Medieval genomes from eastern Mongolia share a stable genetic profile over a millennium

Recent archaeogenomic studies in Mongolia have elucidated the genetic origins of people from the Xiongnu and Mongol eras, but left the Medieval period between them only tangentially explored. Due to this dearth of ancient genomes, the dynamic history of Medieval Mongolia with the rise and fall of numerous polities still lacks a genomic perspective. To fill in this knowledge gap, here we report whole-genome sequences of nine ancient individuals from eastern Mongolia, who were excavated from two nearby cemeteries, Gurvan Dov and Tavan Khailaast. They are distributed from the Xiongnu-Xianbei period (ca. 200 CE) to the Mongol era (ca. 1,400 CE), forming a local time transect encompassing nearly 1,200 years. Remarkably, despite the long-time span, all nine individuals derive most of their ancestry (85–100%) from the eastern Eurasian lineages and show low heterogeneity in their genetic composition. This is in contrast to the general pattern observed in previously published Medieval genomes from central Mongolia, who showed higher heterogeneity and overall less eastern Eurasian ancestry, thus calling for a comprehensive archaeogenetic survey of Medieval Mongolia to fully capture the dynamic genetic history in this period.