Field-based evaluation of scat DNA methods to estimate population abundance of the spotted-tailed quoll (Dasyurus maculatus), a rare Australian marsupial

Wildlife Research

Volumn 36, Issue 8, 2009, Pages 721-736

  Ruibal, Monica ^a   Peakall, Rod ^a   Claridge, Andrew ^b,c   Firestone, Karen ^d  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^b OFFICE OF ENVIRONMENT AND HERITAGE   (Australia)

^c UNIVERSITY OF NEW SOUTH WALES   (Australia)

^d UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ABUNDANCE; AGE STRUCTURE; CARNIVORE; DNA; ENDANGERED SPECIES; GENETIC MARKER; MARSUPIAL; POPULATION ESTIMATION; RARE SPECIES; SCENT MARKING; TRAPPING;

DASYURUS MACULATUS; MAMMALIA; METATHERIA;

EID: 73249150526     PISSN: 10353712     EISSN: None     Source Type: Journal    
DOI: 10.1071/WR09086     Document Type: Article

References (72)

1. Alexander, D. (1980). Diet of the tiger quoll (Dasyurus maculatus Kerr) in an area of New England National Park, northeastern New South Wales. Bachelor of Natural Resources Thesis, University of New England, Armidale.
2. Andrew, D. L. (2005). Ecology of the tiger quoll Dasyurus maculatus maculatus in coastal New South Wales. M.Sc. Thesis, University of Wollongong.
3. 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 microsatellite analysis of faecal DNA. Australian Journal of Zoology 50, 193-204. doi: 10.1071/ZO01072 (Pubitemid 34800996)
4. Banks, S. C., Hoyle, S. D., Horsup, A., Sunnucks, P., and Taylor, A. C. (2003). Demographic monitoring of an entire species (the northern hairy-nosed wombat, Lasiorhinus krefftii) by genetic analysis of non-invasively collected material. Animal Conservation 6, 101-107. doi: 10.1017/ S1367943003003135
5. Begg, C., Begg, K., Du Toit, J., and Mills, M. (2003). Scent-marking behaviour of the honey badger, Mellivora capensis (Mustelidae), in the southern Kalahari. Animal Behaviour 66, 917-929. doi: 10.1006/ anbe.2003.2223
6. Belcher, C. A. (1994). Studies on the diet of the tiger quoll. M.Sc. Thesis, La Trobe University, Melbourne.
7. Belcher, C. A. (2000). Ecology of the tiger quoll Dasyurus maculatus in southeast Australia. Ph.D. Thesis, Deakin University, Melbourne.
8. Belcher, C. A., and Darrant, J. P. (2004). Home range and spatial organisation of the marsupial carnivore, Dasyurus maculatus maculatus (Marsupialia: Dasyuridae) in south-eastern Australia. Journal of Zoology 262, 271-280. doi: 10.1017/S0952836903004631 (Pubitemid 38319245)
9. Boulanger, J., and McLellan, B. (2001). Closure violation in DNA-based mark-recapture estimation of grizzly bear populations. Canadian Journal of Zoology 79, 642-651. doi: 10.1139/cjz-79-4-642 (Pubitemid 32752570)
10. Broquet, T., and Petit, E. (2004). Quantifying genotyping errors in noninvasive population genetics. Molecular Ecology 13, 3601-3608. doi: 10.1111/j.1365-294X.2004.02352.x (Pubitemid 39415689)
11. Bruford, M. W., Hanotte, O., Brookfield, J. F. Y., and Burke, T. (Eds) (1992). 'Single-locus and Multilocus DNA Fingerprinting.' (Oxford University Press: Oxford.)
12. Burnett, S. (2001). Ecology and conservation status of the northern spottailed quoll, Dasyurus maculatus, with reference to the future of Australia's marsupial carnivores. Ph.D. Thesis, James Cook University, Townsville.
13. Burnham, K. P., and Anderson, D. R. (Eds) (1998). 'Model Selection and Multi-model Inference: A Practical Information-Theoretic Approach.' 2nd edn. (Springer-Verlag: New York.)
14. Claridge, A. W., and Mills, D. J. (2007). Aerial baiting for wild dogs has no observable impact on spotted-tailed quolls (Dasyurus maculatus) in a rainshadow woodland. Wildlife Research 34, 116-124. doi: 10.1071/ WR06151
15. Claridge, A. W., Mifsud, G., Dawson, J., and Saxon, M. J. (2004). Use of infra-red digital cameras to investigate the behaviour of cryptic species. Wildlife Research 31, 645-650. doi: 10.1071/WR03072 (Pubitemid 40252849)
16. Claridge, A. W., Paull, D., Dawson, J., Mifsud, G., Murray, A. J., Poore, R., and Saxon, M. J. (2005). Home range attributes of the spotted-tailed quoll (Dasyurus maculatus) a marsupial carnivore, in a rainshadow woodland. Wildlife Research 32, 7-14. doi: 10.1071/WR04031 (Pubitemid 40534697)
17. Creel, S., Spong, G., Sands, J. L., Rotella, J., Zeigle, J., Joe, L., Murphy, K. M., and Smith, D. (2003). Population size estimation in Yellowstone wolves with error-prone noninvasive microsatellite genotypes. Molecular Ecology 12, 2003-2009. doi: 10.1046/j.1365-294X.2003.01868.x (Pubitemid 36815033)
18. Dallas, J. F., Coxon, K. E., Sykes, T., Chanin, P. R. F., Marshall, F., Carss, D. N., Bacon, P. J., Piertney, S. B., and Racey, P. A. (2003). Similar estimates of population genetic composition and sex ratio derived from carcasses and faeces of Eurasian otter Lutra lutra. Molecular Ecology 12, 275-282. doi: 10.1046/j.1365- 294X.2003.01712.x
19. Dawson, J. (2005). Impact of wildfire on the spotted-tailed quoll Dasyurus maculatus in Kosciuszko National Park. M.Sc. Thesis, University of New South Wales, Sydney.
20. Dawson, J., Claridge, A., Mifsud, G., Murray, A., and Poore, R. (2002). Distribution and ecology of the spotted-tailed quoll Dasyurus maculatus in the Kosciuszko region. In 'Proceedings of Celebrating Mountains: An International Year of Mountains Conference'. (Ed. J. Mackay.) pp. 429-437.
21. DEH (2004). 'Listed advice - Dasyurus maculatus maculatus (spot-tailed quoll, spotted-tailed quoll, tiger quoll). Advice to the Minister for the Environment and Heritage from the Threatened Species Scientific Committee on amendments to the list of threatened species under the Environment Protection and Biodiversity Conservation Act 1999.' (Commonwealth Government: Canberra.)
22. Deuter, R., Pietsch, S., Hertel, S., and Muller, O. (1995). A method for preparation of fecal DNA suitable for PCR. Nucleic Acids Research 23, 3800-3801. doi: 10.1093/nar/23.18.3800
23. Dewoody, J., Nason, J. D., and Hipkins, V. D. (2006). Mitigating scoring errors in microsatellite data from wild populations. Molecular Ecology Notes 6, 951-957. doi: 10.1111/j.1471-8286.2006.01449.x (Pubitemid 44807913)
24. Edgar, R., and Belcher, C. (1995). Spotted-tailed quoll Dasyurus maculatus (Kerr, 1792). In 'The Mammals of Australia'. (Ed. R. Strahan.) pp. 67-68. (Reed New Holland: Sydney.)
25. Eggert, L. S., Eggert, J. A., and Woodruff,D. S. (2003). Estimating population sizes for elusive animals: The forest elephants of Kakum National Park, Ghana. Molecular Ecology 12, 1389-1402. doi: 10.1046/j.1365- 294X.2003.01822.x
26. Firestone, K. B. (1999). Isolation and characterization of microsatellites from carnivorous marsupials (Dasyuridae: Marsupialia). Molecular Ecology 8, 1084-1086. doi: 10.1046/j.1365-294X.1999.00655-6.x
27. Frantz, A. C., Pope, L. C., Carpenter, P. J., Roper, T. J., Wilson, G. J., Delahay, R. J., and Burke, T. (2003). Reliablemicrosatellite genotyping of the Eurasian badger (Meles meles) using faecal DNA. Molecular Ecology 12, 1649-1661. doi: 10.1046/j.1365-294X.2003.01848.x (Pubitemid 36708469)
28. Glen, A. S., and Dickman, C. R. (2006). Home range, denning behaviour and microhabitat use of the carnivorous marsupial Dasyurus maculatus in eastern Australia. Journal of Zoology 268, 347-354. doi: 10.1111/j.1469- 7998.2006.00064.x
29. Godsell, J. (1983). Ecology of the eastern quoll Dasyurus viverrinus (Dasyuridae: Marsupialia). Ph.D. Thesis, The Australian National University, Canberra.
30. Henegariu, O., Heerema, N. A., Dlouhy, S. R., Vance, G. H., and Vogt, P. H. (1997). Multiplex PCR: Critical parameters and step-by-step protocol. BioTechniques 23, 504-511.
31. Jones, M., and Rose, R. K. (1996). Preliminary assessment of distribution and habitat associations of the spotted-tailed quoll (Dasyurus maculatus) and eastern quoll (D. viverrinus) in Tasmania to determine conservation and reservation status. Report to the Tasmanian RFA Environment and Heritage Technical Committee. Nature Conservation Branch, Parks and Wildlife Service, Hobart.
32. 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. Biological Sciences 266, 657-663. doi: 10.1098/rspb.1999.0686
33. Körtner, G., Gresser, S., Mott, B., Tamayo, B., Pisanu, P., Bayne, P., and Harden, R. (2004). Population structure, turnover and movement of spotted-tailed quolls on the New England Tablelands. Wildlife Research 31, 475-484. doi: 10.1071/WR03041 (Pubitemid 40117912)
34. Kruuk, H., and Jarman, P. J. (1995). Latrine use by the spotted-tailed quoll (Dasyurus maculatus: Dasyuridae, Marsupialia) in its natural habitat. Journal of Zoology 236, 345-349. doi: 10.1111/j.1469-7998.1995. tb04501.x
35. Lee, A. K., Woolley, P., and Braithwaite, R. W. (1982). Life history strategies of dasyurid marsupials. In 'Carnivorous Marsupials'. (Ed. M. Archer.) pp. 1-396. (Royal Zoological Society of New South Wales: Sydney.)
36. Lindenmayer, D. B., and Franklin, J. F. (2002). 'Conserving Forest Biodiversity: A Comprehensive Multiscaled Approach.' (Island Press: Washington, DC.)
37. Long, K., and Nelson, J. (2008). Draft national recovery plan for Dasyurus maculatus (spotted-tailed quoll) 2005-2009. Department of Environment and Heritage, Canberra.
38. Lukacs, P. M. (2005). Statistical aspects of using genetic markers for individual identification in capture-recapture studies. Ph.D. Thesis, Colorado State University, Fort Collins, CO.
39. Lukacs, P. M., and Burnham, K. P. (2005). Estimating population size from DNA-basedclosed capture-recapture data incorporating genotyping error. The Journal of Wildlife Management 69, 396-403. doi: 10.2193/0022- 541X(2005)0692.0.CO;2
40. McCullagh, P., and Nelder, J. A. (1989). 'Generalized Linear Models.' 2nd edn. (Chapman and Hall: London.)
41. McKelvey, K. S., and Schwartz, M. K. (2005). Dropout: A program to identify problem loci and samples for noninvasive genetic samples in a capturemark- recapture framework. Molecular Ecology Notes 5, 716-718. doi: 10.1111/j.1471-8286.2005.01038.x (Pubitemid 41716894)
42. Miller, C. R., Joyce, P., and Waits, L. P. (2005).Anew method for estimating the size of small populations from genetic mark-recapture data. Molecular Ecology 14, 1991-2005. doi: 10.1111/j.1365-294X.2005.02577.x (Pubitemid 40772418)
43. Molina, R., and Marcot, B. C. (2007). Definitions and attributes of littleknown species. In 'Conservation of Rare or Little-known Species'. (Eds M. G. Raphael and R. Molina.) pp. 67-92. (Island Press: Washington, DC.)
44. 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 HumanGenetics 50, 347-359.
45. Oakwood, M. (2002). Spatial and social organisation of a carnivorous marsupial Dasyurus hallucatus (Marsupialia: Dasyuridae). Journal of Zoology 257, 237-248.
46. Otis, D. L., Burnham, K. P., White, G. C., and Anderson, D. R. (1978). Statistical inference from capture data on closed animal populations. Wildlife Monographs 62, 1-135.
47. Peakall, R., and Smouse, P. E. (2006).GENALEX6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6, 288-295. doi: 10.1111/j.1471-8286.2005.01155.x (Pubitemid 43373825)
48. Peakall, R., Ebert, D., Cunningham, R., and Lindenmayer, D. (2006). Markrecapture by genetic tagging reveals restricted movements by bush rats (Rattus fuscipes) in a fragmented landscape. Journal of Zoology 268, 207-216. doi: 10.1111/j.1469-7998.2005.00011.x
49. Petit, E., and Valiere, N. (2006). Estimating population size with noninvasive capture-mark-recapture data. Conservation Biology 20, 1062-1073. doi: 10.1111/j.1523-1739.2006.00417.x (Pubitemid 44116741)
50. 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. doi: 10.1071/WR02077 (Pubitemid 36579787)
51. Piggott, M. P., Bellemain, E., Taberlet, P., and Taylor, A. C. (2004). A multiplex pre-amplification method that significantly improves microsatellite amplification and error rates for faecal DNA in limiting conditions. Conservation Genetics 5, 417-420. doi: 10.1023/B: COGE.0000031138.67958.44
52. Piggott, M. P., Banks, S. C., Stone, N., Banffy, C., and Taylor, A. C. (2006). Estimating population size of endangered brush-tailed rock-wallaby (Petrogale penicillata) colonies using faecal DNA. Molecular Ecology 15, 81-91. doi: 10.1111/j.1365-294X.2005.02783.x
53. Pollock, K. H., Nichols, J. D., Brownie, C., and Hines, J. E. (1990). Statistical inference for capture-recapture experiments. Wildlife Monographs 107, 1-97.
54. Ruell, E. W., Riley, S. P. D., Douglas,M.R., Pollinger, J. P., and Crooks, K. R. (2009). Estimating bobcat population sizes and densities in a fragmented urban landscape using non-invasive capture-recapture sampling. Journal of Mammalogy 90, 129-135. doi: 10.1644/07-MAMM-A-249.1
55. Ruibal, M. P. (2008). A field implementation and evaluation of non-invasive DNA methods for the spotted-tailed quoll (Dasyurus maculatus). Ph.D. Thesis, The Australian National University, Canberra.
56. Ryon, J., and Brown, R. E. (1990). Urine marking in female wolves: An indicator of dominance status and reproductive state. In 'Chemical Signals in Vertebrates'. 5th edn. (Eds D. W. Macdonald, D. Muller-Schwarze and S. E. Natynczuk.) pp. 346-351. (Oxford University Press: Oxford.)
57. SEFSTQWG (2003). Quolltrack 1: how to spot a spotted-tailed quoll. Pamphlet distributed by South East Forest Spotted-Tailed Quoll Working Group.
58. Smith, D. A., Ralls, K., Hurt, A., Adams, B., Parker, M., and Maldonado, J. E. (2006). Assessing reliability of microsatellite genotypes from kit fox faecal samples using genetic and GIS analyses. Molecular Ecology 15, 387-406. doi: 10.1111/j.1365-294X.2005.02841.x
59. Soderquist, T. R., and Serena, M. (2000). Juvenile behaviour and dispersal of chuditch (Dasyurus geoffroii) (Marsupialia: Dasyuridae). Australian Journal of Zoology 48, 551-560. doi: 10.1071/ZO00029 (Pubitemid 32015422)
60. Solberg, K. H., Bellemain, E., Drageset, O.-M., Taberlet, P., and Swenson, J. E. (2006). An evaluation of field and non-invasive genetic methods to estimate brown bear (Ursus arctos) population size. Biological Conservation 128, 158-168. doi: 10.1016/j.biocon.2005.09.025 (Pubitemid 41831422)
61. Spencer, P., Cardoso, M., How, R. A., Williams, J., Bunce, M., and Schmitt, L. H. (2007). Cross-species amplification at microsatellite loci in Australian quolls including the description of five new markers from the chuditch (Dasyurus geoffroii). Molecular Ecology Notes 7, 1100-1103. doi: 10.1111/j.1471-8286.2007.01791.x (Pubitemid 350059198)
62. Stoddart, D. M. (1976). 'Mammalian Odours and Pheromones.' (Edward Arnold Ltd: London.)
63. Taberlet, P., and Luikart, G. (1999). Non-invasive genetic sampling and individual identification. Biological Journal of the Linnean Society. Linnean Society of London 68, 41-55. doi: 10.1111/j.1095-8312.1999. tb01157.x
64. 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. doi: 10.1093/nar/24.16.3189
65. Triggs, B. (2004). 'Tracks, Scats and Other Traces: A Field Guide to Australian Mammals.' Revised edn. (Oxford University Press: Melbourne.)
66. Valiere, N. (2002). GIMLET: A computer program for analysing genetic individual identification data. Molecular Ecology Notes 2, 377-379. doi: 10.1046/j.1471-8286.2002.00228.x
67. Waits, L. P. (2001). Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Molecular Ecology 10, 249-256. doi: 10.1046/j.1365-294X.2001.01185.x (Pubitemid 32097545)
68. Waits, L. P. (2004). Using noninvasive genetic sampling to detect and estimate abundance of rare wildlife species. In 'Sampling Rare or Elusive Species'. (Ed. W. L. Thompson.) pp. 211-228. (Island Press: Washington, DC.)
69. Waits, L. P., and Leberg, P. (2000). Biases associated with population estimation using molecular tagging. Animal Conservation 3, 191-199. doi: 10.1111/j.1469-1795.2000.tb00103.x
70. Watt, A. (1993). Conservation status and draft management plan for Dasyurus maculatus and D. hallucatus in southern Queensland. Final report to the Queensland Department of Environment and Heritage and The Department of the Environment, Sport and Territories, Brisbane.
71. White, G. C., and Burnham, K. P. (1999). Program MARK: Survival estimation from populations of marked animals. Bird Study 46(Suppl.), 120-138.
72. Wilson, G. J., Frantz, A. C., Pope, L. C., Roper, T. J., Burke, T. A., Cheeseman, C. L., and Delahay, R. J. (2003). Estimation of badger abundance using faecal DNA typing. Journal of Applied Ecology 40, 658-666. doi: 10.1046/j.1365-2664.2003.00835.x (Pubitemid 36914533)