9.D.2 National genotyping facility

A national facility for genotyping invasive animals in Australasia has been developed at the University of Canberra, in collaboration with University of Western Australia and Tasmanian Dept of Primary Industry and Water (DPIW) and the IA CRC’s Uptake Program.

The primary aim of the project is to develop and apply molecular techniques to the analysis of invasive animals in Australia to better inform their management. In particular, the team is focussing on DNA detection and identification approaches for foxes, cats and other animals from trace samples such as faeces (scat), fur or blood. DNA markers, called microsatellites and single nucleotide polymorphisms (‘SNPs’), are being developed to allow a quick and definitive test for animal identification.  From a tiny amount of animal remains, genotyping can reveal which species the animal is, how it’s related to others in the species/population, and potentially even what it has recently eaten.

Information from DNA analyses could have powerful application to field ecology and management by defining mating systems, enabling mark-recapture studies using trace samples, estimating dispersal and defining the spatial units of control. The genotyping facility will be available to all pest animal managers and researchers, to assist in the analysis and management of feral animal populations.

The project is being led by Dr Stephen Sarre at the University of Canberra, with Niccy Aitken, who manages the lab work and the development of new lab facilities, and who is also coordinating a nationwide tissue collection for the DNA profiling of feral cats. Dr Oliver Berry at University of Western Australia has conducted a nationwide collection of over 3200 fox samples, which are now being genotyped.

The new marker techniques were used to identify fox remains in Tasmania, contributing to that state government’s decision to provide $56 million to eradicate foxes. Testing of over 1600 scats and other samples in Tasmania (with DPIW) identified foxes from scats, a blood spot, carcasses and roadside blood spatters. DNA-based scat detection is now central to the surveys being conducted by the DPIW.

The team has tested their multi-species identification approach in Tasmania and found it also to be robust and accurate for cats, dogs, devils and quolls. They have also adapted and optimised DNA markers for fallow deer, possums and feral pigs. Methods have been refined for high throughput of samples.

The feasibility of using microsatellite DNA to measure population structure, connectivity and paternity in fallow deer (Dama dama) on the IA CRC demonstration site of Kangaroo Island has been investigated as a developmental activity. A genotyping analysis of pig samples using microsatellite loci has successfully assessed levels of population structuring and connectivity in feral pigs in the Blue Mountains. A similar study is currently underway on Kangaroo Island.