Northern China harbored the world’s earliest complex societies based on millet farming, in two major centers in the Yellow (YR) and West Liao (WLR) River basins. Until now, their genetic histories have remained largely unknown. Here we present 55 ancient genomes dating to 7500–1700 BP from the YR, WLR, and Amur River (AR) regions. Contrary to the genetic stability in the AR, the YR and WLR genetic profiles substantially changed over time. The YR populations show a monotonic increase over time in their genetic affinity with present-day southern Chinese and Southeast Asians. In the WLR, intensification of farming in the Late Neolithic is correlated with increased YR affinity while the inclusion of a pastoral economy in the Bronze Age was correlated with increased AR affinity. Our results suggest a link between changes in subsistence strategy and human migration, and fuel the debate about archaeolinguistic signatures of past human migration.

Chao Ning, Tianjiao Li, Ke Wang, Fan Zhang, Tao Li, Xiyan Wu, Shizhu Gao, Quanchao Zhang, Hai Zhang, Mark J. Hudson, Guanghui Dong, Sihao Wu, Yanming Fang, Chen Liu, Chunyan Feng, Wei Li, Tao Han, Ruo Li, Jian Wei, Yonggang Zhu, Yawei Zhou, Chuan-Chao Wang, Shengying Fan, Zenglong Xiong, Zhouyong Sun, Maolin Ye, Lei Sun, Xiaohong Wu, Fawei Liang, Yanpeng Cao, Xingtao Wei, Hong Zhu, Hui Zhou, Johannes Krause, Martine Robbeets, Choongwon Jeong, Yinqiu Cui