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

Context: 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. Objectives: 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. Methods: 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. Results: 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. Conclusions: 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.