Carnivore population structure across an urbanization gradient: a regional genetic analysis of bobcats in southern California

In human-dominated landscapes, habitat fragmentation and barriers to movement can interrupt gene flow. While often considered at a local extent, regional analyses are also needed to reveal broader landscape-mediated population processes. To explore the relationship between patterns of gene flow and fragmentation resulting from urbanization across southern California, we used the bobcat as an indicator species. We assembled data for a landscape level genetic analysis across southern California from both archived and new samples, including two northern Californian populations for comparison, to identify local and regional areas affected by isolation. Our regional analyses focused on a dataset of 19 microsatellite loci for 118 individuals and a dataset of 422 individuals genotyped at 11 loci. We examined population genetic structure and examined how pairwise genetic distance of all population clusters aligned with geographic distance. We employed a landscape genetic analysis based on resistance to determine which features of the landscape likely play a role in determining the patterns of genetic structure we observed. Study populations generally exhibited a pattern of isolation by distance and localized areas of genetic isolation. The landscape genetic analysis suggested that, in southern California, these patterns are driven by overall landscape permeability. Although local studies are key to examining the effects of urbanization and habitat fragmentation on populations, we demonstrate the importance of combining local and regional analyses for wide-ranging species to understand and maintain connectivity at local scales, while also improving and establishing sustainable linkages to habitats at the regional scale.