A thorough reconstruction of historical processes is essential for a comprehensive understanding of the mechanisms shaping patterns of genetic diversity. Indeed, past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (Oncorhynchus kisutch) to address two objectives. We demonstrate that a single glacial refugium is the source of most of the present-day genetic diversity, with detectable inputs from a putative secondary micro-refugium. We found statistical support for a scenario whereby ancestral populations located south of the ice sheets expanded recently, swamping out most of the diversity from other putative micro-refugia. Demographic inferences revealed that genetic diversity was also affected by linked selection in large parts of the genome. Moreover, we demonstrate that the recent demographic history of this species generated regional differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations and provides increased support for models of expansion load. We propose that insights from these historical inferences should be better integrated in conservation planning of wild organisms, which currently focuses largely on neutral genetic diversity and local adaptation, with the role of potentially maladaptive variation being generally ignored.

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.

Genetic relationships among 64 spawning populations of chum salmon Oncorhynchus keta in western Alaska were studied using allele frequency data from 40 protein-encoding loci.

Although the number of genetic markers available for fisheries research has steadily increased in recent years, there is limited information on their relative utility. In this study, we compared the preformance of different "classes" of genetic markers (mitochondrial DNA (mtDNA), nuclear DNA (nDNA), and allozymes) in terms of estimating levels and partitioning of genetic variation and of the relative accuracy and precision in estimating population allocations to mixed-stock fisheries. Individuals from eight populations of fall-run chum salmon (Oncorhynchus keta) from the Yukon River in Alaska and Canada were assayed at 25 loci. Significant differences in mitochondrial haplotype and nuclear allele frequencies were observed among five drainages. Populations from the U.S.-Canada border region were not clearly distinguishable based on multilocus allele frequencies. Although estimates of total genetic diversities were higher for the DNA loci (Ht = 0.592 and h = 0.647 for nDNA and mtDNA, respectively) compared with protein allozymes (Ht = 0.250), estimates of the extent of population differentiation were highly concordant across marker classes (mean theta = 0.010, 0.011, and 0.016 for allozymes, nDNA, and mtDNA, respectively). Simulations of mixed-stock fisheries composed of varying contributions of U.S. and Canadian populations revealed a consistent bias for overallocation of Canadian stocks when expected Canadian contributions varied from 0 to 40%, due primarily to misallocations among genetically similar border populations. No single marker class is superior for differentiating populations of this species at the spatial scale examined.

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