Genomic Insights into the Health and Condition of Out-Migrating Salmon Smolts

Our wild ecological genomics program focuses on the elucidation of functional genomic signatures potentially associated with enhanced mortality during transitions between freshwater and saltwater.  In 2006, we combined radio-telemetry, non-destructive biopsies and genetic stock identification on wild caught adult sockeye salmon and identified a genomic signature predictive of premature mortality in the river whether fish were sampled >200 km before river entry, upon entry in the river, or at spawning grounds.  These data showed that adult salmon were already physiologically compromised before they entered the river.  The discovery of this same signature before smolts left natal rearing environments, and the decrease in prevalence of this signature in the first 3 months in the ocean indicates that a similar mechanism may be associated with elevated mortality in juveniles in the ocean.  Functional analysis of the signature revealed a high consistency with a response to a viral infection, and the hunt for a viral pathogen ensued.  Here we provide new data both on the mechanism leading to this powerful, potentially maladaptive signature and the range of stocks and species affected.