Palaeogenomics-informed inferences of European dog admixture enables scalable dingo conservation

Dingoes, mainland Australias sole terrestrial apex mammal for over 3,000 years, are important components of many ecosystems and Indigenous cultural heritage. Yet conflicts with farmers over livestock predation following European colonisation led to widespread lethal control. These measures are further reinforced by perceptions of hybrid ancestry with European dogs. Accurate estimation of European dog ancestry is therefore essential for effective conservation, but existing tests yield highly conflicting results. Leveraging pre-colonial dingo palaeogenomes and a robust ancestry modelling framework, we reassess the genetic ancestry of contemporary populations. Our approach corrects limitations and biases in existing methods, producing consistent estimates even with as few as 10,000 genome-wide transversion genetic markers. Accounting for admixture uncovers population structure that has persisted for over two millennia and reveals patterns of genetic admixture coinciding with human activity during the colonial era. This study underscores the value of palaeogenomes as a vital conservation tool, offering insights unattainable from modern DNA alone. By clarifying ancestry and population structure, our study offers a robust foundation for effective regionally informed dingo management across Australia.