Conservation strategies are often implemented within the jurisdiction of an administrative unit, such as a state or federal agency; however, boundaries between these units may or may not reflect biologically meaningful distinctions. Population genomic data provide a useful way to objectively assess whether boundaries of administrative units coincide with natural population structure, as well as compare future management scenarios within and among said units. Here we used 2658 SNPs generated by a triple-digest reduced representation library preparation method from 171 individuals to determine if genetic population structure of Bog Turtles corresponds with political boundaries. We also estimated gentetic diversity within populations pertinent to setting management priorities and tested for genetic signatures consistent with local adaptation as a preliminary step to assess translocation risk. We found that genetic differentiation among populations was strongly predicted by geographic distance. Fortuitously, the patchy distribution of remaining Bog Turtle sites results in spatial-genetic clusters that do correspond with state boundaries. We observed low genetic diversity within populations and several instances where the census size exceeded our estimates of effective population size. Lastly, we detected 20 outlier loci consistent with signatures of local adaptation, suggesting that outbreeding depression may be a risk in some translocation options. Our approach allowed us to improve population parameter estimates for the federally threatened Bog Turtle to address key recovery plan objectives, some of which had not been addressed previously
