Abstract
BACKGROUND: The lower Yangtze River basin holds a pivotal role in Chinese history. As previous genetic research in this region has primarily focused on modern population datasets, the limited availability of ancient human genomes has hindered our capacity to reconstruct detailed ancient population histories and evaluate the genetic impact of Yellow River-related groups. RESULTS: Here, we present the first set of ancient human genomes from the lower Yangtze River basin, comprising eight individuals from the Song to Qing Dynasties (960-1921 CE). We observed a high degree of genetic homogeneity in most samples, suggesting long-term regional genetic stability. Seven individuals were estimated to derive 69.3-100% of their ancestry from ancient Yellow River-related populations, while the remainder can be attributed to a southern East Asian substrate. Contemporary Han Chinese residing in the lower Yangtze basin can be modelled as direct genetic descendants of historical individuals from this area. Notably, one Qing Dynasty sample reveals a genetic link to the Eastern Mediterranean. CONCLUSIONS: Our findings illustrate enduring genetic continuity in the lower Yangtze River basin throughout historical times. These findings underscore the region's role as a genetic bridge between northern and southern East Asia, retaining local rice-farming ancestry while being shaped by southward expansions of Yellow River-related ancestry.