery that was correlated (R2 = 0.90) with spring Chinook salmon abundance at Bonneville dam (Rkm 235). Salmon travel rates (~8.6 Rkm/day) provided predictions with 2‐week lead time prior to dam passage. Importantly, GSI resolved this predictive ability as finely as the hatchery broodstock level. Lower river stock CPUE in the test fishery was correlated with abundance at Willamette Falls (Rkm 196, R2 = 0.62), but could not be as finely resolved as achieved for upriver stocks. We described steps to combine VSI and GSI to provide timely in‐season information and with prediction accuracy of ~12.4 mean absolute percentage error and high stock resolution to help plan Columbia River mainstem fisheries. [ABSTRACT FROM AUTHOR]

Conserving life‐history variation is a stated goal of many management programs, but the most effective means by which to accomplish this are often far from clear. Early‐ and late‐migrating forms of Chinook salmon (Oncorhynchus tshawytscha) face unequal pressure from natural and anthropogenic forces that may alter the impacts of genetic variation underlying heritable migration timing. Genomic regions of chromosome 28 are known to be strongly associated with migration variation in adult Chinook salmon, but it remains unclear whether there is consistent association among diverse lineages and populations in large basins such as the Columbia River. With high‐throughput genotyping (GT‐seq) and phenotyping methods, we examined the association of genetic variation in 28 markers (spanning GREB1L to ROCK1 of chromosome 28) with individual adult migration timing characteristics gleaned from passive integrated transponder recordings of over 5000 Chinook salmon from the three major phylogeographic lineages that inhabit the Columbia River Basin. Despite the strong genetic differences among them in putatively neutral genomic regions, each of the three lineages exhibited very similar genetic variants in the chromosome 28 region that were significantly associated with adult migration timing phenotypes. This is particularly notable for the interior stream‐type lineage, which exhibits an earlier and more constrained freshwater entry than the other lineages. In both interior stream‐type and interior ocean‐type lineages of Chinook salmon, heterozygotes of the most strongly associated linkage groups had largely intermediate migration timing relative to homozygotes, and results indicate codominance or possibly marginal partial dominance of the allele associated with early migration. Our results lend support to utilization of chromosome 28 variation in tracking and predicting run timing in these lineages of Chinook salmon in the Columbia River. [ABSTRACT FROM AUTHOR]

As life history diversity plays a critical role in supporting the resilience of exploited populations, understanding the genetic basis of those life history variations is important for conservation management. However, effective application requires a robust understanding of the strength and universality of genetic associations. Here, we examine genetic variation of single nucleotide polymorphisms in genomic regions previously associated with migration phenology and age‐at‐maturity in steelhead (Oncorhynchus mykiss) from the Columbia River. We found chromosome 28 markers (GREB1L, ROCK1 genes) explained significant variance in migration timing in both coastal and inland steelhead. However, strength of association was much greater in coastal than inland steelhead (R2 0.51 vs. 0.08), suggesting that genomic background and challenging inland migration pathways may act to moderate effects of this region. Further, we found that chromosome 25 candidate markers (SIX6 gene) were significantly associated with age and size at first return migration for inland steelhead, and this pattern was mediated by sex in a predictable pattern (males R2 = 0.139–0.170; females R2 = 0.096–0.111). While this encourages using these candidate regions in predicting life history characteristics, we suggest that stock‐specific associations and haplotype frequencies will be useful in guiding implementation of genetic assays to inform management. [ABSTRACT FROM AUTHOR]

Stock-specific migration-timing and relative abundance of exploited fish species are critical parameters to estimate for management of mixed stock fisheries. Here, we used parentage-based tagging (PBT) together with mixed stock analyses (MSA) to estimate stock-specific abundance and migration-timing in anadromous adult steelhead (Oncorhynchus mykiss) sampled at Bonneville Dam in the lower Columbia River. Results indicate that natural-origin steelhead was represented by 11 of 13 possible stocks found throughout the Columbia-Snake river basins, while hatchery-origin steelhead was primarily composed of five stocks from the Snake River drainage. Further, migration-timing differentiated stocks and allowed categorization of early, intermediate, and late migrating stocks. Analyses of age and length data for these stocks also showed that late-arriving fish were larger due to older age and originated primarily from the Clearwater River, South Fork Salmon River, and Dworshak Hatchery, all from the Snake River drainage. Sex ratios tended to be skewed towards females and ranged from 51.5 to 68.9% for hatchery stocks and 60.5-71.8% for natural-origin stocks. This suggests that anadromous migration is favored by females while males are more likely to residualize in freshwater. Overall, this study demonstrates how the use of PBT in MSA can reveal important stock-specific differences in migration-timing and relative abundance and provides critical information for management of mixed stock fisheries. [ABSTRACT FROM AUTHOR]

Genetic stock identification (GSI) provides a method of characterizing stock-specific abundance, run timing, and straying as they pertain to the population demographics and behavior of both hatchery and wild fish and thus assists with fisheries management. In this study, tissues were collected and genotyped at 13 microsatellite loci from adult Chinook SalmonOncorhynchus tshawytschathat passed Bonneville Dam during four consecutive migration years (2004–2007). GSI methods were used to estimate the proportions of stocks in a broad genetic baseline, with high-density coverage of Chinook Salmon across the eastern Pacific Rim. The estimates of abundance for interior Columbia River stocks showed widespread decline consistent with a shift to poor ocean conditions during the years when the fish in this study were at sea, but divergent stock- and age-specific patterns were also observed. For example, the upper Columbia River spring-run stock experienced a unique net gain in abundance during this period, and the interior Columbia River summer–fall-run stock experienced a delayed decline of 4-year-olds. Stocks with early run timing shifted to later migrations. However, run timing distributions did not shift unidirectionally for all stocks across years, and stock membership in three major run timing categories was maintained. Of 9,215 total adults sampled, 27 (0.3%) were out-of-basin strays and a quarter of the strays were putatively of wild origin. The general concordance of GSI results with those based on more traditional methods supports the effectiveness of GSI as a tool for fisheries management. Received May 5, 2013; accepted October 23, 2013 [ABSTRACT FROM AUTHOR]

We evaluated the traits and survival to release of reconditioned kelt steelhead Oncorhynchus mykiss in the Yakima River (Washington State, USA). From 2001 to 2011, we captured a total of 9,738 downstream-migrating kelts at an irrigation diversion facility, an average about 27% of each annual wild steelhead return. Captured kelts were reared for 4.5-10 months in an artificial environment, treated for diseases and parasites, and fed both krill and pellets. Surviving reconditioned fish were released into the Yakima River during the peak of the upstream migration of prespawn steelhead. Reconditioned steelhead kelts were predominantly (>92%) female. Annual survival to release ranged from 20% to 62% and averaged 38% over the course of the study, the surviving reconditioned kelts showing increases in FL, weight, and Fulton's K condition factor compared with their preconditioning status. Kelts in good condition and those with bright coloration at the time of collection were more likely to survive than those of poorer status at collection. Postrelease timing of upstream migration by reconditioned kelts was spread over several months and correlated well with the run timing of prespawn migrants upstream. The empirical results we observed demonstrate the potential for kelt reconditioning to provide recovery benefits for repeat spawning imperiled wild populations in highly developed river systems. [ABSTRACT FROM AUTHOR]

Abstract: In the multi-stock Columbia River system, managers estimate fall Chinook salmon, Oncorhynchus tshawytscha (Walbaum), escapements using various combinations of spawning ground surveys, harvest data and fish counts at dams and hatcheries. Our objectives were to improve upon the traditional methods, and to evaluate trade-offs among methods. Using data from radio-tagged (n =4421) and PIT-tagged (n =1950) adult salmon over eight years, we applied a mark-recapture method to estimate population-specific escapements, both aggregating data within year and stratifying them by week. Mark-recapture estimates differed between estimation techniques and from estimates generated using traditional methods. Stratifying data by week measured escapement estimate uncertainty more reasonably than aggregating data within year. Radiotelemetry provided better spatial resolution among populations for tributary spawners whereas PIT tags provided low-cost, easily replicated estimates using an existing detection system. Mark-recapture techniques had several advantages over current practices: quantifying uncertainty, transparent methods and reduced sensitivity to survey biases. [Copyright &y& Elsevier]