Ancient genomes reveal complex genetic history of an international metropolis at Kublai Khan's Upper Capital (Xanadu)

Abstract

AbstractObjectivesAs the political, economic, military, and cultural center of the early Yuan Dynasty, Xanadu attracted people from all over the world. It was thriving and prosperous, composed of residents with different customs and religious beliefs from different social strata. Genetic analysis of Xanadu's residents provides a valuable approach for inferring processes of population movement and exchange during the Yuan period.Materials and MethodsNine skeletons from Zhenzishan cemetery, the largest cemetery near Xanadu, were selected for the whole‐genome shotgun sequencing and capture sequencing of the nonrecombining region of the Y chromosome, three of whom were identified as likely being of European descent based on cranio‐facial morphology.ResultsThere were nine mitochondrial DNA (mtDNA) haplotypes (F1a1, D5b1, B4a3, B5a2a1, H6a1a, T2d1, D4o2a, N9a1, and Z4a) and eight Y‐chromosome DNA haplogroups (G/M201, I/M170, J/M304, L/M20, O/M175, Q/M242, R/M207, and T/M184) identified in the nine ancient individuals. Autosomal analysis further subdivided them into four groups (ZZS_EA, ZZS_CA, ZZS_SA, and ZZS_Cau).DiscussionAs the capital of the Yuan Dynasty, Xanadu was a prosperous city with international influence. The nine skeletons from the Zhenzishan cemetery reflect the high genetic diversity of Xanadu's residents, with clear differences in paternal and maternal origins. The maternal lineages of these residents were mainly East Asian with some western Eurasian features, while the paternal lineages were mainly western Eurasian with fewer East Asian features. These results contribute to a better understanding of the Mongolian Empire's impact on the migration and mixture of people across the Eurasian continent.