National pest animal genotyping facility

Project Leader: Assoc Prof Stephen Sarre, University of Canberra

Aim: To develop a genotyping facility that will provide a service to management agencies for small and large-scale population genetic analyses of pest animals in Australia.

Projects:  9.d.2 

Project summary

This project aims to establish a national facility using cutting-edge DNA technology to identify and genetically characterise key invasive species from tissue or trace samples collected in the field. The applications for this technology include detection of cryptic species, defining units of control, determining barriers to dispersal, estimating population size and other population-level studies for management purposes.

The focus will be on the development of DNA markers for two of the CRC’s target vertebrate pests, cats and pigs, the improvement of technologies for foxes and deer, and the development of processing approaches that will enable genotyping of those animals to be applied to real control situations in a cost effective and efficient manner.

Currently, the application of molecular approaches to wildlife analysis in Australia is piece-meal, dependent on specific project funding, and often reliant upon post-graduate students for method development and sample analysis. Commonwealth and state agencies and would use such technologies but find it difficult to fund the initial development or to obtain ongoing access to the technology.

Population genetic analyses using DNA can provide essential ecological information for the management of pest animals. They are now being applied to the sampling and location of low density and cryptic animals, the analysis of mating systems and dispersal characteristics, population censusing, determining the degree of connectedness among sub-populations as units of eradication or control, assessing species distributions, and predator dietary analysis. Given this range of application, the strength that molecular approaches could add to target control more effectively is substantial.

This project relates to demonstration sites throughout goals one to eight.

Key achievements

  • Multiplex microsatellite genotyping for foxes, cats, fallow deer and pigs has been developed and/or optimised. These DNA technologies have been used this year to analyse feral pigs and fallow deer on Kangaroo Island in South Australia, and feral pig populations in the Blue Mountains, New South Wales.
  • The team has provided ongoing support to the Tasmanian fox eradication project through technical advice, DNA primer development, project direction, facility development, project direction, facility acquisition and sample storage. Over 5000 scats have been screened for fox DNA as part of this project. Of those, 41 have been identified as fox-positive and ten have yielded identifiable and unique genotypes. Results will be used to define management units, estimate dispersal among mainland foxes, and assign possible points of origin for Tasmanian foxes (see also Goal 1 summaries).
  • Large-scale sampling of cats across the continent is continuing with the recruitment of approximately 100 recreational hunters and Government officers to submit feral cat tissues collected as part of their normal activities. To date, over 220 tissue samples have been received from 20 sites.
  • Development of a short course in genetic applications to wildlife management targeting specifically wildlife managers in government agencies.

Key deliverables

  • Continue fox and cat sample collection and analysis.
  • The short course on genetic applications to wildlife management is expected to run in June 2010.

Project partners

IA CRC, University of Canberra.

Further information

Wildlife Genetics Short Course_210610

Berry O, Sarre SD, Farrington L, and Aitken N (2007) Faecal DNA detection of invasive species: the case of feral foxes in Tasmania. CSIRO Publishing (vol 34) (1) 1-7.

Sarre SD, Aitken N, Masters P (2008) Population genetic analysis of feral fallow deer on Kangaroo Island. Report to Kangaroo Island Natural Resource Management Board (unpublished).

Sarre SD (2009) Looking for a needle in a haystack! Using DNA to detect introduced foxes in Tasmania, Australia. Presentation to Bishop Museum, Honolulu.

Sarre SD (2008) DNA detection of foxes to prevent establishment in Tasmania. Presentation to Instituto de Pesquisas Cientificas e Tecnológicas do Estado do Amapá – IEPA, Brazil.

For further information, contact us.