Metapopulation dynamics of a diadromous galaxiid fish and potential effects of salmonid aquaculture

1. Direct ecological effects of biological invasions have been widely documented, but indirect genetic effects on native species are poorly known. In many cases, this is because of the lack of information on the genetic structure of species affected by invasions. 2. We used microsatellite DNA loci to estimate the genetic structure and gene flow patterns of Galaxias maculatus, a galaxiid fish endemic to the southern hemisphere, which is increasingly being threatened by salmonid invasions. 3. Analysis of nine diadromous populations of G. maculatus in Chilean Patagonia (an area heavily impacted by farming of non‐native salmonids) indicates that dispersal is mostly a passive process, seemingly driven by wind and currents and resulting in high gene flow and weak population structuring. 4. Gene flow was asymmetrical, with three populations acting as sources and six populations acting as sinks. Sinks had lower habitat quality and had a greater incidence of adults than sources, which consisted mostly of juveniles. 5. Rivers invaded by salmonid escapees experienced significantly higher aquaculture pressure than rivers where salmonid escapees were apparently absent, but no effect on genetic diversity of G. maculatus could be detected. 6. We discuss whether salmonid aquaculture might affect the demography and connectivity of galaxiid metapopulations: indirectly through habitat alteration and directly through escapes of predatory fish.