Genomes of the Golden Horde Elites

The Golden Horde, the northwestern extension of the Mongol Empire ruled by Genghis Khan's descendants, holds a pivotal place in the history of Central Eurasia and Eastern Europe. Consequently, understanding the genetic legacy of Genghis Khan and his lineage has long been of both academic and public interest, especially concerning the hypothesized association of his Y-chromosome with haplogroup C3* (C2a1a3-F1918). Here, we present novel ancient DNA data from four archaeological individuals—three males and one female—from medieval elite mausoleums of the Golden Horde in the Ulitau region of Kazakstan. Our genomic analyses reveal that the three male individuals are paternally related and share the Y-chromosome haplogroup C3*, providing compelling support for the Genghis Khan haplotype hypothesis first proposed over two decades ago. Additionally, our findings demonstrate that the Golden Horde elites primarily derive their genomes from Ancient Northeast Asians (ANA), with an additional ancestral component from either Ancient North Eurasians (ANE) or a Berel Scythian related population, e.g., the Kipchaks. Archaeological evidence, in turn, sheds light on a medieval population undergoing religious and cultural transition, offering new insights into the societal changes experienced by Mongolian conquerors. Furthermore, through constructing an Identity by Descent (IBD) network, we successfully identify medieval relatives of these individuals on the Mongolian Plateau, linking genetic data to broader population dynamics. In essence, this study provides new ancient DNA evidence that advances our understanding of the genetic background of the Mongolian elites and the population dynamics in Central Eurasia.