Data from: Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan
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...
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2011
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Online Access: | https://doi.org/10.5061/dryad.443t4m1q |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::33d2984441dc4322c1e0ac7cc3b35a22 2023-05-15T18:05:41+02:00 Data from: Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan Shehzad, Wasim Riaz, Tiayyba Miquel, Christian Poillot, Carole Shah, Safdar Coissac, Eric Taberlet, Pierre Nawaz, Muhammad Ali Pompanon, François 2011-01-01 https://doi.org/10.5061/dryad.443t4m1q undefined unknown http://dx.doi.org/10.5061/dryad.443t4m1q https://dx.doi.org/10.5061/dryad.443t4m1q lic_creative-commons oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:82004 oai:easy.dans.knaw.nl:easy-dataset:82004 10.5061/dryad.443t4m1q 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 re3data_____::r3d100000044 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c Life sciences medicine and health care blocking primer DNA metabarcoding mitochondrial DNA ribosomal DNA species identification Ayubia National Park Pakistan Chitral Gol National Park Prionailurus bengalensis Rattus rattus Hyperacrius wynnei Lophura leucomelanos Eoglaucomys fimbriatus Apodemus rusiges Pucrasia macrolopha Crocidura pullata Columba livia Alectoris chukar Paa vicina Lepus capensis Gallus gallus Timaliidae Corvus macrorhynchos Dendrocopos sp Dryomys nitedula Siluriformes Mus musculus envir archeo Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2011 fttriple https://doi.org/10.5061/dryad.443t4m1q 2023-01-22T16:53:39Z 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_datapb_bk_filtered_dataFiltered data obtained with blocking oligonucleotide.pb_sequence_dataFile containing all unique sequences obtained with blocking oligonucleotide.pb_filtered_dataFiltered data obtained with blocking oligonucleotide. Dataset Rattus rattus Unknown Paa ENVELOPE(-53.483,-53.483,66.017,66.017) Chukar ENVELOPE(118.100,118.100,63.700,63.700) |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
Life sciences medicine and health care blocking primer DNA metabarcoding mitochondrial DNA ribosomal DNA species identification Ayubia National Park Pakistan Chitral Gol National Park Prionailurus bengalensis Rattus rattus Hyperacrius wynnei Lophura leucomelanos Eoglaucomys fimbriatus Apodemus rusiges Pucrasia macrolopha Crocidura pullata Columba livia Alectoris chukar Paa vicina Lepus capensis Gallus gallus Timaliidae Corvus macrorhynchos Dendrocopos sp Dryomys nitedula Siluriformes Mus musculus envir archeo |
spellingShingle |
Life sciences medicine and health care blocking primer DNA metabarcoding mitochondrial DNA ribosomal DNA species identification Ayubia National Park Pakistan Chitral Gol National Park Prionailurus bengalensis Rattus rattus Hyperacrius wynnei Lophura leucomelanos Eoglaucomys fimbriatus Apodemus rusiges Pucrasia macrolopha Crocidura pullata Columba livia Alectoris chukar Paa vicina Lepus capensis Gallus gallus Timaliidae Corvus macrorhynchos Dendrocopos sp Dryomys nitedula Siluriformes Mus musculus envir archeo Shehzad, Wasim Riaz, Tiayyba Miquel, Christian Poillot, Carole Shah, Safdar Coissac, Eric Taberlet, Pierre Nawaz, Muhammad Ali Pompanon, François Data from: Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan |
topic_facet |
Life sciences medicine and health care blocking primer DNA metabarcoding mitochondrial DNA ribosomal DNA species identification Ayubia National Park Pakistan Chitral Gol National Park Prionailurus bengalensis Rattus rattus Hyperacrius wynnei Lophura leucomelanos Eoglaucomys fimbriatus Apodemus rusiges Pucrasia macrolopha Crocidura pullata Columba livia Alectoris chukar Paa vicina Lepus capensis Gallus gallus Timaliidae Corvus macrorhynchos Dendrocopos sp Dryomys nitedula Siluriformes Mus musculus envir archeo |
description |
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_datapb_bk_filtered_dataFiltered data obtained with blocking oligonucleotide.pb_sequence_dataFile containing all unique sequences obtained with blocking oligonucleotide.pb_filtered_dataFiltered data obtained with blocking oligonucleotide. |
format |
Dataset |
author |
Shehzad, Wasim Riaz, Tiayyba Miquel, Christian Poillot, Carole Shah, Safdar Coissac, Eric Taberlet, Pierre Nawaz, Muhammad Ali Pompanon, François |
author_facet |
Shehzad, Wasim Riaz, Tiayyba Miquel, Christian Poillot, Carole Shah, Safdar Coissac, Eric Taberlet, Pierre Nawaz, Muhammad Ali Pompanon, François |
author_sort |
Shehzad, Wasim |
title |
Data from: Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan |
title_short |
Data from: Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan |
title_full |
Data from: Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan |
title_fullStr |
Data from: Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan |
title_full_unstemmed |
Data from: Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan |
title_sort |
data from: carnivore diet analysis based on next-generation sequencing: application to the leopard cat (prionailurus bengalensis) in pakistan |
publishDate |
2011 |
url |
https://doi.org/10.5061/dryad.443t4m1q |
long_lat |
ENVELOPE(-53.483,-53.483,66.017,66.017) ENVELOPE(118.100,118.100,63.700,63.700) |
geographic |
Paa Chukar |
geographic_facet |
Paa Chukar |
genre |
Rattus rattus |
genre_facet |
Rattus rattus |
op_source |
oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:82004 oai:easy.dans.knaw.nl:easy-dataset:82004 10.5061/dryad.443t4m1q 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 re3data_____::r3d100000044 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c |
op_relation |
http://dx.doi.org/10.5061/dryad.443t4m1q https://dx.doi.org/10.5061/dryad.443t4m1q |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.443t4m1q |
_version_ |
1766177185372045312 |