The Y-chromosome haplogroup C3*-Star Cluster (revised to C2*-ST in this study) was proposed to be the Y-profile of Genghis Khan. Here, we re-examined the origin of C2*-ST and its associations with Genghis Khan and Mongol populations. We analyzed 34 Y-chromosome sequences of haplogroup C2*-ST and its most closely related lineage. We redefined this paternal lineage as C2b1a3a1-F3796 and generated a highly revised phylogenetic tree of the haplogroup, including 36 sub-lineages and 265 non-private Y-chromosome variants. We performed a comprehensive analysis and age estimation of this lineage in eastern Eurasia, including 18,210 individuals from 292 populations. We discovered that the origin of populations with high frequencies of C2*-ST can be traced to either an ancient Niru’un Mongol clan or ordinary Mongol tribes. Importantly, the age of the most recent common ancestor of C2*-ST (2576 years, 95% CI = 1975–3178) and its sub-lineages, and their expansion patterns, are consistent with the diffusion of all Mongolic-speaking populations, rather than Genghis Khan himself or his close male relatives. We concluded that haplogroup C2*-ST is one of the founder paternal lineages of all Mongolic-speaking populations, and direct evidence of an association between C2*-ST and Genghis Khan has yet to be discovered.

The revolution in large-scale human genomics and advancements in statistical methods have profoundly refined our understanding of genetic diversity and structure within human populations. Y-chromosome variations, with their distinct evolutionary characteristics, play crucial roles in reconstructing the origins and interactions of ancient East Asian paternal lineages. We launched the YanHuang cohort employing a high-resolution capture sequencing panel to explore the evolutionary trajectory of Han Chinese, one of the world’s largest ethnic groups. We generated paternal genomic data for 5020 Han Chinese individuals across 29 Chinese administrative regions. We observed that multiple founding paternal lineages originating from ancient western Eurasia, Siberia, and East Asia contributed significantly to the Han Chinese gene pool. We identified fine-scale paternal genetic structures shaped by interactions among ancient populations and geographic barriers like the Qinling-Huaihe line and the Nanling Mountains. These structures reflect both isolation-enhanced and admixture-driven genetic differentiation, underscoring the complexity of Han Chinese genomic diversity. We observed a strong correlation between the frequency of multiple founding lineages and subsistence-related ancestral sources, including western pastoralists, Holocene Mongolian Plateau populations, and ancient East Asians. This relationship highlights the impact of ancient migrations and admixture on Chinese paternal genomic diversity. We introduced the Weakly-Differentiated Multi-Source Admixture model to clarify the intricate interactions among multiple ancestral sources influencing the Han Chinese paternal landscape. This study provides a comprehensive uniparental genomic resource from the YanHuang cohort, proposes a novel admixture model, and delineates the complex genomic landscape shaped by ancient herders, hunter-gatherers, and farmers integral to Han Chinese ancestry.

Mongolian populations are widely distributed geographically, showing abundant ethnic diversity with geographic and tribal differences. To infer the genetic substructure, admixture and ancient genet...