Data from: Successful carnivore identification with faecal DNA across a fragmented Amazonian landscape

The use of scat surveys to obtain DNA has been well documented in
temperate areas, where DNA preservation may be more effective than in
tropical forests. Samples obtained in the tropics are often exposed to
high humidity, warm temperatures, frequent rain, and intense sunlight, all
of which can rapidly degrade DNA. Despite these potential problems, we
demonstrate successful DNA amplification and sequencing for faeces of
carnivores collected in tropical conditions and quantify how sample
condition and environmental variables influence the success of PCR
amplification and species identification. Additionally the feasibility of
genotyping nuclear microsatellites from jaguar (Panthera onca) faeces was
investigated. From October 2007 to December 2008, 93 faecal samples were
collected in the southern Brazilian Amazon. A total of eight carnivore
species was successfully identified from 71% of all samples obtained.
Information theoretic analysis revealed that the number of PCR attempts
before a successful sequence was an important negative predictor across
all three responses (success of species identification, success of species
identification from the first sequence and PCR amplification success),
whereas the relative importance of the other three predictors (sample
condition, season, and distance from forest) varied between the three
responses. Nuclear microsatellite amplification of DNA from jaguar faeces
had lower success rates (15–44%) compared with those of the mtDNA marker.
Our results show that DNA identification of carnivore species from faecal
samples works efficiently in the Amazon forest and can provide data on
species occurrence as well as a valuable tool for genetic, ecological and
conservation studies.