Genomic Insights Into the Demographic History of the Southern Chinese

Southern China is the birthplace of rice-cultivating agriculture and different language families and has also witnessed various human migrations that facilitated cultural diffusions. The fine-scale demographic history in situ that forms present-day local populations, however, remains unclear. To comprehensively cover the genetic diversity in East and Southeast Asia, we generated genome-wide SNP data from 211 present-day Southern Chinese and co-analyzed them with similar to 1,200 ancient and modern genomes. In Southern China, language classification is significantly associated with genetic variation but with a different extent of predictability, and there is strong evidence for recent shared genetic history particularly in Hmong-Mien and Austronesian speakers. A geography-related genetic sub-structure that represents the major genetic variation in Southern East Asians is established pre-Holocene and its extremes are represented by Neolithic Fujianese and First Farmers in Mainland Southeast Asia. This sub-structure is largely reduced by admixture in ancient Southern Chinese since > similar to 2,000 BP, which forms a Southern Chinese Cluster with a high level of genetic homogeneity. Further admixture characterizes the demographic history of the majority of Hmong-Mien speakers and some Kra-Dai speakers in Southwest China happened similar to 1,500-1,000 BP, coeval to the reigns of local chiefdoms. In Yellow River Basin, we identify a connection of local populations to genetic sub-structure in Southern China with geographical correspondence appearing > similar to 9,000 BP, while the gene flow likely closely related to Southern Chinese Cluster since the Longshan period (similar to 5,000-4,000 BP) forms ancestry profile of Han Chinese Cline.

Automated summary

Southern China is the birthplace of rice-cultivating agriculture and has witnessed various human migrations. This study analyzes genetic data from present-day Southern Chinese individuals along with ancient and modern genomes to uncover the genetic diversity and history of the region. The research reveals a significant association between language classification and genetic variation, particularly among Hmong-Mien and Austronesian speakers, indicating shared genetic history. The findings also suggest a geography-related genetic sub-structure that existed before the Holocene period, shaped by Neolithic populations in Fujian and Mainland Southeast Asia. Admixture events have further influenced the genetic makeup of ancient Southern Chinese populations, leading to a high level of genetic homogeneity. Additional admixture is observed among Hmong-Mien and Kra-Dai speakers in Southwest China, occurring around 1,500-1,000 BP, coinciding with the reigns of local chiefdoms. The study also identifies a connection between local populations in the Yellow River Basin and the genetic sub-structure in Southern China, dating back to around 9,000 BP. Gene flow from the Southern Chinese Cluster has likely contributed to the ancestry profile of the Han Chinese population since the Longshan period.