Genomics Research and Development Initiative

The cultivation of Atlantic salmon has increased exponentially since the late 1960s with expansion into new geographic areas (e.g., Newfoundland) and use of new selectively bred strains from both North America and Europe. Coincident with this expansion has been an increased risk of farmed salmon escapes, which has the potential to impact the diversity of wild Atlantic salmon populations. This project will attempt to identify and apply targete...

Primary investigators: Dr. Ian Bradbury, Lorraine Hamilton, Geoff Perry

The data needed to allow an estimation of mortality rates on individual populations of Pacific salmon species currently depends on the Coded-Wire Tag (CWT) program. However, concern is now growing as the current form of the program conducted by Fisheries and Oceans Canada (DFO) for Chinook Salmon assessment is not financially sustainable and the quality of information delivered by the program is not sufficient for certain fishery management d...

Primary investigators: Dr. Terry Beacham, Dave Willis, Cheryl Lynch

Identifying Redfish stocks which have a diverse ability to adapt to their environment is important for predicting future directions of the stocks, setting conservation priorities, and enabling better long-term management practices. Over the last fifteen years, neutral genetic markers, or those portions of DNA that give no indication of the species ability to adapt, provided a useful tool for defining different redfish species and for stock st...

Primary investigators: Yvan Lambert, Rick Rideout, Don Power, Éric Parent, Jean-Marie Sévigny

Genetic analysis of populations of Atlantic salmon has broken new ground in stock identification; yet regional groups are often large and include populations at various stages of risk for extinction. This does not necessarily meet fisheries management needs and as a result there is increasing domestic and international pressure to explore options for improving the geographic resolution of salmon populations. This project will provide an impro...

Primary investigators: Dr. Ian Bradbury, Lorraine Hamilton, Elizabeth Nagel, Vicki Morris

Salmon enhancement restoration and conservation activities for Pacific salmon intended to support fisheries while maintaining the biological diversity of the many salmon species on Canada’s west coast are becoming increasingly important. Salmon hatchery supplementation and captive breeding of Sockeye and Chinook Salmon have successfully stabilized abundance, retained genetic diversity within target populations, and restored Canadian fisherie...

Primary investigators: Ruth Withler, Dave Willis, Mel Sheng, Wilf Luedke

The European Green Crab (Carcinus maenas) is a high impact aquatic invasive predator which is reported to have commercial (e.g., soft shell clams) and ecosystem (e.g., eelgrass beds) consequences. Sea Scallops (Placopecten magellanicus) are consistently one of the most valuable shellfish species harvested from Canada’s Atlantic waters but connectivity (genetic exchange) between different stocks is not entirely understood. When considered from...

Primary investigators: Dr. Claudio DiBacco, Dr. Ian Bradbury, Lorraine Hamilton, Dr. Cynthia McKenzie, Dr. Stephen Smith, Leslie-Anne Davidson

Climate change, genetic challenges, ecological inconsistency, and disease can all be listed as potential stressors to wild populations of salmon on Canada’s west coast. This project is addressing the physical states of wild populations through the development of a series of “salmon FIT-CHIPs” which will be used as a predictor of salmon condition. The system offers extreme flexibility, allowing biological markers to be easily customized for st...

Primary investigators: Dr. Kristi Miller-Saunders, Paul Pavlidis

Capelin (Mallotus villosus) is a commercially fished, key prey-fish species found in the northern waters of the Pacific and Atlantic oceans. Based on shape analysis, tag returns, and seasonal distribution patterns, four capelin stocks are assumed to inhabit the northwest Atlantic. However, a previous study has suggested that groupings are somewhat different than the current stock structure used for fisheries management and indicate that some ...

Primary investigators: Ellen Kenchington, Lorraine Hamilton, Brian Nakashima, Fran Mowbray

The management goal for fisheries resources, including marine mammals, is the maintenance of populations and stocks that will ensure long term sustainability of the resource. Management questions involving narwhals have dominated requests for marine mammal scientific advice in recent years. At the heart of these questions is the need to be able to resolve stock boundaries for management purposes and attempt to understand the amount of genetic...

Primary investigators: Lianne Postma, Denise Tenkula, Steven Ferguson, Cortney Watt

Environmental DNA (eDNA) or DNA that is isolated from environmental samples (e.g., water, soil) is quickly becoming a tool used by researchers to detect the occurrence of organisms that do not normally belong to an ecosystem. The method is an efficient and cost-effective alternative to standard surveying methods (e.g., netting, electrofishing) over large areas in aquatic environments. Although eDNA methods cannot currently replace standard s...

Primary investigators: Robert Bajno, Karen Dunmall, Tim Gingera, Jim Reist

Since the initial identification of Infectious Salmon Anemia Virus (ISAV), a variety of strains with variable virulence (toxicity) have been discovered. They range from the essentially avirulent strains, such as the HPR0 type, to the highly virulent HPR4 strain and many types in between. The foundation for this research lies in the idea that ISAV-HPR0 can be transmitted among a population and create a state similar to what is referred as “he...

Primary investigators: Nellie Gagné, Francis Leblanc, Mark Laflamme, Brian Glebe, Steve Leadbeater

A majority of salmon populations in the Northwest Atlantic are threatened or at risk of extinction and estimates of the impact of climate change and subsistence harvests are central to rebuilding and recovery strategies. By identifying genes associated with climate change and genetic adaptation in Atlantic salmon, this work provided an opportunity to discover the overall role of climate change in the decline of Atlantic salmon, the strength o...

Primary investigators: Dr. Ian Bradbury, Dr. Patrick O’Reilly

The goal of this project was to develop an improved ability to distinguish Atlantic Cod population structure using genetic techniques, including the Gilbert Bay cod population, and apply this information to improve fisheries management advice. The protected Gilbert Bay Atlantic Cod population has low numbers and the intent of this research was to be able to genetically determine what proportion of cod caught near Gilbert Bay is actually those...

Primary investigators: Corey Morris, Ian Bradbury, Lorraine Hamilton, Laura Park, John Brattey, Robert Gregory, Carl Bradley, John Green, Roland Kemuksigak

A primary goal of this research has been to identify conditional states in wild migrating salmon that may be associated with poor performance as smolts transition to the ocean and adults migrate into freshwater to spawn. Following that theme, in-house large-scale genomics research has led to the discovery of a widespread and powerful genomic signature (mortality related signature or MRS) among adult Sockeye Salmon in the Fraser River. This s...

Primary investigator: Dr. Kristi Miller

This research is expected to benefit the work of the Department in five ways: to help manage endangered and threatened populations and ecosystems; to assist in determining the consequences of interactions between wild and cultured salmon; to help assess the spread of aquatic invasive species in coastal habitats; to provide data on possible adaptive responses of marine species to climate change; and to increase Canada’s genomic and bio-inform...

Primary investigators: Dr. Ian Bradbury, Dr. Claudio DiBacco, Lorraine Hamilton

Climate change and increased variability in the western Arctic is significantly affecting freshwater, anadromous and marine fishes and their respective habitats and ecosystems. With this pressing issue in mind, there were a number of priorities that this project addressed: research to underpin the sustainable management of Arctic fisheries (e.g., Dolly Varden Integrated Fisheries Management Plan), assessing effects/risks of climate change (e...

Primary investigator: Jim Reist

Disease has been identified among a list of factors that may be responsible for declines of Fraser River Sockeye Salmon. There are a variety of pathogens causing disease and death in Sockeye Salmon and among these, infectious hematopoietic necrosis virus (IHNV) is recognized as a lethal contagion. Key questions remain about IHNV regarding the origins, transmission and impact of the virus across salmonid species and stocks. It has been suggest...

Primary investigators: Kyle Garver, Stewart Johnson, Ben Koop, Scott LaPatra

Conservation of Deepwater Redfish across Atlantic fishing zones is important to Canada. New information from this study will assist the development and implementation of management and conservation measures for this species. The geographic distribution of Deepwater Redfish (Sebastes mentella) is essentially continuous across the North Atlantic. Therefore, sustainable management of this resource demands a good understanding of the population s...

Primary investigators: Jean-Marie Sévigny, Don Power, Christoph Stransky

The analysis of environmental DNA (eDNA) has become an effective means to detect the presence of different species in aquatic environments, and an important tool in the management of invasive species and species-at-risk. Ongoing improvements to DNA analysis techniques have generated handheld quantitative PCR (qPCR) devices that can detect, identify, and quantify eDNA in the field.

Primary investigators: Robert Bajno, Jim Reist

The current management of hatchery reared Chinook Salmon in British Columbia relies heavily on coded-wire tagging (CWT) methods to track individuals released into the wild. These tags can be costly on a large scale, and can only be applied to a portion of juvenile fish upon their release.

Primary investigators: Terry Beacham

Despite their cultural, economic, and ecological importance, the population structure and diversity of arctic fishes remains largely unknown. Increasing exploitation of arctic fish species in the absence of a clear understanding of population structure, risks the loss of adaptive diversity, thereby threatening species stability and persistence.

Primary investigators: Ian Bradbury

The analysis of environmental DNA (eDNA) has become an effective means for detecting the presence of different species in aquatic environments and an important tool in the management of invasive species and species-at-risk. DNA quantification technologies, such as quantitative PCR (qPCR) and microfluidics platforms, are used to detect, identify, and quantify the eDNA that is shed from the aquatic organisms into the environment.

Primary investigators: Nellie Gagné, Francis LeBlanc

Understanding stock structure is essential to successful fisheries management. Despite the profound commercial value and cultural significance of Atlantic Cod (Gadus morhua) fisheries, few improvements have been made to update the stock delineation at a micro-scale. However, recent advances in genomic research have made fine-scale spatial analysis of Cod stocks, populations, and sub-populations possible.

Primary investigators: Geneviève Parent, Yanjun Wang