Genomic substructure in Yellow River Basin farmers during the transitional Yangshao-Longshan period

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Abstract: The Yellow River (YR) Basin is a pivotal region for understanding the origins and evolution of Chinese civilization. Previous genomic data here suggest a temporal shift in population genetics towards southern Chinese profiles, possibly due to the introduction of rice agriculture and climatic shifts in the Holocene. Here, we report the ancient genomes of two individuals from the Dahecun site during the Yangshao and transitional Yangshao-Longshan (Longshanization) periods. We found a genetic homogeneity in the Middle Neolithic YR basin, but we have not detected a southern-related ancestry among YR farmers in our sample of the Longshanization period compared with the Middle Neolithic YR farmers. Our results indicate a genomic substructure in YR Basin farmers during the transitional Yangshao-Longshan periods. The initial introduction of rice farming into the Central Plain might not be always accompanied by demic diffusion. The Neolithic Yellow River farmers were suggested to significantly contribute to the formation of modern Han Chinese.