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Effects of time and environmental conditions on the quality of DNA extracted from fecal samples for genotyping of wild deer in a warm temperate broad-leaved forest

Abstract

Extraction of DNA from non-invasive samples (feces) has been used increasingly in genetic research on wildlife. For effective and reliable genetic analyses, knowledge about which samples should be selected in the field is essential. For this reason, we examined the process of DNA degradation in feces of deer. We collected fresh fecal pellets from three wild deer living in a warm temperate forest. We then assessed the effects of time (3, 5, and 10 days) under three environmental conditions (on the forest floor, on exposed ground, and inside the laboratory) on the rates of correct genotyping (CG), amplification failure (NA), genotyping error among positive amplification (ER), false alleles (FA), and allelic dropout (AD) of 15 microsatellite loci. The rate of CG significantly decreased, and those of NA and FA increased with increasing lapse of time. Rates of CG tended to be highest and those of NA, ER, FA, and AD to be lowest in feces kept inside, followed by those on the forest floor. Suitability of samples for DNA extraction was lowest in fecal pellets left on exposed ground, and we suspect that rain may hasten DNA degradation. NA rate could serve as a reliable indicator of the quality of fecal pellets because it was significantly positively correlated with ER rate. For efficient genetic analyses using deer feces in warm temperate zones, we recommend collecting fecal pellets within 3 days of defecation, during periods without rainfall and from under the cover of trees.

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Acknowledgments

Funding was provided by the Leading Graduate Program in Primatology and Wildlife Science, Kyoto University, Japan, as part of the Resilience and Adaptation Program. We thank participants of the programs: B. Z. Katale, E. L. Baking, H. Koba, K. Ichiyama, N. Tajima, and T. Ohkawa for analyses; Dr. H. Sugiura, Dr. K. Agata, Dr. T. Matsuzawa, H. Tajima, K. Yokoyama, and other staff of Kyoto University for supporting this research. We are grateful to the Ministry of the Environment, the Yakushima Forest Environment Conservation Center, and Kagoshima Prefecture for permitting us to conduct this research.

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Correspondence to Yoshimi Agetsuma-Yanagihara.

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Communicated by: Cino Pertoldi

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Agetsuma-Yanagihara, Y., Inoue, E. & Agetsuma, N. Effects of time and environmental conditions on the quality of DNA extracted from fecal samples for genotyping of wild deer in a warm temperate broad-leaved forest. Mamm Res 62, 201–207 (2017). https://doi.org/10.1007/s13364-016-0305-x

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Keywords

  • Amplification failure
  • Cervus nippon yakushimae
  • DNA degradation
  • Genotyping error
  • Microsatellite
  • Non-invasive sampling