The genomic history of East Asian Middle Neolithic millet- and rice-agricultural populations
Jianxue Xiong, Xu Yu, Guoke Chen, Liping Yang, Yawei Zhou, Yiling Pan, Zhiyou Wang, Jiujiang Bai, Baoshuai Zhang, Guanghui Dong, Jingrong Pei, Xiaomin Yang, Liang Chen, Ningwu Kang, Yangyang Wu, Bangyan Wang, Kongyang Zhu, Panxin Du, Xiaolong Li, Hetong Wen, Xiaolin Ma, Tianyou Bai, Wanfa Gu, Ye Yu, Qian Wu, Xin Chang, Jingze Tan, Lei Gao, Ge Dong, Bicheng Li, Yishi Yang, Wei-Wei Feng, Yini Yang, Pengfei Sheng, Hailiang Meng, Rui Wang, Jialin Zheng, Xin Jia, Jin Li, Chuan‐Chao Wang, Shaoqing Wen
Abstract
The Yellow and Yangtze river basins in China are among the world's oldest independent agricultural centers, known for the domestication of millet and rice, respectively, yet their genetic history is poorly understood. Here, we present genome-wide data from 74 Middle Neolithic genetic samples from these regions, showing marked genetic differentiation but bidirectional gene flow, supporting a demic diffusion model of mixed farming. Yellow River populations exhibit distinct genetic substructures resulting from interactions with surrounding groups during the mid-Neolithic expansion of millet agriculture. Upper Yellow River populations are genetically linked to Tibetan Plateau populations and possess the earliest adaptive EPAS1 haplotype (∼5,800 BP) among modern humans. Meanwhile, Yangtze River rice farmers show genetic affinity with Neolithic to present-day southeast coastal China and Austronesian populations, tracing the origins of proto-Austronesians farther north to the Yangtze River. These findings offer new insights into the impact of mid-Neolithic agricultural expansion on human genetic history.