Population Genetics and Functional Connectivity of the Riparian Brush Rabbit (Sylvilagus bachmani riparius): Implications for the Conservation of an Endangered Lagomorph

Changes in landscape composition and connectivity can be powerful drivers of evolutionary change. While many natural changes occur at rates that allow organisms to adapt, anthropogenic changes to landscape often occur rapidly and over large spatial scales, challenging the adaptive potential of native organisms. Wide-spread anthropogenic changes not only decrease the presence and arrangement of habitat (structural connectivity), but also affect habitat quality and how organisms interact with the landscape (functional connectivity). California’s San Joaquin Valley provides an example of changes at both temporal scales. A product of millennia of hydrologic and geologic change, the San Joaquin Valley has experienced substantial changes in landscape composition over the last century, resulting in a highly altered system with isolated remnants of native habitat. The limited availability and connectivity of native habitat can impede gene flow between organismal populations while augmenting genetic drift within populations. Using a combination of molecular data and graph theory approaches, I assessed the genetic diversity, population genetic structure, and structural and functional connectivity of the riparian brush rabbit (Sylvilagus bachmani riparius). Endemic to the riparian forests of the San Joaquin Valley, the riparian brush rabbit has lost over 95 percent of its habitat since European settlement. I find that remnant populations of S. b. riparius share mitochondrial haplotypes, suggestive of historic connectivity throughout their range. However, analyses of contemporary genetic differentiation and structure suggest the presence of three genetic clusters within the subspecies, corresponding to the geographic locations of natural populations, indicating that gene flow is likely limited by habitat fragmentation. Landscape analyses further support these data, indicating strong support for isolation by effective habitat distance and limited connectivity between habitat patches throughout the riparian brush rabbit’s range. While these findings highlight the extensive fragmentation of S. b. riparius’ range, the augmented population at SJRNWR retains high levels of diversity and functional connectivity. As such, S. b. riparius would likely respond favorably to additional augmentation and restoration efforts