Evaluation of fecal DNA preservation techniques and effects of sample age and diet on genotyping success

Journal of Wildlife Management

Volumn 75, Issue 7, 2011, Pages 1616-1624

  Panasci, Michael ^a   Ballard, Warren B ^a   Breck, Stewart ^b   Rodriguez, David ^c   Densmore III, Llewellyn D ^a   Wester, David B ^a   Baker, Robert J ^a  

^a TEXAS TECH UNIVERSITY   (United States)

^b NATIONAL WILDLIFE RESEARCH CENTER   (United States)

^c Cornell University ^*  (United States)

Author keywords

allelic dropout; amplification success; coyote; false allele; fecal preservation; genotyping errors; noninvasive sampling; sample age

Indexed keywords

ALLELE; CANID; CARNIVORE; DIET; ETHANOL; FECES; GENETIC ANALYSIS; GENETIC MARKER; GENETIC RESOURCE; GENOTYPE; HERBIVORE; PLANT PRODUCT; POLYMERASE CHAIN REACTION; PRESERVATION; RELIABILITY ANALYSIS; SAMPLING;

ANIMALIA; CANIS LATRANS; CITHAREXYLUM CAUDATUM; HEXAPODA; JUNIPERUS; MAMMALIA;

EID: 80051871316     PISSN: 0022541X     EISSN: 19372817     Source Type: Journal    
DOI: 10.1002/jwmg.221     Document Type: Article

References (36)

1. Adams, J. R., B. T. Kelly, and, L. P. Waits., 2003. Using faecal DNA sampling and GIS to monitor hybridization between red wolves (Canis rufus) and coyotes (Canis latrans). Molecular Ecology 12: 2175-2186. (Pubitemid 36922329)
2. Albaugh, G. P., V. Iyengar, A. Lohani, M. Malayeri, S. Bala, and, P. P. Nair., 1992. Isolation of exfoliated colonic epithelial cells, a novel, non-invasive approach to the study of cellular markers. International Journal of Cancer 52: 347-350.
3. Breen, M., S. Jouquand, C. Renier, C. S. Mellersh, C. Hitte, N. G. Holmes, A. Chéron, N. Suter, F. Vignaux, A. E. Bristow, C. Priat, E. McCann, C. André, S. Boundy, P. Gitsham, R. Thomas, W. L. Bridge, H. F. Spriggs, E. J. Ryder, A. Curson, J. Sampson, E. A. Ostrander, M. M. Binns, and, F. Galibert., 2001. Chromosome-specific single-locus FISH probes allow anchorage of an 1800-marker integrated radiation-hybrid/linkage map of the domestic dog genome to all chromosomes. Genome Research 11: 1784-1795. (Pubitemid 33040506)
4. Broquet, T., N. Menard, and, E. Petit., 2007. Noninvasive population genetics: a review of sample source, diet, fragment length and microsatellite motif effects on amplification success and genotyping error rates. Conservation Genetics 8: 249-260. (Pubitemid 46035968)
5. Broquet, T., and, E. Petit., 2004. Quantifying genotyping errors in noninvasive population genetics. Molecular Ecology 13: 3601-3608. (Pubitemid 39415689)
6. Camenzind, F. J., 1978. Behavioral ecology of coyotes on the National Elk Refuge, Jackson, Wyoming. Pages 267-294 in, M. Bekoff, editor. Coyotes: biology, behavior, and management. Academic Press, New York, New York, USA.
7. Cariappa, C. A., W. Ballard, S. Breck, A. J. Piaggio, and, M. Neubaum., 2008. Estimating population size of Mexican wolves noninvasively (Arizona). Ecological Restoration 26: 14.
8. Farrell, L. E., J. Roman, and, M. E. Sunquist., 2000. Dietary separation of sympatric carnivores identified by molecular analysis of scats. Molecular Ecology 9: 1583-1590.
9. Francisco, L. V., A. A. Langston, C. S. Mellersh, C. L. Neal, and, E. A. Ostrander., 1996. A class of highly polymorphic tetranucleotide repeats for canine genetic mapping. Mammalian Genome 7: 359-362. (Pubitemid 126426671)
10. Frantz, A. C., L. C. Pope, P. J. Carpenter, T. J. Roper, G. J. Wilson, R. J. Delahay, and, T. Burke., 2003. Reliable microsatellite genotyping of the Eurasian badger (Meles meles) using faecal DNA. Molecular Ecology 12: 1649-1661. (Pubitemid 36708469)
11. Frantzen, M. A. J., J. B. Silk, J. W. H. Ferguson, R. K. Wayne, and, M. H. Kohn., 1998. Empirical evaluation of preservation methods for faecal DNA. Molecular Ecology 7: 1423-1428. (Pubitemid 28472051)
12. Gagneux, P., C. Boesch, and, D. S. Woodruff., 1997. Microsatellite scoring errors associated with noninvasive genotyping based on nuclear DNA amplified from shed hair. Molecular Ecology 6: 861-868. (Pubitemid 27378141)
13. Goossens, B., L. Chikhi, S. S. Utami, J. de Ruiter, and, M. W. Bruford., 2000. A multi-sample, multi-extracts approach for microsatellite analysis of faecal samples in an arboreal ape. Conservation Genetics 1: 157-162.
14. Harrison, D. J., and, J. A. Harrison., 1984. Foods of adult Maine coyotes and their known aged pups. Journal of Wildlife Management 48: 922-926. (Pubitemid 17244778)
15. Kempthorne, O., 1952. The design and analysis of experiments. John Wiley and Sons, New York, New York, USA.
16. Kim, C. S., C. H. Lee, J. S. Shin, Y. S. Chung, and, N. I. Hyung., 1997. A simple and rapid method for isolation of high quality genomic DNA from fruit trees and conifers using PVP. Nucleic Acids Research 25: 1085-1086. (Pubitemid 27298283)
17. Kirk, R., 1995. Experimental design: procedures for the behavioral sciences. Third edition. Brooks/Cole Publishing Company, Pacific Grove, California, USA.
18. Kohn, M. H., and, R. K. Wayne., 1997. Facts from feces revisited. Trends in Ecology and Evolution 12: 223-227. (Pubitemid 27420009)
19. Littell, R. C., G. A. Milliken, W. W. Stroup, and, R. D. Wolfinger., 1996. SAS system for mixed models. SAS Institute, Cary, North Carolina, USA.
20. Longmire, J. L., M. Maltbie, and, R. J. Baker., 1997. Use of "Lysis Buffer" in DNA isolation and its implication for museum collections. Occasional papers, The Museum of Texas Tech University 163: 1-3.
21. Lucchini, V., E. Fabbri, F. Marucco, S. Ricci, L. Boitani, and, E. Randi., 2002. Noninvasive molecular tracking of colonizing wolf (Canis lupus) packs in the western Italian Alps. Molecular Ecology 11: 857-868. (Pubitemid 34519597)
22. McCulloch, C. E., S. R. Searle, and, J. M. Neuhaus., 2008. Generalized, linear and mixed models. Wiley, New York, New York, USA.
23. Monteiro, L., D. Bonnemaison, A. Vekris, K. G. Petry, J. Bonnet, R. Vidal, J. Cabrita, and, F. Mégraud., 1997. Complex polysaccharides as PCR inhibitors in feces: Helicobacter pylori model. Journal of Clinical Microbiology 35: 995-998. (Pubitemid 27146555)
24. Morin, P. A., K. E. Chambers, C. Boesch, and, L. Vigilant., 2001. Quantitative polymerase chain reaction analysis of DNA from noninvasive samples for accurate microsatellite genotyping of wild chimpanzees (Pan troglodytes verus). Molecular Ecology 10: 1835-1844. (Pubitemid 32667738)
25. Murphy, M. A., L. P. Waits, and, K. C. Kendall., 2003. The influence of diet on faecal DNA amplification and sex identification in brown bears (Ursus arctos). Molecular Ecology 12: 2261-2265. (Pubitemid 36922336)
26. Murphy, M. A., L. P. Waits, K. C. Kendall, S. K. Wasser, J. A. Higbee, and, R. Bogden., 2002. An evaluation of long-term preservation methods for brown bear (Ursus arctos) faecal DNA samples. Conservation Genetics 3: 435-440. (Pubitemid 35255373)
27. National Center for Biotechnology Information [NCBI]. 2009. NCBI home page. <>. Accessed 14 May 2009.
28. Nsubuga, A. M., M. M. Robbins, A. D. Roeder, P. A. Morin, C. Boesch, and, L. Vigilant., 2004. Factors affecting the amount of genomic DNA extracted from ape faeces and the identification of an improved sample storage method. Molecular Ecology 13: 2089-2094. (Pubitemid 38847610)
29. Piggott, M. P., 2004. Effect of sample age and season of collection on the reliability of microsatellite genotyping of faecal DNA. Wildlife Research 31: 485-493. (Pubitemid 40117913)
30. Prugh, L. R., C. E. Ritland, S. M. Arthur, and, C. J. Krebs., 2005. Monitoring coyote population dynamics by genotyping faeces. Molecular Ecology 14: 1585-1596. (Pubitemid 40554813)
31. Santini, A., V. Lucchini, E. Fabbri, and, E. Randi., 2007. Ageing and environmental factors affect PCR success in wolf (Canis lupus) excremental DNA samples. Molecular Ecology Notes 7: 955-961. (Pubitemid 350059230)
32. Seutin, G., B. N. White, and, P. T. Boag., 1991. Preservation of avian blood and tissue samples for DNA analyses. Canadian Journal of Zoology 69: 82-90.
33. Taberlet, P., S. Griffin, B. Goossens, S. Questiau, V. Manceau, N. Escaravage, L. Waits, and, J. Bouvet., 1996. Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Research 24: 3189-3194. (Pubitemid 26278559)
34. Taberlet, P., L. P. Waits, and, G. Luikart., 1999. Noninvasive genetic sampling: look before you leap. Trends in Ecology & Evolution 14: 323-327. (Pubitemid 29334432)
35. Waits, L. P., and, D. Paetkau., 2005. Noninvasive genetic sampling tools for wildlife biologists: a review of applications and recommendations for accurate data collection. Journal of Wildlife Management 69: 1419-1433.
36. Wasser, S. K., C. S. Houston, G. M. Koehler, G. G. Cadd, and, S. R. Fain., 1997. Techniques for application of faecal DNA methods to field studies of Ursids. Molecular Ecology 6: 1091-1097. (Pubitemid 27498890)