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.

Substantial genetic divergence was found among chum salmon (Oncorhynchus keta) populations collected from North America and Russia. Five major groups of populations can be identified by geographic region: (1) lower Yukon River summer run; (2) upper Yukon River fall run; (3) Bristol Bay area; (4) Alaska Peninsula; and (5) Russia. Mean heterozygosities were 0.064, 0.062, 0.065, 0.064, and 0.063, respectively; and the percent polymorphic loci values at the 0.99 level were 33.7, 31.3, 32.6, 30.6, and 30.9%, respectively. The hierarchical gene diversity analysis showed that 95.42% of the diversity can be explained by heterogeneity within sites, 1.36% among sites, 0.49% between Yukon River run timing, 1.69% among areas, and 1.04% among countries. The Alaska Peninsula populations are genetically more similar to populations from Russia than to those from western Alaska, and two populations from the upper Yukon River are distinct from other nearby populations. Possible reasons for these findings concern the complex glacial histories of the watersheds.

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We investigated population structure in sockeye salmon, Oncorhynchus nerka, in relation to ecological characteristics and geographical distribution using allozyme allelic frequencies compiled from new and previously published analyses for 71 populations (300 collections) throughout the species' range. Up to 87 protein-coding loci were screened in some samples, but of these, 55% were monomorphic, and another 31% were only slightly polymorphic with variant allele frequencies <0.01. Only 8 loci were moderately or highly polymorphic with variant allele frequencies exceeding 0.10 in at least some collections. The highest variation ever reported in salmon was discovered at LDH-B2* where the *100 allele was fixed in some populations but rare in others. Genetic differentiation was typically greater among populations within regions than among regions. However, stock composition analysis based on patterns of variation at the nine most useful loci appears to be feasible for most major stocks examined in this study. The low level of polymorphism in sockeye despite high variability at a few polymorphic loci is attributed to precise homing to natal rivers and interactions among several colonizing races that survived the Pleistocene ice age in isolated refugia with different habitat characteristics.