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Urbanization is decreasing wildlife habitat and connectivity worldwide, including for apex predators, such as the puma (Puma concolor). Puma populations along California's central and southern coastal habitats have experienced rapid fragmentation from development, leading to calls for demographic and genetic management. To address urgent conservation genomic concerns, we used double‐digest restriction‐site associated DNA (ddRAD) sequencing to analyze 16,285 genome‐wide single‐nucleotide polymorphisms (SNPs) from 401 pumas sampled broadly across the state. Our analyses indicated support for 4–10 geographically nested, broad‐ to fine‐scale genetic clusters. At the broadest scale, the four genetic clusters had high genetic diversity and exhibited low linkage disequilibrium, indicating that pumas have retained genomic diversity statewide. However, multiple lines of evidence indicated substructure, including 10 finer‐scale genetic clusters, some of which exhibited fixed alleles and linkage disequilibrium. Fragmented populations along the Southern Coast and Central Coast had particularly low genetic diversity and strong linkage disequilibrium, indicating genetic drift and close inbreeding. Our results demonstrate that genetically at risk populations are typically nested within a broader‐scale group of interconnected populations that collectively retain high genetic diversity and heterogenous fixations. Thus, extant variation at the broader scale has potential to restore diversity to local populations if management actions can enhance vital gene flow and recombine locally sequestered genetic diversity. These state‐ and genome‐wide results are critically important for science‐based conservation and management practices. Our nested population genomic analysis highlights the information that can be gained from population genomic studies aiming to provide guidance for the conservation of fragmented populations.

Apex predators can influence ecosystems through density and behaviorally mediated effects on herbivores and mesopredators. In many parts of the world, apex predators live in, or are returning to, landscapes that have been modified by people; so, it is important to understand their ecological role in anthropogenic landscapes. We used motion-activated game cameras to compare the activity patterns of humans and 2 mesopredators, coyotes (Canis latrans) and bobcats (Lynx rufus), in areas with and without an apex predator, the gray wolf (Canis lupus), in a multiuse landscape of the northwestern United States. In areas with wolves, there was a significant increase in temporal niche overlap between the mesopredators owing to higher levels of coyote activity at all time periods of the day. Temporal overlap between mesopredators and humans also increased significantly in the presence of wolves. Coyotes exposed to wolves increased their activity during dawn, day, and dusk hours. The increase in coyote activity was greatest during the day, when wolves were least active. The direction of change in bobcat activity in areas with wolves was opposite to coyotes, suggesting a behaviorally mediated cascade between wolves, coyotes, and bobcats, although these findings would need to be confirmed with further research. Our findings suggest that mesopredators in human-dominated systems may perceive humans as less dangerous than apex predators, that humans may be more likely to encounter mesopredators in areas occupied by top predators, and that behaviorally mediated effects of apex predators on mesopredators persist in human-dominated landscapes.