Neutral Loci Reveal Population Structure by Geography, not Ecotype, in Kootenay Lake Kokanee

Abstract

Abstract Genetic tools are often used to define stocks for fisheries management, however, traditional approaches using neutral markers may be inadequate for detecting fine-scale structure when populations have recently diverged. Kokanee Oncorhynchus nerka is a freshwater form of sockeye salmon that exhibits divergent reproductive ecotypes. We used a combination of expressed sequence tag (EST)-linked and non-EST-linked microsatellites to investigate kokanee stock structure and ecotype differentiation in Kootenay Lake, British Columbia. Despite being highly informative in other lakes in the province, the EST-linked loci used in this study did not exhibit outlier behavior relative to neutral loci for distinguishing shore-spawning and stream-spawning ecotypes. We found conflicting evidence for differentiation between ecotypes and strong evidence for geographical structure corresponding to the North Arm and West Arm of Kootenay Lake. These results are consistent with previous findings that neutral markers are ...