Multiple Genetic Origins of Non‐Native, Self‐Sustaining Rainbow Trout Oncorhynchus mykiss in Streams in Baden‐Württemberg, Germany

ABSTRACT Introduced in the late 19th Century, Oncorhynchus mykiss (rainbow trout) has been stocked historically in streams throughout Baden‐Württemberg, Germany, and some populations have become self‐sustaining with unclear impact on native salmonid populations. We sampled 223 rainbow trout from 14 streams and 3 hatcheries, each with different levels of domestication, from which the streams are known to have been stocked. We conducted genomic analyses to uncover evidence confirming self‐sustaining populations, to deduce potential sources of these populations, to compare the genetic diversity of hatchery versus stream populations and to discover genetic differences between stream and hatchery populations. We found genetic population structuring amongst the stream populations, consistent with natural reproduction over several generations, and we inferred multiple genetic origins, potentially including source populations beyond the three hatcheries considered, indicating that naturalisation occurs independently of domestication level and that all lineages pose similar likelihoods of establishing in the wild. We found no significant difference in genetic diversity between stream and hatchery populations, but there were nine loci across four genomic regions associated with naturalisation within or adjacent to immunity, growth and development genes. Whether such genes are under selection in wild stream environments needs still to be determined to inform fisheries and conservation management.