Identification of Neotropical felid faeces using RCP‐PCR

Abstract

Faeces similarity among sympatric felid species has generally hampered their use in distributional, demographic and dietary studies. Here, we present a new and simple approach based on a set of species-specific primers, for the unambiguous identification of faeces from sympatric neotropical felids (i.e. puma, jaguar, jaguarundi and ocelot/ margay). This method, referred to as rapid classificatory protocol-PCR (RCP-PCR), consists of a single-tube multiplex PCR yielding species-specific banding patterns on agarose gel. The method was optimized with samples of known origin (14 blood and 15 fresh faeces) and validated in faecal samples of unknown origin (n = 138), for some of which (n = 40) we also obtained species identification based on mtDNA sequencing. This approach proved reliable and provides high identification success rates from faeces. Its simplicity and cost effectiveness should facilitate its application for routine surveys of presence and abundance of these species.

Monitoring jaguar populationsPanthera oncawith non-invasive genetics: a pilot study in Brazilian ecosystems

“…However, in this study we had similarly high success rates for DNA extraction and PCR amplification for species, sex and individual identification from jaguar faecal samples in two areas with contrasting environmental conditions. Furthermore, species identification rates based on our previously developed method (Roques et al, 2011) were higher (70% for Serra da Capivara National Park and 81% for Caiman Ecological Refuge) than those reported for sequencing methods for faeces of the same species collected in the field (59%, Farrell et al, 2000;55%, Haag et al, 2009). The use of a single pair of Amelogenin-based primers for sex determination also proved to be reliable and a more efficient technique (73-96% success rates) than those previously reported, which were usually based on amplification of the Y-chromosome-linked sexdetermining region gene, using a combination of two pairs of conserved primers (e.g.…”

“…We considered a cumulated probability of identity over loci of , 10 −3 as sufficient for individual identification. Because of the recent divergence between ocelot and margay (Johnson et al, 2006), it was not possible to differentiate scat from these species with the approach used (Roques et al, 2011).…”

Combining camera-trapping and noninvasive genetic data in a spatial capture–recapture framework improves density estimates for the jaguar

“…DNA was extracted using protocols based on the GuSCN/silica method (Boom et al, 1990;Höss and Pääbo, 1993;Frantz et al, 2003). Posterior species identification was carried out using an optimized PCR-based protocol as described in Roques et al (2011). Sex was identified using the method proposed by Pilgrim et al (2005) based on the size difference between the male and female Amelogenin gene, but using newly design primers (Roques et al, accepted for publication).…”

Note on the diet of the jaguar in central Brazil

“…We quantified jaguar diet based on 39 genetically identified jaguar scats collected with the aid of scat detector dogs (14 collected by the Jaguar Conservation Fund-JCF-in 2009 (Sollmann 2011) and analysed as described in Roques et al (2011); 25 collected and analysed as described in Vynne et al (2011Vynne et al ( , 2012 between 2004 and 2008) along 3,500 km of transects in ENP. Because yearly sample sizes were too small for separate analysis, we pooled samples across years.…”