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Background  Pathogens are growing threats to wildlife. The rapid growth of marine salmon farms over the past two decades has increased host abundance for pathogenic sea lice in coastal waters, and wild juvenile salmon swimming past farms are frequently infected with lice. Here we report the first investigation of the potential role of salmon farms in transmitting sea lice to juvenile sockeye salmon ( Oncorhynchus nerka ).    Methodology/Principal Findings  We used genetic analyses to determine the origin of sockeye from Canada's two most important salmon rivers, the Fraser and Skeena; Fraser sockeye migrate through a region with salmon farms, and Skeena sockeye do not. We compared lice levels between Fraser and Skeena juvenile sockeye, and within the salmon farm region we compared lice levels on wild fish either before or after migration past farms. We matched the latter data on wild juveniles with sea lice data concurrently gathered on farms. Fraser River sockeye migrating through a region with salmon farms hosted an order of magnitude more sea lice than Skeena River populations, where there are no farms. Lice abundances on juvenile sockeye in the salmon farm region were substantially higher downstream of farms than upstream of farms for the two common species of lice:  Caligus clemensi  and  Lepeophtheirus salmonis , and changes in their proportions between two years matched changes on the fish farms. Mixed-effects models show that position relative to salmon farms best explained  C .  clemensi  abundance on sockeye, while migration year combined with position relative to salmon farms and temperature was one of two top models to explain  L .  salmonis  abundance.    Conclusions/Significance  This is the first study to demonstrate a potential role of salmon farms in sea lice transmission to juvenile sockeye salmon during their critical early marine migration. Moreover, it demonstrates a major migration corridor past farms for sockeye that originated in the Fraser River, a complex of populations that are the subject of conservation concern.

Sea Louse Infection of Juvenile Sockeye Salmon in Relation to Marine Salmon Farms on Canada's West Coast