Data from: Application of a GT-seq SNP panel to quantify interannual variation in mixed-stock composition in the largest commercial fishery for Arctic Charr (<em>Salvelinus alpinus</em>) in Canada

Aquatic resources are central to the global food supply and economy, particularly in the Arctic, where Inuit communities have long depended on wild resources. In the 1960s, the community of Iqaluktuuttiaq (Cambridge Bay, Nunavut, Canada) established commercial fisheries targeting Arctic Char (Salvelinus alpinus, L.), providing key employment and income. In a rapidly changing Arctic, molecular tools can enhance sustainable fisheries management. We applied a GT-seq (Genotyping-in-Thousands) panel of 377 SNP loci to distinguish five local stocks (Ekalluk, Halokvik, Jayko, Lauchlan, and Surrey) and quantify their contributions to annual harvests. A total of 1387 samples collected from four commercial sites over eight years (2012–2020) were analyzed to assess temporal variation in stock composition. Results revealed unequal stock contributions, with Ekalluk and Halokvik comprising over 75 % of catches. Spring harvests showed stable stock composition across years, while fall harvests exhibited significant interannual variation (p &lt; 0.05). Environmental factors such as ice breakup timing (IB) and duration of 50 % marine ice cover (I50) had no significant influence on stock contribution variability, likely due to limited data. Thus, GTseq offers the opportunity to explore more adaptive management by capturing interannual variability in stock mixing.