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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 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]

Genetic stock identification (GSI) from genotyping‐by‐sequencing of single nucleotide polymorphism (SNP) loci has become the gold standard for stock of origin identification in Pacific salmon. The sequencing platforms currently applied require large batch sizes and multiday processing in specialized facilities to perform genotyping by the thousands. However, recent advances in third‐generation single‐molecule sequencing platforms, such as the Oxford Nanopore minION, provide base calling on portable, pocket‐sized sequencers and promise real‐time, in‐field stock identification of variable batch sizes. Here we evaluate utility and comparability to established GSI platforms of at‐sea stock identification of coho salmon (Oncorhynchus kisutch) using targeted SNP amplicon sequencing on the minION platform during a high‐sea winter expedition to the Gulf of Alaska. As long read sequencers are not optimized for short amplicons, we concatenate amplicons to increase coverage and throughput. Nanopore sequencing at‐sea yielded data sufficient for stock assignment for 50 out of 80 individuals. Nanopore‐based SNP calls agreed with Ion Torrent‐based genotypes in 83.25%, but assignment of individuals to stock of origin only agreed in 61.5% of individuals, highlighting inherent challenges of Nanopore sequencing, such as resolution of homopolymer tracts and indels. However, poor representation of assayed salmon in the queried baseline data set contributed to poor assignment confidence on both platforms. Future improvements will focus on lowering turnaround time and cost, increasing accuracy and throughput, as well as augmentation of the existing baselines. If successfully implemented, Nanopore sequencing will provide an alternative method to the large‐scale laboratory approach by providing mobile small batch genotyping to diverse stakeholders. [ABSTRACT FROM AUTHOR]

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Wild Pacific salmon, including Chinook salmon Oncorhynchus tshawytscha, have been supplemented with hatchery propagation for over 50 years in support of increased ocean harvest, mitigation for hydroelectric development, and conservation of threatened populations. In Canada, the Wild Salmon Policy for Pacific salmon was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision‐making. For policy implementation, a new approach to the assessment and management of Chinook salmon and the associated hatchery production and fisheries management are needed. Implementation of genetic stock identification (GSI) and parentage‐based tagging (PBT) for marine fisheries assessment may overcome problems associated with coded‐wire tag‐based (CWT) assessment and management of Chinook salmon fisheries, providing at a minimum information equivalent to that derived from the CWT program. GSI and PBT were used to identify Chinook salmon sampled in 2018 and 2019 marine fisheries (18,819 individuals genotyped) in British Columbia to specific conservation units (CU), populations, and broodyears. Individuals were genotyped at 391 single nucleotide polymorphisms via direct sequencing of amplicons. Very high accuracy of assignment to population and age (>99.5%) via PBT was observed for 1994 Chinook salmon of ages 2–4 years, with a 105,722–individual, 380–population baseline available for assignment. Application of a GSI‐PBT system of identification to individuals in 2019 fisheries provided high‐resolution estimates of stock composition, catch, and exploitation rate by CU or population, with fishery exploitation rates directly comparable to those provided by CWTs for 13 populations. GSI and PBT provide an alternate, cheaper, and more effective method in the assessment and management of Canadian‐origin Chinook salmon relative to CWTs, and an opportunity for a genetics‐based system to replace the current CWT system for salmon assessment. [ABSTRACT FROM AUTHOR]

The article discusses determination of population structure and stock identification is a ubiquitous problem in fisheries assessment and management. Topics include pacific salmon fishery management regimes are evolving to require higher resolution of stock composition on increasingly smaller reporting units; and a genetics-based assessment system provides an opportunity for conservation-based management of Canadian coho salmon.

We have generated a high-density, high-throughput genotyping array for characterizing genome-wide variation in Arctic charr (Salvelinus alpinus). Novel single nucleotide polymorphisms (SNPs) were identified in charr from the Fraser, Nauyuk and Tree River aquaculture strains, which originated from northern Canada and fish from Iceland using high coverage sequencing, reduced representation sequencing and RNA-seq datasets. The array was designed to capture genome-wide variation from a diverse suite of Arctic charr populations. Cross validation of SNPs from various sources and comparison with previously published Arctic charr SNP data provided a set of candidate SNPs that generalize across populations. Further candidate SNPs were identified based on minor allele frequency, association with RNA transcripts, even spacing across intergenic regions and association with the sex determining (sdY) gene. The performance of the 86,503 SNP array was assessed by genotyping Fraser, Nauyuk and Tree River strain individuals, as well as wild Icelandic Arctic charr. Overall, 63,060 of the SNPs were polymorphic within at least one group and 36.8% were unique to one of the four groups, suggesting that the array design allows for characterization of both within and across population genetic diversity. The concordance between sdY markers and known phenotypic sex indicated that the array can accurately determine the sex of individuals based on genotype alone. The Salp87k genotyping array provides researchers and breeders the opportunity to analyze genetic variation in Arctic charr at a more detailed level than previously possible. [ABSTRACT FROM AUTHOR]

Genetic stock identification (GSI) and parentage-based tagging (PBT) are being increasingly applied to salmon fisheries and hatchery broodstock management and assessment in Canada. GSI and PBT with single nucleotide polymorphisms (SNPs) were applied in assessment of 2020 Chinook salmon fisheries and hatchery broodstocks in British Columbia (BC), Canada, with 9234 individuals successfully genotyped in fishery samples and 2250 PBT identifications made (24.4% individual identification rate). As PBT identifications provided age of the individual and sex was determined from a SNP in the SNP panel, it was possible to evaluate sex ratios by age observed in the fishery sampling. Fishery catch sex ratios at age two and three years were male-biased, whereas those at age four and five years were female-biased. The combined age and sex information derived from genetics-based fishery sampling illustrates the ancillary information that becomes available relative to coded-wire tag (CWT) sampling if biological sampling of the catch is not conducted. There were 20,342 individuals genotyped in 65 hatchery broodstocks from which 6080 PBT identifications were made. Population-specific contributions to mixed-stock fisheries and exploitation rates were estimated with CWTs and GSI-PBT technologies for 13 populations, and close agreement of estimated population-specific exploitation rates between CWT and genetic methods for the 13 populations was observed (r2 (11) = 0.951, P < 0.001). We conclude that a genetic approach can improve upon the results available from the current CWT program for assessment and management of Chinook salmon fisheries and hatchery broodstocks in BC, as well as provide ancillary information to improve wild Chinook salmon assessment and conservation by providing fishery impacts by conservation unit for any fishery in Canada. [ABSTRACT FROM AUTHOR]