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Urbanization reduces genetic connectivity in bobcats (Lynx rufus) at both intra- and inter-population spatial scales

Cite this dataset

Kozakiewicz, Christopher P et al. (2019). Urbanization reduces genetic connectivity in bobcats (Lynx rufus) at both intra- and inter-population spatial scales [Dataset]. Dryad.


Urbanization is a major factor driving habitat fragmentation and connectivity loss in wildlife. However, the impacts of urbanization on connectivity can vary among species and even populations due to differences in local landscape characteristics, and our ability to detect these relationships may depend on the spatial scale at which they are measured. Bobcats (Lynx rufus) are relatively sensitive to urbanization and the status of bobcat populations is an important indicator of connectivity in urban coastal southern California. We genotyped 271 bobcats at 13,520 SNP loci to conduct a replicated landscape resistance analysis in five genetically distinct populations. We tested urban and natural factors potentially influencing individual connectivity in each population separately, as well as study-wide. Overall, landscape genomic effects were most frequently detected at the study-wide spatial scale, with urban land cover (measured as impervious surface) having negative effects and topographic roughness having positive effects on gene flow. The negative effect of urban land cover on connectivity was also evident when populations were analyzed separately despite varying substantially in spatial area and the proportion of urban development, confirming a pervasive impact of urbanization largely independent of spatial scale. The effect of urban development was strongest in one population where stream habitat had been lost to development, suggesting that riparian corridors may help mitigate reduced connectivity in urbanizing areas. Our results demonstrate the importance of replicating landscape genetic analyses across populations and considering how landscape genetic effects may vary with spatial scale and local landscape structure.


This dataset comprises raw sequencing reads from double-digest restriction-site-associated DNA sequencing of 286 bobcat (Lynx rufus) blood and tissue samples collected from coastal southern California between 1997 and 2012. Reads have been demultiplexed, trimmed, and quality-filtered using the process_radtags module from Stacks 1.42 using default settings. 

Usage notes

Each fq.gz file contains sequences for one sample, named according to sample ID. This dataset includes 15 samples that were filtered out from the final analysis due to poor sequencing coverage.


National Science Foundation, Award: EF 0723676

National Science Foundation, Award: DEB 1413925

Australian Government Research Training Program Scholarship

The Nature Conservancy

California Department of Transportation

Ecosystems Mission Area of the U.S. Geological Survey