Extensive evaluation of faecal preservation and DNA extraction methods in Australian native and introduced species

Australian Journal of Zoology

Volumn 51, Issue 4, 2003, Pages 341-355

  Piggott, Maxine P ^a   Taylor, Andrea C ^a  

^a MONASH UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; EXTRACTION; FECES; GENETIC ANALYSIS; INTRODUCED SPECIES; MARSUPIAL; NATIVE SPECIES;

AUSTRALASIA; AUSTRALIA;

DASYURUS; MAMMALIA; METATHERIA; PENICILLATA; PETROGALE; PETROGALE PENICILLATA; THYLOGALE; THYLOGALE BILLARDIERII; VULPES; VULPES VULPES;

EID: 0345581714     PISSN: 0004959X     EISSN: None     Source Type: Journal    
DOI: 10.1071/ZO03012     Document Type: Article

References (41)

1. Banks, S. C., Piggott, M. P., Hansen, B. D., Robinson, N. A., and Taylor, A. C. (2002). Wombat coprogenetics: enumerating a common wombat population by analysis of faecal DNA. Australian Journal of Zoology 50, 193-204.
2. Bayes, M. K., Smith, K. L., Alberts, S. C., Altmann, J., and Bruford, M. W. (2000). Testing the reliability of microsatellite typing from faecal DNA in the savannah baboon. Conservation Genetics 1, 173-176.
3. Browning, T. L., Taggart, D. A., Rummery, C., Close, R. L., and Eldridge, M. D. B. (2001). Multifaceted genetic analysis of the "Critically Endangered" brush-tailed rock-wallaby Petrogale penicillata in Victoria, Australia: implications for management. Conservation Genetics 2, 145-156.
4. Constable, J. L., Ashley, M. V., Goodall, J., and Pusey, A. E. (2001). Noninvasive paternity assignment in Gombe chimpanzees. Molecular Ecology 10, 1279-1300.
5. Deuter, R., Pietsch, S., Hertel, S., and Müller, O. (1995). A method for preparation of fecal DNA suitable for PCR. Nucleic Acids Research 23, 3800-3801.
6. Ernest, H. B., Penedo, M. C. T., May, B. P., Syvanen, M., and Boyce, W. M. (2000). Molecular tracking of mountain lions in the Yosemite Valley region in California: genetic analysis using microsatellites and faecal DNA. Molecular Ecology 9, 433-441.
7. Farrell, L. E., Roman, J., and Sunquist, M. E. (2000). Dietary separation of sympatric carnivores identified by molecular analysis of scats. Molecular Ecology 9, 1583-1590.
8. Fernando, P., Pfrender, M. E., Encalada, S. E., and Lande, R. (2000). Mitochondrial DNA variation, phylogeography and population structure of the Asian elephant. Heredity 84, 362-372.
9. Firestone, K. (1999). Isolation and characterisation of microsatellites from carnivorous marsupials (Dasyuridae: Marsupialia). Molecular Ecology 8, 1084-1086.
10. Firestone, K., Houlden, B. A., Sherwin, W. B., and Geffen, E. (2000). Variability and differentiation of microsatellites in the genus Dasyurus and conservation implications for the large Australian carnivorous marsupials. Conservation Genetics 1, 115-133.
11. Flagstad, Ø., Røed, K., Stacy, J. E., and Jakobsen, K. S. (1999). Reliable noninvasive genotyping based on excremental PCR of nuclear DNA purified with a magnetic bead protocol. Molecular Ecology 8, 879-883.
12. Frantzen, M. A. J., Silk, J. B., Ferguson, J. W. H., Wayne, R. K., and Kohn, M. H. (1998). Empirical evaluation of preservation methods for faecal DNA. Molecular Ecology 7, 1423-1428.
13. Garnier, J. N., Bruford, M. W., and Goossens, B. (2001). Mating system and reproductive skew in the black rhinocerous. Molecular Ecology 10, 2031-2041.
14. Gerloff, U., Hartung, B., Fruth, B., Hohmann, G., and Tautz, D. (1999). Intracommunity relationships, dispersal pattern and paternity success in a wild living community of bonobos (Pan paniscus) determined from DNA analysis of faecal samples. Proceedings of the Royal Society of London, Series B 266, 1189-1195.
15. Goossens, B., Chikhi, L., Utami, S. S., de Ruiter, J., and Bruford, M. W. (2000). A multi-samples, multi-extracts approach for microsatellite analysis of faecal samples in an aboreal ape. Conservation Genetics 1, 157-162.
16. Holmes, N. G., Mellersh, C. S., Humphreys, S. J., Binns, M. M., Holliman, A., Curtis, R., and Sampson, J. (1993). Isolation and characterisation of microsatellites from the canine genome. Animal Genetics 24, 289-292.
17. Hoss, M., Kohn, M., Pääbo, S., Knauer, F., and Schröder, W. (1992). Excrement analysis by PCR. Nature 359, 199.
18. Jensen-Seaman, M. I., and Kidd, K. K. (2001). Mitochondrial DNA variation and biogeography of eastern gorillas. Molecular Ecology 10, 2241-2247.
19. Kohn, M., Knauer, F., Stoffella, A., Schröder, W., and Pääbo, S. (1995). Conservation genetics of the European brown bear - a study using excremental PCR of nuclear and mitochondrial sequences. Molecular Ecology 4, 95-103.
20. Kohn, M. H., and Wayne, R. K. (1997). Facts from feces revisted. Trends in Evolution and Ecology 12, 223-227.
21. Kohn, M. H., York, E. C., Kamradt, D. A., Haught, G., Sauvajot, R. M., and Wayne, R. K. (1999). Estimating population size by genotyping faeces. Proceedings of the Royal Society of London, Series B 266, 657-663.
22. Lade, J. A., Murray, N. D., Marks, C. A., and Robinson, N. A. (1996). Microsatellite differentiation between Phillip Island and mainland Australian populations of the red fox Vulpes vulpes. Molecular Ecology 5, 81-87.
23. Lucchini, V., Fabri, E., Marucco, F., Dricci, S., Biotani, L., and Randi, E. (2002). Noninvasive molecular tracking of colonising wolf (Canis lupus) packs in the western Italian Alps. Molecular Ecology 11, 857-868.
24. Monteiro, L., Bonnemaison, D., Vekris, A., Petry, K. G., Bonnet, J., Vidal, R., Cabrita, J., and Mégraud, F. (1997). Complex polysaccharides as PCR inhibitors in feces: Helicobacter pylori model. Journal of Clinical Microbiology 35, 995-998.
25. Morin, P. A., Chambers, K. E., Boesch, C., and Vigilant, L. (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.
26. Murphy, M. A., Waits, L. P., Kendall, K. C., Wasser, S. K., Higbee, J. A., and Bogden, R. (2002). An evaluation of long-term preservation methods for brown bear (Ursus arctos) faecal samples. Conservation Genetics 3, 435-440.
27. Navidi, W., Arnheim, N., and Waterman, M. S. (1992). A multiple-tubes approach for accurate genotyping of very small DNA samples by using PCR: statistical considerations. American Journal of Human Genetics 50, 347-359.
28. Ostrander, E. A., Sprague, G. F., and Rine, J. (1993). Identification and characterisation of dinucleotide repeat (CA)n markers for genetic mapping in dog. Genomics 16, 207-213.
29. Piggott, M. P., and Taylor, A. C. (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.
30. Reed, J. Z., Tollit, D. J., Thompson, P. M., and Amos, W. (1997). Molecular scatology: the use of molecular genetic analysis to assign species, sex and individual identity to seal faeces. Molecular Ecology 6, 225-234.
31. Rudi, K., Kroken, M., and Dahlberg, O. J. (1997). Rapid universal method to isolate PCR-ready DNA using magnetic beads. Biotechniques 22, 506-511.
32. Smith, K. L., Alberts, S. C., Bayes, M. K., Bruford, M. W., Altmann, J., and Ober, C. (2000). Cross-species amplification, non-invasive genotyping, and non-Mendelian inheritance of human STRPs in savannah baboons. American Journal of Primatology 51, 219-227.
33. Spencer, P. B. S., Odorico, M. D., Jones, S. J., Marsh, H., and Miller, D. J. (1995). Highly variable microsatellites in isolated colonies of the rock-wallaby (Petrogale assimilis). Molecular Ecology 4, 523-525.
34. Sunnucks, P., and Hales, D. F. (1996). Numerous transposed sequences of mitochodrial cytochrome oxidase I-II in aphids of the genus Sitobion (Hemiptera: Aphididae). Molecular Biology and Evolution 13, 510-524.
35. Taberlet, P., Griffin, S., Goossens, B., Questiau, S., Manceau, V., Escaravage, N., Waits, L. P., and Bouvet, J. (1996). Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Research 24, 3189-3194.
36. Taberlet, P., Camarra, J.-J., Griffin, S., Uhrès, E., Hanotte, O., Waits, L. P., Dubois-Paganon, C., Burke, T., and Bouvet, J. (1997). Noninvasive genetic tracking of the endangered Pyrenean brown bear population. Molecular Ecology 6, 869-876.
37. Taberlet, P., Waits, L. P., and Luikart, G. (1999). Noninvasive genetic sampling: look before you leap. Trends in Ecology and Evolution 14, 323-327.
38. Taylor, A. C., and Cooper, D. W. (1998). A set of unlinked microsatellites from the Tammar wallaby Macropus eugenii. Molecular Ecology 7, 925-926.
39. Valière, N., Berthier, P., Mouchiroud, D., and Pontier, D. (2002). GEMINI: software for testing the effects of genotyping errors and multitubes approach for individual identification. Molecular Ecology Notes 2, 83-86.
40. Vigilant, L., Hofreiter, M., Siedel, M., and Boesch, C. (2001). Paternity and relatedness in wild chimpanzee communities. Proceedings of the National Academy of Sciences USA 98, 12890-12895.
41. Wasser, S. K., Houston, C. S., Koehler, G. M., Cadd, G. G., and Fain, S. R. (1997). Techniques for application of faecal DNA methods to field studies of ursids. Molecular Ecology 6, 1091-1097.