A multi-species mixed-stock analysis reveals latitudinal differences in stock overlap with implications for supporting local indigenous fisheries

Abstract Indigenous subsistence fisheries are critical to food security and cultural continuity in northern communities but often lack tools to monitor stock contributions to mixed-stock fisheries. We used population-level genetic differentiation to quantify lake whitefish and brook charr relative stock contributions to Cree First Nations subsistence harvests along the eastern coast of James Bay, Canada, which spans >400 km. Using two Genotyping-in-Thousands by sequencing panels, we characterized the genetic composition of ~3800 harvested fish from multiple coastal sites over 5 years. Our analyses revealed a pronounced latitudinal gradient in stock mixing, with the two southernmost sites exhibiting higher levels of inter-population mixing and the northern sites displaying a more homogeneous stock composition for both species. Notably, up to 10% of individuals in southern harvests originated from northern stocks, suggesting extensive southward oceanic movements, particularly for lake whitefish, perhaps driven by ecological factors such as access to productive feeding areas and longer growing seasons. In contrast, we detected no southern fish in the north, indicating a predominantly southward, asymmetric movement pattern. This spatial stock structure supports localized management in most areas but highlights challenges for stock-specific monitoring and the need for integrated, coast-wide strategies in highly mixed southern fisheries. Our study underscores the ecological complexity of stock connectivity and its implications for the sustainability of culturally and economically vital northern fisheries. Keywords: indigenous fisheries; fisheries management; GT-seq, genetic stock identification; mixed-stock analysis; migration; anadromous salmonids