<p>Many salmonid populations are supported through captive breeding programs in which hatchery production supplies fish for reintroduction or supplementation efforts. In Lake Champlain, Atlantic salmon (Salmo salar) are the subject of a reintroduction effort that is complicated by the occurrence of thiamine (vitamin B1) deficiency in adult salmon returning to spawn. This deficiency results in high offspring mortality rates that must be mitigated by hatchery interventions (reviewed in Chapter 1). I used an experimental transcriptomics approach coupled with survival analyses to assess genetic variation in thiamine deficiency outcomes (i.e., survival at the family level) and identified candidate genes that may comprise a putatively adaptive response to selection imposed by thiamine deficiency (Chapter 2). Using sequence data from this study, I next compared patterns of genetic variation in the Lake Champlain population against two other populations to identify signatures of selection associated with hatchery rearing environment and differences in life history strategies (Chapter 3). Finally, I surveyed salmonid populations for density-dependent effects of adult spawning density on per capita fitness and found that in many cases, hatchery releases can contribute to decreased individual fitness. Using genotype data for returning adults in multiple populations, I also tested for reductions in effective population size (Ne) associated with hatchery supplementation and describe how increasing hatchery contribution to a population decreases Ne (Chapter 4). Together, my results demonstrate the powerful influences of hatchery supplementation on salmonid populations and suggest that specific modifications to hatchery practices can limit negative impacts of captive breeding on population genetic and demographic characteristics.</p>