Abstract
Increasing rates of hybridization and introgression in managed populations of freshwater fish are a major threat to the long-term viability of native species. The conservation challenge begins with identifying native gene pools. For brown trout (Salmo trutta Linnaeus, 1758) in the Upper Danube drainage, this task is complicated by the presence of both naturally and anthropogenically induced admixture of highly divergent lineages (Atlantic and Danubian). Herein, a ddRADseq protocol was used to type 377 individuals from 24 populations in the Upper Danube in Austria and Germany, and from reference populations from adjacent drainages and commercial hatcheries. High genetic differentiation at small geographic scales was found among pure Danubian-lineage populations, especially in the Kalkalpen National Park (Austria). In the Upper Danube drainage of Germany, as well as in the Rhine and Elbe drainages, brown trout populations were predominantly of Atlantic-lineage origin – as were those of all commercial hatcheries. Most populations, however, showed various degrees of admixture between Danubian and Atlantic lineages, hypothesized to be the result of both natural and anthropogenic processes. We highlight the conservation value of pure Danubian-lineage populations, and the challenges promoting conservation of naturally admixed populations, while discouraging continued stocking and admixture via management activities