The applicability of DNA barcoding for dietary analysis of sika deer

Abstract

AbstractIn 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.