Domestic dog introgression in Australian dingoes: environmental drivers and evolutionary consequences

Hybridization between wild and domestic canids is a widespread phenomenon with important implications for genetic diversity, local adaptation, and conservation management. In Australia, hybridization between dingoes and domestic dogs presents a dual conservation challenge—threatening the genetic integrity of dingoes while allowing potential adaptive introgression. To investigate the genetic and environmental drivers of this process, we analyzed 170,465 SNPs genotyped with a high-density SNP array in 336 dingoes and 396 European and Australian domestic dogs. Principal component analysis and ADMIXTURE revealed clear genetic differentiation between dingoes and domestic dogs, as well as regional structuring among dingo populations. Using local ancestry inference and genome–environment association (GEA) analyses, we found that dingoes from remote areas such as the Big Desert and Western Australia exhibited low levels of dog introgression, while higher levels were observed in eastern and southern populations. These patterns correlated with proximity to human settlements and environmental modifications. Key variables—including maximum temperature of the warmest month, mean temperature of the driest quarter, and the Human Footprint Index—were significant predictors of introgression. We identified genomic regions with overrepresented dog ancestry, including a large introgressed haplotype block on chromosome 27, along with small blocks on chromosomes 13, 14, and 24. Several genes within these regions showed signatures of purifying or positive selection, suggesting adaptive introgression. Together, these results highlight the complex interplay between hybridization, human influence, and local adaptation in dingoes, offering valuable insights for conserving the evolutionary potential of this apex predator in increasingly modified landscapes.