Riverscape genetics of non-native Brook Trout to inform native Cutthroat Trout conservation

Understanding how riverscape features influence gene flow is crucial for managing population connectivity in freshwater species. We examined the spatial genetic structure of non-native brook trout (Salvelinus fontinalis) in a headwater stream network proposed for the reintroduction of federally threatened greenback cutthroat trout (Oncorhynchus virginalis stomias). Brook trout were used as a surrogate species to evaluate the suitability of this habitat for supporting a native trout metapopulation. Using 12 microsatellite loci, we genotyped 757 individual brook trout from 22 sampling sites and modelled the effects of physical riverscape features on gene flow. Genetic clustering analysis identified four distinct tributary groups, while pairwise genetic differentiation (mean FST = 0.04; mean Jost's D = 0.06) indicated some genetic connectivity across the network. Vertical barriers and steep stream gradients impeded gene flow, whereas high-order mainstem streams facilitated trout movement. Gene flow was stronger in the downstream direction, and streams with barriers and steeper gradients showed increased asymmetry between upstream and downstream movement. Results suggest that this stream network provides sufficient genetic connectivity to support a metapopulation of native trout. Managers should prioritize habitats with gradual stream gradients and fewer barriers to promote genetic connectivity in reintroduced native trout.