| California's San Joaquin Valley has faced dramatic changes in land composition over the last century, offering an example of a highly altered system with few isolated native remnants. Over time, changes in habitat size and connectivity can impede gene flow between populations of species and augment genetic drift resulting in long-term evolutionary consequences. Such is the case for the riparian brush rabbit (Sylvilagus bachmani riparius), a subspecies of brush rabbit endemic to the San Joaquin Valley. S.b. riparius has experienced substantial declines due primarily to habitat loss and fragmentation but also periodic flooding, drought, and wildfire, resulting in its listing as an endangered species. We identified current genetic diversity and population genetic structure of five remnant S.b. riparius populations and two populations of the neighboring S.b. macrorhinus. We find moderate levels of genetic diversity within the populations. Bayesian clustering indicates the presence of three distinct genetic clusters corresponding to the geographic locations of the populations, though isolation by distance is only modestly supported by these data. As such, we anticipate that habitat configuration and landscape features play important roles in determining the distribution of genetic variation, and are central to the success of future recovery efforts. |