Salish Sea Marine Survival Project

79 RESEARCH TOPIC OUTCOMES Predation Studies Salmon have a number of predators and several studies focussed on the role of predation, particularly from harbour seals, on the survival of juvenile salmon. Novel methods were developed during SSMSP including the development of PIT tag scanner "beanies" affixed to the heads of seals to allow for the first direct estimation of predation (in this case, by PIT tagging of Big Qualicum hatchery Coho); collec- tions of seal scat from the Strait of Georgia for 2012-2018 to assess diet using DNA, hardparts, and novel metabarcoding methods; and GPS backpacks to study seal feeding strategies. Studies were done to determine how many Chinook and Coho smolts are consumed in the Strait of Georgia by harbour seals. Harbour seal abundance has increased 7X in the Salish Sea since receiving protection under the Marine Mammal Protection Act of 1972. SSMSP analyses suggest this harbour seal abundance trend is negatively related to changes in productivity or marine survival of Chinook, Coho and steelhead. Harbour seals appear to target Coho, Chinook and Sockeye smolts in the spring, while largely ignoring juvenile Chum and Pink smolts — but primarily take adult Pink and Chum in the fall. For smolts, this may be due to the comparatively larger size at outmigration. Seal predation on smolts in estuaries occurs primarily at dusk. Only a small portion of the seal population specialises in feeding on smolts exiting rivers and entering saltwater. In the seal "beanie" experiment, only a portion (~18%) of the seals appeared to target the releases of hatchery Coho at the mouth of the Big Qualicum and took about 6% of the release, while ignoring a subsequent release of smaller Chinook smolts. While juvenile salmon are a minor component of the overall seal diet (<5% juvenile salmon and ~2% juvenile Chinook in the spring diet), the high abundance of seals and their energetic demands can still result in a significant total impact. Results to date suggest that seals may be taking about 40% juvenile Coho and Chinook in the Strait of Georgia, but there is significant year to year and spatial variability. Additionally, most sampling focused on estuary environments, where those salmon species may be more commonly taken than in nearshore sites not associated with estuaries. Strategic Salmon Health Initiative (PSF, DFO Science, and Genome BC) This is the largest study of pathogens in BC salmon (wild, hatchery-reared, and aquaculture) and applied new genomic tools to study viruses, bacteria, fungi and protists. The study addressed whether pathogens/disease is contributing to the reduced productivity of juvenile salmon in the Salish Sea and return migrants in the Fraser River, and investigated the potential interaction of aquaculture salmon with wild/hatchery salmon in BC's coastal waters. We developed and applied new technologies to the surveillance of pathogens in BC salmon. We identified 15 previously uncharacterized viruses, and conducted surveillance on 60 infectious agents known to infect salmon globally (including 9 newly discovered). Fifty pathogens were confirmed in BC salmon. Predation studies with bull trout (Chilko Lake) and Rhinoceros Auklets (coastal BC) demonstrate that predators disproportionately feed on salmon infected with pathogens. This study was the first to demonstrate the presence of Piscine orthoreovirus (PRV ) and associated diseases in BC's aquaculture salmon (Atlantic and Chinook salmon). Modeling shows that PRV infection in wild Chinook salmon is associated with farm exposure and negatively correlated with ocean survival. Models based on almost a decade of juvenile surveillance depict ocean temperature as the most important driver of infection risk to BC salmon. Models have also identified over a dozen pathogens associated with condition and/or year-class strength for Chinook, Sockeye and Coho salmon. Our analyses tested 31,000 fish; we did not detect any "Reportable pathogens" not known previously to exist in BC (IHN known previously). During this research, genomic tools were developed to recognize specific disease and stress response states, and may assist in hatchery production and understanding of cumulative effects in Nature.

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