Genetic analysis of non-invasive samples is an important wildlife management tool, and is especially useful to inform management of rare or cryptic species. Here, we describe how genetic tools for species detection and individual identification can be applied within a management context, to find and monitor an invasive predator and understand its impacts on native wildlife.
The introduced red fox (Vulpes vulpes) has been implicated in extinctions and declines of many Australian vertebrates, and fox management remains a challenge to conservation across much of the continent. The island of Tasmania was considered to be fox-free, but from the late 1990s increasing evidence pointed to a fox incursion. Tasmania is home to species that have declined or become extinct elsewhere in Australia and are at particular risk of fox predation.
Since 2007, we have used genetics to study Australian foxes. We have conducted landscape-scale surveys for predator scats in Tasmania, and used a PCR and sequencing test to identify scats containing fox DNA. We have also used blind trials and bioinformatic tools to evaluate the sensitivity and specificity of this fox DNA test. Microsatellite and SNP genotyping have improved our understanding of Australian fox population structure, and we are now developing better genotyping tools for non-invasive mark-recapture studies.
Finally, DNA metabarcoding analysis of scats reveals the diets of introduced and native predators, including foxes, cats, Tasmanian devils and quolls. Scat metabarcoding also has great potential as a survey method for rare native species. To improve data interpretation we conducted captive feeding trials, analysing scats from predators fed controlled diets. We have also developed a reference DNA sequence database, which includes mitochondrial sequences from a wide range of Australian vertebrates, including almost all Tasmanian terrestrial mammals.