Evaluating DNA degradation rates in faecal pellets of the endangered pygmy rabbit

Molecular Ecology Resources

Volumn 13, Issue 4, 2013, Pages 654-662

  Demay, Stephanie M ^a   Becker, Penny A ^b   Eidson, Chad A ^b   Rachlow, Janet L ^a   Johnson, Timothy R ^a   Waits, Lisette P ^a  

^a UNIVERSITY OF IDAHO   (United States)

^b WASHINGTON DEPARTMENT OF FISH AND WILDLIFE   (United States)

Author keywords

Brachylagus idahoensis; DNA degradation; Genotyping error; Noninvasive genetic sampling; Pygmy rabbit

Indexed keywords

MICROSATELLITE DNA; MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; CHEMISTRY; FECES; GENETICS; LABORATORY DIAGNOSIS; LAGOMORPH; METABOLISM; METHODOLOGY; POLYMERASE CHAIN REACTION; TEMPERATURE; TIME;

ANIMALS; DNA, MITOCHONDRIAL; FECES; LAGOMORPHA; MICROSATELLITE REPEATS; POLYMERASE CHAIN REACTION; SPECIMEN HANDLING; TEMPERATURE; TIME FACTORS;

BRACHYLAGUS; BRACHYLAGUS IDAHOENSIS; ORYCTOLAGUS CUNICULUS;

EID: 84879415314     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12104     Document Type: Article

References (38)

1. Adams JR, Goldberg CS, Bosworth WR, Rachlow JL, Waits LP (2011) Rapid species identification of pygmy rabbits (Brachylagus idahoensis) from faecal pellet DNA. Molecular Ecology Resources, 11, 808-812.
2. Beja-Pereira A, Oliveira R, Alves PC, Schwartz MK, Luikart G (2009) Advancing ecological understandings through technological transformations in noninvasive genetics. Molecular Ecology Resources, 9, 1279-1301.
3. Broquet T, Petit E (2004) Quantifying genotyping errors in noninvasive population genetics. Molecular Ecology, 13, 3601-3608.
4. Broquet T, Ménard N, Petit E (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.
5. Buchan JC, Archie EA, Van Horn RC, Moss CJ, Alberts SC (2005) Locus effects and sources of error in noninvasive genotyping. Molecular Ecology Notes, 5, 680-683.
6. De Barba M, Waits L, Garton E et al. (2010) The power of genetic monitoring for studying demography, ecology and genetics of a reintroduced brown bear population. Molecular Ecology, 19, 3938-3951.
7. Dobler FC, Dixon KR (1990) The pygmy rabbit Brachylagus idahoensis. In: Rabbits, Hares, and Pikas: Status Survey and Conservation Action Plan (eds Chapman JA & Flux JEC), pp. 111-115. IUCN/SSC Lagomorph Specialist Group, Gland.
8. Estes-Zumpf WA, Rachlow JL (2007) Evaluation of radio-transmitters on juvenile rabbits: application to the semifossorial pygmy rabbit (Brachylagus idahoensis). Western North American Naturalist, 67, 133-136.
9. Estes-Zumpf WA, Rachlow JL (2009) Natal dispersal by the pygmy rabbit (Brachylagus idahoensis). Journal of Mammalogy, 90, 363-372.
10. Estes-Zumpf WA, Rachlow JL, Waits LP (2008) Permanent Genetic Resources: ten polymorphic microsatellite markers for the pygmy rabbit (Brachylagus idahoensis). Molecular Ecology Resources, 8, 360-362.
11. Estes-Zumpf WA, Rachlow JL, Waits LP, Warheit KI (2010) Dispersal, gene flow, and population genetic structure in the pygmy rabbit (Brachylagus idahoensis). Journal of Mammalogy, 91, 208-219.
12. Federal Register (2003) Endangered and threatened wildlife and plants; final rule to list the Columbia Basin distinct population segment of the pygmy rabbit (Brachylagus idahoensis) as endangered. Federal Register, 68, 10388-10409.
13. Green JS, Flinders JT (1980) Habitat and dietary relationships of the Pygmy Rabbit. Journal of Range Management, 33, 136-142.
14. Hoffman JI, Amos W (2005) Microsatellite genotyping errors: detection approaches, common sources and consequences for paternal exclusion. Molecular Ecology, 14, 599-612.
15. Kovach AI, Litvaitis MK, Litvaitis JA (2003) Evaluation of fecal mtDNA analysis as a method to determine the geographic range of a rare lagomorph. Wildlife Society Bulletin, 31, 1061-1065.
16. Litvaitis JA, Tash JP, Litvaitis MK, Marchand MN, Kovach AI, Innes R (2006) A range-wide survey to determine the current distribution of New England cottontails. Wildlife Society Bulletin, 34, 1190-1197.
17. 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. Molecular Ecology, 11, 857-868.
18. Maudet C, Luikart G, Dubray D, von Hardenberg A, Taberlet P (2004) Low genotyping error rates in wild ungulate faeces sampled in winter. Molecular Ecology Notes, 4, 772-775.
19. Mougel F, Mounolou J, Monnerot M (1997) Nine polymorphic microsatellite loci in the rabbit, Oryctolagus cuniculus. Animal Genetics, 28, 59.
20. Murphy MA, Waits LP, Kendall KC (2003) The influence of diet on faecal DNA amplification and sex identification in brown bears (Ursus arctos). Molecular Ecology, 12, 2261-2265.
21. Murphy MA, Kendall KC, Robinson A, Waits LP (2007) The impact of time and field conditions on brown bear (Ursus arctos) faecal DNA amplification. Conservation Genetics, 8, 1219-1224.
22. 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. Molecular Ecology, 13, 2089-2094.
23. Panasci M, Ballard WB, Breck S et al. (2011) Evaluation of fecal DNA preservation techniques and effects of sample age and diet on genotyping success. Journal of Wildlife Management, 75, 1616-1624.
24. Piggott MP (2004) Effect of sample age and season of collection on the reliability of microsatellite genotyping of faecal DNA. Wildlife Research, 31, 485-493.
25. Piggott MP, Taylor AC (2003) Remote collection of animal DNA and its applications in conservation management and understanding the population biology of rare and cryptic species. Wildlife Research, 30, 1-13.
26. Rico C, Rico I, Webb Smith S, Bell D, Hewitt G (1994) Four polymorphic microsatellite loci for the European wild rabbit Oryctolagus cuniculus. Animal Genetics, 25, 367.
27. Sanchez DM, Rachlow JL, Robinson AP, Johnson TR (2009) Survey indicators for pygmy rabbits: temporal trends of burrow systems and pellets. Western North American Naturalist, 69, 426-436.
28. Santini A, Lucchini V, Fabbri E, Randi E (2007) Ageing and environmental factors affect PCR success in wolf (Canis lupus) excremental DNA samples. Molecular Ecology Notes, 7, 955-961.
29. Scarlata C, Elias B, Godwin J et al. (2011) Characterizing gonadal and adrenal activity by fecal steroid analyses in pygmy rabbits (Brachylagus idahoensis). General and Comparative Endocrinology, 171, 373-380.
30. Schwartz MK, Luikart G, Waples RS (2007) Genetic monitoring as a promising tool for conservation and management. Trends in Ecology & Evolution, 22, 25-33.
31. Shipley LA, Davila TB, Thines NJ, Elias BA (2006) Nutritional requirements and diet choices of the pygmy rabbit (Brachylagus idahoensis): a sagebrush specialist. Journal of Chemical Ecology, 32, 2455-2474.
32. Siegel Thines NJ, Shipley LA, Sayler RD (2004) Effects of cattle grazing on ecology and habitat of Columbia Basin pygmy rabbits (Brachylagus idahoensis). Biological Conservation, 119, 525-534.
33. Stenglein JL, Waits LP, Ausband DE, Zager P, Mack CM (2010) Efficient, noninvasive genetic sampling for monitoring reintroduced wolves. Journal of Wildlife Management, 74, 1050-1058.
34. Surridge AK, Bell DJ, Rico C, Hewitt GM (1997) Polymorphic microsatellite loci in the European rabbit (Oryctolagus cuniculus) are also amplified in other lagomorph species. Animal Genetics, 28, 302-305.
35. Taberlet P, Luikart G (1999) Non-invasive genetic sampling and individual identification. Biological Journal of the Linnean Society, 68, 41-55.
36. Taberlet P, Waits LP, Luikart G (1999) Noninvasive genetic sampling: look before you leap. Trends in Ecology & Evolution, 14, 323-327.
37. Waits LP, Paetkau D (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.
38. Washington Department of Fish and Wildlife (2011) Addendum to Washington State Recovery Plan for the Pygmy Rabbit (1995): 2011 Columbia Basin Pygmy Rabbit Reintroduction and Genetic Management Plan. Washington Department of Fish and Wildlife, Olympia, WA.