Ancient East Asian dog lineage is revealed by genome of ancient Korean dogs.

Dogs form a monophyletic clade comprising three major sublineages: Eastern Eurasian, Western Eurasian, and sled dog lineages. While ancient genomic studies have clarified relationships within the latter two, the internal structure of the Eastern Eurasian lineage remains unclear. The dingo and New Guinea Singing Dog (NGSD) are regarded as its least admixed members, but it is uncertain whether they were the sole representatives in East Eurasia. Here, we sequenced ancient genomes from three dogs excavated at the Neuk-do site (3rd century BCE-early 1st century CE) in Sacheon and one dog from the Bonghwang-dong site (4th-6th century CE) in Gimhae. Average genomic coverages for the Neuk-do dogs were 0.5 × , 0.73 × , and 0.64 × , and 0.3× for the Bonghwang-dong dog. Phylogenetic analyses, outgroup-f₃ statistics, and principal component analysis (PCA) of dogs and wolves showed that ancient Korean dogs were closely related to the dingo and NGSD. However, dog-only PCA separated ancient Korean dogs from dingo/NGSD, indicating a distinct lineage within Eastern Eurasia. The detection of Western Eurasian ancestry in the Neuk-do dogs demonstrates that admixture had begun before the 3rd century BCE. The higher proportion of this ancestry in the Bonghwang-dong dog suggests that additional admixture occurred by the 4th to 6th centuries CE. These findings reveal that ancient Korean dogs represent a separate Eastern Eurasian lineage that had already experienced Western Eurasian gene flow by the late first millennium BCE, providing new insights into the evolutionary history of dogs in Eastern Eurasia.