Ancient genomes provide insight into the Paleolithic-to-Neolithic transition in northern East Asia

The Paleolithic-to-Neolithic transition (PNT), which coincided with the Holocene warming trend after the last Ice Age, significantly transformed human cultural and genetic landscapes around the world. However, the genetic dynamics of this transitional period in northern East Asia have yet to be fully investigated. Here, we reported mitochondrial genomes from three individuals and genome-wide data from two individuals from the Donghulin site located in western Beijing, China (∼11-9 thousand years ago). This represents the earliest genetic evidence, together with archaeological context, of Neolithization in northern East Asia. We identify a newly discovered deep northern East Asian (nEA) lineage represented by the ∼11,000-year-old DHL_M1, which diverged early in the Late Pleistocene. We also identify the genetic changes at the Donghulin site over approximately 2,000 years during the post-glacial warming period. These findings highlight the genetic diversity and complex population dynamics during the Neolithization process in northern East Asia, indicating a unique PNT trajectory in this region.