title: Evaluating the consequences of hybridization among divergent farmed and wild Atlantic salmon (Salmo salar) populations
Creators: name: Islam, Shahinur S. 
Publisher: name: Memorial University of Newfoundland
Year: 2022

description: Multi-generation domestication selection and distinct geographic and ancestral relationships have raised concerns about potential genetic and ecological interactions between escaped farmed and wild populations. In Newfoundland (NF), Canada, most aquaculture sites use North American (NA) Saint John River strain. However, recently, site-specific permission has been approved to farm a strain of European origin (EO). It has already been documented that if reproductively viable farmed EO salmon escape, it is likely that they will be able to breed successfully and interact genetically and ecologically with local wild populations. In my thesis, using common-garden experiments, I assessed the consequences of interbreeding of divergent EO and NA farmed with NF wild salmon populations. Firstly, in chapter two, I compared a series of early-life fitness-related traits (e.g., development time, size, growth, survival) among them. I then (in chapter three) examined their gene expression profiles at the late yolk sac fry stage, using 44K microarrays and qPCR validation. Subsequently, at the juvenile stage (in chapter four), using two complementary experiments, I investigated their fitness-related traits (e.g., dominance, growth, and survival) differences across the contrasting tank and stream environments. Finally, in chapter five, I compared their behaviour in four different contexts (e.g., exploration, response to a novel object, boldness under predation risk, and aggression). Significant differences were observed in early-life development time, survival, growth, and energy conversion among farmed, F₁ hybrid, and wild populations. All pure farmed strains and wild populations differed among themselves, but I found few differences in fitness-related traits between F₁ hybrids and their maternal wild/farmed strains. The late yolk sac fry gene expression study indicates that the wild population showed greater transcriptome differences from the EO farmed strain than that of NA farmed strain. I also found the largest differences in global gene expression between the two farmed strains. I detected fewer significantly differentially expressed transcripts between F1 hybrids and domesticated/wild maternal strains. At the juvenile stage, I found Farm.NA fish were more dominant and less subordinate than NF wild conspecifics, with hybrids being intermediate, not differing from wild fish. Farm.EO fish also tended to dominate NF wild fish. I did not find any differences in the growth of wild fish in sympatry versus allopatry in the tank environment. However, in the stream environment, wild fish in sympatry with Farm.NA and hybrids fish outgrew those in allopatry. Within sympatric treatments, both EO and NA farmed fish similarly outgrew wild fish in the tank environment, but not necessarily always in the stream environment (e.g., Farm.NA). F₁ hybrids tended to display intermediate growth performance relative to farmed and wild fish both in tank and stream environments. No survival differences were detected among cross types both in tank and stream environments. I also found both NA and EO farmed fish were equally more explorative, responsive to a novel object, bold, and aggressive than wild fish and related hybrids. Overall, these findings suggest that early-life fitness-related trait differences among fish of EO and NA farmed, NF wild, and related F₁ hybrid origins are generated by the geographic and ancestral relationship and maternal effects of egg size, but later stage juvenile fitness-related trait differences are mainly generated by domestication selection. Also, the gene transcriptome and fitness-related trait findings suggest that the consequences of hybridization would be greater from escaped EO farmed than NA farmed salmon and may have effects on productivity and viability for local NF populations.