Molecular tracking of mountain lions in the Yosemite Valley region in California: genetic analysis using microsatellites and faecal DNA

Abstract

Twelve microsatellite loci were characterized in California mountain lions (Puma concolor) and sufficient polymorphism was found to uniquely genotype 62 animals sampled at necropsy. Microsatellite genotypes obtained using mountain lion faecal DNA matched those from muscle for all of 15 individuals examined. DNA from potential prey species and animals whose faeces could be misidentified as mountain lion faeces were reliably distinguished from mountain lions using this microsatellite panel. In a field application of this technique, 32 faecal samples were collected from hiking trails in the Yosemite Valley region where seven mountain lions previously had been captured, sampled, and released. Twelve samples yielded characteristic mountain lion genotypes, three displayed bobcat-type genotypes, and 17 did not amplify. The genotype of one of the 12 mountain lion faecal samples was identical to one of the mountain lions that previously had been captured. Three of the 12 faecal samples yielded identical genotypes, and eight new genotypes were detected in the remaining samples. This analysis provided a minimum estimate of 16 mountain lions (seven identified by capture and nine identified by faecal DNA) living in or travelling through Yosemite Valley from March 1997 to August 1998. Match probabilities (probabilities that identical DNA genotypes would be drawn at random a second time from the population) indicated that the samples with identical genotypes probably came from the same mountain lion. Our results demonstrate that faecal DNA analysis is an effective method for detecting and identifying individual mountain lions.

Remote collection of animal DNA and its applications in conservation management and understanding the population biology of rare and cryptic species

“…Other species, such as tammar and parma wallabies, can exhibit strong trap avoidance (Vujcich 1979) and repeated trapping drives in an area may increase trap wariness (Lentle et al 1997). Animals with large home ranges and mobility, such as large carnivores and elephants, are difficult to observe or capture (Grigione et al 1999;Kohn et al 1999;Woods et al 1999;Ernest et al 2000). In any case, the latter may pose unacceptable safety risks to both humans and animals (e.g.…”

“…Such DNA has successfully been analysed from a variety of animals including primates (Constable et al 1995;Gerloff et al 1999;Utami et al 2002), mountain lions (Ernest et al 2000), coyotes (Kohn et al 1999), bears (Taberlet et al 1997), ungulates (Flagstad et al 1999), dolphins (Parsons et al 1999), bats (Vege and McCracken 2001), common wombats (Banks et al 2002a) and black rhinos (Garnier et al 2001). More unusual sources of DNA have been wolf urine in snow (Valiere and Taberlet 2000), chimpanzee buccal cells from chewed food remnants (wadges) (Sugiyama et al 1993;Takenaka et al 1993;Hashimoto et al 1996;Morin and Woodruff 1996), sloughed skin from cetaceans (Bricker et al 1996;Valsecchi et al 1998) and for birds, nest materials, feathers, eggshells and urine (Morin et al 1994a;Pearce et al 1997;Nota and Takenaka 1999).…”

“…Microsatellite profiling and sexing of faeces (in combination with footprint measurements to estimate age) collected from the dwindling Pyrenean brown bear (Ursus arctos) population gave an estimated population size of at least one yearling (male), three adult males and one adult female (Taberlet et al 1997). A combination of faecal DNA typing and trapping provided a minimum estimate of 16 mountain lions (seven by capture and nine by faecal DNA analysis) living in, or travelling through, the Yosemite Valley during an 18-month period (Ernest et al 2000).…”

“…This necessitates the use of more laborious and costly DNA extraction procedures than are required for blood and tissue samples Ernest et al 2000). Furthermore, the ramifications of contamination with highquality DNA from other sources are sufficiently severe that extra precautions are required during DNA extraction, such as working in a laboratory separate from that in which high quality DNA samples are handled or stored.…”

“…Thus, all currently used mammalian-sexing primers will amplify sequences in a wide variety of mammals. For example, the fact that faeces from known mountain lion females produced a Y-specific PCR product was probably due to the presence of male mammalian prey DNA in the faeces (Ernest et al 2000). To a lesser degree, accurate microsatellite genotyping (and therefore individual identification) may be hampered when the diet of the target species includes individuals of the same or a closely related species.…”