Abstract
The Lake Sturgeon is a long‐lived, late‐maturing fish that declined significantly in abundance over the past 150 years. Since the 1990s, stocking has been used to recover numerous Lake Sturgeon populations across North America. Ill‐informed genetic mixing among populations can have unintended negative consequences, so a genotype‐by‐sequencing (GBS) study was undertaken to help guide the stocking strategy for Lake Sturgeon on the 653‐km‐long Nelson River, Manitoba. Tissue samples collected from 416 adults captured from 12 locations along the Nelson River, and from the Hayes and Churchill rivers that also empty into Hudson Bay, were sequenced using Illumina technology. A bioinformatics pipeline yielded 5637 high‐quality filtered markers. Genetic differentiation (overall mean F ST of 0.028; a range of means: 0–0.16) revealed spatial structuring among and within rivers. Two populations were found in the upper Nelson River, two more in the middle Nelson, and one in the lower Nelson. Discriminant analysis of principal components revealed first‐generation migrants and a general lack of effective dispersal, which raises questions about historical versus contemporary influence. Lake Sturgeon stocking in northern Manitoba should avoid mixing among rivers and among Nelson River sections.