Ancient genomes provide insights into the genetic history in the historical era of southwest China

Southwest China was characterized by its ethnic, cultural, and linguistic diversity, but the genetic profile and dynamic history of past populations in this region are not well attested. Here, we present genome-wide ancient DNA data from seven Ming Dynasty (1368 CE–1644 CE) individuals from the heart of southwest China, Guizhou province. To the best of our knowledge, this is the first ancient genomic data from the region. We found that compared to other published historical genomes from southwest China, the Ming Dynasty Dasongshan individuals in Guizhou share more affinity with northern Chinese, and were genetically admixed by ancient populations from southern China and northern China agriculturalists from the Yellow River region. Analysis of short runs of homozygosity fragments suggests that the Dasongshan people constituted a small-sized population with probable exogamous customs. Furthermore, present-day Tibeto-Burman, Tai-Kadai, and Hmong-Mien groups in southwest China carry additional ancestry associated with ancient Yellow River agriculturists, indicating a genetic influx from northern China within recent centuries.