Describing Fine‐Scale Patterns of Genetic Structure and Introgression of Redband Trout in a Complex River System

The conservation status of Redband Trout Oncorhynchus mykiss gairdneri has been an increasing concern of fish managers. Effective fish management first requires an understanding of the spatial distribution of distinct populations and the processes influencing gene flow. We performed a genetic analysis of Redband Trout from the Deschutes River basin in central Oregon to discern population genetic structure and the genetic impacts of an extensive hatchery stocking program and several potential barriers to dispersal. Conducting surveys in lateral habitats, we sampled over 1,400 young-of-the-year Redband Trout and genotyped them at a panel of 269 SNPs using genotyping-in-thousands by sequencing. We found that within this section of the Deschutes River basin there were multiple distinct genetic groups of Redband Trout, with an irrigation diversion dam and only one of eight waterfalls in the study area acting as complete barriers to gene flow. Within these distinct genetic groups there was a strong signal of isolation by distance. Despite the extensive stocking of large numbers out-of-basin hatchery Rainbow Trout Oncorhynchus mykiss, our results indicated that introgression of wild fish occurred only with a locally derived hatchery strain of Redband Trout. Hatchery influence was greatest in Fall River and in neighboring portions of the Deschutes River. The combination of spatially explicit sampling in lateral habitat with genotyping via high-throughput sequencing provided an effective sampling design for this large river and its tributaries. Such an approach may be useful elsewhere for identifying genetic management units of Redband Trout and other widespread freshwater fishes.