Nucleic acid isolation from ecological samples - Animal scat and other associated materials

Methods in Enzymology

Volumn 395, Issue , 2005, Pages 73-82

  Eggert, Lori S ^a   Maldonado, Jesús E ^a   Fleischer, Robert C ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEIC ACID;

ARTICLE; BIOLOGY; COST EFFECTIVENESS ANALYSIS; DNA DETERMINATION; DNA EXTRACTION; ECOLOGY; EXTRACTION; ISOLATION PROCEDURE; MEDICAL RESEARCH; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL;

ANIMALIA; SCATOPHAGUS ARGUS;

EID: 19944374433     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(05)95006-4     Document Type: Article

References (63)

1. Adams J.R., Kelly B.T., Waits L.P. Using faecal DNA sampling and GIS to monitor hybridization between red wolves (Canis rufus) and coyotes (Canis latrans). Mol. Ecol. 12:2003;2175-2186
2. Alpers D.L., Taylor A.C., Sunnucks P., Bellman S.A., Sherwin W.B. Pooling hair samples to increase DNA yield for PCR. Cons. Gen. 4:2003;779-788
3. Banks S.C., Piggott M.P., Hansen B.D., Robinson N.A., Taylor A.C. Wombat coprogenetics: Enumerating a common wombat population by microsatellite analysis of faecal DNA. Aust. J. Zool. 50:2002;193-204
4. Bayes M.K., Smith K.L., Alberts S.C., Altmann J., Bruford M.W. Testing the reliability of microsatellite typing from faecal DNA in the Savannah baboon. Cons. Gen. 1:2000;173-176
5. Boom R., Sol C.J.A., Salimans M.M.M., Jansen C.L., van Dillen Werthien P.M.E., van der Noordaa J. Rapid and simple method for purification of nucleic acids. J. Clin. Microbiol. 28:1990;495-503
6. Bradley B.J., Boesch C., Vigilant L. Identification and redesign of human microsatellite markers for genotyping wild chimpanzee (Pan troglodytes verus) and gorilla (Gorilla gorilla gorilla) DNA from faeces. Cons. Gen. 1:2000;289-292
7. Bradley B.J., Chambers K.E., Vigilant L. Accurate DNA-based sex identification of apes using non-invasive samples. Cons. Gen. 2:2001;179-181
8. Constable J.L., Ashley M.V., Goodall J., Pusey A.E. Noninvasive paternity assignment in Gombe chimpanzees. Mol. Ecol. 10:2001;1279-1300
9. Creel S., Spong G., Sands J.L., Rotella J., Zeigle J., Joe L., Murphy K.M., Smith D. Population size estimation in Yellowstone wolves with error-prone noninvasive microsatellite genotypes. Mol. Ecol. 12:2003;2003-2009
10. Dalén L., Götherström A., Angerbjörn A. Identifying species from pieces of faeces. Cons. Gen. 5:2004;1-3
11. Dallas J.F., Carss D.N., Marshall F., Koepfli K.-P., Kruuk H., Piertney S.B., Bacon P.J. Sex identification of the Eurasian otter Lutra lutra by PCR typing of spraints. Cons. Gen. 1:2000;181-183
12. Dallas J.F., Coxon K.E., Sykes T., Chanin P.R.F., Marshall F.A., Carss D.N., Bacon P.J., Piertney S.B., Racey P.A. Similar estimates of population genetic composition and sex ratio derived from carcasses and faeces of Eurasian otter Lutra lutra. Mol. Ecol. 12:2003;275-282
13. Ding B., Zhang Y.-P., Ryder O.A. Extraction, PCR amplification, and sequencing of mitochondrial DNA from scent mark and feces in the giant panda. Zoo Biol. 17:1998;499-504
14. Eggert L.S., Rasner C.A., Woodruff D.S. The evolution and phylogeography of the African elephant (Loxodonta africana), inferred from mitochondrial DNA sequence and nuclear microsatellite markers. Proc. R. Soc. Lond. B. 269:2002;1993-2006
15. Eggert L.S., Eggert J.A., Woodruff D.S. Estimating population sizes for elusive animals: The forest elephants of Kakum National Park, Ghana. Mol. Ecol. 12:2003;1389-1402
16. Farrell L.E., Roman J., Sunquist M.E. Dietary separation of sympatric carnivores identified by molecular analysis of scats. Mol. Ecol. 9:2000;1583-1590
17. Fernando P., Vidya T.N.C., Rajapakse C., Dangolla A., Melnick D.J. Reliable noninvasive genotyping: Fantasy or reality? J. Heredity. 94:2003;115-123
18. Flagstad Ø., Røed K., Stacy J.E., Jakobsen K.S. Reliable noninvasive genotyping based on excremental PCR of nuclear DNA purified with a magnetic bead protocol. Mol. Ecol. 8:1999;879-883
19. Frantz A.C., Pope L.C., Carpenter P.J., Roper T.J., Wilson G.J., Delahay R.J., Burke T. Reliable microsatellite genotyping of the Eurasian badger (Meles meles) using faecal DNA. Mol. Ecol. 12:2003;1649-1661
20. Frantzen M.A.J., Silk J.B., Ferguson J.W.H., Wayne R.K., Kohn M.H. Empirical evaluation of preservation methods for faecal DNA. Mol. Ecol. 7:1998;1423-1428
21. Garnier J.N., Bruford M.W., Goossens B. Mating system and reproductive skew in the black rhinoceros. Mol. Ecol. 10:2001;2031-2041
22. Gerloff U., Schlötterer C., Rassmann K., Rambold I., Hohmann F., Fruth B., Tautz D. Amplification of hypervariable simple sequence repeats (microsatellites) from excremental DNA of wild living bonobos (Pan paniscus). Mol. Ecol. 4:1995;515-518
23. Goossens B., Funk S.M., Vidal C., Latour S., Jamart A., Ancrenaz M., Wickings E.J., Tutin C.E.G., Bruford M.W. Measuring genetic diversity in translocation programmes: Principles and application to a chimpanzee release project. Anim. Conserv. 5:2002;225-236
24. Greenwood A.D., Pääbo S. Nuclear insertion sequences of mitochondrial DNA predominate in hair but not in blood of elephants. Mol. Ecol. 8:1999;133-137
25. Hofreiter M., Poinar H.N., Spaulding W.G., Bauer K., Martin P.S., Possnert G., Pääbo S. A molecular analysis of ground sloth diet through the last glaciation. Mol. Ecol. 9:2000;1975-1984
26. Höss M., Pääbo S. DNA extraction from Pleistocene bones by a silica-based purification method. Nucleic Acids Res. 21:1993;3913-3914
27. Huber S., Bruns U., Arnold W. Sex determination of red deer using polymerase chain reaction of DNA from feces. Wildlife Soc. Bull. 30:2002;208-212
28. Idaghdour Y., Broderick D., Korrida A. Faeces as a source of DNA for molecular studies in a threatened population of great butards. Cons. Gen. 4:2003;789-792
29. Kohn M., Knauer F., Stoffella A., Schröder W., Pääbo S. Conservation genetics of the European brown bear - a study using excremental PCR of nuclear and mitochondrial sequences. Mol. Ecol. 4:1995;95-103
30. Kohn M.H., York E.C., Kamradt D.A., Haught G., Sauvajot R.M., Wayne R.K. Estimating population size by genotyping faeces. Proc. Roy. Soc. Lond. B. 266:1999;657-663
31. Kuch M., Rohland N., Betancourt J.L., Latorre C., Steppan S., Poinar H.N. Molecular analysis of a 11,700-year-old rodent midden from the Atacama Desert, Chile. Mol. Ecol. 11:2002;913-924
32. Ledl F., Schleicher E. Die Maillard Reaktion in Lebensmitteln und im menschlichen Körper - neue Ergebnisse zur Chemie, Biochemie und Medizin. Angewandte Chem. 102:1992;597-626
33. Lucchini V., Fabbri E., Marucco F., Ricci S., Boitani L., Randi E. Noninvasive molecular tracking of colonizing wolf (Canis lupus) packs in the western Italian Alps. Mol. Ecol. 11:2002;857-868
34. Mills L.S., Pilgrim K.L., Schwartz M.K., McKelvey K. Identifying lynx and other North American felids based on mtDNA analysis. Cons. Gen. 1:2000;285-288
35. Morin P.A., Chambers K.E., Boesch C. and Vigilant, L. Quantitative polymerase chain reaction analysis of DNA from noninvasive samples for accurate microsatellite genotyping of wild chimpanzees (Pan troglodytes verus). Mol. Ecol. 10:2001;1835-1844
36. Morin P.A., Woodruff D.S. Paternity exclusion using multiple hypervariable microsatellite loci amplified from nuclear DNA of hair cells. Martin R.D., Dixson A.F., Wickings E.J. "Paternity in Primates: Genetic Tests and Theories" 1992;63-81 Karger, Basel
37. Mowat G., Paetkau D. Estimating marten Martes americana population size using hair capture and genetic tagging. Wildlife Biol. 8:2002;201-209
38. Mowat G., Strobeck C. Estimating population size of grizzly bears using hair capture, DNA profiling, and mark-recapture analysis. J. Wildlife Manag. 64:2000;183-193
39. Murakami T. Species identification of mustelids by comparing partial sequences on mitochondrial DNA from fecal samples. J. Vet. Med. Sci. 64:2002;321-323
40. Murphy M.A., Waits L.P., Kendall K.C., Wasser S.K., Higbee J.A., Bogden R. An evaluation of long-term preservation methods for brown bear (Ursus arctos) faecal DNA samples. Cons. Gen. 3:2002;435-440
41. Murphy M.A., Waits L.P., Kendall K.C. The influence of diet on faecal DNA amplification and sex identification in brown bears (Ursus arctos). Mol. Ecol. 12:2003;2261-2265
42. Parsons K. Reliable microsatellite genotyping of dolphin DNA from faeces. Mol. Ecol. 1:2001;341-344
43. Parsons K.M., Dallas J.F., Claridge D.E., Durban J.W., Balcomb K.C. III, Thompson P.M., Noble L.R. Amplifying dolphin mitochondrial DNA from faecal plumes. Mol. Ecol. 8:1999;1753-1768
44. Paxinos E., McIntosh C., Ralls K., Fleischer R. A noninvasive method for distinguishing among canid species: Amplification and enzyme restriction of DNA from dung. Mol. Ecol. 6:1997;483-486
45. Pearce J.M., Fields R.L., Scribner K.T. Nest materials as a source of genetic data for avian ecological studies. J. Field Ornith. 68:1997;471-481
46. Pires A.E., Fernandes M.L. Last lynxes in Portugal? Molecular approaches in a pre-extinction scenario. Cons. Gen. 4:2003;525-532
47. Poinar H.N., Hofreiter M., Spaulding W.G., Martin P.S., Stankiewicz B.A., Bland H., Evershed R.P., Possnert G., Pääbo S. Molecular coproscopy: Dung and diet of the extinct ground sloth Nothrotheriops shastensis. Science. 281:1998;402-406
48. Poinar H.N., Kuch M., Sobolik K., Barnes I., Stankiewicz B.A., Kuder T., Spaulding W.G., Bryant V.M., Cooper A., Pääbo S. A molecular analysis of dietary diversity for three archaic Native Americans. Proc. Natl. Acad. Sci. USA. 98:2001;4317-4322
49. Reed J.Z., Tollit D.J., Thompson P.M., Amos W. Molecular scatology: The use of molecular analysis to assign species, sex and individual identity to seal faeces. Mol. Ecol. 6:1997;225-234
50. Riddle A.E., Pilgrim K.L., Mills L.S., McKelvey K.S., Ruggiero L.F. Identification of mustelids using mitochondrial DNA and non-invasive sampling. Cons. Gen. 4:2003;241-243
51. Sambrook J., Fritsch E.F., Maniatis T. "Molecular Cloning: A Laboratory Manual." 1989;Cold Spring Harbor Laboratory Press, New York
52. Sloane M.A., Sunnucks P., Alpers D., Beheregaray L.B., Taylor A.C. Highly reliable genetic identification of individual northern hairy nosed wombats from single remotely collected hairs: A feasible censusing method. Mol. Ecol. 9:2000;1233-1240
53. Smith D.A., Ralls K., Hurt A., Adams B., Parker M., Davenport B., Smith M.C., Maldonado J.E. Detection and accuracy rates of dogs trained to find scats of San Joaquin kit foxes (Vulpes macrotis mutica). Anim. Cons. 6:2003;339-346
54. Taberlet P., Matlock H., Dubois-Paganon C., Bouvet J. Sexing free-ranging brown bears Ursus arctos using hairs found in the field. Mol. Ecol. 2:1993;399-403
55. Taberlet P., Griffin S., Goossens B., Questiau S., Manceau V., Escaravage N., Waits L.P., Bouvet J. Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Res. 24:1996;3189-3194
56. Taberlet P., Camarra J.-J., Griffin S., Uhrès E., Hanotte O., Waits L.P., Dubois-Paganon C., Burke T., Bouvet J. Noninvasive genetic tracking of the endangered Pyrenean brown bear population. Mol. Ecol. 6:1997;869-876
57. Taberlet P., Waits L.P., Luikart G. Noninvasive genetic sampling: Look before you leap. Trends Ecol. Evol. 14:1999;323-327
58. Telfer P.T., Souquière S., Clifford S.L., Abernethy K.A., Bruford M.W., Disotell T.R., Sterner K.N., Roques P., Marx P.A., Wickings E.J. Molecular evidence for deep phylogenetic divergence in Mandrillus sphinx. Mol. Ecol. 12:2003;2019-2024
59. Walsh P.S., Metzger D.A., Higuchi R. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. BioTechniques. 10:1991;506-513
60. Wasser S.K., Houston C.S., Koehler G.M., Cadd G.G., Fain S.R. Techniques for application of faecal DNA methods to field studies of Ursids. Mol. Ecol. 6:1997;1091-1097
61. Whittier C.A., Dhar A.K., Stem C., Goodall J., Alcivar-Warren A. Comparison of DNA extraction methods for PCR amplification of mitochondrial cytochrome c oxidase subunit II (COII) DNA from primate fecal samples. Biotechnol. Tech. 13:1999;771-779
62. Wilson G.J., Frantz A.C., Pope L.C., Roper T.J., Burke T.A., Cheeseman C.L., Delahay R.J. Estimation of badger abundance using faecal DNA typing. J. Applied Ecol. 40:2003;658-666
63. Woods J.G., Paetkau D., Lewis D., McLellan B.N., Proctor M., Strobeck C. Genetic tagging of free-ranging black and brown bears. Wildlife Soc. Bull. 27:1999;616-627