title: Successful carnivore identification with faecal DNA across a fragmented Amazonian landscape.
abstract: 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 mtDNA 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 edge) varied between the three responses. Nuclear microsatellite amplification from jaguar faeces had lower success rates (15-44%) compared with those of the mtDNA marker. Our results show that DNA obtained from faecal samples works efficiently for carnivore species identification in the Amazon forest and also shows potential for nuclear DNA analysis, thus providing a valuable tool for genetic, ecological and conservation studies.
authors.affiliation: Department of Ecology, Bioscience Institute, University of São Paulo, Rua do Matão 321, Travessa 14, São Paulo, SP 05508-900, Brazil. fmichalski@procarnivoros.org.br
authors.forename: Fernanda
authors.initials: F
authors.lastname: Michalski
authors.forename: Fernanda Pedone
authors.initials: FP
authors.lastname: Valdez
authors.forename: Darren
authors.initials: D
authors.lastname: Norris
authors.forename: Chris
authors.initials: C
authors.lastname: Zieminski
authors.forename: Cyntia Kayo
authors.initials: CK
authors.lastname: Kashivakura
authors.forename: Cristine S
authors.initials: CS
authors.lastname: Trinca
authors.forename: Heath B
authors.initials: HB
authors.lastname: Smith
authors.forename: Carly
authors.initials: C
authors.lastname: Vynne
authors.forename: Samuel K
authors.initials: SK
authors.lastname: Wasser
authors.forename: Jean Paul
authors.initials: JP
authors.lastname: Metzger
authors.forename: Eduardo
authors.initials: E
authors.lastname: Eizirik
mesh_terms: D000818:Animals; D001938:Brazil; D002335:Carnivora / Q000235:genetics*; D016000:Cluster Analysis; D017931:DNA Primers / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics / Q000302:isolation & purification*; D005243:Feces / Q000737:chemistry*; D005819:Genetic Markers / Q000235:genetics; D018895:Microsatellite Repeats / Q000235:genetics; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods; D013045:Species Specificity; D014329:Tropical Climate
chemical_list: D017931:DNA Primers; D004272:DNA, Mitochondrial; D005819:Genetic Markers