title: Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan.
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.
authors.affiliation: Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble, France.
authors.forename: Wasim
authors.initials: W
authors.lastname: Shehzad
authors.forename: Tiayyba
authors.initials: T
authors.lastname: Riaz
authors.forename: Muhammad A
authors.initials: MA
authors.lastname: Nawaz
authors.forename: Christian
authors.initials: C
authors.lastname: Miquel
authors.forename: Carole
authors.initials: C
authors.lastname: Poillot
authors.forename: Safdar A
authors.initials: SA
authors.lastname: Shah
authors.forename: François
authors.initials: F
authors.lastname: Pompanon
authors.forename: Eric
authors.initials: E
authors.lastname: Coissac
authors.forename: Pierre
authors.initials: P
authors.lastname: Taberlet
mesh_terms: D000818:Animals; D001522:Behavior, Animal; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D004272:DNA, Mitochondrial / Q000032:analysis / Q000235:genetics*; D004032:Diet; D005243:Feces / Q000737:chemistry; D045989:Felidae / Q000502:physiology*; D009841:Oligonucleotides / Q000235:genetics; D011235:Predatory Behavior; D012335:RNA, Ribosomal / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity
chemical_list: D004272:DNA, Mitochondrial; D009841:Oligonucleotides; D012335:RNA, Ribosomal; C075526:RNA, ribosomal, 12S