Skip to main content

Advertisement

Log in

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

  • Short Communication
  • Published:
Conservation Genetics Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig 1

References

  • Alaback PB (1982) Dynamics of understory biomass in Sitka spruce-western hemlock forests of southeast Alaska. Ecology 63:1932–1948. doi:10.2307/1940131

    Article  Google Scholar 

  • Alaska Climate Research Center (2008) Climate normals. Available via http://climate.gi.alaska.edu/Climate/Normals/Index.html Accessed Dec 2008

  • Arevalo E, Holder DA, Derr JN, Bhebbe E, Linn RA, Ruvuna F, Davis SK, Taylor JF (1994) Caprine microsatellite dinucleotide repeat polymorphisms at the SR-CRSP-1, SR-CRSP-2, SR-CRSP-3, SR-CRSP-4, SR-CRSP-5 loci. Anim Genet 25:202

    Article  CAS  PubMed  Google Scholar 

  • Ball MC, Pither R, Manseau M, Clark J, Petersen SD, Kingston S, Morrill N, Wilson P (2007) Characterization of target nuclear DNA from faeces reduces technical issues associated with the assumptions of low-quality and quantity template. Conserv Genet 8:577–586. doi:10.1007/s10592-006-9193-y

    Article  Google Scholar 

  • Barendse W, Armitage SM, Kossarek I, Shalom A, Kirkpatrick BW, Ryan AM, Clayton D, Li L, Nelbergs HL, Zhang N, Grosse WM, Weiss J, Creighton P, McCarthy F, Ron M, Teale AJ, Fries R, McGraw RA, Moore SS, Georges M, Soller M, Womack JE, Hetzel DJS (1994) A genetic linkage map of the bovine genome. Nat Genet 6:227–235. doi:10.1038/ng0394-227

    Article  CAS  PubMed  Google Scholar 

  • Bellemain E, Swenson JE, Tallmon D, Brunberg S, Taberlet P (2005) Estimating population size of elusive animals with DNA from hunter-collected feces: four methods for brown bears. Conserv Biol 19:150–161. doi:10.1111/j.1523-1739.2005.00549.x

    Article  Google Scholar 

  • Bishop MD, Kappes SM, Keele JW, Stone RT, Sunden SLF, Hawkins GA, Toldo SS, Fries R, Grosz MD, Yoo J, Beattie CW (1994) A genetic linkage map for cattle. Genetics 136:619–639

    CAS  PubMed  Google Scholar 

  • Bonin A, Bellemain E, Bronken Eidesen P, Pompanon F, Brochmann C, Taberlet P (2004) How to track and assess genotyping errors in population genetics studies. Mol Ecol 13:3261–3273. doi:10.1111/j.1365-294X.2004.02346.x

    Article  CAS  PubMed  Google Scholar 

  • Buchan JC, Archie EA, VanHorn RC, Moss CJ, Alberts SC (2005) Locus effects and sources of error in noninvasive genotyping. Mol Ecol Notes 5:680–683. doi:10.1111/j.1471-8286.2005.01002.x

    Article  CAS  Google Scholar 

  • Creel S, Spong G, Sands JL, Rotella J, Zeigle J, Joe L, Murphy KM, Smith D (2003) Population size estimation in Yellowstone wolves with error-prone noninvasive microsatellite genotypes. Mol Ecol Notes 12:2003–2009

    Google Scholar 

  • Farrell LE, Roman J, Sunquist ME (2000) Dietary separation of sympatric carnivores identified by molecular analysis of scats. Mol Ecol 9:1583–1590. doi:10.1046/j.1365-294x.2000.01037.x

    Article  CAS  PubMed  Google Scholar 

  • Fisch G (1979) Deer pellet deterioration. In: Wallmo OC, Schoen JW (eds) Sitka black-tailed deer, USDA Forest Service Conference Proceedings, Series No R10–48, Juneau, pp 207–218

  • Harestad AS, Bunnell FL (1987) Persistence of black-tailed deer fecal pellets in coastal habitats. J Wildl Manage 51:33–37. doi:10.2307/3801624

    Article  Google Scholar 

  • Holder DA, Arevalo E, Holder MT, Taylor JF, Davis SK (1994) Bovine microsatellite dinucleotide repeat polymorphisms at the TEXAN-1, TEXAN-2, TEXAN-3, TEXAN-4, and TEXAN-5 loci. Anim Genet 25:201

    Article  CAS  PubMed  Google Scholar 

  • Jones KC, Levine KF, Banks JD (2000) DNA-based genetic markers in black-tailed and mule deer for forensic applications. Calif Fish Game 86:115–126

    Google Scholar 

  • Lucchini V, Fabbri E, Marucco F, Ricci S, Boitani L, Randi E (2002) Noninvasive molecular tracking of colonizing wolf (Canis lupus) packs in the western Italian Alps. Mol Ecol 11:857–868. doi:10.1046/j.1365-294X.2002.01489.x

    Article  CAS  PubMed  Google Scholar 

  • Maudet C, Luikart G, Dubray D, Von Hardenberg A, Taberlet P (2004) Low genotyping error rates in wild ungulate feces sampled in winter. Mol Ecol Notes 4:772–775. doi:10.1111/j.1471-8286.2004.00787.x

    Article  CAS  Google Scholar 

  • McKelvey KS, Schwartz MK (2004) Providing reliable and accurate genetic capture-mark-recapture estimates in a cost-effective way. J Wildl Manage 68:453–456. doi:10.2193/0022-541X(2004)068[0453:PRAAGC]2.0.CO;2

    Article  Google Scholar 

  • McKelvey KS, Schwartz MK (2005) DROPOUT: a program to identify problem loci and samples for noninvasive genetic samples in a capture-mark-recapture framework. Mol Ecol Notes 5:716–718. doi:10.1111/j.1471-8286.2005.01038.x

    Article  CAS  Google Scholar 

  • Meredith EP, Rodzen JA, Levine KF, Banks JD (2005) Characterization of an additional 14 microsatellite loci in California elk (Cervus elaphus) for use in forensic and population applications. Cons Gen 6:151–153. doi:10.1007/s10592-004-7735-8

    Article  Google Scholar 

  • Miller CR, Joyce P, Waits LP (2002) Assessing allelic dropout and genotype reliability using maximum likelihood. Genetics 160:357–366

    PubMed  Google Scholar 

  • Morin PA, Chambers KE, Boesch C, Vigilant L (2001) Quantitative polymerase chain reaction analysis of DNA from noninvasive samples for accurate microsatellite genotyping of wild chimpanzees (Pan troglodytes verus). Mol Ecol 10:1835–1844. doi:10.1046/j.0962-1083.2001.01308.x

    Article  CAS  PubMed  Google Scholar 

  • Murphy MA, Waits LP, Kendall KC (2003) Influence of diet on faecal DNA amplification and sex identification in brown bears (Ursus arctos). Mol Ecol 12:2261–2265. doi:10.1046/j.1365-294X.2003.01863.x

    Article  CAS  PubMed  Google Scholar 

  • Murphy MA, Kendall KC, Robinson A, Waits LP (2007) The impact of time and field conditions on brown bear (Ursus arctos) faecal DNA amplification. Conserv Genet 8:1219–1224. doi:10.1007/s10592-006-9264-0

    Article  Google Scholar 

  • Nsubuga AM, Robbins MM, Roeder AD, Morin PA, Boesch C, Vigilant L (2004) Factors affecting the amount of genomic DNA extracted from ape faeces and the identification of an improved sample storage method. Mol Ecol 13:2089–2094. doi:10.1111/j.1365-294X.2004.02207.x

    Article  CAS  PubMed  Google Scholar 

  • Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295. doi:10.1111/j.1471-8286.2005.01155.x

    Article  Google Scholar 

  • Piggot MP (2004) Effect of sample age and season of collection on the reliability of microsatellite genotyping of faecal DNA. Wildl Res 31:485–493. doi:10.1071/WR03096

    Article  Google Scholar 

  • Schwartz MK, Monfort SL (2008) Genetic and endocrine tools for carnivore surveys. In: Long RA, Mackay P, Zielinski WJ, Ray JC (eds) Noninvasive survey methods for carnivores. Island Press, Washington DC, pp 238–262

    Google Scholar 

  • Schwartz MK, Cushman SA, McKelvey KS, Hayden J, Engkjer C (2006) Detecting genotyping errors and describing American black-bear movement in northern Idaho. Ursus 17(2):138–148. doi:10.2192/1537-6176(2006)17[138:DGEADA]2.0.CO;2

    Article  Google Scholar 

  • Sefc KM, Payne RB, Sorenson MD (2003) Microsatellite amplification from museum feather samples: effects of fragment size and template concentration of genotyping errors. Auk 120:982–989. doi:10.1642/0004-8038(2003)120[0982:MAFMFS]2.0.CO;2

    Article  Google Scholar 

  • Taberlet P, Griffin S, Goossens B, Questlau S, Manceau V, Escaravage N, Waits LP, Bouvet J (1996) Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Res 24:3189–3194. doi:10.1093/nar/24.16.3189

    Article  CAS  PubMed  Google Scholar 

  • Ulizio TJ, Squires JR, Pletscher DH, Schwartz MK, Claar JJ, Ruggiero LF (2006) The efficacy of obtaining genetic-based identifications from putative wolverine snow tracks. Wildl Soc Bull 34(5):1326–1332. doi:10.2193/0091-7648(2006)34[1326:TEOOGI]2.0.CO;2

    Article  Google Scholar 

  • Valiere N, Berthier P, Mouchiroud D, Pontier D (2002) GEMINI: software for testing the effects of genotyping errors and multitubes approach for individual identification. Mol Ecol Notes 2:83–86

    CAS  Google Scholar 

  • Van Vliet N, Nasi R, Lumaret JP (2008a) Factors influencing duiker dung decay in north-east Gabon: are dung beetles hiding duikers? Afr J Ecol. doi:10.1111/j.1365-2028.2007.00913.x

    Google Scholar 

  • Van Vliet N, Zundel S, Miquel C, Taberlet P, Nasi R (2008b) Distinguishing dung from blue, red and yellow-backed duikers through noninvasive genetic techniques. Afr J Ecol 46:411–417. doi:10.1111/j.1365-2028.2007.00879.x

    Article  Google Scholar 

  • Waits LP, Paetkau D (2005) Noninvasive genetic sampling of wildlife. J Wildl Manage 69:1419–1433. doi:10.2193/0022-541X(2005)69[1419:NGSTFW]2.0.CO;2

    Article  Google Scholar 

  • Wilson GA, Strobeck C, Wu L, Coffin JW (1997) Characterization of microsatellite loci in caribou Rangifer tarandus, and their use in other artiodactyls. Mol Ecol 6:697–699. doi:10.1046/j.1365-294X.1997.00237.x

    Article  CAS  PubMed  Google Scholar 

Download references

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.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Todd J. Brinkman.

Rights and permissions

Reprints and permissions

About this article

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

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

Keywords

Navigation