Data from: Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan

• Main Authors: Shehzad, Wasim, Riaz, Tiayyba, Miquel, Christian, Poillot, Carole, Shah, Safdar, Coissac, Eric, Taberlet, Pierre, Nawaz, Muhammad Ali, Pompanon, François
• Format: Other/Unknown Material
• Language: unknown
• Published: Zenodo 2011
• Subjects: Mus musculus; ribosomal DNA; Columba livia; Crocidura pullata; Lepus capensis; Hyperacrius wynnei; Pucrasia macrolopha; Corvus macrorhynchos; Timaliidae; Dendrocopos sp; Eoglaucomys fimbriatus; Dryomys nitedula; Prionailurus bengalensis; Paa vicina; Siluriformes; species identification; Lophura leucomelanos; Alectoris Chukar; Apodemus rusiges; blocking primer; Rattus rattus; Gallus gallus
• Online Access: https://doi.org/10.5061/dryad.443t4m1q

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 feces. Here, we developed a methodology for carnivore diet analyses based on 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 analyzed a total of 38 leopard cat feces. 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, simple to implement, and allows the possibility of very large-scale analyses. pb_bk_sequence_data pb_bk_filtered_data Filtered data obtained with blocking oligonucleotide. pb_sequence_data File containing all unique sequences obtained with blocking oligonucleotide. pb_filtered_data Filtered data obtained with blocking oligonucleotide.