Osuna-Mascaro, C.; Cairns, K.; Doan, K.; Flores-Manzanero, A.; Nesbitt, B. J.; Newsome, T. M.; Pilot, M.

Introgressive hybridization between wild and domestic animals is a widespread phenomenon with important implications for genetic diversity, local adaptation, and conservation management. The causes and consequences of this process are poorly understood. 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 environmental drivers of this process, we analyzed high-density SNP array data in 390 dingoes and 396 domestic dogs. Dingo populations showed regional genetic structure and were clearly differentiated from domestic dogs. Using local ancestry inference and genome-environment association analyses, we found low levels of dog introgression in dingoes from remote areas in Central and Western Australia, and moderate levels in Eastern and Southern populations. Climatic variables (maximum temperature of the warmest month, mean temperature of the driest quarter) and the Human Footprint Index (reflecting density of human populations and environmental modifications) were significant predictors of introgression. We identified four genomic regions with overrepresented dog ancestry, including a large introgressed block on chromosome 27, which contained an olfactory receptor gene showing signatures of positive selection, suggesting adaptive introgression. In addition, a chromosomal inversion previously described in dogs and absent in dingoes was initially identified as an introgressed block. We also detected eight genomic regions nearly free of dog ancestry, suggesting purifying selection against maladaptive variants. Together, these results highlight the complex interplay between introgression, human influence, and local adaptation in dingoes, offering valuable insights for conserving the evolutionary potential of this apex predator in increasingly modified landscapes.