Genomic Signatures of Within-Generation Selection in Coho Salmon (Oncorhynchus kisutch) under Enriched Hatchery-Rearing Practices and in the Wild
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2023-09-13
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Abstract
Salmonids occupy central roles in the ecological and human communities in which they occur. As such, many salmonid populations are heavily managed for conservation and to support their harvest. This often involves hatcheries, which typically use captured mature adults to produce fertilized eggs which are reared to the smolt life-history stage, with resultant smolts released into the wild. Despite a history of over 150 years of hatchery use, fundamental questions remain about the ecological and evolutionary impacts of hatcheries on released fish and on the wild populations released fish interact with. Chief among these questions is the role and impact of selection in hatchery fish compared to wild fish and if domesticating processes are inevitable. In this thesis, I present a detailed investigation of the population genomics of an integrated hatchery-wild coho salmon (Oncorhynchus kisutch) population subjected to long-term experimental rearing under conventional hatchery environments, and under enriched hatchery environments designed to mimic aspects of the wild environment in efforts to mitigate potential effects of hatchery rearing. Specifically, I investigated (1) if spatial genetic structuring occurs among wild fish in this system, (2) if selection is detectable for survival-at-sea and for survival across the lifecycle within a single generation, and (3) if such selection depends on the rearing environment fish experience in the hatchery. I additionally reviewed what is known about gene expression under domestication in salmonids. I found no evidence for spatial genetic structuring among wild fish, indicating the typical strategy of restricted sampling of wild fish for inclusion in the hatchery broodstock should not drive differentiation between hatchery and wild fish. I also found evidence for within-generation selection for both survival-at-sea and survival across the lifecycle, and most importantly, that these signatures of selection differed between hatchery fish reared under different environments. Notably, signatures of selection for fish reared under enriched environments were not more similar to those observed in wild fish, compared to conventionally reared fish, indicating work remains in designing hatchery environments that mimic those aspects of the wild environment required to produce wild-like fish, and with implications for captive rearing programs more broadly.
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Bull, J. K. (2023). Genomic signatures of within-generation selection in coho salmon (Oncorhynchus kisutch) under enriched hatchery-rearing practices and in the wild (Doctoral thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca.