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Mol Ecol ; 21(8): 1951-65, 2012 Apr.
Article in English | MEDLINE | ID: mdl-22250784

ABSTRACT

Diet analysis is a prerequisite to fully understand the biology of a species and the functioning of ecosystems. For carnivores, traditional diet analyses mostly rely upon the morphological identification of undigested remains in the faeces. Here, we developed a methodology for carnivore diet analyses based on the next-generation sequencing. We applied this approach to the analysis of the vertebrate component of leopard cat diet in two ecologically distinct regions in northern Pakistan. Despite being a relatively common species with a wide distribution in Asia, little is known about this elusive predator. We analysed a total of 38 leopard cat faeces. After a classical DNA extraction, the DNA extracts were amplified using primers for vertebrates targeting about 100 bp of the mitochondrial 12S rRNA gene, with and without a blocking oligonucleotide specific to the predator sequence. The amplification products were then sequenced on a next-generation sequencer. We identified a total of 18 prey taxa, including eight mammals, eight birds, one amphibian and one fish. In general, our results confirmed that the leopard cat has a very eclectic diet and feeds mainly on rodents and particularly on the Muridae family. The DNA-based approach we propose here represents a valuable complement to current conventional methods. It can be applied to other carnivore species with only a slight adjustment relating to the design of the blocking oligonucleotide. It is robust and simple to implement and allows the possibility of very large-scale analyses.


Subject(s)
DNA Barcoding, Taxonomic/methods , DNA, Mitochondrial/genetics , Felidae/physiology , Predatory Behavior , RNA, Ribosomal/genetics , Sequence Analysis, DNA/methods , Animals , Behavior, Animal , DNA, Mitochondrial/analysis , Diet , Feces/chemistry , Oligonucleotides/genetics , Species Specificity
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