UBC Theses and Dissertations

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UBC Theses and Dissertations

Population genomics in species conservation : tools for the study of local adaptation and fisheries management in kokanee (Oncorhynchus nerka) Kirk, Stephanie Lynn


The Okanagan Lake kokanee (Oncorhynchus nerka) population has experienced a dramatic decline in numbers since the late 1960’s, making it the focus of significant conservation efforts. Despite the decline, two sympatric ecotypes adapted to different reproductive environments continue to exist. This thesis aims to determine whether divergent selection is driving fine-scale genomic differentiation between the two ecotypes and explore whether the use of adaptive genetic markers for stock identification and population assessment would improve the accuracy and reduce the error associated with conventional kokanee fishery management. Genomic scans using expressed sequence tag-linked microsatellite markers identified 57 gene regions of adaptive significance, of which seven loci displayed outlier behaviour associated with local adaptation to different spawning environments. The utility of these outlier loci in genetics-based classifications of Okanagan Lake kokanee stocks is evaluated and the uncertainty surrounding the optimal class and number of genetic markers for differentiating kokanee ecotypes is addressed. Results from individual assignment and mixture composition analyses show outlier loci consistently perform better than all other classes of markers. The use of adaptive genetic markers for stock identification and assessment show great promise for improving the accuracy of fundamental abundance estimates and the results suggest a genetics-based approach to stock assessment may be a better alternative to achieving an effective and sustainable kokanee fishery in Okanagan Lake. This thesis presents the first study to directly infer signatures of selection that may be associated with observed variation between Okanagan Lake kokanee ecotypes and presents one of the first applications of population genomics to a natural population of conservation concern.

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