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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"Comparative fecal DNA preservation studies for carnivores were conducted primarily for canids and ursids (e.g., Wasser et al. 1997, Murphy et al. 2000, 2002, Panasci et al. 2011). For felids, a wide variety of fecal DNA methods have been applied, including freezing (e.g., Ernest et al. 2002, Sugimoto et al. 2006), air drying (e.g., Farrell et al. 2000, Weckel et al. 2006), silica desiccation (e.g., Haag et al. 2009, Jane cka et al. 2011), or liquid storage using buffer solutions (e.g., 20% dimethyl sulfoxide buffer, Vynne et al. 2012) or ethanol (EtOH; e.g., Mondol et al. 2009, Michalski et al. 2011, see also online Supporting Information Table S1). Yet, only a handful of comparative fecal DNA preservation studies examined the effectiveness of different methods on amplification of fecal DNA for felids (e.g., for mtDNA for wild tigers [Panthera tigris]; Bhagavatula and Singh 2006) and nuclear DNA (nDNA) markers for captive tigers (Reddy et al. 2012). "
"The molecular tools developed in this study thus provide certain advantages over earlier approaches used in carnivore studies (Cossíos and Angers 2006; Sugimoto et al. 2006; Bidlack et al. 2007; Livia et al. 2007; Haag et al. 2009; Roques et al. 2010). The approaches proposed here facilitate rapid screening of large number of samples using fewer steps in sample processing (DNA extraction, single multiplex PCR, electrophoresis), reduced species/sex misidentifications , and are cheaper than PCR–RFLP (Nagata Table 1 Details of the speciesspecific mtDNA primers designed in this study "
[Show abstract][Hide abstract] ABSTRACT: Assessing the distribution, abundance and demographic ratios of endangered and elusive co-occurring carnivore species at a landscape level is important for their continued survival. Despite potential to determine distribution and dietary analyses, use of faecal samples has been relatively limited in the context of multiple sympatric species living at large landscapes. We developed and optimized a range of novel non-invasive molecular techniques for species, gender and individual identification of tiger (Panthera tigris) and leopard (Panthera pardus). We collected a large number of faecal samples as part of a pilot occupancy survey in the Malenad-Mysore Tiger Landscape, Western Ghats, India. We could genetically ascertain species and gender for 88 and 57 % of the field-collected samples respectively. Additionally, we also determined a panel of nine and eight polymorphic loci for tiger and leopard individual identification, resulting in 18 tigers and 39 leopards from varied quality field-collected samples. Our pilot study suggest such molecular approaches will help in future efforts to gather landscape level distribution, demographic and other ecological information on tigers and leopards across their distribution.
"This can be particularly important when the focal species of the study occurs in sympatry with related taxa . Analyses based on faecal DNA have been applied to a broad range of taxa to address questions from occupancy and food habits to abundances, species distribution, and habitat use       . "
[Show abstract][Hide abstract] ABSTRACT: Abstract
The Guinean Forests are renowned for their primate diversity, with nearly 30 distinct species. These forests have been identified as some of Africa's most critical primate conservation areas. However, intensive poaching pressure and habitat degradation cause severe threats to these species. The remaining primate populations have low population densities, have secretive habitats, and are wary of humans. This can make ﬁeld studies and direct observation difﬁcult. To develop a reliable, sensitive and simple molecular identiﬁcation method using Polymerase
Chain Reaction (PCR), we sequenced the mitochondrial D-loop Hypervariable 1 region (HVR1) of Diana monkey (Cercopithecus diana) and Campbell monkey (Cercopithecus campbelli). From these sequences and their orthologs within Eastern black-and-white colobus (Colobus guereza) obtained from GenBank, we designed species-speciﬁc primers to amplify fragments of the mitochondrial D-loop HVR1 gene from faecal samples. These primers allow us to differentiate between Diana monkey (C. diana), Campbell monkey (C. campbelli), lesser spot-nosed monkey (Cercopithecus petaurista), Red colobus (Piliocolobus badius), Olive colobus (Procolobus verus), King colobus (C. polykomos), and Geoffroy’s black-and-white colobus (C. vellerosus), demonstrating their potential for the identification of West African threatened primates.