Search

Many natural and managed organisms will require substantial functional genetic variation to respond to selection in the face of rapid environmental change. Pacific salmon have experienced strong fluctuations in critical fitness traits over the past five decades. We examined genetic and phenotypic variability over three generations in a pedigreed hatchery population of coho salmon (Oncorhynchus kisutch) by monitoring seven fitness-related traits. Three-year-old adult return numbers varied more than fivefold, and jack (2-year-old males) numbers varied 13-fold. Body sizes of Inch Creek coho salmon decreased consistently such that fish were only 40.7% as heavy in 2015 as in 2006, and female reproductive traits also decreased. During the study period, the majority of families produced returning adult progeny, and effective population size was relatively constant. Heritability estimates for phenotypic traits were significantly greater than zero except for condition factor, and the estimated heritability for jacking was 0.42. The Inch Creek coho salmon population harbours substantial heritability for fitness and reproductive traits and thus likely retains substantial capacity for adaptation despite many years of hatchery propagation. De nombreux organismes naturels et faisant l'objet d'une gestion necessiteront une variation genetique fonctionnelle considerable pour reagir a la selection decoulant de changements environnementaux rapides. Les saumons du Pacifique ont presente de fortes fluctuations de caracteres cles associes a l'aptitude au cours des cinq dernieres decennies. Nous examinons la variabilite genetique et phenotypique sur trois generations dans une population d'ecloserie de saumons cohos (Oncorhynchus kisutch) de genealogie connue, en examinant sept caracteres relies a l'aptitude. Le nombre de retours d'adultes de 3 ans varie par un facteur de plus de cinq et le nombre de males furtifs (de 2 ans) varie par un facteur de treize. La taille du corps des saumons cohos d'Inch Creek a diminue de maniere soutenue, de sorte que, en 2015, la masse des poissons n'etait que de 40,7 % de celle de 2006, et des caracteres associes a la reproduction des femelles ont egalement diminue. Durant la periode d'etude, la majorite des familles ont produit une progeniture comptant des adultes de retour, et la taille effective de la population etait relativement constante. Des estimations de l'heritabilite pour des caracteres phenotypiques sont significativement superieures a zero, sauf pour le facteur d'embonpoint, et l'heritabilite estimee de la maturation sexuelle des males est de 0,42. La population de saumons cohos d'Inch Creek presente une heritabilite considerable en ce qui concerne des caracteres associes a l'aptitude et a la reproduction et conserve donc probablement une capacite significative d'adaptation, malgre des annees de propagation en ecloserie. [Traduit par la Redaction], Introduction Many organisms are facing rapid environmental changes that may require adjustments of basic life history phenotypes to maintain high levels of fitness (Crozier et al. 2008). Before extreme conditions [...]

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 [...]

Objective: The kokanee Oncorhynchus nerka (nonanadromous life‐history form of Sockeye Salmon) uses lacustrine habitat in watersheds draining into the north Pacific Ocean. Kokanee also have been widely introduced into reservoirs following impoundment of rivers consequent to the construction of hydroelectric dams. Genetically divergent subpopulations of kokanee should be identified and evaluated when implementing watershed‐level fishery management strategies. Methods: We analyzed the genetic population structure of kokanee in the Williston watershed, north‐central British Columbia, where native populations were present in the reservoir and headwater lakes prior to stocking Columbia River‐origin fish in the 1990s using microsatellite markers. Result: We determined that native Williston Reservoir kokanee were divergent from only one of the headwater lake populations. Native populations in headwater lakes remain entirely separate from the reservoir populations, and there was no indication of past or current introgression with the introduced stock. We identified all fish collected from 2006 to 2019 as introduced Columbia River‐origin genotypes, and there was no evidence of genetic divergence by spawning location. Conclusion: As native Williston kokanee have not been sampled from the reservoir in survey efforts since 2000, it is likely that this population has been extirpated from the reservoir perhaps through competition with the introduced Columbia River‐origin lineage. Impact statementColumbia River‐origin kokanee that were introduced into the Williston Reservoir watershed in the 1990s show no indication of introgression with native kokanee populations in headwater lakes, but native kokanee within the reservoir do not appear to have persisted. [ABSTRACT FROM AUTHOR]

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. Une etude a ete menee pour determiner si un programme d'etiquetage base sur l'ascendance (PBT) et l'identification genetique au stock (GSI) pourrait reproduire les resultats d'un programme existant devaluation a l'aide de micromarques codees (CWT) en Colombie-Britannique. L'approche PBT-GSI a ete utilisee pour identifier des saumons quinnats (Oncorhynchus tshawytscha) a leurs populations et annees d'eclosion, dans laquelle 36 241 individus de 45 populations ont fait l'objet d'un genotypage sur 321 polymorphismes mononucleotidiques (SNP). Des poissons juveniles d'un an d'origine et d'age connus issus de sept populations ont ete affectes par l'approche PBT (deux genotypes parentaux requis, 538 juveniles sur 656 affectes; un genotype parental requis, 636 juveniles sur 656 affectes) avec une exactitude minimum de 99,9 %. L'exactitude de l'affectation par l'approche PBT de 1026 saumons quinnats de 1, 2 et 3 ans retournant a neuf populations en 2015 et 2016 (deux genotypes parentaux requis, 556 individus sur 1026 affectes; un genotype parental requis, 898 juveniles sur 1026 affectes) etait d'au moins 99,8 %. Un systeme PBT-GSI ou PBT d'identification pourrait constituer une methode d'identification moins couteuse pour revaluation et la conservation des saumons quinnats d'origine canadienne comparativement au programme de CWT existant, offrant notamment une tres haute resolution pour les echantillons tires de peches de stocks melanges contenant des populations sauvages (nageoires adipeuses presentes) et issues d'alevinieres (nageoires adipeuses retirees). [Traduit par la Redaction], Introduction Assignment of individuals to specific populations can be an important component of analysis of mixed-stock salmon fisheries and other applications, with identification of individuals conducted either through physical tags [...]

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 Le marquage base sur l'ascendance (PBT) et l'identification genetique des stocks (GSI) ont ete utilises pour relier des saumons cohos (Oncorhynchus kisutch) individuels a des populations et annees d'eclosion precises. Au total, 20 242 individus issus de 117 populations ont ete genotypes sur 304 polymorphismes nucleotidiques (SNP) par sequencage direct d'amplicons. Des saumons cohos issus de 15 populations ont ete affectes par une analyse de l'ascendance qui necessitait les genotypes des deux parents. L'exactitude globale de l'affectation de 1939 saumons cohos a la bonne population etait de 100 %, et a la bonne annee d'eclosion au sein de la population, egalement de 100 %. L'inclusion d'individus necessitant seulement un genotype parental pour l'identification s'est traduite par l'affectation de 2101 individus, avec une exactitude de 99,95 % (2000-2001) a la bonne population, et de 100 % a la bonne classe d'age. En tenant compte des 23 regions definies par le programme de micromarques magnetisees codees (CWT) et en excluant de l'analyse les individus presentant une probabilite d'affectation de, Introduction Coho salmon (Oncorhynchus kisutch) are produced in hatcheries in British Columbia, Canada, with approximately seven million juveniles released annually. In some hatcheries, a portion of the juveniles is marked [...]

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]

Temporally stable genetic structure among salmonid populations has been reported in many studies, although the time span evaluated in most studies is limited to 10 years or less. This result has important implications in conservation and management of Pacific salmon (Oncorhynchus spp.) and ramifications for the construction and application of genetic databases for stock identification of fish sampled from mixed-stock fisheries. Walter et al. (2009. Can. J. Fish. Aquat. Sci. 66: 167-176) failed to consider recent studies providing evidence that their conclusion 'the overall magnitude of temporal within-population variation exceeding that of among-population variation' for the populations under study may be invalid for Fraser River Chinook salmon (Oncorhynchus tshawytscha) populations. Their estimation of rates and patterns of migration among Chinook salmon populations also provided results that are difficult to reconcile with published information. Evaluation of the experimental designed employed by Walter et al. (2009) indicates that their sample sizes were too small to estimate reliably genetic variation among or within populations. Extrapolation of their conclusions relating temporal instability of population structure to other Chinook salmon populations or indeed other salmonid species is unwarranted. Resume: On a signale une structure genetique stable dans le temps dans les populations de salmonides dans plusieurs etudes, bien que la periode de temps etudie dans la plupart des cas soit limitee a dix annees ou moins. Cette observation a des consequences serieuses sur la conservation et la gestion des saumons du Pacifique (Oncorhynchus spp.) et des implications dans la construction et l'application de bases de donnees genetiques pour l'indentification des stocks de poissons echantillonnes dans des peches constituees de plusieurs stocks. Walter et al. (2009. J. can. sci. halieut. aquat. 66: 167-176) ont neglige certaines etudes recentes qui fournissent des donnees selon lesquelles leur conclusion voulant que l'importance globale de la variation temporelle au sein des populations depasse la variation entre les populations qu'ils ont etudiees pourrait ne pas s'appliquer aux populations de saumons Chinook (Oncorhynchus tshawytscha) du fleuve Fraser. Leur estimation des taux et des patrons de migration chez les populations de saumons Chinook fournit aussi des resultats qui sont difficiles a reconcilier avec les donnees deja publiees. Une evaluation du plan d'experience utilise par Walter et al. (2009) indique que la taille de leurs echantillons est trop petite pour permettre une evaluation stable de la variation genetique au sein des populations et entre les populations. L'extrapolation de leurs conclusions au sujet de l'instabilite temporelle de la structure de population a d'autres populations de saumons Chinook et evidemment a d'autres especes de salmonides est injustifiee. [Traduit par la Redaction], ********** Considerable effort has been directed towards surveying the population structure of Chinook salmon (Oncorhynchus tshawytscha) in North America, initially through allozymes (Utter et al. 1989; Waples et al. 2004) [...]

Abstract--A new method of finding the optimal group membership and number of groupings to partition population genetic distance data is presented. The software program Partitioning Optimization with Restricted Growth Strings [...]

ABSTRACT As the number of native species targeted for aquaculture and enhancement in British Columbia (BC) rises, fisheries managers must develop policies and species-specific management plans that facilitate industry expansion [...]

Abstract--Variation at 13 microsatellite loci was previously surveyed in approximately 7400 chinook salmon (Oncorhynchus tshawytscha) sampled from 50 localities in the Fraser River drainage in southern British Columbia. Evaluation of [...]

Abstract--We surveyed variation at 13 microsatellite loci in approximately 7400 chinook salmon sampled from 52 spawning sites in the Fraser River drainage during 1988-98 to examine the spatial and temporal [...]