Early history of Chinese domestic sheep indicated by ancient DNA analysis of Bronze Age individuals

China has a long history of sheep husbandry, and has several indigenous sheep breeds. However, the exact geographic origin of Chinese domestic sheep remains unclear. To provide valuable genetic information for origin of Chinese domestic sheep, we performed an ancient DNA study on 22 sheep excavated from four Bronze Age archaeological sites in Northern China. Two lineages (A and B) were observed in ancient Chinese sheep, of which lineage A was predominant reaching a frequency of 95.5%. Furthermore, phylogenetic network showed that the most frequent haplotype in ancient sheep was the founder of lineage A. These results suggest that Lineage A may hold the key to understanding the origin of Chinese domestic sheep. Sequence sharing and principal component analysis showed that the ancient Chinese sheep had a close affinity to modern Chinese sheep. However, there was no significant breed structure among three modern Chinese sheep groups, making it difficult to determine their relationship to ancient Chinese sheep. Lastly, our results imply that ancient DNA analysis could provide a new way to investigate prehistoric East-West contact.