Genetic continuity and dietary change during the emergence of millet farming in northern China

Abstract

How agriculture emerged in East Asia and the demographic and social dynamics associated with this transition remain incompletely understood. Here, we present genome-wide data from eleven individuals from the Xinglong site in northern China, directly dated to ~9,000–5,000 cal. before present (BP), together with stable carbon and nitrogen isotope compositions from bone collagen. Genetic analyses show that these individuals share a homogeneous genetic profile with the nearby Yumin individual, indicating a shared regional ancestry profile consistent with population interactions across the Mongolian Plateau during the Early Holocene, and that this profile persisted for at least 1,500 years (9,000–7,500 cal. BP) at Xinglong. This long-term regional demic stability provides a backdrop for a transition toward millet cultivation, as suggested by isotopic and macrofossil evidence dated to ~7,500 cal. BP. Between 7,500 and 5,500 cal. BP, early millet-associated populations across northern China exhibit heterogeneous genetic structures, suggesting that early millet-associated populations in northern China were genetically heterogeneous and did not derive from a single homogeneous population. By 5,500 cal. BP, individuals from Xinglong show admixture with Middle Neolithic Yellow River millet farmers while retaining affinities with earlier Xinglong and Baikal-related ancestries. Co-buried individuals from residential burials dated to ~9,000 and ~7,500 cal. BP, respectively, both show first-degree kinship, suggesting possible continuity in biologically kin-based residential burial practices. Together, these findings suggest that dietary change was not necessarily accompanied by major demographic replacement or by a genetically detectable shift in kin-based residential burial practices at Xinglong.