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Direct DNA sequencing is powering a revolution in the application of genetics to resource management, with parentage-based tagging (PBT) increasingly applied to salmon fisheries and hatchery brood stock management and assessment. Genetic stock identification (GSI) and PBT were applied to assessment of 2018 coho salmon (Oncorhynchus kisutch) ocean fisheries and hatchery brood stocks in British Columbia (BC), Canada, with 6391 individuals successfully genotyped in fishery samples and 7805 individuals genotyped in 40 hatchery brood stocks. Population-specific contributions to mixed-stock fisheries and exploitation rates were estimated with coded-wire tags (CWTs) and GSI–PBT technologies for six populations. PBT assignments, verified by CWTs, were 100% accurate for 308 individuals with respect to population of origin and age. There was generally reasonably close agreement of estimated population-specific exploitation rates between CWT and genetic methods. We conclude that a genetic approach can improve upon the results available from the current CWT program for assessment and management of coho salmon fisheries and hatchery brood stocks in BC and provide information critical to aid in implementation of Canada’s Policy for Conservation of Wild Pacific Salmon.

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.

For Pacific salmon, the key fisheries management goal in British Columbia (BC) is to maintain and restore healthy and diverse Pacific salmon populations, making conservation of salmon biodiversity the highest priority for resource management decision‐making. Salmon status assessments are often conducted on coded‐wire‐tagged subsets of indicator populations based on assumptions of little differentiation within or among proximal populations. In the current study of southern BC coho salmon (Oncorhynchus kisutch) populations, parentage‐based tagging (PBT) analysis provided novel information on migration and life‐history patterns to test the assumptions of biological homogeneity over limited (generally, Salmon status assessments are often conducted on coded‐wire‐tagged subsets of indicator populations based on the assumptions of little differentiation within or among proximal populations. In the current study of southern BC coho salmon (Oncorhynchus kisutch) populations, parentage‐based tagging (PBT) analysis provided novel information on migration and life‐history patterns to test the assumptions of biological homogeneity over small geographic distances and, potentially, to inform management of fisheries and hatchery broodstocks.

In salmonid parentage‐based tagging (PBT) applications, entire hatchery broodstocks are genotyped, and subsequently, progeny can be nonlethally sampled and assigned back to their parents using parentage analysis, thus identifying their hatchery of origin and brood year (i.e., age). Inter‐ and intrapopulation variability in migration patterns, life history traits, and fishery contributions can be determined from PBT analysis of samples derived from both fisheries and escapements (portion of a salmon population that does not get caught in fisheries and returns to its natal river to spawn). In the current study of southern British Columbia coho salmon (Oncorhynchus kisutch) populations, PBT analysis provided novel information on intrapopulation heterogeneity among males in the total number of progeny identified in fisheries and escapements, the proportion of progeny sampled from fisheries versus escapement, the proportion of two‐year‐old progeny (jacks) produced, and the within‐season return time of progeny. Fishery recoveries of coho salmon revealed heterogeneity in migration patterns among and within populations, with recoveries from north and central coast fisheries distinguishing “northern migrating” from “resident” populations. In northern migrating populations, the mean distance between fishery captures of sibs (brothers and sisters) was significantly less than the mean distance between nonsibs, indicating the possible presence of intrapopulation genetic heterogeneity for migration pattern. Variation among populations in productivity and within populations in fish catchability indicated that population selection and broodstock management can be implemented to optimize harvest benefits from hatcheries. Application of PBT provided valuable information for assessment and management of hatchery‐origin coho salmon in British Columbia.

Wild Pacific salmon, including Coho salmon Onchorynchus kisutch, have been supplemented with hatchery propagation for over 50 years in support of increased ocean harvest 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. A new approach to the assessment and management of wild coho salmon, and the associated hatchery production and fishery management is needed. Implementation of parentage‐based tagging (PBT) may overcome problems associated with coded‐wire tag‐based (CWT) assessment and management of coho salmon fisheries, providing at a minimum information equivalent to that derived from the CWT program. PBT and genetic stock identification (GSI) were used to identify coho salmon sampled in fisheries (8,006 individuals) and escapements (1,692 individuals) in British Columbia to specific conservation units (CU), populations, and broodyears. Individuals were genotyped at 304 single nucleotide polymorphisms (SNPs) via direct sequencing of amplicons. Very high accuracy of assignment to population (100%) via PBT for 543 jack (age 2) assigned to correct age and collection location and 265 coded‐wire tag (CWT, age 3) coho salmon assigned to correct age and release location was observed, with a 40,774—individual, 267—population baseline available for assignment. Coho salmon from un‐CWTed enhanced populations contributed 65% of the catch in southern recreational fisheries in 2017. Application of a PBT‐GSI system of identification to individuals in 2017 fisheries and escapements provided high‐resolution estimates of stock composition, catch, and exploitation rate by CU or population, providing an alternate and more effective method in the assessment and management of Canadian‐origin coho salmon relative to CWTs, and an opportunity for a genetic‐based system to replace the current CWT system for coho salmon assessment.

A study was undertaken to evaluate whether a parentage-based tagging (PBT) and genetic stock identification (GSI) program has the potential to emulate the results from an existing coded-wire tag (CWT) assessment program in British Columbia. A PBT–GSI approach was used to identify Chinook salmon (Oncorhynchus tshawytscha) to specific populations and brood years where 36 241 individuals from 45 populations were genotyped at 321 single nucleotide polymorphisms (SNPs). Known-origin and known-age age 1 juveniles from seven test populations were assigned via PBT (two parental genotypes required, 538 of 656 juveniles assigned; one parental genotype required, 636 of 656 juveniles assigned) with a minimum accuracy of 99.9%. Assignment accuracy via PBT of 1026 ages 1, 2, or 3 Chinook salmon returning to nine populations in 2015 or 2016 (two parental genotypes required, 556 of 1026 individuals assigned; one parental genotype required, 898 of 1026 individuals assigned) was a minimum of 99.8%. A PBT–GSI or PBT system of identification may provide an alternate cost-effective method of identification in the assessment and conservation of Canadian-origin Chinook salmon relative to the existing CWT program, thereby providing very high resolution of mixed-stock fishery samples containing both hatchery-origin (adipose fin clipped) and wild-origin (unclipped) populations.

Parentage-based tagging (PBT) and genetic stock identification (GSI) were used to identify individual coho salmon (Oncorhynchus kisutch) to specific populations and brood years. In total, 20 242 individuals from 117 populations were genotyped at 304 single nucleotide polymorphisms (SNPs) via direct sequencing of amplicons. Coho salmon from 15 populations were assigned via parentage analysis that required the genotypes of both parents. The overall accuracy of assignment for 1939 coho salmon to the correct population was 100%, and to correct brood year within population was also 100%. Inclusion of individuals requiring only a single parental genotype for identification resulted in assignments of 2101 individuals, with an accuracy of 99.95% (2000–2001) to population and 100.0% to age. With 23 regions defined by the coded-wire tag (CWT) program, and individuals displaying an assignment probability

Conservation scientists rarely have the information required to understand changes in abundance over more than a few decades, even for important species like Pacific salmon. Such lack of historical information can underestimate the magnitude of decline for depressed populations. We applied genetic tools to a unique collection of 100‐year‐old salmon scales to reveal declines of 56%–99% in wild sockeye populations across Canada's second largest salmon watershed, the Skeena River. These analyses reveal century‐long declines that are much greater than those based on modern era abundance data, which suggested that only 7 of 13 populations declined over the last five decades. Populations of larger‐bodied fish have declined the most in abundance, likely because of size‐selective commercial fisheries. Our findings illustrate how a deep historical perspective can expand our understanding of past abundances to a time before species incurred significant losses from fishing, and help inform conservation for diminished populations.

Determination of run timing is an important component of salmonid fisheries management and was the major focus of the current study. Population structure of Sockeye Salmon Oncorhynchus nerka was examined in the Skeena River, northern British Columbia. Variation at 14 microsatellites was surveyed for 27 populations in the drainage. There were 9,473 individuals sampled in a lower river test fishery during 2000–2011 in order to provide information on relative abundance and time of arrival of specific populations or stocks near the mouth of the river. Within-lake or within-river tributary structuring of populations was the general pattern observed, with 10 populations from Babine Lake clustering together in 91% of dendrograms evaluated, and two populations from Lakelse Lake clustering together in 100% of dendrograms evaluated. The 27 populations sampled were arranged in 12 reporting groups for genetic stock identification applications. The estimated stock composition of known-origin mixtures was withi...

Variation at 14 microsatellite loci, one major histocompatibility complex (MHC) locus, and 49 single nucleotide polymorphism (SNPs) loci was surveyed in 44 populations of sockeye salmon ( Oncorhynchus nerka ) over 16 regions from southern and central British Columbia, Canada. Sequential addition of the five highest rated SNPs to the suite of 14 microsatellites provided the equivalent average accuracy when compared with the current suite of microsatellites and MHC. Six microsatellites provided the equivalent average stock identification resolution and individual assignment accuracy compared with 46 SNPs. For regional stock compositions, 53–104 SNPs were projected to be required to provide accuracy and precision equivalent to the microsatellites. For population-specific stock compositions, 75–79 SNPs were projected to be required to provide accuracy and precision equivalent to the microsatellites. Equivalency in individual assignment accuracy to region was estimated to require 100 SNPs of the quality evaluated in the study, whereas equivalent accuracy in assignment to specific populations was estimated to require 124 SNPs. Applications that incorporate the existing power of a combined microsatellite–SNP approach are the best current technique available for sockeye salmon stock identification applications in southern British Columbia.

The population structure of sockeye salmon Oncorhynchus nerka from Russia was determined from a survey of the variation of 14 microsatellite loci among approximately 3,750 sockeye salmon from 56 populations. The populations from Avacha Bay and the Palana River were quite distinct. Genetic differentiation among the populations surveyed was observed, the mean value of the differentiation index (F ST) for all loci being 0.038 (SD = 0.007). Regional structuring of the populations surveyed was observed, multiple populations sampled within a lake being more similar to each other than to populations in other lakes or rivers. River drainage of origin was a significant unit of population structure. Populations spawning in rivers without access to a nursery lake for juvenile rearing displayed greater genetic variation than did populations with access to nursery lakes. Within Kurilskoye Lake, genetic differentation was observed between populations spawning in tributaries to the lake and those populations sp...

The variation at 14 microsatellite loci and one major histocompatibility complex (MHC) locus was surveyed for over 48,000 sockeye salmon Oncorhynchus nerka sampled from 299 localities ranging from the Columbia River to Japan. For the microsatellite loci, the number of alleles observed at a locus was related to the power of the locus in providing accurate estimates of stock composition of single-population mixtures. In an analysis of single-population mixtures where the Pacific Rim baseline was used for estimation of stock identification, 80% accuracy for the average population was achieved by employing approximately 80 alleles in the analysis. Increasing the accuracy of estimated stock compositions to 90% for the average population required approximately 400 microsatellite alleles. When all loci were used to estimate stock compositions, estimates were above 80% for all sampling sites or populations, above 90% for the lake of origin, and generally above 95% for the region of origin. Analysis of kn...

The variation at 14 microsatellite loci and 1 major histocompatibility complex locus was surveyed in 12,000 sockeye salmon Oncorhynchus nerka from 35 populations in the Skeena and Nass River drainages in British Columbia and 20 populations from Southeast Alaska. Genetic differentiation among populations was observed, with an overall F ST of the microsatellite loci of 0.104. Evaluation of the utility of the microsatellite loci for stock identification applications indicated that the accuracy and precision of the estimated stock compositions generally increased as the number of observed alleles at the loci increased. Analysis of simulated mixtures of sockeye salmon from the Nass River, Skeena River, and Southeast Alaska indicated that DNA variation provides a practical way to estimate stock composition, yielding population and regional estimates within 1–3% of the actual values. The validity of the results from the simulated mixtures was evaluated with an analysis of a sample of known origin. Estim...

Population structure of sockeye salmon, Oncorhynchus nerka (Walbaum, 1792), from coastal lakes in British Columbia was determined from a survey of variation of 14 microsatellite loci, with approximately 6400 sockeye salmon analyzed from 40 populations. Populations from the Queen Charlotte Islands displayed fewer alleles per locus than did populations in other regions. Genetic differentiation among the populations surveyed was observed, with the mean FSTfor all loci being 0.077 (SD = 0.006). Differentiation among populations was approximately 13 times greater than annual variation within populations. Regional structuring of the populations surveyed was observed. The accuracy and precision of the estimated stock compositions generally increased as the number of observed alleles at the loci increased. Simulated mixed-stock samples generated from observed population frequencies in different regions suggested that variation at microsatellite loci provided reasonably accurate and precise estimates of stock composition for potential samples from marine or freshwater fisheries.

The utility of DNA-based variation for stock identification was evaluated for Fraser River sockeye salmon Oncorhynchus nerka. For this evaluation, the variation at 14 microsatellite loci and one major histocompatibility complex (MHC) locus was determined from approximately 13,000 fish from 47 populations in the drainage. Genetic differentiation among the populations was observed, the overall F ST value for the 14 microsatellite loci surveyed being 0.054 and that for the MHC locus being 0.215. The variation among regions and populations within regions was approximately 20 times as great as that of the annual variation within populations for the microsatellite loci and 28 times as great for the MHC locus. The power of a microsatellite locus for population-specific identification in simulated mixture samples was positively correlated with the number of observed alleles at the locus. Analysis of simulated mixtures indicated that the mean percentage error of estimated stock compositions was less than ...

The population structure of 'lake-type' and 'river-type' sockeye salmon Oncorhynchus nerka, primarily in transboundary rivers in northern British Columbia, was examined with a survey of microsatellite variation. Variation at 14 microsatellite loci was surveyed from c. 3000 lake-type and 3200 river-type sockeye salmon from 47 populations in six river drainages in British Columbia. The mean F ST for the 14 microsatellite loci and 47 populations was 0.068, and 0.034 over all river-type populations. River-type sockeye salmon were more genetically diverse than lake-type sockeye salmon. with expected heterozygosity of river-type sockeye salmon 0.72 and with an average 12.7 alleles observed per locus, whereas expected heterozygosity of lake-type sockeye salmon was 0.65 with and average 10.5 alleles observed per locus. River drainage of origin was a significant unit of population structure. There was clear evidence of genetic differentiation among river-type populations of sockeye salmon from different drainages over a broad geographic range in British Columbia.

Population structure of sockeye salmon Oncorhynchus nerka in Barkley Sound, British Columbia, Canada was examined by analysis of microsatellite variation at 14 loci in three populations sampled in each of 3 years. The mean FST over all 14 loci was 0·063. Differences among populations accounted for 12 times the variation observed among years within populations. The number of alleles present at a locus was related to the power of the locus to provide accurate identification of individuals to population. The more alleles that were present at a locus, the greater was the power of the locus for individual identification. Individuals were correctly classified to one of three lakes of origin at a rate of 89%, and to one of two river drainages at a rate of 96%.