Assessments of population genetic structure and diversity can be of value in formulating management plans for threatened species. Using randomly amplified polymorphic DNA markers, we found evidence of significant genetic structure among black rat snakes ( Elaphe obsoleta) sampled at three spatial scales. Highly isolated (1500–1900 km apart) populations were strongly divergent (FST = 0.242–0.323), whereas populations more proximal (465 km apart) although currently isolated, exhibited far less divergence (FST = 0.019). A considerable proportion (80%) of total genetic diversity was due to differences among individuals within populations, although differences among populations (8%) also were significant. At the scale of sub‐populations (local populations 15–50 km apart), differentiation was generally moderate (FST = 0.058). Our estimates of Nei’s genetic distance for sub‐populations (0.014) approximated (mean = 0.044) those obtained in other studies that have assessed differentiation between snake populations based on variation in allozymes. The majority (ca. 86%) of total genetic variance across five sub‐populations was attributable to differences among individuals, although differences among sub‐populations (ca. 13%) also were significant. We found little evidence of genetic structure (FST = 0.006) between pairs of hibernacula, our finest spatial scale (samples 1–2 km apart), if they were located in natural habitats. In contrast, a pair of hibernacula sampled in an urban area exhibited genetic structure equivalent to some sub‐population differences (FST = 0.039), suggesting interrupted gene flow related to urban development. Our results have direct implications for ranking populations in terms of their conservation value and the genetic management of threatened snakes.
Blood samples were taken and snakes marked