Ancient mitogenomes reveal maternal lineage diversity in Neolithic dogs of southwestern China

Yunnan lies at the junction of the Tibetan Plateau, southern China, and mainland Southeast Asia and has long connected populations, farming traditions, and domestic animals moving between East and Southeast Asia. As the first domesticated animal to accompany humans widely across prehistoric landscapes, dogs preserve genetic records of human mobility, exchange, and settlement. Ancient-human genomic and archaeological records document repeated population movements across this region, but ancient-DNA evidence for domestic animals remains scarce, and no ancient dog genomic data have previously been reported from southwestern China. We investigated four dogs from the late-Neolithic Dadunzi site to characterize their maternal diversity and assess how Yunnan relates to the East Asian lineages associated with dogs in Island Southeast Asia and the Pacific. The dogs carried three distinct maternal lineages: DDZ4 belonged to A2a, DDZ7 to A5, and DDZ9 and DDZ11 to A1a1, revealing substantial diversity at a single southwestern Chinese site. Phylogenetic analysis placed DDZ4 on an early-diverging mainland branch related to, but outside, the sampled Pacific-associated cluster. Divergence dating separated this lineage and the Australia–New Guinea cluster from the later radiation of Pacific-associated lineages, providing a temporal framework for the proposed multi-stage dispersal history. The Dadunzi dogs document substantial maternal-lineage diversity in Neolithic Yunnan and provide an ancient southwestern Chinese reference for the deeper maternal history of dogs associated with Island Southeast Asia and the Pacific. We propose a multi-stage dispersal model in which related dog lineages may have moved southward from East Asia through Yunnan and mainland Southeast Asia before a later dispersal through Island Southeast Asia into Remote Oceania.