Wildlife Research Wildlife Research Society
Ecology, management and conservation in natural and modified habitats

Evaluating exotic predator control programs using non-invasive genetic tagging

Maxine P. Piggott A E , Rebecca Wilson B , Sam C. Banks C , Clive A. Marks D , Frank Gigliotti B and Andrea C. Taylor A

A Australian Centre for Biodiversity, School of Biological Sciences, Monash University, Clayton,Victoria 3800, Australia.

B Vertebrate Pest Research Unit, Department of Primary Industries (Victoria), PO Box 49, Frankston, Victoria 3199, Australia.

C The Fenner School of Environment and Society, The Australian National University, Canberra, ACT 0200, Australia.

D Nocturnal Wildlife Research Pty Ltd, PO Box 2126, Wattletree Road Post Office, East Malvern, Victoria 3145, Australia.

E Corresponding author. Email: mpiggott@bio.mq.edu.au

Wildlife Research 35(7) 617-624 http://dx.doi.org/10.1071/WR08040
Submitted: 13 March 2008  Accepted: 17 June 2008   Published: 17 November 2008


Carnivorous predators are difficult to detect using conventional survey methods, especially at low levels of abundance. The introduced red fox (Vulpes vulpes) in Australia is monitored to determine the effectiveness of control programs, but assessing population parameters such as abundance and recruitment is difficult. We carried out a feasibility study to determine the effectiveness of using faecal DNA analysis methods to identify individual foxes and to assess abundance before and after lethal control. Fox faeces were collected in two sampling periods over four separate transects, and genotyped at five microsatellite loci. Two transects were subject to lethal control between collection periods. DNA was extracted from 170 fox faeces and, in total, 54 unique genotypes were identified. Fifteen biopsy genotypes from 30 foxes killed during lethal control were detected among the faecal genotypes. Overall, a similar number of genotypes were detected in both sampling periods. The number of individuals sampled in both periods was low (n = 6) and new individuals (n = 24) were detected in the second collection period. We were also able to detect animals that avoided lethal control, and movement of individuals between transects. The ability to identify individual foxes using these DNA techniques highlighted the shortcomings of the sample design, in particular the spatial scale and distances between transects. This study shows that non-invasive DNA sampling can provide valuable insight into pre and post fox abundance in relation to lethal control, individual behaviour and movement, as well as sample design. The information gained from this study will contribute to the design of future studies and, ultimately, control strategies.


Adams J. R. Waits L. P. 2007 An efficient method for screening faecal DNA genotypes and detecting new individuals and hybrids in the red wolf (Canis rufus) experimental population area. Conservation Genetics 8 123 131 doi:10.1007/s10592-006-9154-5

Adams J. R. Lucash C. Schutte L. Waits L. P. 2007 Locating hybrid individuals in the red wolf (Canis rufus) experimental population area using a spatially targeted sampling strategy and faecal DNA genotyping. Molecular Ecology 16 1823 1834 doi:10.1111/j.1365-294X.2007.03270.x

Baker P. J. Funk S. M. Bruford M. W. Harris S. 2004 Polygynandry in a red fox population: implications for the evolution of group living in canids? Behavioral Ecology 15 766 778 doi:10.1093/beheco/arh077

Banks S. C. Horsup A. Wilton A. N. Taylor A. C. 2003 a Genetic marker investigation of the source and impact of predation on a highly endangered species. Molecular Ecology 12 1663 1667 doi:10.1046/j.1365-294X.2003.01823.x

Banks S. C. Hoyle S. D. Horsup A. Sunnucks P. Taylor A. C. 2003 b Demographic monitoring of an entire species by genetic analysis of non-invasively collected material. Animal Conservation 6 101 107 doi:10.1017/S1367943003003135

Berry O. Sarre S. D. Farrington L. Aitken N. 2007 Faecal DNA detection of invasive species: the case of feral foxes in Tasmania. Wildlife Research 34 1 7 doi:10.1071/WR06082

Buckland S. T. , Anderson D. R. , Burnham K. P. , and Laake J. L. (1993). ‘Distance sampling: estimating abundance of biological populations’. (Chapman and Hall: London).

Busana F. Gigliotti F. Marks C. A. 1998 Modified M-44 ejector for the baiting of red foxes. Wildlife Research 25 209 215 doi:10.1071/WR96096

Coman B. J. Robinson J. Beaumont C. 1991 Home range, dispersal and density of red foxes (Vulpes vulpes L.) in Central Victoria. Wildlife Research 18 215 223 doi:10.1071/WR9910215

Dann P. 1992 Distribution, population trends and factors influencing the population size of little penguins (Eudyptula minor) on Phillip Island, Victoria. Emu 91 263 272

Dexter N. Meek P. 1998 An analysis of bait-take and non-target impacts during a fox-control exercise. Wildlife Research 25 147 155

Dickman C. R. 1996 Impact of exotic generalist predators on the native fauna of Australia. Wildlife Biology 2 185 195

Ernest H. B. Penedo M. C. D. May B. P. Syvanen M. 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

Flagstad Ø. Hedmark E. Landa A. Broseth H. Persson J. Andersen R. Segerstrom P. Ellegren H. 2004 Colonization history and noninvasive monitoring of a re-established wolverine population. Conservation Biology 18 676 688 doi:10.1111/j.1523-1739.2004.00034.x

Francisco L. V. Langston A. A. Mellersh C. S. Neal C. L. Ostrander E. A. 1996 A class of highly polymorphic tetranucleotide repeats for canine genetic mapping. Mammalian Genome 7 359 362 doi:10.1007/s003359900104

Gompper M. E. Kays R. W. Ray J. C. Lapoint S. D. Bogan D. A. Cryan J. R. 2006 A comparison of noninvasive techniques to survey carnivore communities in northeastern North America. Wildlife Society Bulletin 34 1142 1151 doi:10.2193/0091-7648(2006)34[1142:ACONTT]2.0.CO;2

Goossens B. Chikhi L. Utami S. S. de Ruiter J. Bruford M. W. 2000 A multi-samples, multi-extracts approach for microsatellite analysis of faecal samples in an arboreal ape. Conservation Genetics 1 157 162 doi:10.1023/A:1026535006318

Holmes N. G. Dickens H. F. Parker H. L. Binns M. M. Mellersh C. S. Sampson J. 1995 Eighteen canine microsatellites. Animal Genetics 24 132 133

Kohn M. H. York E. C. Kamradt D. A. Haught G. Sauvajot R. M. Wayne R. K. 1999 Estimating population size by genotyping faeces. Proceedings of the Royal Society of London. Series B. Biological Sciences 266 657 663

Lade J. A. Murray N. D. Marks C. A. Robinson N. A. 1996 Microsatellite differentiation between Phillip Island and mainland Australian populations of the red fox Vulpes vulpes. Molecular Ecology 5 81 87 doi:10.1111/j.1365-294X.1996.tb00293.x

Lucchini V. Fabbri E. Marucco F. Ricci S. Biotani L. Randi E. 2002 Noninvasive molecular tracking of colonising wolf (Canis lupus) packs in the western Italian Alps. Molecular Ecology 11 857 868 doi:10.1046/j.1365-294X.2002.01489.x

Macdonald D. W. 1980 Patterns of scent marking with urine and faeces amongst carnivore communities. Symposium of the Zoological Society, London 45 107 139

Mahon P. S. Banks P. B. Dickman C. R. 1998 Population indices for wild carnivores: a critical study in sand-dune habitat, south-western Queensland. Wildlife Research 25 11 22 doi:10.1071/WR97007

Marks C. A. , and Gigliotti F. (1996). ‘Cyanide baiting manual: practices and guidelines for the destruction of red foxes (Vulpes vulpes).’ (Ropet Printing: Tynong North, Victoria).

Marks C. A. Gigliotti F. Busana F. 2003 Field performance of the M-44 ejector for red fox (Vulpes vulpes) control. Wildlife Research 30 601 609 doi:10.1071/WR01032

May S. A. Norton T. W. 1996 Influence of fragmentation and disturbance on the potential impact of feral predators on native fauna in Australian forest ecosystems. Wildlife Research 23 387 400 doi:10.1071/WR9960387

Morrison S. A. Macdonald N. Walker K. Lozier L. Shaw M. R. 2007 Facing the dilemma at eradication’s end: uncertainty of absence and the Lazarus effect. Frontiers in Ecology and the Environment 5 271 276 doi:10.1890/1540-9295(2007)5[271:FTDAEE]2.0.CO;2

Norman F. I. 1971 Predation by the fox (Vulpes vulpes L.) on colonies of the Short-tailed Shearwater (Puffinus tenuirostris (Temminck)) in Victoria, Australia. Journal of Applied Ecology 8 21 32 doi:10.2307/2402124

Ostrander E. A. Mapa F. Yee M. Rine J. 1995 One hundred new simple sequence repeat-based markers for the canine genome. Mammalian Genome 6 192 195 doi:10.1007/BF00293011

Peakall R. Lindenmayer D. 2006 Genetic insights into population recovery following experimental perturbation in a fragmented landscape. Biological Conservation 132 520 532 doi:10.1016/j.biocon.2006.05.013

Peakall R. Smouse P. E. 2006 GenAlEx 6: 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

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 doi:10.1071/WR03096

Piggott M. P. Taylor A. C. 2003 Extensive evaluation of faecal preservation and DNA extraction methods in Australian native and introduced species. Australian Journal of Zoology 51 341 355 doi:10.1071/ZO03012

Piggott M. P. Banks S. C. Stone N. Banffy C. S. Taylor A. C. 2006 a 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

Piggott M. P. Banks S. C. Taylor A. C. 2006 b Genetic analysis of the population structure of Petrogale penicillata colonies in Wollemi National Park using faecal DNA, and implications for management. Molecular Ecology 15 93 105 doi:10.1111/j.1365-294X.2005.02784.x

Rolls E. C. (1969) ‘They All Ran Wild: The Story of Pests on the Land in Australia.’ (Angus and Robertson: Sydney).

Saunders G. , and McLeod L. (2007). ‘Improving Fox Management Strategies in Australia’. (Bureau of Rural Sciences: Canberra).

Sharp A. Norton M. Marks A. Holmes K. 2001 An evaluation of two indices of red fox (Vulpes vulpes) abundance in an arid environment. Wildlife Research 28 419 424 doi:10.1071/WR00075

Smith D. A. Ralls K. Hurt A. Adams B. Parker M. 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

Sunnucks P. Hales D. F. 1996 Numerous transposed sequences of mitochondrial cytochrome oxidase I–II in aphids of the genus Sitobion (Hemiptera: Aphididae). Molecular Biology and Evolution 13 510 524

Thompson J. A. Fleming P. J. S. 1994 Evaluation of the efficacy of 1080 poisoning of red foxes using visitations to non-toxic baits as an index of fox abundance. Wildlife Research 21 27 39

Valière N. Berthier P. Mouchiroud D. Pontier D. 2002 GEMINI: software for testing the effects of genotyping errors and multitubes approach for individual identification. Molecular Ecology Notes 2 83 86

Waits L. P. Luikart G. Taberlet P. 2001 Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Molecular Ecology 10 249 256

Wandeler P. Funk S. M. 2006 Short microsatellite DNA markers for the red fox (Vulpes vulpes). Molecular Ecology Notes 6 98 100 doi:10.1111/j.1471-8286.2005.01152.x

Wandeler P. Funk S. M. Largiadér C. R. Gloor S. Breitenmoser U. 2003 The city-fox phenomenon: genetic consequences of a recent colonization of urban habitat. Molecular Ecology 12 647 656 doi:10.1046/j.1365-294X.2003.01768.x

White G. C. Burnham K. P. 1999 Program MARK: Survival estimation from populations of marked animals. Bird Study 46 Suppl. 120 138

White J. G. Gubiani R. Smallman N. Snell K. Morton A. 2006 Home range, habitat selection and diet of foxes (Vulpes vulpes) in a semi-urban riparian environment. Wildlife Research 33 175 180

Witmer G. W. 2005 Wildlife population monitoring: some practical considerations. Wildlife Research 32 259 263 doi:10.1071/WR04003

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