| Summary: | An understanding of the level of both genetic and morphological diversity within a taxon and how that diversity is structured within and across habitats is important when determining the conservation value of that taxon and for successful habitat management programs to be developed. Atlin Lake is a large lake in northern British Columbia and is one of the largest lakes that contain relatively unperturbed populations of lake trout (Salvelinus namaycush). As the top aquatic predator, lake trout in Atlin Lake are a key component of the lake’s fish community and are important for local fisheries. I assayed lake trout from Atlin Lake and other western lake trout populations at eight microsatellite DNA loci and for body morphology to determine: (i) the level of genetic variation present, (ii) the level of substructure that occurs in Atlin Lake, and (iii) whether there was a relationship between the genetic and morphological variation present. STRUCTURE analysis identified five subpopulations within Atlin Lake. Morphological analysis was used to differentiate between the samples collected throughout Atlin Lake. Cluster analysis of size corrected data separated the fish into two groups making Atlin Lake the smallest lake identified to date to possess more than one morphotype. Genetic and morphological groupings were found not to be correlated with each other. Finally, I was interested in whether each of the genetic subpopulations contributed equally to the local fisheries catches. A mixed stock analysis of samples collected from the commercial fishery and recreational anglers indicated that all of the genetic subpopulations contribute to the fishery along with lake trout subpopulations in the interconnecting Tagish Lake; suggesting that no one subpopulation is being depleted by the fisheries. Continued genetic monitoring, however, is necessary to see if the trends in fishery contribution are temporally stable. Future studies should focus on understanding the source of the morphological variation and maintenance of genetic substructure.
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