Conventional thought holds that in formerly glaciated areas straying of anadromous fish from nearby unglaciated areas established contemporary salmon populations. An additional explanation for patterns of salmon life-history diversity and population structure derives from isolation of populations in proglacial lakes. We evaluate evidence for these potentially complementary hypotheses in chum salmon from two previously glaciated North American regions: the southern Alaska Peninsula/upper Cook Inlet and the Salish Sea of northwestern Washington and southern British Columbia. Some chum salmon populations in the southern Alaska Peninsula are genetic outliers compared with other nearby populations, while Salish Sea chum salmon populations have greater region-wide genetic divergence and lower gene diversity. Within-population genetic diversity and among-population divergence in both study areas support a hypothesis of salmon persistence relying on cryptic isolation and freshwater-resident (trout-like) life histories in proglacial lakes. We find that ice age adaptation of salmon to a trout life history helps explain aspects of contemporary population structure and life-history diversity.

Hatcheries are vital to many salmon fisheries, with inherent risks and rewards. While hatcheries can increase the returns of adult fish, the demographic and evolutionary consequences for natural populations interacting with hatchery fish on spawning grounds remain unclear. This study examined the impacts of stray hatchery-origin pink salmon on natural population productivity and resilience. We explored temporal assortative mating dynamics using a quantitative genetic model that assumed the only difference between hatchery- and natural-origin adults was their return timing to natural spawning grounds. This model was parameterized with empirical data from an intensive multi-generational study of hatchery-wild interactions in the world's largest pink salmon fisheries enhancement program located in Prince William Sound, Alaska. Across scenarios of increasing hatchery fish presence on spawning grounds, our findings underscore a trade-off between demographic enhancement and preservation of natural population diversity. While enhancement bolstered natural population sizes towards local carrying capacities, hatchery introgression reduced variation in adult return timing by up to 20%. Results indicated that hatchery-origin alleles can rapidly assimilate into natural populations, despite the reduced fitness of hatchery fish attributable to phenotypic mismatches. These findings elucidate the potential for long-term demographic and evolutionary consequences arising from specific hatchery-wild interactions, emphasizing the need for management strategies that balance demographic enhancement with the conservation of natural diversity.

Previous studies generally report that hatchery-origin Pacific Salmon (Oncorhynchus spp.) have lower relative reproductive success (RRS) than their natural-origin counterparts. We estimated the RRS of Pink Salmon (O. gorbuscha) in Prince William Sound (PWS), Alaska using incomplete pedigrees. In contrast to other RRS studies, Pink Salmon have a short freshwater life history, freshwater habitats in PWS are largely unaltered by development, and sampling was conducted without the aid of dams or weirs resulting in incomplete sampling of spawning individuals. Pink Salmon released from large-scale hatchery programs in PWS have interacted with wild populations for more than 15 generations. Hatchery populations were established from PWS populations but have subsequently been managed as separate broodstocks. Gene flow is primarily directional, from hatchery strays to wild populations. We used genetic-based parentage analysis to estimate the RRS of a single generation of stray hatchery-origin Pink Salmon in two streams, and across the odd- and even-year lineages. Despite incomplete sampling, we assigned 1745 offspring to at least one parent. Reproductive success (RS), measured as sampled adult offspring that returned to their natal stream, was significantly lower for hatchery- vs. natural-origin parents in both lineages, with RRS ranging from 0.03 to 0.47 for females and 0.05 to 0.86 for males. Generalized linear modeling for the even-year lineage indicated that RRS was lower for hatchery-origin fish, ranging from 0.42 to 0.60, after accounting for sample date (run timing), sample location within the stream, and fish length. Our results strongly suggest that hatchery-origin strays have lower fitness in the wild. The consequences of reduced RRS on wild productivity depend on whether the mechanisms underlying reduced RRS are environmentally driven, and likely ephemeral, or genetically driven, and likely persistent across generations.

The Alaska salmon hatchery program is intended to supplement salmon fisheries without supplanting wild stocks. Hatchery-origin Chum Salmon Oncorhynchus keta spend most of their lives interacting with wild salmon, including some degree of straying to spawning streams. Our study was designed and implemented to measure the extent and annual variability of straying by hatchery-produced, summer-run Chum Salmon in Southeast Alaska from 2013 to 2015 by sampling in individual streams to estimate the proportion of hatchery strays. In the sampled index streams, the proportion ranged from 0.000 to 0.854 over the 3 years. Unbiased estimates of the proportions of hatchery-origin fish spawning in each of the three management units ranged from 0.016 to 0.081, and the estimated hatchery proportions spawning across Southeast Alaska ranged from 0.032 to 0.060. The proportion of hatchery strays decreased as the distance from hatchery release sites increased; proportions were highest at streams located within 50 km of the nearest release site. The proportion of hatchery-origin spawners was negatively related to the index of spawning escapement in a stream. A hatchery donor stray rate of 0.8-4.8% was estimated. Hatchery-origin Chum Salmon occur at low levels in most Chum Salmon systems in Southeast Alaska and at higher levels in systems close to hatchery release sites.

Pacific salmon hatcheries support important commercial fisheries for Pink Salmon Oncorhynchus gorbuscha and Chum Salmon O. keta in Prince William Sound (PWS), Alaska. State policy mandates that hatchery-produced fish must not negatively impact natural populations, which can occur during mixed fisheries and via ecological and genetic interactions. Therefore, we quantified the spatial and temporal overlap of natural- and hatchery-origin salmon (1) as they migrated into PWS and (2) in PWS spawning streams. Intensive sampling during 2013-2015, combined with ancillary agency harvest and hatchery composition data, also allowed us to estimate the hatchery, natural, and total run sizes. Estimated annual proportions (SE in parentheses) of hatchery fish in the preharvest run ranged from 0.55 (0.01) to 0.86 (0.03) for Pink Salmon and from 0.51 (0.03) to 0.73 (0.02) for Chum Salmon. Proportions of hatchery fish across all sampled PWS spawning streams were much lower, ranging from 0.05 (0.03) to 0.15 (0.07) for Pink Salmon and from 0.03 (0.03) to 0.09 (0.03) for Chum Salmon. In both species, relatively high instream proportions of hatchery fish tended to be geographically localized, while many streams exhibited low proportions. The estimated total PWS runs were 50-142 million Pink Salmon and 2.3-5.4 million Chum Salmon. Commercial fisheries harvested 94-99% of hatchery-origin fish of both species, 27-50% of natural-origin Pink Salmon, and 17-20% of natural-origin Chum Salmon. Despite very high harvest rates on hatchery-produced fish, an estimated 0.8-4.5 million hatchery Pink Salmon and 30,000-90,000 hatchery Chum Salmon strayed into PWS spawning streams. Our findings provide context for further research on the relative productivity of hatchery- and natural-origin salmon spawning in streams, density-dependent survival, improvements in fidelity to hatchery release sites, the influence of hatchery production on escapement management and policy, and refinements in harvest management precision in PWS.

Salmon are an important natural, economic, and cultural resource for many people across the northern Pacific Rim, including all five North Pacific Anadromous Fish Commission (NPAFC) member nations.Monitoring and understanding the status of salmon stocks is critical to the management and conservation of this shared resource, especially within the context of a changing and increasingly variable environment that these stocks interact in (e.g., ocean warming and ocean acidification).It is unclear what the future holds for our salmon populations, but we need to think about, and prepare for, the inevitable changes.

Chinook salmon (Oncorhynchus tshawytscha) are migratory fish that are highly valued for subsistence, sport, and commercial fisheries throughout their native range. Populations of Chinook salmon in western Alaska have exhibited long-term declines, leading to restrictions on harvests. Management priorities require greater resolution for genetic stock identification (GSI) than is available with current methods. We leveraged RADseq, TaqMan, and GT-seq data originating from multiple sources, collected through time, to develop a set of GT-seq panels containing 1092 single nucleotide polymorphisms (SNPs) that improved GSI resolution in western Alaska for at-sea and in-river sampling. We generated a dense linkage map to ensure that markers selected for panels spanned the entire genome. In addition, we identified multiple RADseq markers that were associated with sex; these aligned to a 5-centimorgan (cM) region on the sex chromosome. Finally, we developed a bioinformatic pipeline to streamline analysis of GT-seq data that is capable of genotyping microhaplotypes and paralogs, both of which can improve GSI resolution over traditional single-SNP data. Our panels and pipeline provide tools for management agencies to rapidly and easily analyze large-scale genotyping projects.

Pink salmon, the most abundant Pacific salmon, have an obligate 2-year life cycle that leads to reproductively isolated even-and odd-year lineages. Using new and existing data, we examined the genetic structure of both lineages across their distributional range by genotyping 16 681 single-nucleotide polymorphisms for 383 individuals originating from seven pairs of even-and odd-year populations. Distinct differences in standing pools of genetic variation were identified between the lineages; we observed higher levels of heterozygosity, allelic richness, and significantly more private alleles in the odd-year lineage. However, the patterns of population structure were concordant between lineages: the Asian and northern Alaska populations displayed little differentiation but differed significantly from populations in southcentral Alaska and the Pacific Northwest. Our population structure results, in the context of known paleoecological information, suggest that both lineages occupied a northern Beringial refugium as well as a Cascadian refugium in North America during the Last Glacial Maximum. These results highlight the influence of historical patterns of habitat availability on contemporary population structure and support the hypothesis of a pre-glacial origin of the lineages.

The Yukon River is one of the largest producers of chum salmon (Oncorhynchus keta) in western Alaska. Management of Yukon River chum salmon is complex. One of the current concerns is overharvesting of the fall-run component. An earlier and typically more abundant summer-run type spawns in the lower to middle reaches of the drainage, whereas the genetically distinct fall-run type spawns in the middle to upper reaches in Alaska and Canada. Juvenile chum salmon migrate from the Yukon River in the spring and are found in the pelagic waters on the eastern Bering Sea shelf during summer and fall months. We genetically analyzed juvenile chum salmon caught on the eastern Bering Sea shelf during the 2003–2007 Bering-Aleutian Salmon International Surveys. Juvenile chum salmon were predominately from coastal western Alaska and upper/middle Yukon River populations. The relative proportions of fall and summer Yukon chum salmon varied considerably across years. The proportion of fall-run chum salmon in the juvenile collections was positively correlated with the proportion of fall-run chum salmon in the adult returns to the Yukon River, suggesting that the brood-year strength of Yukon River summer and fall-run chum salmon is determined early in the fi rst year of life.

Juvenile Chinook Salmon (Oncorhynchus tshawytscha) abundance in the northern Bering Sea is used to provide insight into future returns and fisheries in the Yukon River. The status of Yukon River Chinook Salmon is of concern due to recent production declines and subsequent closures of commercial, sport, and personal use fisheries, and severe restrictions on subsistence fisheries in the Yukon River. Surface trawl catch data, mixed layer depth adjustments, and genetic stock mixtures are used to estimate juvenile abundance for the Canadian-origin stock group from the Yukon River. Abundance ranged from a low of 0.62 million in 2012 to a high of 2.58 million in 2013 with an overall average of 1.5 million from 2003 to 2015. Although abundance estimates indicate that average survival is relatively low (average of 5.2%), juvenile abundance was significantly correlated (r=0.87, p=0.005) with adult returns, indicating that much of the variability in survival occurs during early life-history stages (freshwater and initial marine). Juvenile abundance in the northern Bering Sea has increased since 2013 due to an increase in early life-history survival (average juveniles-per-spawner increased from 29 to 59). The increase in juvenile abundance is projected to produce larger runs and increased subsistence fishing opportunities for Chinook Salmon in the Yukon River as early as 2016.

Summary Genetic tools are commonly used for conservation and management of at‐risk species. Individuals are often sampled from mixtures that are composed of many populations, which creates a need to assign individuals to their source. This can be problematic when the genetic divergence among source populations is weak but can be improved using adaptive genetic loci, which should show stronger levels of divergence. We previously reported a signature of positive selection in the mitochondrial‐encoded ND5 subunit of complex I in diverse taxa. The respiratory machinery of the mitochondria in salmonids is composed of more than 80 nuclear genes and there is substantial interaction between nuclear and mitochondrial expressed gene products. Recent studies report adaptive variation in mitochondrial function as well as co‐evolution between mitochondrial and nuclear genomes. We used potentially adaptive ND5‐based mitochondrial haplotypes to identify nuclear loci that would display increased levels of genetic divergence compared to neutral nuclear loci in chum salmon (Oncorhynchus keta). Populations in a geographic area the size of France have previously demonstrated weak genetic divergence even after substantial discovery efforts by multiple laboratories for allozymes, microsatellites and SNPs over the last two decades. We used RAD‐based next‐generation sequencing and identified a nuclear‐encoded subunit of mitochondrial complex I that was a significant FST outlier and 14 other divergent nuclear markers that improve genetic assignment of individuals to their population of origin relative to assignments based on neutral markers alone. This work demonstrates how a known adaptive marker can be leveraged to increase the probability of identifying divergent markers for applied genetics tools that may be biologically linked to it.

We examined genetic diversity patterns among 55 collections of Chum Salmon from the northeastern Pacific Ocean using 89 single nucleotide polymorphisms (SNPs). The distribution of Chum Salmon samples extended from the Nass River along the coast of British Columbia and along the coast of Washington as far south as the Columbia River. Chum Salmon represented three previously defined run-groups: fall (primarily), summer, and winter. Genetic variation at SNP loci, as measured by FST, ranged from 0.002 to 0.279 over all collections and averaged 0.062 over all loci. Similar to the genetic patterns detected with microsatellites and allozymes, genetic variation followed a regional structure along geographic distance, with genetic diversity being highest in the north and decreasing southward, then increasing in and near the Columbia River. Within Puget Sound, Washington, genetic variation was structured further according to run timing (fall, summer, and winter) and shared ancestry. Simulations indicated that this suite of SNPs is powerful for identifying regional components in a Chum Salmon mixed fishery. Because of the transferability of SNP data, the growing SNP baseline for Chum Salmon will be useful for multiple agencies managing Chum Salmon around the Pacific Rim.Received December 19, 2014; accepted May 20, 2015

Recent advances in population genomics have made it possible to detect previously unidentified structure, obtain more accurate estimates of demographic parameters, and explore adaptive divergence, potentially revolutionizing the way genetic data are used to manage wild populations. Here, we identified 10 944 single‐nucleotide polymorphisms using restriction‐site‐associated DNA (RAD) sequencing to explore population structure, demography, and adaptive divergence in five populations of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. Patterns of population structure were similar to those of past studies, but our ability to assign individuals back to their region of origin was greatly improved (>90% accuracy for all populations). We also calculated effective size with and without removing physically linked loci identified from a linkage map, a novel method for nonmodel organisms. Estimates of effective size were generally above 1000 and were biased downward when physically linked loci were not removed. Outlier tests based on genetic differentiation identified 733 loci and three genomic regions under putative selection. These markers and genomic regions are excellent candidates for future research and can be used to create high‐resolution panels for genetic monitoring and population assignment. This work demonstrates the utility of genomic data to inform conservation in highly exploited species with shallow population structure.

We estimated the genetic structure and diversity of Japanese Chum Salmon Oncorhynchus keta populations using single-nucleotide polymorphism (SNP) markers to support the management and assessment of the Japanese salmon hatchery program. A total of 5,571 individuals from 57 Japanese Chum Salmon populations were genotyped with 52 markers. A neighbor-joining tree, principal coordinate analysis, analysis of molecular variance, and average pairwise F-ST values indicated the existence of eight regional groups, six in Hokkaido and two in Honshu. Weak but significant isolation by distance was found within the populations of Hokkaido and the Pacific Ocean coast of Honshu. These results suggest that the genetic differentiation among the eight regional groups is small but distinct and occurred through low or restricted gene flow. Furthermore, our results also suggest the persistence of the historical genetic structure (or remnants of it) in extant populations in Japan despite the operation of a hatchery program for about 120 years. The genetic framework of the Japanese Chum Salmon populations that we observed using SNP markers is basically similar to that found by previous studies using other molecular markers but the populations along the western Pacific Ocean coast of Hokkaido are separated into two regional groups.

Genetic stock identification (GSI), an important tool for fisheries management that relies upon the ability to differentiate stocks of interest, can be difficult when populations are closely related. Here we genotyped 11 850 single-nucleotide polymorphisms (SNPs) from existing DNA sequence data available in five closely related populations of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. We then converted a subset of 96 of these SNPs displaying high differentiation into high-throughput genotyping assays. These 96 SNPs (RAD96) and 191 SNPs developed previously (CTC191) were screened in 28 populations from western Alaska. Regional assignment power was evaluated for five different SNP panels, including a panel containing the 96 SNPs with the highest F-ST across the CTC191 and RAD96 panels (F(ST)96). Assignment tests indicated that SNPs in the RAD96 were more useful for GSI than those in the CTC191 and that increasing the number of reporting groups in western Alaska from one to three was feasible with the F(ST)96. Our approach represents an efficient way to discover SNPs for GSI and should be applicable to other populations and species.

Identifying the spatial distribution of genetic variation across the landscape is an essential step in informing species conservation. Comparison of closely related and geographically overlapping species can be particularly useful in cases where landscape may similarly influence genetic structure. Congruent patterns among species highlight the importance that landscape heterogeneity plays in determining genetic structure whereas contrasting patterns emphasize differences in species-specific ecology and life-history or the importance of species-specific adaptation to local environments. We examined the interacting roles of demography and adaptation in determining spatial genetic structure in two closely related and geographically overlapping species in a pristine environment. Using single nucleotide polymorphism (SNP) loci exhibiting both neutral and putative adaptive variation, we evaluated the genetic structure of sockeye salmon in the Copper River, Alaska; these data were compared to existing data for Chinook salmon from the same region. Overall, both species exhibited patterns of isolation by distance; the spatial distribution of populations largely determined the distribution of genetic variation across the landscape. Further, both species exhibited largely congruent patterns of within- and among-population genetic diversity, highlighting the role that landscape heterogeneity and historical processes play in determining spatial genetic structure. Potential adaptive differences among geographically proximate sockeye salmon populations were observed when high FST outlier SNPs were evaluated in a landscape genetics context. Results were evaluated in the context of conservation efforts with an emphasis on reproductive isolation, historical processes, and local adaptation.

The dynamic Quaternary geology of the Pacific Ring of Fire created substantial challenges for biogeography. Fish life history and population genetic variation were shaped by climate change, repeated formation and subsidence of ice sheets, sea-level change, volcanism and tectonics, isostatic rebound, and now human activities. It is widely recognized in Chinook salmon (Oncorhynchus tshawytscha) that parallel evolution and phenotypic plasticity have obscured range-wide patterns of life-history segregation with evolutionary lineage, yet the idea of the lineages themselves persists. We employed a large, internationally standardized, microsatellite data set to explore population structure at coast-wide scale and test for two divergent lineages, whether or not related to life history. We found at least 27 distinct lineages. However, relationships among groups were poorly resolved - essentially a star phylogeny. We found pervasive isolation by distance among groups, complicating cluster analysis. Only in the interior Columbia River (east of the Cascade Mountains) is there a deep genetic bifurcation that supports both the two-lineage hypothesis and the life-history segregation hypothesis. This broad-scale perspective helps reconcile different views of Chinook salmon phylogeography and life-history distribution.

Low genetic divergence at neutral loci among populations is often the result of high levels of contemporary gene flow. Western Alaskan summer-run chum salmon (Oncorhynchus keta) populations demonstrate weak genetic structure, but invoking contemporary gene flow as the basis for the low divergence is problematic because salmon home to their natal streams and some of the populations are thousands of kilometers apart. We used genotypes from microsatellite and single nucleotide polymorphism loci to investigate alternative explanations for the current genetic structure of chum salmon populations from western Alaska. We also estimated current levels of gene flow among Kuskokwim River populations. Our results suggest that weak genetic structure is best explained by physical connections that occurred after the Holocene Thermal Maximum among the Yukon, Kuskokwim, and Nushagak drainages that allowed gene flow to occur among now distant populations.