Neolithic dogs in southwestern China carried three distinct maternal lineages

Ancient mitochondrial genomes from four dogs buried at a late-Neolithic site in Yunnan, southwestern China, have revealed three distinct maternal lineages at a single location, according to a study published in BMC Ecology and Evolution. The dogs came from the Dadunzi site, and their mitogenomes place them in lineages A2a, A5 and A1a1. No ancient dog genomic data had previously been reported from southwestern China, making the Dadunzi animals the first such reference for the region.

Yunnan occupies a pivotal position at the junction of the Tibetan Plateau, southern China and mainland Southeast Asia. The region has long connected populations, farming traditions and domestic animals moving between East and Southeast Asia. Dogs, as the first domesticated animal to accompany humans widely across prehistoric landscapes, preserve genetic records of human mobility, exchange and settlement. Ancient-human genomic and archaeological records already document repeated population movements across this region, but ancient-DNA evidence for domestic animals remained scarce until now.

The research team, led by Shao-Jie Zhang, Zheng-Fei Cai and Zhen-Zhen Wang with Min-Sheng Peng as senior author, sequenced the mitochondrial genomes of the four Dadunzi dogs to characterize their maternal diversity. Mitochondrial DNA is inherited only through the maternal line, so each dog’s mitogenome traces a single maternal lineage back through generations of female dogs. This property makes mitogenomes a powerful tool for reconstructing the deeper maternal history of dog populations, even when nuclear genomes are not preserved.

The results showed substantial diversity at the single site. Dog DDZ4 belonged to lineage A2a, dog DDZ7 to lineage A5, and dogs DDZ9 and DDZ11 to lineage A1a1. Three distinct maternal lineages among only four animals suggests that Neolithic dogs in Yunnan drew on a broad pool of maternal ancestry rather than descending from a single founding female line.

Phylogenetic analysis placed DDZ4 on an early-diverging mainland branch that is related to, but outside, the sampled Pacific-associated cluster. This position matters for understanding how East Asian dog lineages relate to those carried into Island Southeast Asia and the Pacific. The Dadunzi dog’s branch diverged before the later radiation of the Pacific-associated lineages, indicating that maternal relatives of the Pacific dogs existed on the East Asian mainland at an earlier stage.

Divergence dating separated the DDZ4 lineage and the Australia–New Guinea cluster from the later radiation of Pacific-associated lineages. This temporal framework supports a proposed multi-stage dispersal history, in which related dog lineages moved at different times rather than in a single wave. The dating results provide a chronological anchor for comparing the Dadunzi dogs with the maternal lineages found further south and east.

On the basis of these findings, the researchers propose a multi-stage dispersal model. In this model, related dog lineages may have moved southward from East Asia through Yunnan and mainland Southeast Asia before a later dispersal carried dogs through Island Southeast Asia into Remote Oceania. 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.

The study is published as an open access article and was shared early to provide faster access to peer-reviewed, accepted research. It is citable and carries a permanent DOI, though this version remains subject to further edits before the final Version of Record replaces it. The work involved researchers from multiple institutions, including contributors affiliated with the Kunming Institute of Zoology and collaborators in Thailand working on comparative genomics.

For archaeologists and geneticists studying dog domestication, the Dadunzi mitogenomes fill a geographic gap in the ancient-DNA record. Southwestern China had been a blank space on the map of ancient dog genomics, despite its documented role as a corridor for human and animal movement. The three lineages recovered from a single late-Neolithic site now anchor the maternal diversity of the region and offer a reference point against which other ancient and modern dog genomes from East and Southeast Asia can be compared.

Subject of Research: Ancient mitochondrial genomes of Neolithic dogs from a southwestern Chinese site reveal maternal lineage diversity relevant to dog dispersal in East and Southeast Asia.

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

Article References: Zhang, S.-J., Cai, Z.-F., Wang, Z.-Z., Zhao, Y., Li, H., Zeng, Z.-H., Singchat, W., Srikulnath, K., Ji, X., Zhang, X., Zhang, Y.-P., & Peng, M.-S. (2026). Ancient mitogenomes reveal maternal lineage diversity in Neolithic dogs of southwestern China. BMC Ecology and Evolution. https://doi.org/10.1186/s12862-026-02611-y

Image Credits: AI Generated

DOI: 10.1186/s12862-026-02611-y

Keywords: ancient DNA, mitogenomes, Neolithic dogs, Yunnan, Dadunzi site, maternal lineages, dog dispersal, Island Southeast Asia, Pacific, phylogenetics, BMC Ecology and Evolution, southwestern China