Ecological and epigenomic consequences of alternative rearing strategies for coho salmon in a Pacific salmon enhancement program
Committee MemberYeaman, Samuel
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AbstractUnderstanding how the environment and genome interact to produce phenotypic variation is a fundamental challenge of ecology and evolution. Epigenetic modifications are environmentally sensitive processes that can modify gene expression, but the role of these processes in adaptive evolution is not established. Pacific salmon reared in hatcheries represent a model to study how phenotypes change during adaptation to a captive environment and the involvement of epigenetics. I studied coho salmon (Oncorhynchus kisutch) from the Nitinat River Hatchery reared in a semi-natural environment intended to mitigate domestication compared to fish reared in a conventional hatchery environment and to wild counterparts. Hatchery fish were otolith marked to differentiate treatments. I fit generalized linear mixed models to assess survival differences between hatchery treatments for 2002-2004 and 2012-2015 cohorts using count data on smolt releases and adult returns. Models suggested that semi-natural rearing may be leading to higher survival, but statistical power was low and the results inconclusive. To elucidate if epigenetics contributed to phenotypic changes under rearing environments, I used reduced representation bisulfite sequencing to examine cytosine methylation between wild and hatchery treatments. Treatments showed multiple differentially methylated regions (DMRs). Analysis suggested semi-natural rearing may encourage a more wild methylation profile, but overall hatchery fish were more similar to one another than to wild fish signifying a shared hatchery influence. DMRs discovered in smolts were not found in adults, however, de novo methylation maintained treatment specific patterns and increased differentiation between wild and conventional treatments not mirrored in semi-natural fish, suggesting a propagated impact of rearing treatment. Effects of family and sex resulted in many DMRs comparable to the effect of treatment, indicating the importance of accounting for these covariates in epigenetic analyses. Further research on this population requires quantifying phenotypes and linkage of methylation changes to gene expression to establish the prevalence and importance of this process. This study supported the knowledge that epigenetic mechanisms may contribute to phenotypic change in natural populations and should be considered in resource management, as the importance of these processes remain unclear in adaptive evolution.
CitationBokvist, J. (2022). Ecological and epigenomic consequences of alternative rearing strategies for coho salmon in a Pacific salmon enhancement program (Unpublished master's thesis). University of Calgary, Calgary, AB.
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