Colin G. Wallace

Seasonal Stock-Specific Migrations of Juvenile Sockeye Salmon along the West Coast of North America: Implications for Growth

Abstract Knowledge of the migratory habits of juvenile Pacific salmon Oncorhynchus spp. is required to test the hypothesis that ocean food resources are a limiting factor in their production. Using DNA stock identification techniques, we reconstructed the regional and seasonal changes in the stock composition of juvenile sockeye salmon O. nerka (n = 4,062) collected from coastal Washington to the Alaska Peninsula in coastal trawl surveys from May to February 1996–2007. Individuals were allocated to 14 regional populations. The majority were allocated to stocks from the Fraser River system (42%), while west coast Vancouver Island stocks accounted for 15% of the total catch; Nass and Skeena River sockeye salmon constituted 14% and Rivers Inlet 6% of the total. The remainder of the stocks identified individually contributed less than 5% of the sockeye salmon analyzed. These proportions generally reflected the abundance of those populations. In spring and summer, the majority of fish were caught in close prox...

Life History and Seasonal Stock-Specific Ocean Migration of Juvenile Chinook Salmon

Abstract The ocean feeding grounds of juvenile Pacific salmon Oncorhynchus spp. range over several thousand kilometers in which ocean conditions, prey quality and abundance, and predator assemblages vary greatly. Therefore, the fate of individual stocks may depend on where they migrate and how much time they spend in different regions. Juvenile (n = 6,266) and immature (n = 659) Chinook salmon Oncorhynchus tshawytscha were collected from coastal Washington to Southeast Alaska in coastal trawl surveys from February to November 1998–2008, which allowed us to reconstruct changes in stock composition for seasons and regions by means of DNA stock identification techniques. Individuals were allocated to 12 regional stocks. The genetic stock assignments were directly validated by showing that 96% of the 339 known-origin, coded-wire-tagged fish were accurately allocated to their region of origin. Overall, the analyses performed in this study support the main findings of previous work based on tagging. However, gi...

Stock‐Specific Migration Pathways of Juvenile Sockeye Salmon in British Columbia Waters and in the Gulf of Alaska

AbstractWe outlined the route and relative timing of juvenile Sockeye Salmon Oncorhynchus nerka migration by analyzing stock composition and relative CPUE in marine sampling conducted in coastal British Columbia and the Gulf of Alaska. Variation at 14 microsatellites was analyzed for 10,500 juvenile Sockeye Salmon obtained from surveys conducted during 1996–2011. Using a 404-population baseline, we identified the sampled individuals to 47 populations or stocks of origin. Stock compositions of the mixtures increased in diversity in more northerly sampling locations, indicating a general northward movement of juveniles. The primary migration route of Columbia River and Washington stocks was northward along the west coast of Vancouver Island, with a majority of the juveniles subsequently migrating through Queen Charlotte Sound and Dixon Entrance. Fraser River stocks migrated principally through the Strait of Georgia and Johnstone Strait. Some Fraser River populations, such as the Cultus Lake population, appe...

Stock-Specific Size of Juvenile Sockeye Salmon in British Columbia Waters and the Gulf of Alaska

AbstractThe variation at 14 microsatellites was analyzed for 10,500 juvenile Sockeye Salmon Oncorhynchus nerka obtained from coastal British Columbia and Gulf of Alaska surveys during 1996–2011. A 404-population baseline was used to determine the individual identifications of the fish sampled, with individuals being identified to 47 populations or stocks of origin. Columbia River and Washington juveniles were consistently larger than those from British Columbia and Alaska. During July, larger individuals from the same Fraser River stock were observed in more northerly locations compared with those in the Strait of Georgia. There was a relationship between the timing of northward migration from the Strait of Georgia and juvenile body size, with individuals from larger populations or stocks migrating earlier than individuals from smaller stocks which remain resident for longer. There was a wide divergence among stocks in juvenile size and dispersion among sampling locations.Received August 1, 2013; accepted...

Microsatellite Stock Identification of Chum Salmon on a Pacific Rim Basis

Abstract The variation at 14 microsatellite loci was analyzed for more than 53,000 chum salmon Oncorhynchus keta from 381 locations ranging from Korea to Washington State and used to estimate the stock composition of mixed-stock fishery samples. High resolution of the samples was possible, the number of reporting groups being distributed as follows: Korea = 1, Japan = 7, Russia = 8, Alaska = 15, Canadian Yukon River = 5, British Columbia = 16, and Washington State = 5. The number of alleles observed at a locus was related to the power of the locus in providing accurate estimates of the stock composition of single population mixtures. Approximately 800 alleles were observed across the 14 microsatellites, providing the basis for high-resolution stock identification. Analysis of known-origin samples indicated that accurate regional estimates of stock composition were obtained. The estimated stock compositions of mixed-fishery samples from coastal Japan, the Sea of Okhotsk, the western Pacific Ocean, the Gulf...

Population Structure and Run Timing of Sockeye Salmon in the Skeena River, British Columbia

AbstractDetermination of run timing is an important component of salmonid fisheries management and was the major focus of the current study. Population structure of Sockeye Salmon Oncorhynchus nerka was examined in the Skeena River, northern British Columbia. Variation at 14 microsatellites was surveyed for 27 populations in the drainage. There were 9,473 individuals sampled in a lower river test fishery during 2000–2011 in order to provide information on relative abundance and time of arrival of specific populations or stocks near the mouth of the river. Within-lake or within-river tributary structuring of populations was the general pattern observed, with 10 populations from Babine Lake clustering together in 91% of dendrograms evaluated, and two populations from Lakelse Lake clustering together in 100% of dendrograms evaluated. The 27 populations sampled were arranged in 12 reporting groups for genetic stock identification applications. The estimated stock composition of known-origin mixtures was withi...

A Comparison of Stock and Individual Identification for Chinook Salmon in British Columbia Provided by Microsatellites and Single-Nucleotide Polymorphisms

Abstract The following questions were addressed in this study: (1) If a suite of 12–15 microsatellites were used in the genetic stock identification (GSI) of Chinook salmon Oncorhynchus tshawytscha, which microsatellites should be in the suite? (2) How many microsatellites are required to provide stock identification resolution equivalent to that of 72 single-nucleotide polymorphisms (SNPs)? (3) How many SNPs are required to replace the current microsatellite baselines used in GSI applications? (4) If additional GSI power is required for microsatellite baselines, what is the incremental increase provided by SNPs and microsatellites? The variation at 29 microsatellite loci and 73 SNP loci was surveyed in 60 populations of Chinook salmon in 16 regions in British Columbia. Microsatellites with more observed alleles provided more accurate estimates of stock composition than those with fewer alleles. The options available for improving the accuracy and precision of stock composition estimates for a 12-locus Fisheries and Oceans Canada (DFO) microsatellite suite range include adding either 4 microsatellites or 25 SNPs to the existing suite to achieve an overall population-specific accuracy of 86% across 60 populations. For the 13-locus Genetic Analysis of Pacific Salmon (GAPS) microsatellites, either 2 microsatellites or 20–25 SNPs can be added to the existing suite to achieve approximately 86% population-specific accuracy in estimated stock composition. The enhanced DFO (16 loci) and GAPS (15 loci) microsatellite baselines were projected to require 179 and 166 SNPs, respectively, for equivalent precision of the population-specific estimates. The level of regional accuracy of individual assignment available from the enhanced DFO and GAPS suites of microsatellites was projected to require 90 and 82 SNPs, respectively. The level of individual assignment to specific populations available from the enhanced DFO and GAPS suites of microsatellites was projected to require 137 and 121 SNPs, respectively.

Advantages and Challenges of Genetic Stock Identification in Fish Stocks with Low Genetic Resolution

AbstractGenetic stock identification (GSI) is widely applied to mixed-stock fisheries for many commercially exploited species. However, the accuracy of GSI depends on the level of differentiation among stocks. To evaluate our ability to estimate contributions in mixed-stock fisheries of Pink Salmon Oncorhynchus gorbuscha, a species with limited population genetic differentiation, we analyzed 46 odd-year Pink Salmon stocks belonging to a baseline of genotypes from southern British Columbia, the Fraser River, and Puget Sound. Samples were obtained without replacement from the baseline (known mixtures), and 16 microsatellite loci were used for analysis with two software packages (cBayes and ONCOR) to evaluate the accuracy of using this marker set to identify the correct region, subregion, and spawning site. The correct subregion was identified for Pink Salmon from southern British Columbia and Puget Sound. However, incorrect assignments were observed for the Fraser River subregions and the stock-specific est...

Population Structure and Run Timing of Steelhead in the Skeena River, British Columbia

Abstract Identification of population-specific run timing is an important component of salmonid fisheries management and was a major focus of our study. Population structure of steelhead Oncorhynchus mykiss was examined in the Skeena River of northern British Columbia. Variation at 14 microsatellites was surveyed in 3,062 steelhead sampled from 17 populations in the drainage. During 1998–2010, 6,691 individuals were sampled in a lower river test fishery to obtain information on relative abundance and time of arrival of specific populations near the river mouth. The genetic differentiation index F ST calculated over all populations and loci was 0.021; individual locus values ranged from 0.017 to 0.045. Differentiation in steelhead allele frequencies among populations was approximately 14 times the differentiation observed among years within populations. A regional structuring of populations was the general pattern observed, with steelhead populations from the upper portion of the drainage clustering togeth...

Microsatellite Mixed-Stock Identification of Coho Salmon in British Columbia

Abstract Variation at 17 microsatellite loci was analyzed for about 50,000 coho salmon Oncorhynchus kisutch sampled from 274 locations ranging from Russia to California (but largely from British Columbia), and the variation was applied to estimate stock composition in mixed-stock fishery samples. High resolution of mixed-stock samples was possible; accurate estimates of stock composition were available for coho salmon originating from 39 regions (Russia, 1 region; Yukon River, 1; southeast Alaska, 1; British Columbia, 28; Washington, 5; Columbia River, 1; Oregon, 1; California, 1). The power of a locus in providing accurate estimates of stock composition of simulated single-population mixtures was related to the number of alleles observed at the locus. Approximately 800 alleles were observed across the 17 microsatellites. Analysis of known-origin samples indicated that accurate regional estimates of stock composition were obtained; estimates from 37 of 39 regions had accuracy greater than 90%. Estimated stock compositions of five mixed-fishery samples collected in British Columbia and the San Juan Islands (Washington) reflected the presence and timing of migration of the local populations. Microsatellites provided accurate estimates of stock composition from many locations in the British Columbia distribution of coho salmon.