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Development and testing of an optimized method for DNA-based identification of jaguar (Panthera onca) and puma (Puma concolor) faecal samples for use in ecological and genetic studies

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Abstract

The elusive nature and endangered status of most carnivore species imply that efficient approaches for their non-invasive sampling are required to allow for genetic and ecological studies. Faecal samples are a major potential source of information, and reliable approaches are needed to foster their application in this field, particularly in areas where few studies have been conducted. A major obstacle to the reliable use of faecal samples is their uncertain species-level identification in the field, an issue that can be addressed with DNA-based assays. In this study we describe a sequence-based approach that efficiently distinguishes jaguar versus puma scats, and that presents several desirable properties: (1) considerably high amplification and sequencing rates; (2) multiple diagnostic sites reliably differentiating the two focal species; (3) high information content that allows for future application in other carnivores; (4) no evidence of amplification of prey DNA; and (5) no evidence of amplification of a nuclear mitochondrial DNA insertion known to occur in the jaguar. We demonstrate the reliability and usefulness of this approach by evaluating 55 field-collected samples from four locations in the highly fragmented Atlantic Forest biome of Brazil and Argentina, and document the presence of one or both of these endangered felids in each of these areas.

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Acknowledgments

We would like to thank all the institutions and people who helped with collection of biological samples used in this study, including those mentioned in Table 1, as well as Warren E. Johnson, Stephen J. O’Brien, Peter G. Crawshaw Jr., Laury Cullen Jr., Alessandra Nava, Leonardo R. Viana, Adriano G. Chiarello, Cristian Corio, Esteban Hasson, Agustín Paviolo and Mario Di Bitteti. We especially thank Paulo B. Chaves for technical assistance and suggestions, as well as access to unpublished data on ocelot ATP6 sequences. We are also grateful to the Centro Nacional de Pesquisas para a Conservação de Predadores Naturais (CENAP/ICMBio), Instituto Pró-Carnívoros, Companhia Energética de São Paulo (CESP) and Instituto Ambiental Vale for having supported this project, and the Laboratorio de Evolución, Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, for help in the analysis of scat samples from Argentina. T. Haag is supported by a fellowship from Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Brazil.

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Authors and Affiliations

  1. Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil

    Taiana Haag

  2. Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Av. Ipiranga 6681, CEP 90619-900, Porto Alegre, Rio Grande do Sul, Brazil

    Taiana Haag, Anelisie S. Santos & Eduardo Eizirik

  3. National Research Council of Argentina (CONICET) and Asociación Civil Centro de Investigaciones del Bosque Atlántico (CeIBA), Buenos Aires, Argentina

    Carlos De Angelo

  4. Instituto Ambiental Vale, Linhares, Vitoria, Espírito Santo, Brazil

    Ana Carolina Srbek-Araujo

  5. Instituto Pró-Carnívoros, Atibaia, São Paulo, Brazil

    Dênis A. Sana, Ronaldo G. Morato & Eduardo Eizirik

  6. CENAP/ICMBio, Atibaia, São Paulo, Brazil

    Ronaldo G. Morato

  7. Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil

    Francisco M. Salzano

  8. Laboratory of Genomic Diversity, NCI, Frederick, MD, USA

    Eduardo Eizirik

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  1. Taiana Haag
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  2. Anelisie S. Santos
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Correspondence to Eduardo Eizirik.

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Haag, T., Santos, A.S., De Angelo, C. et al. Development and testing of an optimized method for DNA-based identification of jaguar (Panthera onca) and puma (Puma concolor) faecal samples for use in ecological and genetic studies. Genetica 136, 505–512 (2009). https://doi.org/10.1007/s10709-008-9347-6

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