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The applicability of DNA barcoding for dietary analysis of sika deer

Fumiko Nakahara / Haruko Ando
  • Corresponding author
  • Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba 305-8506, Japan
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/ Hideyuki Ito / Asako Murakami / Naoki Morimoto / Michimasa Yamasaki
  • Laboratory of Forest Biology, Division of Forest an Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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/ Atsushi Takayanagi
  • Laboratory of Forest Biology, Division of Forest an Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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/ Yuji Isagi
  • Laboratory of Forest Biology, Division of Forest an Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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Published Online: 2015-11-26 | DOI: https://doi.org/10.1515/dna-2015-0021


In Japan, overgrazing by sika deer (Cervus nippon) has been suggested to cause a decline in forest understory vegetation. DNA barcoding has become an accepted method for analyzing the diets of animals and may be useful for evaluating the impact of sika deer on vegetation. However, the applicability of DNA barcoding in the dietary analysis of sika deer, particularly whether all of the food plants can be detected with sufficient taxonomic resolution and whether the results can be evaluated quantitatively, has not been investigated. We conducted a feeding trial by feeding five plant species to a captive sika deer and sequenced the chloroplast trnL P6 loop region from the sika deer’s fecal DNA using the Ion PGM sequencer. We detected the sequences of all of the food plants at the species level using the local (selfproduced) database and at the genus or family level with the global database. Although the sequences of some major food plants were detected with high frequency, the proportion of consumed food plants did not match the proportion of sequences obtained from fecal DNA. With further technical advances and the further completeness of the sequence database for vegetation, DNA barcoding will be a useful tool for the dietary study of sika deer.

Keywords: Cervus nippon; feeding trial; high-throughput sequencing; trnL P6 loop


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About the article

Received: 2015-02-27

Accepted: 2015-10-01

Published Online: 2015-11-26

Published in Print: 2015-01-01

Citation Information: DNA Barcodes, Volume 3, Issue 1, Pages 200–206, ISSN (Online) 2299-1077, DOI: https://doi.org/10.1515/dna-2015-0021.

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© 2015. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License. BY-NC-ND 3.0

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