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RESEARCH ARTICLE
Contents Vol 36(8)

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

Monica Ruibal A E , Rod Peakall A , Andrew Claridge B C and Karen Firestone D
+ Author Affiliations
- Author Affiliations

A Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia.

B Department of Environment and Climate Change, Parks and Wildlife Group, Planning and Performance Unit, Southern Branch, Queanbeyan, NSW 2620, Australia.

C School of Physical, Environmental and Mathematical Sciences, University of New South Wales, Australian Defence Force Academy, Northcott Drive, Canberra, ACT 2620, Australia.

D School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia.

E Corresponding author. Email: monica.ruibal@anu.edu.au

Wildlife Research 36(8) 721-736 https://doi.org/10.1071/WR09086
Submitted: 29 June 2009  Accepted: 14 November 2009   Published: 16 December 2009

Abstract

Context. DNA extracted non-invasively from remotely collected scat samples has been used successfully to enumerate populations of a few endangered mammal species. However, scat DNA surveys relying on scent-marking behaviours need to identify if age- or sex-specific variations or seasonal changes in scat scent-marking patterns affect population estimates. Furthermore, owing to the low quantity and quality of scat DNA, a thorough assessment of the technique is needed when it is applied to different species to ensure that individual identification is reliable.

Aims. In the current study, microsatellite genetic profiles derived from 208 remotely collected scats of the spotted-tailed quoll (Dasyurus maculatus), a rare Australian marsupial carnivore, were compared with DNA profiles from tissue of 22 live-trapped individuals from the same study area to critically assess the reliability of the non-invasive method to estimate population abundance.

Methods. Scat samples were collected at scent-marking sites over 4 consecutive months (April–July 2005), 7 weeks of which overlapped with the trapping program to allow direct comparisons of population estimates.

Key results. Combining a multiple-tubes approach with error checking analyses provided reliable genetic tags and resulted in the detection of the majority of the live-trapped population (18 of 22 individuals). Ten additional individuals not known from trapping were also observed from scat DNA. A longer-term sampling regime was required for scats than for trapping to allow direct detection of a large proportion of the population and to provide a comparable population estimate. Critically, the 4-month scat collection period highlighted the importance of performing scat surveys during the mating season when scat scent marking is more frequent, and to avoid sex and age biases in scat marking patterns.

Implications. Non-invasive scat DNA sampling methods that rely on scent-marking behaviours need to consider the duration of the sampling period and temporal differences in behaviours by the sexes and age groups to ensure that meaningful population estimates are achieved.


Acknowledgements

We thank Debbie Claridge, Doug Mills, Fred Ford, Ross Meggs and Pam O’Brien for their assistance in the trapping program, and Alex Martin and Chris Howard and two anonymous reviewers for improving earlier drafts of the manuscript. Funding for this project was provided to M. Ruibal from The Australian National University, Sophie Danforth Conservation Biology Fund, The Australian Academy of Science, M.A Ingram Trust, Estate of the Late Winifred Violet Scott, Wildlife Protection Society of Australia and NSW National Parks and Wildlife Service; K. Firestone and W. Sherwin received an ARC grant linkage grant LP0454947. The primary author was supported by an APA PhD scholarship. All fieldwork and tissue collections were conducted under ethics approvals from the Animal Experimentation Ethics Committee, The Australian National University, F.BTZ.75.04 & F.BTZ.78.04, and under the auspices of a NSW National Parks and Wildlife Service Section 120 Scientific Investigation Licence (S11472).


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Appendix 1.  Primer details for re-designed microsatellite loci for amplifying non-invasive DNA from spotted-tailed quolls
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Appendix 2.  Locus fluorescent labels and PCR multiplex groupings used to genotype tissue and scat DNA
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Appendix 3.  PCR conditions and final concentrations used for tissue and scat DNA
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Appendix 4.  The sequential PCR approach applied to score the microsatellite molecular profiles from scat DNA
This approach was based on the comparative procedure of Frantz et al. (2003)
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