I have overseen a diverse molecular genetics research program within DFO for over 15 years. The overarching goal of my program is the development and application of molecular genetic tools that can be applied towards sustainable fisheries management and aquaculture development of aquatic species. Population genetics research has been applied to establish management and conservation units within species, develop stock identification databases in salmon, and in forensic identification for enforcement. Genetic studies have been conducted on a variety of marine fish and shellfish species, including salmonids, rockfish, sablefish, Atlantic cod, herring, urchins, geoduck, and abalone. While we have developed and utilized a variety of molecular markers, including minisatellite and microsatellite loci and mitochondrial DNA, my main interest is in adaptive variation. The Major Histocompatibility Complex (MHC) is the premiere adaptive gene complex in vertebrates, and my lab has conducted extensive research on MHC gene discovery in teleosts, adaptive population genetics of MHC genes in salmon, and mechanisms of selection on the MHC in teleosts. My group has also developed genetic markers and techniques for species identification and applied these in forensic analysis for enforcement, scat analysis in stellar sea lions, and identification of escaped farmed salmon. Our work on bacterial typing has been applied to the development of probiotics for aquaculture, delineation of bacterial complexity in salmon streams and lakes, and pathogen screening in fish. For aquaculture, we have developed quantitative RT-PCR assays for pathogens, identified the Kudoa thyrsites protein responsible for the post-mortem liquefication of salmon tissue, and identified “expressed” QTLs associated with rapid muscle growth in scallops.
In 2004, with the introduction of the first GRASP (Genomics Research on Atlantic Salmon Project; Ben Koop and Willie Davidson) salmon cDNA microarray, I initiated the formation of a new functional genomics program, the Marine Ecological Genomics and Adaptation Group, within the Molecular Genetics Laboratory. This new program expands my interest in adaptive evolution to the molecular control of phenotypic adaptation. Research within this program has included species-specific salmonid host response to the IHN virus, aimed at elucidating effective host responses for targeted vaccine research, salmon migration physiology, to identify physiological profiles associated with river entry timing and fate of late-run Fraser river sockeye salmon, and density stress in pen-reared salmon, to identify stress biomarkers for aquaculture. This program focuses largely, although not exclusively, on wild ecological genomics research to elucidate phenotype-environment interactions and limits to adaptability. See the MEGA tab under the Molecular Genetics Laboratory for more details.