Urbanization is a substantial force shaping the genetic and demographic structure of natural populations. Urban development and major highways can limit animal movements, and thus gene flow, even in highly mobile species. Characterizing varying species responses to human activity and fragmentation is important for maintaining genetic continuity in wild animals and for preserving biodiversity. As one of the only common and wide-ranging large wild herbivores in much of urban North America, deer play an important ecological role in urban ecosystems, yet the genetic impacts of development on deer are not well known.

We assessed genetic connectivity for mule deer to understand their genetic response to habitat fragmentation, due to development and highway barriers, in an increasingly urbanized landscape.

Using non-invasive sampling across a broad region of southern California, we investigated genetic structure among several natural areas that were separated by major highways and applied least-cost path modelling to determine if landscape context and highway attributes influence genetic distance for mule deer.

We observed significant yet variable differentiation between subregions. We show that genetic structure corresponds with highway boundaries in certain habitat patches, and that particular landscape configurations more greatly limit gene flow between patches.

As a large and highly mobile species generally considered to be well adapted to human activity, mule deer nonetheless showed genetic impacts of intensive urbanization. Because of this potential vulnerability, mule deer and other ungulates may require further consideration for effective habitat management and maintenance of landscape connectivity in human-dominated landscapes.