DNA found in species’ scat can help create a roadmap for effective population and conservation management. Applying genetic sampling techniques enables the collection of important information on species such as genetic diversity, relatedness, and effective population size. Traditional techniques to obtain these data are often challenging, relying on trapping and disturbing the species’ and their environment.
Scat samples are known to contain degraded or low-quality DNA which has previously made genotyping challenging. However due to technological advancements, the level of data that can be derived from scat samples has drastically improved. This provides a powerful advancement for environmental managers looking to understand wildlife population health.
Cesar Australia partnered with the Department of Energy, Environment and Climate Change (DEECA) to apply these techniques for the development of a non-invasive sampling strategy for dingoes (Canis lupus dingo) in Western Victoria. The team improved on previous methods for both sample collection and DNA genotyping using a panel of genomic single nucleotide polymorphisms (SNP). This approach overcame the traditional sampling challenges, allowing the project team to gain valuable genetic insights.
Understanding fragmented populations
Dingoes are the largest native terrestrial predator across mainland Australia. Population numbers have likely been suppressed since European settlement, and remaining populations have become somewhat fragmented due to habitat clearing, lethal control and the imposition of other barriers including construction of the dingo fence in the 1880s.
It is suspected this may have led to some remnant populations being small and isolated, such as the dingo population in western Victoria. This leads to concerns around genetic drift and inbreeding, which can impact overall population fitness. In this project, new knowledge of species in western Victoria, in the Big Desert Wilderness Area and Wyperfield National Park.
Known culturally as Wilkurr across the sampling area, Barengi Gadjin Land Council Aboriginal Corporation and DEECA collaborators including Deakin University, have undertaken the collection of Wilkurr scat samples. Cesar Australia molecular scientists successfully developed a SNP genotyping array (using MassARRAY® SNP technology) for processing the non-invasive samples and a scat sampling method that limits further degradation of DNA. Analyses have been undertaken on scats collected from western Victoria, as well as some dingo scat samples from eastern Victoria to make sure the method can be applied across the state of Victoria.
Low quality samples to precise results
Genomic single nucleotide polymorphism (SNP) data is now becoming the new standard in conservation genetics due to the increased sensitivity for determining genetic parameters. We undertake SNP genotyping that allows high accuracy and precision and can ensure that genotyping results are reliable, even when working with low-quality samples.
From scat samples, we can identify individuals, determine their sex, and assess overall population structure. This data can be used to inform environmental management in the wild and also mitigate the negative effects of inbreeding in small captive populations. This is useful data as breeding programs must prioritise genetic diversity through careful management of breeding pairs.
Cesar Australia has developed a number of non-invasive genetic sampling strategies based on utilising SNP technologies. We have worked on projects for native species such as the central rock rat, spot-tailed quolls, bush stone curlews and also invasive red foxes. These projects form exciting developments for environmental managers to efficiently and cost-effectively access species’ genetic population data.
Acknowledgements
Thank you to the Department of Energy, Environment and Climate Change (DEECA), Barengi Gadjin Land Council Aboriginal Corporation and Deakin University for their efforts and collaboration.
