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Abstract:Noninvasive sampling methods provide a means for studying species such as large mammalian carnivores that are difficult to survey using traditional techniques. Focusing on bobcat (Lynx rufus), we compared the effectiveness of noninvasive hair and scat genetic sampling in terms of field sample collection, species identification, and individual identification. We describe a novel hair-snare design and sampling protocol that successfully sampled 4 sympatric carnivore species, bobcat, mountain lion (Felis concolor), coyote (Canis latrans), and gray fox (Urocyon cinereoargenteus), in 3 habitat blocks in coastal southern California, USA. Scat surveys were also successful at sampling bobcats and other carnivores in the area. Hair and scat sampling methods had similar species identification success (81% and 87%, respectively) using mitochondrial DNA amplification and restriction enzyme digestion patterns. Therefore, for studies focused on the distribution and activity of a suite of carnivore species, we recommend a combination of noninvasive methodologies, for example, targeting hair and scat surveys toward species and sites where they are most effective. Because of a higher success rate for scat (85%) than for hair samples (10%) when using 4 microsatellite loci and a multiple-tubes approach to verify individual genotypes, we suggest scat sampling is a better choice for studies that require individual identification of bobcats.

This corrects the article DOI: 10.1038/nature15256

Fragmentation of wildlife populations can have detrimental effects, including genetic differentiation of populations, loss of genetic diversity, and inbreeding depression. We evaluated the genetic structure among isolated colonies of black-tailed prairie dogs (Cynomys ludovicianus) along an urban gradient in southern Denver, Colorado. Urban colonies are important ecologically and for educational purposes, and they serve as source populations for relocation efforts. Levels of genetic differentiation between colonies were high relative to colonies in natural habitat at comparable or greater distances. Prairie dog colonies depend on dispersal among colonies for long-term persistence, and we found evidence for reduced but measurable rates of movement of individual prairie dogs among urban fragments. We observed a trend for smaller and more isolated colonies to exhibit lower genetic diversity, but we did not detect inbreeding in any of the colonies sampled. Isolation-by-distance measures, including measures based on permeability of various features of urban habitat such as roads and development, did not explain genetic differences. Our system represents a possible end point in the genetic consequences of continued loss and isolation of prairie dog colonies as fragmentation increases in both urban and natural landscapes. Urban development could affect dispersal in unexpected and complex ways and requires further study, but prairie dog colonies and their associated wildlife communities in urban areas have the potential for long-term persistence if not extirpated by human activity.

Bobcats (Lynx rufus) are valuable indicators of connectivity in the highly fragmented landscape of coastal southern California, yet their population sizes and densities are largely unknown. Using noninvasive scat sampling in a capture–recapture framework, we estimated population sizes for 2 similar areas of natural habitat with differing levels of isolation by human development in Santa Monica Mountains National Recreation Area, California. We used scat transects with geographic information system land-use layers and home-range sizes of bobcats to estimate effective sampling area and population densities. Estimates of population size in the study area connected to a much larger habitat area (26–31 individuals) were similar to estimates for the area that was completely surrounded by development (25–28 individuals). Bobcat densities for the 2 study areas also were similar (ranging from 0.25 to 0.42 bobcat/km2) and likely represent recent population declines because of notoedric mange likely interacting with toxicants. These methods proved effective despite particularly low densities of bobcats and may be especially useful when study areas are geographically isolated, reducing the uncertainty in size of the sampling area.