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Harvesting from admixed populations is a common practice in contemporary fisheries. However, monitoring stock health in such mixed-stock fisheries remains challenging, with accurately identifying stock composition a critical first step. Fortunately, genetic tools have improved our ability to quantify stock composition ("genetic stock identification" or GSI). A commercial Arctic char (Salvelinus alpinus) fishery has been proposed for the King William Island region of the Lower Northwest Passage (LNWP), Nunavut, Canada, an area that heretofore has had only subsistence fisheries. Previous studies identified two major char genetic clusters in this region with evidence of stock mixing in some rivers and estuaries. We developed a panel of 181 autosomal single nucleotide polymorphisms and one sex marker using Genotyping-in-Thousands by sequencing (GTseq) to facilitate GSI and sex identification and contribute to development of a sustainable fishery. Applying population genetics and population assignment tests to a pilot set of 48 samples, our panel proved effective in GSI with an assignment success rate of 95.8–100%, and in sex determination with a success rate of 93.6%. Our panel of 182 markers provides a cost- and time-efficient means to perform GSI and sex identification in char in the LNWP, which in turn can be used for effective, continuous monitoring of Arctic char in this region. Collectively, a sustainable Arctic char fishery could bring both long-term revenue and a stable food source to the Inuit community of Gjoa Haven. • Arctic char populations from King William Island and adjacent Chantrey Inlet, Nunavut are genetically differentiated. • A new char fishery requires tools for effective fisheries management of the two identified stocks. • We develop and test a multi-amplicon GTseq tool to facilitate stock identification and sex determination. • Our GTSeq panel allows for fast and accurate stock composition assessment for future fisheries management. [ABSTRACT FROM AUTHOR]

The identification of food fish bearing anthropogenic contaminants is one of many priorities for Indigenous peoples living in the Arctic. Mercury (Hg), arsenic (As), and persistent organic pollutants including polychlorinated biphenyls (PCBs) are of concern, and these are reported, in some cases for the first time, for fish sampled in and around King William Island, located in Nunavut, Canada. More than 500 salmonids, comprising Arctic char, lake trout, lake whitefish, and ciscoes, were assayed for contaminants. The studied species are anadromous, migrating to the ocean to feed in the summers and returning to freshwater before sea ice formation in the autumn. Assessments of muscle Hg levels in salmonids from fishing sites on King William Island showed generally higher levels than from mainland sites, with mean concentrations generally below guidelines, except for lake trout. In contrast, mainland fish showed higher means for As, including non-toxic arsenobetaine, than island fish. Lake trout were highest in As and PCB levels, with salmonid PCB congener analysis showing signatures consistent with the legacy of cold-war distant early warning stations. After DNA-profiling, only 4–32 Arctic char single nucleotide polymorphisms were needed for successful population assignment. These results support our objective to demonstrate that genomic tools could facilitate efficient and cost-effective cluster assignment for contaminant analysis during ocean residency. We further suggest that routine pollutant testing during the current period of dramatic climate change would be helpful to safeguard the wellbeing of Inuit who depend on these fish as a staple input to their diet. Moreover, this strategy should be applicable elsewhere. [ABSTRACT FROM AUTHOR]