The black‐tailed prairie dog (Cynomys ludovicianus) is considered an indicator species for the short grass prairie of North America; however, this species currently occupies an estimated 2% of its original distribution. Persistent and pervasive poisoning, and sylvatic plague have fragmented the remaining populations. It is not well understood how these population fragments are connected in a heterogeneous landscape of land use practices and land cover types, but quantifying population isolation and individual measures of dispersal across the landscape are essential to predicting both the vulnerability of extinction due to stochastic processes and the probability of disease emergence. To better understand how land use practices and grassland productivity affect individual dispersal and population connectivity, we conducted a population genetic analysis of black‐tailed prairie dogs across the longitudinal breadth of the Great Plains Landscape Conservation Cooperative (GPLCC), from the core of their distribution in the short grass prairie of Colorado to the eastern periphery of their distribution in the mixed grass prairie of Kansas. Our experimental design was hierarchical in nature in order to assess the relative importance of migration among colonies, complexes, and regions. Estimates of gene flow, effective number of migrants, and spatial autocorrelation indicated that colonies throughout the GPLCC are highly connected to one another, although colonies on the western periphery of the distribution of black‐tailed prairie dogs were less connected to one another and to the core than colonies within core. We provide an estimate of the appropriate size for a prairie dog management unit based on results from spatial autocorrelation (40‐60 km), and demonstrate that, while isolation by distance predicts genetic distance at broad spatial scales, at hierarchically sampled regional locations, distance alone did not perform as well, nor did models incorporating habitat features that were implicated as complete or semipermeable barriers in a previous study. Overall, our results suggest that prairie dogs are not as sensitive to the effects of fragmentation as other grassland species.
