Reconstructing the genetic history of ancient populations on the Mongolian Steppe through ancient DNA

Abstract

Gene flow, the movement of genetic material between populations, plays a central role in evolutionary biology by shaping genetic diversity, influencing adaptation through both the spread and dilution of adaptive alleles, and counteracting the effects of drift and inbreeding. Understanding gene flow is therefore essential for reconstructing the evolutionary and demographic histories of populations. However, repeated and complex gene flow can obscure these historical patterns, making ancient genomes a unique window into past population interactions. While several thousand ancient human genomes have now been reported, most studies have focused on western Eurasia, leaving the Mongolian Steppe comparatively understudied despite its biological and historical importance. Situated at the crossroads of Eurasia, this region has long served as a corridor for human migration, cultural exchange, and genomic interactions. It also played a central role in the spread and development of pastoralist societies, whose seasonal mobility and long-distance movements facilitated genetic connectivity across broad regions. Therefore, integrating ancient DNA with archaeological and mortuary data from pastoralist populations on the Eurasian Steppe can provide a clearer understanding of how subsistence strategies and social structures shaped patterns of gene flow, offering crucial insights into both the evolutionary and cultural history of the region. To address these questions, I analyzed genome-wide data of ancient pastoralists from multiple time periods in Mongolia. First, I examined individuals from the Late Bronze Age (LBA) and Early Iron Age (EIA) in central Mongolia to explore the relationship between mortuary traditions and genetic structure. During the LBA, dairy pastoralism expanded alongside diverse burial practices, including the Deer Stone–Khirgisuur Complex and figure-shaped/Ulaanzuukh burials. By combining genomic and mortuary data from individuals associated with both burial traditions, I identified two genetically distinct clusters corresponding to the different burial types. This finding indicates limited gene flow between these coexisting groups, revealing the persistence of cultural boundaries despite spatial and temporal overlap. The later expansion of the Slab Grave tradition during the EIA was associated with the replacement of these earlier populations, illustrating a significant demographic turnover and the introduction of new gene flow into the region. Analyses further refine the genetic origin of the LBA Deer Stone–Khirgisuur Complex populations, tracing minor western Eurasian ancestry back to Eneolithic and Early Bronze Age Afanasievo and Khemtseg populations, suggesting episodic long-distance gene flow connecting Mongolia to western Eurasian gene pools. Next, I focused on the Xiongnu Empire (ca. 200 BCE–100 CE) to investigate patterns of genetic diversity under the context of imperial formation and social stratification. While previous studies documented high genetic diversity across the empire, local-scale patterns of gene flow and population structure remained unclear. Genome-wide analyses of individuals from aristocratic and local elite cemeteries on the western frontier reveal that genetic heterogeneity was high even within single cemeteries. Notably, higher-status individuals exhibited lower genetic diversity, whereas lower-status individuals showed greater heterogeneity, indicating that elite groups may have maintained more restricted gene flow, while integration of diverse lineages occurred predominantly among lower-status populations. These patterns highlight the interplay between social hierarchy and gene flow, showing how mobility and admixture were structured by sociopolitical status within a nomadic empire. Finally, I analyzed nine individuals from eastern Mongolia spanning the Medieval period (ca. 200–1,400 CE), covering the Xiongnu–Xianbei through the Mongol eras. Despite nearly 1,200 years of temporal depth, these individuals show remarkable genetic continuity dominated by eastern Eurasian lineages, with limited heterogeneity, contrasting with previously reported Medieval populations from central Mongolia that exhibited higher heterogeneity and lower proportions of eastern Eurasian ancestry. These results suggest regionally variable patterns of gene flow, with eastern Mongolia experiencing relative genetic stability, while other regions saw increased admixture, reflecting localized mobility, migration, and demographic events. Together, these findings provide a fine-scale archaeogenetic perspective on Mongolia from the Late Bronze Age through the Medieval period, highlighting how pastoralist expansion, imperial formation, and regional continuity were shaped by patterns of mobility, social organization, and gene flow. By integrating genomic, archaeological, and mortuary data, this study demonstrates that gene flow in the Mongolian Steppe was neither uniform nor random, but structured by cultural practices, geographic proximity, and social hierarchies, offering a nuanced understanding of the forces that shaped the evolutionary history of humans over millennia.