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Objective: Genetic stock identification (GSI) can be an effective tool for fisheries management, but development of reference baselines for species with broad geographic distributions can be challenging. Mixed‐stock fisheries for Chinook Salmon Oncorhynchus tshawytscha have utilized GSI analyses for decades with various genetic baselines, but these have largely become outdated with advances in technology that enable more efficient genotyping. Thus, our goals were to (1) create nested baselines of genotypic data for Chinook Salmon throughout their entire natural range using existing data from multiple sources and (2) evaluate the utility of those nested baselines to conduct accurate hierarchical GSI of mixture proportions or the stock identification of individual fish. Methods: In this study, we compiled a large genetic baseline of single‐nucleotide polymorphism (SNP) markers for 389 populations that encompass the entire geographic range of Chinook Salmon. We used cross validation and realistic mixture simulations to test the accuracy of the baseline in generating GSI estimates. Result: We demonstrated that a multi‐tiered assignment approach can provide high accuracy at both tier 1 (broadscale, with three coastwide reporting groups; 97.8% mean accuracy) and tier 2 (fine‐scale regional reporting groups; up to 97.7% mean accuracy) levels. Realistic mixture simulations showed that this multi‐tiered approach can provide highly effective GSI results for several common mixed‐stock fisheries applications in the Pacific Ocean. Conclusion: This new SNP baseline and the multi‐tiered assignment approach provide the most comprehensive rangewide GSI baseline for Chinook Salmon over any previous application and enable highly accurate estimates for GSI purposes. Impact statementA Chinook Salmon genetic stock identification baseline encompassing the species' entire range has broad applications in fishery management and harvest allocation as well as in basic research. [ABSTRACT FROM AUTHOR]

Determination of population structure and stock identification is a general problem in fisheries assessment and management. Pacific salmon fishery management regimes are evolving to require higher resolution of stock composition on increasingly smaller reporting units. For Chinook salmon (Oncorhynchus tshawytscha), a stock identification baseline comprised of some 125 198 individuals from 369 populations ranging from Russia to California was employed for genetic stock identification (GSI). GSI analysis based on variation at up to 547 single nucleotide polymorphisms (SNPs) was demonstrated to provide accurate estimates of stock composition for 68 conservation units (CUs) in British Columbia, 23 reporting groups in the United States, and one reporting group in Russia. In many instances, accurate population-specific estimates of stock composition within a CU were possible in fishery samples, as well as identifying individuals to some specific populations. A genetics-based assessment system provides an opportunity for conservation-based management of Canadian Chinook salmon. La determination de la structure des populations et l'identification au stock constituent un probleme general en evaluation et en gestion des peches. Les regimes de gestion des peches aux saumons du Pacifique necessitent des donnees sur la composition des stocks de resolution croissante visant des unites de declaration de plus en plus petites. Pour le saumon chinook (Oncorhynchus tshawytscha), une base de donnees de reference d'identification au stock comprenant quelque 125 198 specimens issus de 369 populations allant de la Russie a la Californie a ete utilisee pour l'identification genetique au stock (IGS). Il est demontre que l'analyse d'IGS basee sur les variations aux sites de jusqu'a 547 polymorphismes mononucleotidiques (SNP) fournit des estimations exactes de la composition des stocks pour 68 unites de conservation (UC) en Colombie-Britannique, 23 groupes de declaration aux Etats-Unis et un groupe de declaration en Russie. Dans de nombreux cas, des estimations exactes de la composition des stocks dans des populations donnees au sein d'une UC sont possibles dans des echantillons issus de la peche, ainsi que l'identification d'individus a des populations precises. Un systeme devaluation reposant sur la genetique permet une gestion basee sur la conservation du saumon chinook canadien. [Traduit par la Redaction], Introduction In Canada, the Policy for Conservation of Wild Pacific Salmon (WSP) was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of [...]

Determination of population structure and stock identification is a ubiquitous problem in fisheries assessment and management. Pacific salmon fishery management regimes are evolving to require higher resolution of stock composition on increasingly smaller reporting units. For coho salmon (Oncorhynchus kisutch), a stock identification baseline composed of some 57 982 individuals from 332 populations ranging from southeast Russia to California was employed for genetic stock identification (GSI). GSI analysis based upon variation at up to 480 single nucleotide polymorphisms (SNPs) was demonstrated to provide accurate estimates of stock composition for 37 conservation units (CU) in British Columbia, 13 reporting groups in the United States, and one reporting group in Russia. In many instances, accurate population-specific estimates of stock composition within a CU were possible in fishery samples, as well as identifying individuals to some specific populations. A genetics- based assessment system provides an opportunity for conservation-based management of Canadian coho salmon. La determination de la structure des populations et l'identification au stock sont des problemes generalises en evaluation et en gestion des peches. Les regimes de gestion des peches aux saumons du pacifique evoluent pour exiger une plus haute resolution de la composition des stocks dans des unites de declaration de plus en plus petites. Pour le saumon coho (Oncorhynchus kisutch), une base de reference pour l'identification au stock comprenant quelque 57 982 individus provenant de 332 populations allant du sud-est de la Russie a la Californie a ete utilisee pour l'identification genetique au stock (IGS). Il est demontre que l'analyse IGS basee sur les variations de jusqu'a 480 polymorphismes mononucleotidiques (SNP) fournit des estimations exactes de la composition des stocks pour 37 unites de conservation (UC) en Colombie-Britannique, 13 groupes de declaration aux Etats-Unis et un groupe de declaration en Russie. Dans de nombreux cas, des estimations propres a la population exactes de la composition des stocks au sein d'une UC sont possibles pour des echantillons tires de la peche, ainsi que l'affectation des individus a certaines populations precises. Un systeme devaluation reposant sur la genetique offre la possibilite d'une gestion basee sur la conservation des saumons cohos canadiens. [Traduit par la Redaction], Introduction The general objective of genetic stock identification (GSI) for Pacific salmon is to provide the optimal resolution among stocks or populations present when applied to mixed-stock fishery and forensic [...]

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. see also the Perspective by Rebekah L. Horn and Shawn R. Narum [ABSTRACT FROM AUTHOR]

Abstract Background The products of cyp19, dax, foxl2, mis, sf1 and sox9 have each been associated with sex-determining processes among vertebrates. We provide evidence for expression of these regulators very early in salmonid development and in tissues outside of the hypothalamic-pituitary-adrenal/gonadal (HPAG) axis. Although the function of these factors in sexual differentiation have been defined, their roles in early development before sexual fate decisions and in tissues beyond the brain or gonad are essentially unknown. Results Bacterial artificial chromosomes containing salmon dax1 and dax2, foxl2b and mis were isolated and the regulatory regions that control their expression were characterized. Transposon integrations are implicated in the shaping of the dax and foxl2 loci. Splice variants for cyp19b1 and mis in both embryonic and adult tissues were detected and characterized. We found that cyp19b1 transcripts are generated that contain 5'-untranslated regions of different lengths due to cryptic splicing of the 3'-end of intron 1. We also demonstrate that salmon mis transcripts can encode prodomain products that present different C-termini and terminate before translation of the MIS hormone. Regulatory differences in the expression of two distinct aromatases cyp19a and cyp19b1 are exerted, despite transcription of their transactivators (ie; dax1, foxl2, sf1) occurring much earlier during embryonic development. Conclusions We report the embryonic and extragonadal expression of dax, foxl2, mis and other differentiation factors that indicate that they have functions that are more general and not restricted to steroidogenesis and gonadogenesis. Spliced cyp19b1 and mis transcripts are generated that may provide regulatory controls for tissue- or development-specific activities. Selection of cyp19b1 transcripts may be regulated by DAX-1, FOXL2 and SF-1 complexes that bind motifs in intron 1, or by signals within exon 2 that recruit splicing factors, or both. The potential translation of proteins bearing only the N-terminal MIS prodomain may modulate the functions of other TGF β family members in different tissues. The expression patterns of dax1 early in salmon embryogenesis implicate its role as a lineage determination factor. Other roles for these factors during embryogenesis and outside the HPAG axis are discussed.