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Effects of time and rainfall on PCR success using DNA extracted from deer fecal pellets

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Abstract

Non-invasive wildlife research using DNA from feces has become increasingly popular. Recent studies have attempted to solve problems associated with recovering DNA from feces by investigating the influence of factors such as season, diet, collection method, preservation method, extraction protocol, and time. To our knowledge, studies of this nature have not addressed DNA degradation over time in wet environments, and have not been performed on fecal pellets of ungulates. Therefore, our objective was to determine the length of time a fecal pellet from a Sitka black-tailed deer (Odocoileus hemionus sitkensis) could remain in the field in a temperate rainforest environment before the DNA became too degraded for individual identification. Pellets were extracted from the rectum of recently killed deer and placed in an environment protected from rainfall and in an environment exposed to rainfall. Pellets from each treatment group were sampled at intervals of 2, 7, 14, 21, and 28 days after deer harvest. DNA was extracted from sampled pellets and individual samples were genotyped using microsatellite markers. Amplification failure and errors (dropout and false alleles) were recorded to determine extent of DNA degradation. Eighty percent of samples in the protected environment and 22% of samples in the exposed environment were successfully genotyped during the 28-day experiment. With no samples being successfully genotyped in the exposed environment after 7 days, our study showed that rainfall significantly increases degradation rates of DNA from ungulate pellets.

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Acknowledgments

Funding was provided by the Alaska Trappers Association; the Resilience and Adaptation Program (Interdisciplinary Graduate Education Research Training, National Science Foundation 0114423), the Bonanza Creek Long Term Ecological Research funded jointly by National Science Foundation grant 0423442 and United States Department of Agriculture Forest Service, Pacific Northwest Research Station (grant PNW01-JV11261952-231); and the University of Alaska Fairbanks Biology and Wildlife Department and the Institute of Arctic Biology.

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Authors and Affiliations

  1. 211 Irving I, Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA

    Todd J. Brinkman & Kris J. Hundertmark

  2. USDA Forest Service, Rocky Mountain Research Station, Missoula, MT, USA

    Michael K. Schwartz & Kristine L. Pilgrim

  3. Alaska Department of Fish & Game, Division of Wildlife Conservation, Ketchikan, AK, USA

    David K. Person

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  1. Todd J. Brinkman
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  2. Michael K. Schwartz
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  4. Kristine L. Pilgrim
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Correspondence to Todd J. Brinkman.

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Brinkman, T.J., Schwartz, M.K., Person, D.K. et al. Effects of time and rainfall on PCR success using DNA extracted from deer fecal pellets. Conserv Genet 11, 1547–1552 (2010). https://doi.org/10.1007/s10592-009-9928-7

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  • DOI: https://doi.org/10.1007/s10592-009-9928-7

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