Résumé
The European colonial expansion had dramatic consequences on both Indigenous Peoples and local fauna. In Australia, the degree to which the arrival of Europeans and their dogs impacted the ecology and ancestry of dingoes is contentious. To test for gene flow with European dogs, we sequenced genomes of 18 ancient Australian dingoes from the Nullarbor Plain, two early 20th-century New Guinean dingoes, a mid-19th-century kangaroo hound, and 33 contemporary dingoes from across Australia. To quantify dietary shifts after the arrival of the First Fleet (AD1788), we generated stable isotopic ( δ 13 C, δ 15 N) data for 55 directly dated ancient Australian dingoes spanning the last ~2,300 y. We show that the diet of Nullarbor Plain dingoes shifted soon after European arrival, possibly due to shifts in prey abundance. Our genomic analyses demonstrated that pre-European dingoes were more inbred than most contemporary dog breeds, possibly as a result of population bottlenecks. We also showed that many dingoes, particularly those from Southeast Australia, experienced admixture with European dogs. Although we detected European ancestry dating to the early 18th-century, the majority of gene flow events coincided with the initiation of landscape-scale population control in the 1960s. Furthermore, some European dog alleles may have provided adaptive benefits to dingoes and alleviated inbreeding depression. Despite the existence of gene flow with European dogs, dingoes have maintained their distinctiveness. This suggests that management strategies should prioritize maintenance of substantial population sizes across Australia to both facilitate effective purifying and positive selection on introgressed alleles, and mitigate inbreeding.