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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.

Natural-origin steelhead trout (Oncorhynchus mykiss (Walbaum, 1792)) in the Pacific Northwest, USA, are threatened by a number of factors including habitat destruction, disease, decline in marine survival, and a potential erosion of genetic viability due to introgression from hatchery strains. Our major goal was to use a recently developed SNP array containing ∼57 000 SNPs to identify a subset of SNPs that differentiate hatchery and natural-origin populations. We analyzed 35 765 polymorphic SNPs in nine populations of steelhead trout sampled from Puget Sound, Washington, USA. We then conducted two outlier tests and found 360 loci that were candidates for divergent selection between hatchery and natural-origin populations (mean FCT = 0.29, maximum = 0.65) and 595 SNPs that were candidates for selection among natural-origin populations (mean FST = 0.25, maximum = 0.51). Comparisons with a linkage map revealed that two chromosomes (Omy05 and Omy25) contained significantly more outliers than other chromosomes, suggesting that regions on Omy05 and Omy25 may be of adaptive significance. Our results highlight several advantages of the 57 000 SNP array as a tool for population and conservation genomics studies.

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.

Understanding population-specific spawner–recruit relationships is necessary for sustainable salmon management. Where multiple populations are harvested together, run reconstruction methods partition mixed-stock catches and allocate recruits back to their populations of origin. Traditional run reconstruction methods often use age composition data to inform catch partitioning. However age-only methods do not account for stock-specific differences in the availability of fish to harvest within fishing areas or the incidental harvest of nontarget stocks in nearby fishing areas. Advances in molecular genetic techniques permit genetic stock identification (GSI) of both contemporary and historical catch samples. We present a statistical model for salmon run reconstruction that utilizes both age composition and GSI data to estimate differences in the availability of stocks within, and interception rates among, terminal fisheries. When applied to the commercial sockeye salmon (Oncorhynchus nerka) fishery in Bristol Bay, Alaska, new estimates of population productivity differed from those generated using previous age-only methods by 0.1%–155.1%, with stock-specific mean absolute percent differences of 9.7%–38.7% across years, underscoring the value of genetic data for run reconstruction. With more accurate run reconstruction methods, spawner–recruit relationships can be identified more precisely, thus providing more accurate management targets for salmon fisheries.

A common challenge for fisheries management is resolving the relative contribution of closely related populations where accuracy of genetic assignment may be limited. An overlooked method for increasing assignment accuracy is the use of multi-SNP (single nucleotide polymorphism) haplotypes rather than single-SNP genotypes. Haplotypes increase power for detecting population structure, and loci derived from next-generation sequencing methods often contain multiple SNPs. We evaluated the utility of multi-SNP haplotyping for mixture analysis in western Alaska Chinook salmon (Oncorhynchus tshawytscha). Multi-SNP haplotype data increased the accuracy of mixture analysis for closely related populations by up to seven percentage points relative to single-SNP genotype data for a set of 500 loci; 90% accuracy was achievable with as few as 150 loci with multi-SNP haplotypes but required at least 300 loci with single-SNP genotypes. Individual assignment to reporting groups showed an even greater increase in accuracy of up to 17 percentage points when multi-SNP haplotypes were used. Haplotyping multiple SNPs shows promise to improve the accuracy of assigning unknown fish to population of origin whenever haplotype data are available.

We genotyped nuclear and mitochondrial single nucleotide polymorphisms (SNPs) in six paired archived and contemporary collections of Alaskan sockeye salmon ( Oncorhynchus nerka ) to evaluate the stability of allele frequencies over 25–42 years (4.9–8.4 generations). First, our results show that temporal changes were dramatically (between 40- and 250-fold) smaller than spatial differences in allele frequencies when based on nuclear SNPs. Second, the magnitude of temporal change was consistent with a model of genetic drift: (i) SNPs with high levels of differentiation (large θ) and candidates for diversifying selection were not more likely to show significant temporal changes than small-θ SNPs; and (ii) the fraction of single-locus significant tests was consistent with theoretical predictions relating sample size and the annual number of breeders (Nb). Third, estimates of Nbwere bound by infinitely large upper 95% confidence intervals, except for one paired collection with unique life-history attributes of both a smoltification phase and generation time shorter than the other paired collections. Use of multigenerational SNP data sets seems a safe practice in management of Alaska sockeye salmon that could be extended to other large, wild aquatic populations.

We assessed genetic differentiation among populations of weathervane scallop (Patinopecten caurinus) in the northeastern Pacific, extending over 2500 km in the Gulf of Alaska and southeastern Bering Sea. Variability was surveyed at nuclear loci with allozyme, microsatellite, and single nucleotide polymorphism (SNP) methods, and at mitochondrial (mt)DNA loci with SNPs and nucleotide sequencing. High levels of gene diversity were detected for allozymes (H = 0.080), microsatellites ( H= 0.734), and mtDNA (h = 0.781). Genotypes at nuclear loci generally fit Hardy-Weinberg pro- portions, except for some microsatellite loci, for which null-allele frequencies of 0.02 to 0.34 were estimated. No allele- frequency differences were detected among samples, except for the allozyme loci Gpi and Pep-4. Overall levels of differ- entiation ranged from FST = 0.0004 for allozymes, FST = 0.0008 for mtDNA to FST = 0.0004 for microsatellites. No isola- tion by distance was found for any of the markers. A unimodal mtDNA mismatch distribution and significant excesses of low-frequency variants for allozymes, microsatellites, and mtDNA may reflect a post-glacial population expansion. The lack of genetic differentiation measured by neutral markers does not preclude the existence of locally adapted, self- sustaining populations that are important in the harvest management of this species. Resume´ : Nous avons evaluela differenciation genetique dans des populations du petoncle geant du Pacifique, Patinopec- ten caurinus, dans le nord-est du Pacifique sur plus de 2500 km dans le golfe de l'Alaska et le sud-est de la mer de Be ´- ring. La variabilitedes locus nucleaires a etedeterminee par les methodes des allozymes, des microsatellites et du polymorphisme mononucleotidique (SNP) et celle des locus d'ADNmt mitochondrial par les methodes de SNP et de se ´- quencage des nucleotides. De fortes valeurs de diversitegenique sont decelables chez les allozymes (H = 0,080), les mi- crosatellites (H = 0,734) et l'ADNmt (h = 0,781). Les genotypes aux locus nucleaires suivent generalement les proportions de Hardy-Weinberg, al'exception de certains locus microsatellites chez lesquels des frequences d'alleles nuls de 0,02 a ` 0,34 ont eteestimees. Il n'y a pas de differences de frequences d'alleles entre les echantillons, exceptepour les locus d'al- lozymes Gpi et Pep-4. Les valeurs globales de differenciation vont de FST = 0,0004 pour les allozymes et FST = 0,0008 pour l'ADNmt a FST = 0,0004 pour les microsatellites. Aucun isolement par distance ne se retrouve chez les marqueurs. Une distribution des differences (mismatch distribution) unimodale de l'ADNmt et des surplus significatifs des variantes de faible frequence des allozymes, des microsatellites et de l'ADNmt peuvent etre le reflet d'une expansion postglaciaire des populations. L'absence de differenciation genetique mesureeal'aide des marqueurs neutres n'exclut pas l'existence de populations adaptees localement et autosuffisantes qui sont importantes dans la gestion de la recolte chez cette espece. (Traduit par la Redaction)

We found that salt water induces ploidy alterations in salmonid embryos. Flow cytometry analysis revealed significantly higher frequencies of haploids, triploids, heteroploid mosaics, and aneuploids in rainbow trout (Oncorhynchus mykiss) embryos experimentally exposed to salt water from fertilization to the two- and eight-cell stages of development. Heteroploid mosaics have been reported in diploid and triploid salmonid hybrids, although none were observed in the triploid coho salmon or diploid and triploid coho salmon (O. kisutch) × chinook salmon (O. tshawytscha) hybrids we examined. No mosaics were observed in intertidally spawned pink salmon (O. gorbuscha) embryos. Salt water could induce ploidy alterations by causing chromosome segregation errors during meiosis, mitosis, or both. Heteroploid embryos appeared morphologically normal although they may possess physiological deficiencies not immediately apparent.

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.

Sterile hybrid and triploid fish may provide hatchery programs with a tool to reduce the risk of genetic contamination of wild stocks, provided these fish have acceptable performance characteristics. We examined growth, survival, and deformities in diploid and triploid families of coho salmon (Oncorhynchus kisutch) and hybrids between coho salmon females × chinook salmon (O. tshawytscha) males. Data were collected from the half-sibling families through day 387. A reparameterized Gompertz growth model showed that conspecific coho salmon grew faster than hybrids, regardless of ploidy. No difference in growth rates was found between diploids and triploids. Abnormalities were significantly associated with the male parent but not with ploidy component, in contrast to previous observations of reduced deformity occurrence in triploid hybrids. Food conversion was better for conspecifics than hybrids during initial feeding, but not different during the second half of the experiment. No ploidy or cross × ploidy interaction effects on food conversion efficiency were observed. Finally, conspecifics had better posthatching survival than hybrids, regardless of ploidy. Of the treatments studied, conspecific triploid coho salmon may be the most viable alternative for sterile fish production: they performed as well as the conspecific diploids and better than either diploid or triploid hybrids.

We studied the genetic relationships and postglacial dispersal of northern pike (Esox lucius) populations in North America using allozyme data. Allelic products of up to 65 protein coding loci were examined in eight populations: five from drainages in western Canada, flowing into Hudson Bay and the Beaufort Sea; two from the Missouri River drainage, flowing into the Mississippi River; and one from the upper Mississippi River drainage, flowing into the Gulf of Mexico. Only two polymorphic loci were identified, Est-1 and Ck-1, and the average observed heterozygosity was only 0.001, much lower than that observed in most teleosts. All of the populations from the drainages in western Canada and the Missouri River were genetically identical. The Mississippi River population was unique, expressing Ck-1 (140), an allele nearly absent in all other populations, at a frequency of 0.99. Our data suggest that the Missouri River drainage, during the period when it was isolated from the Mississippi River, was the southern refugium from which northern pike radiated during deglaciation.