Genomic Signatures of Within-Generation Selection in Coho Salmon (Oncorhynchus kisutch) under Enriched Hatchery-Rearing Practices and in the Wild

Bull, James Kenneth

Genomic Signatures of Within-Generation Selection in Coho Salmon (Oncorhynchus kisutch) under Enriched Hatchery-Rearing Practices and in the Wild

dc.contributor.advisor	Rogers, Sean Michael
dc.contributor.author	Bull, James Kenneth
dc.contributor.committeemember	Miller, Kristina
dc.contributor.committeemember	Munkittrick, Kelly Roland
dc.contributor.committeemember	Poissant, Jocelyn
dc.contributor.committeemember	Narum, Shawn
dc.date	2023-11
dc.date.accessioned	2023-09-22T14:57:30Z
dc.date.available	2023-09-22T14:57:30Z
dc.date.issued	2023-09-13
dc.description.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.
dc.identifier.citation	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.
dc.identifier.uri	https://hdl.handle.net/1880/117070
dc.language.iso	en
dc.publisher.faculty	Science
dc.publisher.institution	University of Calgary
dc.rights	University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission.
dc.subject.classification	Genetics
dc.title	Genomic Signatures of Within-Generation Selection in Coho Salmon (Oncorhynchus kisutch) under Enriched Hatchery-Rearing Practices and in the Wild
dc.type	doctoral thesis
thesis.degree.discipline	Biological Sciences
thesis.degree.grantor	University of Calgary
thesis.degree.name	Doctor of Philosophy (PhD)
ucalgary.thesis.accesssetbystudent	I do not require a thesis withhold – my thesis will have open access and can be viewed and downloaded publicly as soon as possible.