A new genomics tool for monitoring Arctic char (Salvelinus alpinus) populations in the Lower Northwest Passage, Nunavut

Abstract

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.