Research Projects

Pacific salmon gene expression during the critical early marine period
NSERC Postdoctoral research; advised by Dr. Kristi Miller (Saunders), Dr. Scott Hinch, and Dr. Tony Farrell

Salmonids have a complex life cycle, transitioning from freshwater to marine environments and migrating long distances to feeding grounds and back to reproduce. Beyond the osmotic challenges and other stressors associated with transition between environments, salmon must grow rapidly and accrue sufficient fat to escape predation and migrate. In southern British Columbia (BC), many wild salmon populations are in decline, in part due to environmental changes associated with climate warming. Reduced survival of fish during early marine residence is associated with the declines, possibly due to enhanced environmental stressors and/or sensitivity to stress during this critical transition period. However, there is a paucity of information on salmon physiology during this critical period, including physiological changes associated with seasonal behaviours and stressors. Hatchery programs are used to supplement shrinking wild populations and augment fisheries, but hatchery-bred fish released into the wild tend to experience higher mortality than wild fish. Physiological differences between hatchery and wild fish have not been described.

Chinook salmon smolt from
Sarita Estuary
Hundreds of hatchery and wild Sockeye salmon (Oncorhynchus nerka), Chinook salmon (O. tshawytscha), and Coho salmon (O. kisutch) smolts (in freshwater) and post-smolts (in seawater) were collected along their migration route over multiple years. The gene expression of four tissues (gill, liver, white muscles, and brain) was previously quantified using a 44K cDNA microarray to assess genome-wide physiology at the Fisheries and Oceans (DFO) Molecular Genetics Lab, Pacific Biological Station, Nanaimo, BC. Here, I will use multivariate analyses to identify shifts in gene expression over migration, and identify profiles associated with shifting seasons (spring, summer, fall) and source (hatchery and wild). The genes that significantly differ between seasons and source will be used to produce qPCR biomarkers for physiological fish condition, including smoltification (seawater preparedness) and domestication (hatchery vs. wild). These biomarkers will be validated with additional tissue samples and challenge experiments using wild and hatchery fish.

Pacific Salmon Foundation
Genome Brtitish Columbia

Restoration of native biodiversity in altered environments
Doctoral thesis; supervised by Dr. Bryan Neff

Historical Lake Ontario
Atlantic salmon rivers

Atlantic salmon (Salmo salar) were once abundant in Lake Ontario. Reports suggest that Lake Ontario Atlantic salmon were so abundant that people could walk on their backs during spawning runs, kill them with pitchforks and clubs, and capture over one thousand fish in a night! Unfortunately, this prolific population was extirpated by 1900 because of human-mediated habitat degradation and overfishing.

The habitat in Lake Ontario and its tributaries has been largely revitalized and should now support Atlantic salmon; however, recent attempts to restore Atlantic salmon have yet to succeed in producing a self-sustaining population, suggesting that other genetic and ecological factors should be considered for restoration. Here, I will examine the performance of three source populations of Atlantic salmon that differ in the extent of genetic and ecological suitability to the current Lake Ontario environment.

Dr. Chris Wilson, Ontario Ministry of Natural Resources
Dr. Daniel Heath and Xiaoping He, University of Windsor
Dr. Pedro Peres-Neto and Andrew Smith, Université du Québec à Montréal
Dr. Trevor Pitcher and Craig Black, University of Windsor

Relative risks of inbreeding and outbreeding
Master's thesis; supervised by Dr. Jeff Hutchings

The negative consequences associated with inbreeding depression in small populations may be similar in scope to those associated with outbreeding depression (a detrimental result that may arise from mixing populations to avoid inbreeding issues). An evaluation of the relative costs of inbreeding and outbreeding is needed for the genetic management of small populations.

Surviving juvenile at 5 months
after release
Inter-population hybrid and inbred Atlantic salmon juveniles from three populations were released into their native rivers to test for inbreeding and outbreeding depression and evaluate whether inbreeding or outbreeding may be worse for the persistence of these populations in the wild.

This was one of few studies that have examined the risks of inbreeding and outbreeding using wild reciprocal transplants as a tool in addressing conservation issues in small fish populations. The study was a collaborative project with the Department of Fisheries and Oceans (Dr. Pat O'Reilly) and Dr. Dylan Fraser. Other studies on the subject are usually confined to testing for outbreeding and inbreeding depression in a common-garden environment which may be too benign to detect fitness effects and are not an ideal representation of the native environments.

Ecological interactions between hybrids of farmed and wild Atlantic salmon
Honour's thesis; supervised by Dr. Jeff Hutchings and Dr. Dylan Fraser

Semi-natural stream environment
Continual wild-farmed interbreeding, due to escaped farmed salmon, may have detrimental effects on the persistence of wild populations. That is, interbreeding wild and domestic fishes may generate wild-farmed hybrids with behaviours that reduce their individual survival as well as reduce the survival of wild fish in the wild.

We evaluated the anti-predator responses of juveniles from two divergent wild Atlantic salmon populations, the major farmed strain used in regional aquaculture, and their wild-farmed hybrids (F1, F2, and wild backcross). We also evaluated the competitive abilities of each cross using pair-wise aggression contests and tested whether these contests could be used to predict survival in semi-natural stream environments varying in the proportion of wild-farmed hybrids.



Research Projects

Pacific salmon
gene expression

Lake Ontario
Atlantic salmon



Last updated January 2018
© Aimee Lee Houde