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Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutch) across its entire North American range. We hypothesized that extensive spatial variation in environmental conditions and the species homing behavior may promote the establishment of local adaptation. We genotyped 7,829 individuals representing 217 sampling locations at more than 100,000 high-quality RADseq loci to investigate how recombination might affect the detection of loci putatively under selection and took advantage of the precise description of the demographic history of the species from our previous work to draw accurate population genomic inferences about local adaptation. Results indicated that genetic differentiation scans and genetic-environment association analyses were both significantly affected by variation in recombination rate as low recombination regions displayed an increased number of outliers. By taking these confounding factors into consideration, we revealed that migration distance was the primary selective factor driving local adaptation and partial parallel divergence among distant populations. Moreover, we identified several candidates SNP associated with long distance migration and altitude including a gene known to be involved in adaptation to altitude in other species. The evolutionary implications of our findings are discussed along with conservation applications.

Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutch) across its entire North American range. We hypothesized that extensive spatial variation in environmental conditions and the species' homing behaviour may promote the establishment of local adaptation. We genotyped 7829 individuals representing 217 sampling locations at more than 100,000 high-quality RADseq loci to investigate how recombination might affect the detection of loci putatively under selection and took advantage of the precise description of the demographic history of the species from our previous work to draw accurate population genomic inferences about local adaptation. The results indicated that genetic differentiation scans and genetic-environment association analyses were both significantly affected by variation in recombination rate as low recombination regions displayed an increased number of outliers. By taking these confounding factors into consideration, we revealed that migration distance was the primary selective factor driving local adaptation and partial parallel divergence among distant populations. Moreover, we identified several candidate single nucleotide polymorphisms associated with long-distance migration and altitude including a gene known to be involved in adaptation to altitude in other species. The evolutionary implications of our findings are discussed along with conservation applications.

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.

A thorough reconstruction of historical processes is essential for a comprehensive understanding 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 in postglacial time, 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.

Lake trout Salvelinus namaycush is a slow-growing, late-maturing, cold-water-adapted species whose native distribution is described by the glaciated regions of North America. Southwestern Alaska, the western limit of the species range, has undergone repeated episodes of glacial advance and retreat. In this study, lake trout were sampled from 15 lakes in six drainages on or near Togiak National Wildlife Refuge (TNWR) in southwestern Alaska. Data from 14 microsatellite loci were used to test for genetic evidence that lake trout survived the most recent glacial advance in a local refugium, and to test the effect of habitat size, elevation, and drainage on within- and among-population variation. We could not infer that unglaciated lakes within the TNWR served as a refugium during the most recent glacial maximum. In a neighbor-joining tree, populations largely clustered by drainage, suggesting a single founding source for each drainage. An exception occurred in the Nushagak and Kuskokwim rivers, where evidence for stream capture was detected. Among-population variation, as measured by FST, was 0.35; pairwise FST within drainages ranged from 0.05 to 0.47, indicative of low gene flow, even within drainages, though individual-based analysis detected movement of lake trout among lakes within the Kanektok, Goodnews, and Nushagak rivers. Lake surface area was positively associated with allele richness, and negatively associated with FIS, indicating that smaller lakes in the TNWR harbor less genetic diversity and may have more limited adaptive potential.

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.

Fishery resources are often studied when individuals from multiple stocks are aggregated. For that reason, mixed-stock analysis (MSA), i.e., estimation of the stock composition of a mixture of individuals, is an important component of many research programs. Although many characteristics can be used in MSA, DNA loci, particularly microsatellites, have become extremely common. Microsatellite loci usually have a greater number of potential expressions, or alleles, than other marker types. A high degree of polymorphism can enhance the power of MSA, but allele proportions are estimated less precisely and rare alleles are absent or observed in very small numbers in typically sized samples. The reduced precision and presence of rare alleles can degrade the performance of some analytic methods. Although the effect can be reduced by binning alleles, which is common, an objective method of doing so has not been available previously. We present a method for binning alleles that reduces the number of rare alleles, largely preserves the genetic relationships observed among stocks, and modestly improves the performance of mixed-stock and individual-assignment analyses. The method is illustrated with data from Yukon River chum salmon (Oncorhynchus keta) and western Alaska Dolly Varden (Salvelinus malma).

The geographic distribution pattern of mitochondrial DNA (control region) sequence polymorphisms from 73 populations of a salmonid fish, Dolly Varden Salvelinus malma, over most of its range in the North Pacific rim, was examined to assess how its spatial population genetic structure has been molded. The observed 68 haplotypes were grouped into three main lineages, which correspond to western, central, and eastern regions in the North Pacific. The two outlier-haplotype groups gave close agreement with DNA types from two congeneric species, white-spotted charr S. leucomaenis and Arctic charr S. alpinus, respectively. These results suggest that the present-day genetic structure of S. malma reflects historical patterns of isolation and re-colonization, and also historical hybridization with co-distributed species. We also placed the haplotypes of S. malma within our study areas into a pre-existing evolutionary relationship of S. alpinus and S. malma throughout the Northern Hemisphere. Phylogenetic analysis revealed that the Western Lineage S. malma was basal to all other lineages of S. malma and S. alpinus. Our data serve as a biogeographic hypothesis for salmonid fishes that the Sea of Japan and/or Sea of Okhotsk regions represents a place of origin for S. malma and S. alpinus groups currently distributed in circumpolar regions.

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. Two major lineages of chum salmon inhabiting Alaska were detected using clustering and multidimensional scaling analyses of Cavalli-Sforza and Edwards' chord distances. Populations of the northwest Alaska lineage occur in the largely unglaciated areas of Alaska north of the Alaska Peninsula (Beringia, the Beringian Refugium), and the Alaska Peninsula–Gulf of Alaska lineage occurs in the glaciated and unglaciated areas of the Alaska Peninsula, Kodiak Island, and southcentral Alaska. The two lineages come into contact in the 150-km area separating Herendeen Bay and Port Heiden on the northern Alaska Peninsula; this area may represent a major zoogeographic contact zone. Genetic data also suggest the lineages come in contact in upper Cook Inlet; the population representing the Susitna River drainage, which drains into Cook Inlet...

A representative baseline of allozyme allele frequencies of 69 stock groupings covering the entire range of chum salmon Oncorhynchus keta was evaluated for its ability to estimate stock of origin of Asian and North American chum salmon in complex mixtures. We estimated the origin of 2,000 chum salmon harvested incidentally in fisheries for sockeye salmon O. nerka along the south side of the Alaska Peninsula in the northern Pacific Ocean in 1993 and 1994 using a maximum likelihood algorithm. Of eight major regions (Japan, Russia, northwest Alaska summer run, Yukon River fall run, Alaska Peninsula–Kodiak Island, southeast Alaska, British Columbia, and Washington) reported, northwest Alaska summer-run populations predominated in the fishery with estimates ranging from 0.52 to 0.72. A mitochondrial DNA (mtDNA) marker capable of distinguishing the Japanese component from the rest of the Pacific Rim stocks was assayed in 400 of the 1994 samples. Estimates from the allozyme and mtDNA data were similar. ...

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 iclassesi 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.nCanada 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 θ= 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. Resume : Ces dernires annOes, de nouveaux marqueurs gOnOtiques sont rOgulirement venus enrichir la panoplie dioutils dont dispose la recherche dans le domaine des pŒches; toutefois, liutilitO relative de ces instruments reste en grande partie ‡ dOterminer. Nous avons comparO la performance de diffOrentes « classes » de marqueurs gOnOtiques (ADN mitochondrial (ADNmt), ADN nuclOaire (nADN) et alloenzymes) diaprs leurs propriOtOs de diffOrenciation et le degrO de variation gOnOtique quiils permettent de mettre en Ovidence et diaprs leur exactitude et leur prOcision relatives pour liestimation de la distribution des populations dans les pŒche de stocks mixtes. Nous avons OtudiO 25 locus chez des spOcimens prOlevOs dans huit populations de saumon kOta (Oncorhynchus keta) ‡ montaison automnale du fleuve Yukon, en Alaska et au Canada. Lianalyse des haplotypes mitochondriaux et des frOquences allOliques nuclOaires a permis de mettre en Ovidence des

We studied phylogenetic relationships in the genus Salvelinus with emphasis on S. alpinus, S. malma, and S. confluentus. Sixty allozyme loci were resolved in 422 individuals representing six species from a worldwide distribution. We used phenetic (UPGMA), phylogenetic (Fitch and Margoliash), and maximum-likelihood techniques to derive estimates of Salvelinus phylogeny. Three almost identical topologies were produced, but we chose the Fitch and Margoliash topology as the best phylogenetic estimate. The distances used to construct this tree assume that gene frequencies are affected only by genetic drift, which we argued was the dominant speciation force in Salvelinus. This topology was also the shortest. Jackknifing the Fitch and Margoliash tree resolved the branching order among the three Salvelinus subgenera: S. [Baione], S. [Cristivomer], and S. [Salvelinus]. It also revealed two sister groups within the Salvelinus subgenus: S. leucomaenis – S. confluentus and S. alpinus – S. malma.

Wild stocks of chum salmon, Oncorhynchus keta, have experienced recent declines in some areas of their range. Also, the release of hatchery chum salmon has escalated to nearly three billion fish annually. The decline of wild stocks and the unknown effects of hatchery fish combined with the uncertainty of future production caused by global climate change have renewed interest in the migratory patterns of chum salmon on the high seas. We studied the composition of high-seas mixtures of maturing and immature individuals using baseline data for 20 allozyme loci from 356 populations from throughout the Pacific Rim. Composition estimates were made from three time series. Two of these time series were from important coastal migratory corridors: the Shumagin Islands south of the Alaska Peninsula and the east coast of the Kamchatka Peninsula. The third was from chum salmon captured incidentally in the Bering Sea trawl fishery for walleye pollock. We also analyzed geographically dispersed collections of chum salmon captured in the month of July. The time series show dynamic changes in stock composition. The Shumagin Island corridor was used primarily by Northwest Alaskan and Asian populations in June; by the end of July stocks from the Alaska Peninsula and southern North America dominated the composition. The composition along the Kamchatka coast changed dramatically from primarily Russian stocks in May to primarily Japanese stocks in August; the previously undocumented presence of stocks from the Alaska Peninsula and Gulf of Alaska was also demonstrated. Immature chum salmon from throughout the Pacific Rim, including large proportions of southern North American stocks, contributed to the Bering Sea bycatch during the months of September and October. The migration routes of North American stocks is far more widespread than previously observed, and the Bering Sea is an important rearing area for maturing and immature chum salmon from throughout the species’ range.