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Most information about Chinook salmon genetic diversity and life history originates from studies from the West Coast USA, western Canada and southeast Alaska; less is known about Chinook salmon from western and southcentral Alaska drainages. Populations in this large area are genetically distinct from populations to the south and represent an evolutionary legacy of unique genetic, phenotypic and life history diversity. More genetic information is necessary to advance mixed stock analysis applications for studies involving these populations. We assembled a comprehensive, open-access baseline of 45 single nucleotide polymorphisms (SNPs) from 172 populations ranging from Russia to California. We compare SNP data from representative populations throughout the range with particular emphasis on western and southcentral Alaska. We grouped populations into major lineages based upon genetic and geographic characteristics, evaluated the resolution for identifying the composition of admixtures and performed mixed stock analysis on Chinook salmon caught incidentally in the walleye pollock fishery in the Bering Sea. SNP data reveal complex genetic structure within Alaska and can be used in applications to address not only regional issues, but also migration pathways, bycatch studies on the high seas, and potential changes in the range of the species in response to climate change.

The extent to which stray, hatchery-reared salmon affect wild populations is much debated. Although experiments show that artificial breeding and culture influence the genetics of hatchery salmon, little is known about the interaction between hatchery and wild salmon in a natural setting. Here, we estimated historical and contemporary genetic population structures of chum salmon (Oncorhynchus keta) in Prince William Sound (PWS), Alaska, with 135 single nucleotide polymorphism (SNP) markers. Historical population structure was inferred from the analysis of DNA from fish scales, which had been archived since the late 1960’s for several populations in PWS. Parallel analyses with microsatellites and a test based on Hardy-Weinberg proportions showed that about 50% of the fish-scale DNA was cross-contaminated with DNA from other fish. These samples were removed from the analysis. We used a novel application of the classical source-sink model to compare SNP allele frequencies in these archived fish-scales (1964–1982) with frequencies in contemporary samples (2008–2010) and found a temporal shift toward hatchery allele frequencies in some wild populations. Other populations showed markedly less introgression, despite moderate amounts of hatchery straying. The extent of introgression may reflect similarities in spawning time and life-history traits between hatchery and wild fish, or the degree that hybrids return to a natal spawning area. The source-sink model is a powerful means of detecting low levels of introgression over several generations.

We developed a hierarchical Bayesian model (HBM) to estimate missing counts of Chinook salmon (Oncorhynchus tshawytscha (Walbaum in Artedi, 1792)) at a weir on the Kogrukluk River, Alaska, between 1976 and 2015. The model assumed that fish passage during a breach of the weir was typical of passage during normal operations. Counts of fish passing the weir were missing for some days during the runs, or only partial counts for a given 24-hour period were available. The HBM approach provided more defensible estimates of missing data and total escapement than ad hoc or year-by-year model estimates, because estimates of passage for a given year were informed not only by counts for the current year, but also by counts for all previous years. The results of the HBM yielded less variable estimates of escapement than did ad hoc or year-by-year model estimates. The HBM represents a standardized approach to estimate missing counts and total escapement and eliminates the need for ad hoc estimates of missing counts. The model also provides managers with a measure of uncertainty around estimates of escapement and around estimates of hyper-parameters to define run curves in subsequent years with incomplete fish counts.

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