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 Taiana Haag Æ Anelisie S. Santos Æ Carlos De Angelo Æ Ana Carolina Srbek-Araujo Æ De ˆnis A. Sana Æ Ronaldo G. Morato Æ Francisco M. Salzano Æ Eduardo Eizirik Received: 27 June 2008 / Accepted: 11 December 2008 / Published online: 10 January 2009 Ó Springer Science+Business Media B.V. 2009 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 ampli- fication 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. Keywords Faecal DNA Á Mitochondrial DNA Á Panthera onca Á Puma concolor Á Species identification Introduction The jaguar (Panthera onca) and puma (Puma concolor) are the only large felids currently present in the Neotropics. Both species are now threatened by habitat loss and frag- mentation, along with direct persecution by ranchers due to conflict over livestock depredation (Nowell and Jackson 1996). Resilience to human disturbance varies between them, with the jaguar being considerably more sensitive to anthropogenic threats (Polisar 2002; Novack 2003; Silveira 2004). To maintain viable populations of these felids, urgent conservation efforts are needed in several areas, and T. Haag Programa de Po ´s-Graduac ¸a ˜o em Gene ´tica e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil T. Haag Á A. S. Santos Á E. Eizirik (&) Laborato ´rio de Biologia Geno ˆmica e Molecular, Faculdade de Biocie ˆncias, Pontifı ´cia Universidade Cato ´lica do Rio Grande do Sul, Av. Ipiranga 6681, CEP 90619-900 Porto Alegre, Rio Grande do Sul, Brazil e-mail: eduardo.eizirik@pucrs.br C. De Angelo National Research Council of Argentina (CONICET) and Asociacio ´n Civil Centro de Investigaciones del Bosque Atla ´ntico (CeIBA), Buenos Aires, Argentina A. C. Srbek-Araujo Instituto Ambiental Vale, Linhares, Vitoria, Espı ´rito Santo, Brazil D. A. Sana Á R. G. Morato Á E. Eizirik Instituto Pro ´-Carnı ´voros, Atibaia, Sa ˜o Paulo, Brazil R. G. Morato CENAP/ICMBio, Atibaia, Sa ˜o Paulo, Brazil F. M. Salzano Departamento de Gene ´tica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil E. Eizirik Laboratory of Genomic Diversity, NCI, Frederick, MD, USA 123 Genetica (2009) 136:505–512 DOI 10.1007/s10709-008-9347-6