GENERAL RESEARCH THEME

The research conducted in our laboratory is unified by the program of the Canadian Research Chair in Genomics and Conservation of Aquatic Resources. Many projects also contribute to internationally renowned research centers, including Ressources Aquatiques Québec (RAQ, http://raq.uqar.ca/), Québec-Océan (Groupe interinstitutionnel de recherches océanographiques du Québec, http://www.quebec-ocean.ulaval.ca/) and ArcticNet (http://www.arcticnet.ulaval.ca/). In addition to our major projects on freshwater and marine organisms, we also collaborate with many other national and international partners on a range of projects, including the characterization of genetic diversity in white-tailed deer, census size estimation in black bears, and the determinants of dispersal patterns in wandering albatross.

The Canadian Research Chair in Genomics and Conservation of Aquatic Resources has three major objectives.

1) The first objective is to increase our fundamental knowledge about the evolutionary processes responsible for generating and maintaining genetic diversity within populations of aquatic animals. This research will contribute to the sustainable maintenance and the long term economic viability of aquatic species in three complementary domains of activity: recreational and commercial fisheries, the conservation of biodiversity, and aquaculture.

2) The second objective is to provide high-quality training for students, researchers, and research professionals in areas of high priority for Canada, including evolutionary and conservation genomics and bioinformatics.

3) The third objective is to increase public awareness of how academic researchers are working to improve the strategies we use to conserve and manage natural populations.

Our research projects are characterized by an integrative approach that combines quantitative and functional genomics, population genomics, bioinformatics, ecology and physiology. These projects include topics that can be sources of conflict among conservation biologists, resource managers and industry. For instance, we work to address questions of interest to fisheries managers, the aquaculture industry and conservation biologists. These three sectors are facing common problems concerning the erosion of genetic diversity and all require further knowledge of the processes that generate and maintain genetic diversity and must collaborate to enable sustainable resource management. We aim to fill this gap in our knowledge and provide these actors with the information required to best manage our country's biological resources.

OVERVIEW OF ONGOING RESEARCH PROJECTS

Our ongoing research projects are grouped into six research themes. A summary of each project, as well as the names of collaborators, are presented in the people section of our webpage.

1) Understanding the mechanisms leading to adaptive divergence and the origin of new species. Our multidisciplinary approach is based on the integration of techniques in ecology, physiology, population genomics and functional genomics. Our principal study system is the Lake Whitefish (Coregonus clupeaformis, Salmonidae), which contains ‘dwarf’ and ‘normal’ populations that have recently diverged. Populations in different lakes vary in their levels of reproductive isolation and in their level of specialization toward distinct ecological niches.

2) Understanding adaptations to human activities and their evolutionary implications. Specifically, we aim to elucidate the genetic changes that occur as a result of fishing, stocking, domestication and habitat disturbance, including pollution and habitat fragmentation. As with our first research theme, we use a multidisciplinary approach that includes population and functional genomics, transcriptomics, ecological measures, and physiological data. Our principal species of study are the Atlantic salmon (Salmo salar), Brook Char (Salvelinus fontinalis), American Eel (Anguilla rostrata) and Yellow Perch (Perca flavescens).

3) Using population genomics to determine genetic structure and identifying conservation units. Our studies aim to identify the role of ecological determinism (neutral and selective) on genetic and phenotypic variability within and among populations for many species including the Atlantic Salmon (Salmo salar), Brook Char (Salvelinus fontinalis), American Eel (Anguilla rostrata), Muskellunge (Esox masquinongy), Lake Trout (Salvelinus namaycush), American Lobster (Homarus americanus), and Sea Cucumber (Parastichopus parvimensis).

4) Clarifying the molecular bases of various ecological processes (ecological genomics). Our studies use genomic and transcriptomic tools on non-model species to identify the molecular bases underlying various processes including local adaptation to pathogens and contamination, population divergence, and the functional effects of hybridisation. The species studied are American and European Eel (Anguilla rostrata and Anguilla anguilla), Atlantic Salmon (Salmo salar), Brook Char (Salvelinus fontinalis), and Yellow Perch (Perca flavescens).

5) Creating techniques to identify and monitor organisms using genetic barcoding. We work in collaboration with the Canadian Barcode of Life Network to establish a genetic barcode database for all North America freshwater fishes. This database is a reference for the environmental DNA (eDNA) studies that are in development in our laboratory to monitor biodiversity using meta-barcoding, detect rare species, detect invasive species, and estimate species abundance. These studies are conducted with government and private collaborators and also monitor invertebrate species. We are currently conducting research as part of the ArcticNet and Coastal SEES Collaborative Research Network to detect the biodiversity changes and the introduction of invasive species in the Arctic.

6) Developing safe, secure and sustainable Coho salmon (Oncorhynchus kisutch) aquaculture. The ‘Enhanced Production in Coho: Culture, Community, Catch’ (EPIC4) project is funded by Genome Canada, Genome BC and Genome Quebec to develop a new aquaculture industry in Canada, improve food and cultural security for First Nations, enhance employment and incomes in associated communities, help rebuilt wild fisheries with an effective hatchery system and maintain genetic variation within this species. This multidisciplinary project uses cutting-edge genomic techniques to address challenges facing the development of aquaculture and population management of Coho salmon and our main objective is to identify genetic variation among salmon populations from across this species’ range to identify the different conservation units needed to maintain genetic variation in this species. We will also help to assess the ability of hatcheries to conserve and enhance Coho salmon populations. This project is a collaboration between Canadian and Chilean researchers, and includes members from Simon Fraser University, the University of British Colombia, the University of Victoria, Vancouver Island University, Universidad de Chile, the Pacific Salmon Foundation, Spring Salmon SP, Aquainnovo, Fisheries and Oceans Canada, Thermo Fisher, Ressources Aquatiques Québec, and the Institute for Integrative and Systems Biology at Université Laval.