Across the Canadian North, Arctic Char, Salvelinus alpinus, are culturally important and critical for maintaining subsistence lifestyles and ensuring food security for Inuit. Arctic Char also support economic development initiatives in many Arctic communities through the establishment of coastal and inland commercial char fisheries. The Halokvik River, located near the community of Cambridge Bay, Nunavut, has supported a commercial fishery for anadromous Arctic Char since the late 1960s. The sustainable management of this fishery, however, remains challenging given the lack of biological data on Arctic Char from this system and the limited information on abundance and biomass needed for resolving sustainable rates of exploitation. In 2013 and 2014, we enumerated the upstream run of Arctic Char in this system using a weir normally used for commercial harvesting. Additionally, we measured fish length and used T-bar anchor tags to mark a subset of the run. Subsequently, we estimated population size using capture-mark-recapture (CMR) methods. The estimated number of Arctic Char differed substantially between years. In 2013, 1967 Arctic Char were enumerated whereas in 2014, 14,502 Arctic Char were enumerated. We attribute this marked difference primarily to differences in weir design between years. There was also no significant relationship between daily mean water temperature and number of Arctic Char counted per day in either year of the enumeration. The CMR population estimates of Arctic Char (those ≥450mm in length) for 2013 and 2014 were 35,546 (95% C.I 30,513-49,254) and 48,377 (95% C.I. 37,398-74,601) respectively. The 95% CI overlapped between years, suggesting that inter-annual differences may not be as extreme as what is suggested by the enumeration. The population estimates reported here are also the first estimates of population size for an Arctic Char stock in the Cambridge Bay region using CMR methodology. Overall, the results of this study will be valuable for understanding how population size may fluctuate over time in the region and for potentially providing advice on the sustainable rates of harvest for Halokvik River Arctic Char. Additionally, the results generated here may prove valuable for validating current stock assessment models that are being explored for estimating biomass and abundance for commercial stocks of Arctic Char in the region.

Single Nucleotide Polymorphism (SNP) panels are powerful tools for assessing genetic population structure and dispersal of fishes and can enhance management practices for commercial, recreational, and subsistence mixed-stock fisheries. Arctic Char (Salvelinus alpinus), Brook Trout (Salvelinus fontinalis), and Lake Whitefish (Coregonus clupeaformis) are amongst the most harvested and consumed fish species in northern Indigenous communities in Canada, contributing significantly to food security, culture, tradition, and economy. However, genetic resources supporting Indigenous fisheries have not been widely accessible to northern communities (e.g., Inuit, Cree, and Dene). Here, we developed Genotyping-in-Thousands by sequencing (GT-seq) panels for population assignment and mixed-stock analyses of three salmonids, to support fisheries stewardship or co-management in northern Canada. Using low-coverage Whole Genome Sequencing data from 943 individuals across source populations in Cambridge Bay (Nunavut), Great Slave Lake (Northwest Territories), James Bay (Québec), and Mistassini Lake (Québec), we developed a bioinformatic SNP filtering workflow to select informative SNP markers from genotype likelihoods. These markers were then used to design GT-seq panels, thus enabling high-throughput genotyping for these species. The three GT-seq panels yielded an average of 413 autosomal loci and were validated with an average assignment accuracy of 83.03%. Thus, these GT-seq panels are powerful tools for assessing population structure and quantifying the relative contributions of populations/stocks in mixed stock fisheries across multiple regions. Interweaving these genomic-derived tools with Traditional Ecological Knowledge will ensure the sustainable harvest of three culturally important salmonids in Indigenous communities, contributing to food security programs and the economy in northern Canada. Methods 793 fish samples were genotyped using GT-seq panel developed in this study. After filtering (SNP with >50% missing data; samples with>30% missing data) the final datasets were converted in rubias format for each of the five (5) species/region datasets used in our paper for estimating assignment accuracies for GSI studies.

Microsatellite dataGenepop file (3 digit format) containing all microsatellite data. Population names are listed in Table 1 of the paper.Genepop 3 Digit

The Arctic Char Salvelinus alpinus is widely considered the most important subsistence fish species in the Canadian Arctic. Throughout the species’ range, commercial fisheries for Arctic Char also exist, the management of which primarily follows river-specific harvest strategies. Such an approach, however, may not be appropriate if the management unit or stock does not accurately reflect a demographically independent population or if mixtures of populations are being harvested. We assayed microsatellite DNA variation among 744 Arctic Char from the Cambridge Bay region, Nunavut, where the largest commercial fishery for the species exists, in order to identify the most appropriate spatial scale at which these stocks should be managed. Our sampling design specifically mirrored that of the commercial fishery in order to describe patterns of genetic structure and genetic variation within and among the harvested component. We also included Arctic Char from more geographically distant sampling...

Dans tout le nord du Canada, l’omble chevalier (Salvelinus alpinus) revêt une importance culturelle et est essentiel pour maintenir les modes de subsistance et assurer la sécurité alimentaire des Inuits. L’omble chevalier permet aussi d’appuyer les initiatives de développement économique dans de nombreuses collectivités de l’Arctique, notamment par l’établissement de pêches commerciales de l’omble dans les eaux côtières et intérieures. La rivière Halokvik, située près de la collectivité de Cambridge Bay, au Nunavut, fait l’objet d’une pêche commerciale de l’omble chevalier anadrome depuis la fin des années 1960. Toutefois, la gestion durable de cette pêche demeure un défi en raison de l’absence de données biologiques sur l’omble chevalier dans ce réseau, ainsi que des renseignements limités sur l’abondance et la biomasse nécessaires pour atteindre des taux d’exploitation viables. En 2013 et 2014, nous avons eu recours à une fascine habituellement utilisée dans la pêche commerciale pour dénombrer les ombles chevaliers qui effectuaient la montaison dans ce réseau. Nous avons aussi mesuré la longueur des poissons et utilisé des étiquettes à ancrage en T pour marquer un sous-ensemble d’individus qui effectuaient la montaison. Par la suite, nous avons estimé la taille de la population à l’aide des méthodes de capture-marquage-recapture (CMR). Le nombre d’ombles chevaliers varie grandement d’une année à l’autre. En 2013, 1 967 ombles chevaliers ont été dénombrés tandis qu’en 2014, 14 502 ombles chevaliers ont été dénombrés. Nous attribuons cet écart marqué principalement aux différences dans la conception des fascines d’une année à l’autre. De plus, pour les deux années du dénombrement, il n’y a aucun lien important entre la température quotidienne moyenne de l’eau et le nombre d’ombles chevaliers dénombrés par jour. Les estimations de la population d’ombles chevaliers (longueur ≥450 mm) selon les méthodes de capture-marquage-recapture en 2013 et 2014 étaient de 35 546 (intervalle de confiance à 95 %; 30 513-49 254) et 48 377 (intervalle de confiance à 95 %; 37 398-74 601) respectivement. L’intervalle de confiance à 95 % se chevauche pour les deux années, ce qui laisse supposer que les différences interannuelles ne sont peut-être pas aussi importantes que celles indiquées par le dénombrement. Dans le présent document, nous donnons aussi les premières estimations de la taille de la population qui ont été faites à l’aide des méthodes de capture-marquage-recapture pour un stock d’ombles chevaliers dans la région de Cambridge Bay. Dans l’ensemble, les résultats de cette étude permettront de comprendre les possibles fluctuations de la taille de la population dans la région au fil du temps, et éventuellement de fournir des avis sur les taux de durabilité de la pêche de l’omble chevalier dans la rivière Halokvik. En outre, les résultats présentés ici pourront servir à valider les modèles d’évaluation du stock qui sont actuellement étudiés pour estimer la biomasse et l’abondance des stocks commerciaux d’ombles chevaliers dans la région.