Abstract

Limited stocking efforts to introduce Atlantic salmon Salmo salar into Chilean rivers and streams were unsuccessful during the 20th century. Following the arrival of the aquaculture industry during the 1980s, escaped Atlantic salmon have presented an ecological risk to native taxa through predation, competition, and transmission of pathogens or parasites. However, whether commercial aquaculture strains represent the likely source of free-living Atlantic salmon in marine and freshwater environments is unclear. We used 272 single nucleotide polymorphisms to characterize free-living Atlantic salmon (n = 80) captured from 12 marine and freshwater locations in southern Chile. These were compared with 8 reference collections, 6 known commercial strains, and 2 wild populations of Atlantic salmon. We evaluated genetic structure among free-living Atlantic salmon and assessed individual ancestry and origin by assigning mixture samples to reference collections. We found evidence for genetic structure (number of clusters, K = 3) among free-living salmon unexplained by geography, environment, or life stage, but consistent with the number of clusters among commercial aquaculture strains. Most free-living Atlantic salmon had a close ancestry with farmed Norwegian strains, the most widely used by the industry, pointing to recent aquaculture escapes as their origin. Yet recent establishment of self-sustaining populations weakly differentiated from aquaculture broodstock cannot be ruled out. We propose increasing monitoring efforts of free-living Atlantic salmon in remote sites as well as in watersheds located in densely stocked aquaculture areas.