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RESEARCH ARTICLE
Contents Vol 57(2)

Faecal DNA analysis enables genetic monitoring of the species recovery program for an arid-dwelling marsupial

Steve Smith A C D , Peter McRae B and Jane Hughes A
+ Author Affiliations
- Author Affiliations

A Griffith School of Environment, Griffith University, 170 Kessels Road, Nathan, Qld 4111, Australia.

B Queensland Parks and Wildlife Service, PO Box 149, Charleville, Qld 4470, Australia.

C Present address: Research Institute for Wildlife Ecology, Savoyenstraße 1, A-1160 Vienna, Austria.

D Corresponding author. Email: steve.smith@fiwi.at

Australian Journal of Zoology 57(2) 139-148 https://doi.org/10.1071/ZO09035
Submitted: 3 April 2009  Accepted: 6 July 2009   Published: 13 August 2009

Abstract

The greater bilby, Macrotis lagotis, is a species of conservation significance in the arid and semiarid zones of Australia. A species recovery program has been underway since the mid-1990s but the incorporation of molecular genetic data within the program has been difficult due to the problems of obtaining regular, population-wide samples of this trap-shy and sparsely distributed species. In this study, we demonstrate that faecal pellets collected from around burrows in the dry, arid habitat of western Queensland provide a viable source for DNA extraction and analysis. Faecal DNA was used to generate population-level estimates of microsatellite and mtDNA diversity for comparison with previous estimates for the natural population derived from tissue samples. Data were used to assess both the reliability of faecal-derived genotypes and the extent of any diversity loss since the previous study. Microsatellite diversity recorded from eight polymorphic markers for the natural population (A = 4.31 ± 0.30, HE = 0.76 ± 0.03) was comparable with the previous study, indicating little change in genetic diversity for the natural population in the 10-year interim. Faecal genotypes generated for the recently reintroduced population matched the known number of founders as well as a known genotype, providing support for the reliability of the faecal DNA approach. The captive and reintroduced populations had significantly lower diversity levels than the natural population (A = 3.59 ± 0.28, HE = 0.68 ± 0.03; A = 3.57 ± 0.20, HE = 0.65 ± 0.03 respectively). Mitochondrial control region analysis, incorporating nested clade phylogeographic analysis (NCPA), agrees with earlier findings that populations of bilbies across the arid zone in Australia have only recently become fragmented, but the case for Queensland bilbies being strongly differentiated from other regions is diminished. Implications from this study include the need to further supplement the captive and reintroduced populations with additional out-bred individuals and that faecal DNA can be used effectively for ongoing monitoring and management of this species.

Additional keywords: bilby, captive breeding, Macrotis lagotis, microsatellites, mtDNA, non-invasive samples, reintroduction.


Acknowledgements

We thank Doug Shooter for his assistance in sample collection and two anonymous reviewers for helpful comments that improved the quality of this manuscript. This study was partly funded by the Queensland Government’s ‘Smartstate PhD Research Grant Scheme’ grant to SS. The study was conducted with the approval of the Griffith University Animal Ethics Committee (GU Ref No. AES/03/03/AEC).


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