Genetic affinity of cave burial and Hmong-Mien populations in Guangxi inferred from ancient genomes

Cave burial has been prevalent in southern China for thousands of years since the Shang and Zhou Dynasties (3600 − 2200 BP). The population history and the genetic contribution of cave burial groups to the formation of present-day southern minorities are largely unknown due to the lack of ancient genomic data. Here, we present the genomic data from four ancient individuals from cave burial sites Baitaishan and Huatudong from the Late Yuan to Ming Dynasties (650 − 300 BP) in Guangxi. We observed a close genetic affinity between the four individuals and published contemporaneous cave burial samples. However, our studied individuals received gene flows from northern East Asians compared to the cave burial groups around 1600 − 1400 years ago. We identified a strong genetic link between these ancient cave burial groups and present-day Hmong-Mien-speaking populations, particularly the geographically adjacent Baiku Yao population, indicating population stability in the mountainous region of southern China over the past few centuries.