We examined the assumption that landscape heterogeneity similarly influences the spatial distribution of genetic diversity in closely related and geographically overlapping species. Accordingly, we evaluated the influence of watershed affiliation and nine habitat variables from four categories (spatial isolation, habitat size, climate, and ecology) on population divergence in three species of Pacific salmon (Oncorhynchus tshawytscha, O. kisutch, and O. keta) from three contiguous watersheds in subarctic North America. By incorporating spatial data we found that the three watersheds did not form the first level of hierarchical population structure as predicted. Instead, each species exhibited a broadly similar spatial pattern: a single coastal group with populations from all watersheds and one or more inland groups primarily in the largest watershed. These results imply that the spatial scale of conservation should extend across watersheds rather than at the watershed level which is the scale for fishery management. Three independent methods of multivariate analysis identified two variables as having influence on population divergence across all watersheds: precipitation in all species and subbasin area (SBA) in Chinook. Although we found general broad-scale congruence in the spatial patterns of population divergence and evidence that precipitation may influence population divergence in each species, we also found differences in the level of population divergence (coho [ Chinook and chum) and evidence that SBA may influence population divergence only in Chinook. These differences among species support a species-specific approach to evaluating and planning for the influence of broad-scale impacts such as climate change.

In a cooperative project among three agencies, variation at 30 microsatellite loci was surveyed for 19 populations of Chinook salmon Oncorhynchus tshawytscha from the Yukon River. The observed number of alleles per locus ranged from 2 to 63. Loci with a greater number of alleles displayed lower genetic differentiation index (F ST ) values, but loci with lower F ST values also tended to provide more-accurate estimates of stock composition. The observed number of alleles was related to the power of the locus for providing accurate estimates of stock composition of simulated single-population samples. Mean estimated stock compositions for these mixtures ranged from 38.9% for simulations of single loci with fewer than 10 alleles to 85.5% for simulated loci with more than 60 alleles. Reliable population-specific estimation of stock composition was obtained with a minimum of five loci. Comparison of microsatellite stock identification power with an existing nine-locus single-nucleotide polymorphism (SNP) baseline indicated that nine SNPs or a single microsatellite locus can provide accurate and reasonably precise estimates of stock composition to country of origin. In comparisons of population-specific estimation, the nine-SNP baseline was approximately equivalent to a single microsatellite locus with 17-22 alleles. Mixed-stock analysis applying the microsatellite baseline outlined in this study can accurately and precisely allocate Chinook salmon to units useful for management, such as region or major drainage, providing managers with a powerful tool for assessing and regulating fisheries.

We used 20 microsatellite loci to compare genetic diversity and patterns of isolation-by-distance among three groups of chum salmon ( Oncorhynchus keta ) from two physically distinct watersheds in western Alaska, USA. The results were consistent with the hypothesis that gene flow decreases as the complexity of the hydrographic system increases. Specifically, higher gene flow was inferred among 11 populations from a nonhierarchical collection of short coastal rivers in Norton Sound compared with 29 populations from a complex hierarchical network of inland tributaries of the Yukon River. Within the Yukon River, inferred gene flow was highest among 15 summer-run populations that spawn in the lower drainage, compared with 14 fall-run populations that spawn in the upper drainage. The results suggest that the complexity of the hydrographic system may influence population connectivity and hence the level of genetic diversity of western Alaska chum salmon. Finally, evidence of isolation-by-time, when controlling for geographic distance, supported the hypothesis that genetic divergence in Yukon River chum salmon is influenced by seasonal run timing. However, evidence of isolation-by-distance, when controlling for season run timing, indicated the populations are not sufficiently isolated, spatially or temporally, to prevent gene flow. Dispersal among summer- and fall-run populations may play a role in maintaining genetic diversity.