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.

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.

The Pacific Rim population structure of Chinook salmon Oncorhynchus tshawytscha was examined with a survey of microsatellite variation. Variation at 13 microsatellite loci was surveyed for over 52,000 Chinook salmon sampled from over 320 localities ranging from Russia to California. The genetic differentiation index (F ST ) over all populations and loci was 0.063; individual locus values ranged from 0.026 to 0.130. The most genetically diverse Chinook salmon were observed from northern British Columbia, Washington (Puget Sound and coastal populations), and the upper Columbia River (spring run). Chinook salmon from the Alsek River, northern British Columbia, and the Klamath River, California, displayed the fewest number of alleles relative to Chinook salmon in other regions surveyed. Differentiation in Chinook salmon allele frequencies among river drainages and populations within river drainages was approximately 13 times greater than that of annual variation within populations. We observed a general pattern of regional structuring of populations, and Chinook salmon spawning in different tributaries within a major river drainage or in smaller rivers within a geographic area were generally more similar to each other than to populations in different major river drainages or geographic areas. Population structure of Chinook salmon on a Pacific Rim basis supports the concept of a minimum of two refuges, northern and southern, during the last glaciation. The distribution of microsatellite variation of Chinook salmon on a Pacific Rim basis reflects the origins of salmon radiating from refuges after the last glaciation period.

The Pacific Rim population structure of sockeye salmon Oncorhynchus nerka was examined with a survey of microsatellite variation. Variation at 14 microsatellite loci was surveyed for over 48,000 sockeye salmon sampled from 299 localities ranging from the Columbia River to Japan. The value of the genetic differentiation index FST over all populations and loci was 0.097; individual locus values ranged from 0.038 to 0.154. Sockeye salmon from the Queen Charlotte Islands and the Columbia River displayed the least number of alleles relative to sockeye salmon from other regions in the Pacific Rim distribution of the species. Conversely, sockeye salmon displaying the greatest allelic diversity were observed in Southeast Alaska and the central coast of British Columbia. Sockeye salmon from these two regions displayed approximately 30% more alleles than did sockeye salmon from the Queen Charlotte Islands and the Columbia River. Sockeye salmon from Russia and western Alaska were, on average, less diverse than sockeye salmon from Southeast Alaska and more southerly locations in North America. A regional structuring of populations was generally observed among the sockeye salmon populations sampled, and populations were clustered within lakes and river drainages. At the Pacific Rim scale of population structure, there were two major groups of populations. The first group included populations from Russia, Bristol Bay, Kodiak Island, the Alsek River, and the Queen Charlotte Islands. The second group generally included populations from Southeast Alaska, British Columbia, and Washington. The distribution of microsatellite variation of sockeye salmon on a Pacific Rim basis reflected the origins of sockeye salmon radiating from refuges after the last glaciation period.

Genetic differentiation among subpopulations of sockeye salmon (Oncorhynchus nerka) was investigated within nine intensively sampled lake systems located throughout the species' range using allozyme allelic frequency data collected by researchers in Canada, Russia, and the United States. Allelic frequencies at up to nine highly polymorphic loci were used to examine genetic diversity among 163 samples collected from 68 distinct spawning sites and to identify subpopulation structure within lakes. Significant heterogeneity was detected among sites within all lakes. The greatest differentiation was evident among subpopulations exhibiting different run timing (earlier vs. later) or utilizing different spawning habitat (tributary vs. littoral). These findings indicate that sockeye home precisely to natal streams, not just to lake systems, and underscore the importance of conserving individual spawning sites within sockeye populations.