We genotyped 7,588 brook trout representing 406 collections from across the State of North Carolina (Figure 1) at 12 microsatellite loci (King et al. 2012). The vast majority of
collections appeared to represent single populations, based on general conformance to HardyWeinberg equilibrium and limited evidence for linkage-disequilibrium. Allelic diversity was low to moderate relative to Brook Trout Salvelinus fontinalis populations endemic to higher latitudes. Effective population sizes varied widely among populations, but were often very small and indicate that many populations are at risk of losing diversity through genetic drift. Remarkable levels of genetic differentiation exist among populations, which suggests that little, if any, gene flow occurs among most populations. Analysis of molecular variance (AMOVA) revealed that a substantial portion of the observed genetic variation was attributed to differences among patches (44.8%), and there was some variation (11.2%) even among collections within a single patch. These results, taken in conjunction with high levels of genetic differentiation among populations, suggest that the fundamental unit of management for Brook Trout should be the
population. Interestingly, despite extensive stocking across the state, the vast majority of wild populations show limited evidence of introgression by northern origin hatchery strains. These results represent a valuable baseline for management and restoration efforts, and can be used to (a) select suitable donor streams for translocation efforts, (b) identify streams with low effective population sizes that may be vulnerable to extirpation, and (c) target stocking efforts into watersheds where extensive introgression has already occurred. All data associated with this manuscript has been publicly released (Kazyak et al. 2017).