Recovery plans for endangered southern resident killer whales Orcinus orca have identified reduced prey availability as a risk to the population. In order to better assess this risk, we studied prey selection from 2004 to 2008 in 2 regions of the whales' summer range: San Juan Islands, Washington and the western Strait of Juan de Fuca, British Columbia. Following the whales in a small boat, we collected fish scales and tissue remains from predation events, and feces, using a fine mesh net. Visual fish scale analysis and molecular genetic methods were used to identify the species consumed. Chinook salmon, a relatively rare species, was by far the most frequent prey item, confirming previous studies. For Chinook salmon prey, we used genetic identification methods to estimate the spawning region of origin. Of the Chinook salmon sampled, 80 to 90% were inferred to have originated from the Fraser River, and only 6 to 14% were inferred to have originated from Puget Sound area rivers. Within the Fraser River, the Upper Fraser, Middle Fraser, South Thompson River and Lower Fraser stocks were inferred to currently be sequentially important sources of Chinook salmon prey through the summer. This information will be of significant value in guiding management actions to recover the southern resident killer whale population.
The variation at 14 microsatellite loci and one major histocompatibility complex (MHC) locus was surveyed for over 48,000 sockeye salmon Oncorhynchus nerka sampled from 299 localities ranging from the Columbia River to Japan. For the microsatellite loci, the number of alleles observed at a locus was related to the power of the locus in providing accurate estimates of stock composition of single‐population mixtures. In an analysis of single‐population mixtures where the Pacific Rim baseline was used for estimation of stock identification, 80% accuracy for the average population was achieved by employing approximately 80 alleles in the analysis. Increasing the accuracy of estimated stock compositions to 90% for the average population required approximately 400 microsatellite alleles. When all loci were used to estimate stock compositions, estimates were above 80% for all sampling sites or populations, above 90% for the lake of origin, and generally above 95% for the region of origin. Analysis of known‐origin samples indicated that accurate lake or regional estimates of stock composition were obtained. The accuracy of identification of individual fish to the correct lake of origin was above 90%, regardless of whether the lakes were geographically widespread or within a single watershed. The estimated stock compositions of mixed‐fishery samples from the western Bering Sea, from the continental shelf near Kodiak Island in the Gulf of Alaska, from Southeast Alaska, and from Johnstone Strait in southern British Columbia were markedly different among samples. These stock compositions reflected geographical variation in fishery locations and variation in the migration pathways of either juvenile or maturing sockeye salmon. Variation of DNA enabled us to estimate accurately the origin of individual fish and the composition of mixed‐stock samples from any location in the Pacific Rim distribution of sockeye salmon.
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 ¼ 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 proximity to their rivers of origin, lending further support to the allocations. By fall, sockeye salmon were caught as far north and west as the Alaska Peninsula, the majority being caught from central British Columbia to Southeast Alaska. Juvenile sockeye salmon generally disappeared from the coast by winter, suggesting dispersion into the Gulf of Alaska. Within each region, the proportional stock composition changed as the seasons progressed, with northward (and in some cases, rapid) migration along the coast. We also demonstrated stock-specific differences in migration patterns. For each stock identified, body size and energy density were higher at northern latitudes, suggesting that there is an environmental or food web influence on growth or that faster growing fish initiated their northward migration earlier.
Variation at 13 microsatellite loci was surveyed for over 52,000 Chinook salmon Oncorhynchus tshawytscha sampled from 325 localities ranging from Russia to California; the variation was applied to estimate stock composition in mixed-stock fishery samples. A rapid increase in the accuracy of estimated stock composition in simulated mixtures with respect to population sample size was observed for sample sizes of up to about 75 individuals, at which point a 90% accuracy of assignment to population was achieved. 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. In analysis of single-population mixtures where the Pacific Rim baseline was used for estimation of stock identification, 75% accuracy for the average population was achieved by employing approximately 55 alleles in the analysis. Increasing the accuracy of the estimated stock composition to 90% for the average population required approximately 350 microsatellite alleles. The precision of estimated stock composition increased rapidly for approximately the first 100 alleles used; standard deviations declined from 20.0% to 8.0%. Analysis of known-origin samples indicated that accurate regional estimates of stock composition were obtained. The accuracy of assigning individuals to a specific region or river drainage averaged 84% for 54 populations in multipopulation samples. The estimated stock compositions of mixed-fishery samples from northern and southern locations in British Columbia were quite different among samples and reflected whether samples were derived from migrating or resident Chinook salmon. Microsatellites have the ability to provide accurate estimates of stock composition from many fisheries in the Pacific Rim distribution of Chinook salmon.
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