Successful carnivore identification with faecal DNA across a fragmented Amazonian landscape

Authors

  • FERNANDA MICHALSKI,

    1. Department of Ecology, Bioscience Institute, University of São Paulo, Rua do Matão 321, Travessa 14, São Paulo, SP 05508-900, Brazil
    2. Instituto Pró-Carnívoros, C.P. 10, Atibaia, SP 12940-970, Brazil
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  • FERNANDA PEDONE VALDEZ,

    1. Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Avenida Ipriranga 6681, Porto Alegre, RS 90619-900, Brazil
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  • DARREN NORRIS,

    1. Departamento de Ecologia, Laboratório de Biologia da Conservação, Universidade Estadual Paulista, C.P. 199, Rio Claro, SP 13506-900, Brazil
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  • CHRIS ZIEMINSKI,

    1. Department of Biology, Center for Conservation Biology, Box 351800, University of Washington, Seattle, WA 98195-1800, USA
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  • CYNTIA KAYO KASHIVAKURA,

    1. Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Drive N.W., Calgary, AB, Canada T2N 4N1
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  • CRISTINE S. TRINCA,

    1. Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Avenida Ipriranga 6681, Porto Alegre, RS 90619-900, Brazil
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  • HEATH B. SMITH,

    1. Department of Biology, Center for Conservation Biology, Box 351800, University of Washington, Seattle, WA 98195-1800, USA
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  • CARLY VYNNE,

    1. Department of Biology, Center for Conservation Biology, Box 351800, University of Washington, Seattle, WA 98195-1800, USA
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  • SAMUEL K. WASSER,

    1. Department of Biology, Center for Conservation Biology, Box 351800, University of Washington, Seattle, WA 98195-1800, USA
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  • JEAN PAUL METZGER,

    1. Department of Ecology, Bioscience Institute, University of São Paulo, Rua do Matão 321, Travessa 14, São Paulo, SP 05508-900, Brazil
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  • EDUARDO EIZIRIK

    1. Instituto Pró-Carnívoros, C.P. 10, Atibaia, SP 12940-970, Brazil
    2. Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Avenida Ipriranga 6681, Porto Alegre, RS 90619-900, Brazil
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Fernanda Michalski, Fax: +55 96 33121757; E-mail: fmichalski@procarnivoros.org.br

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.

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