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

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

As 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 Methods
Nine 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.

There 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).

As 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.

ZZS26   G1a1/Z3175   G-Z3175*

ZZS68   I2a1b1a2a2a2b~/S23937   I-S23937*

ZZS10   J2b2b~/CTS6812   J-Z42957*, downstream of J-CTS6812

ZZS60   L1a1b3c~/SK1433   L-SK1433 (xY24982, xY28521, xY31217)

ZZS25   O2a2b1a2a1a1b1b2b2a/CTS335   O-CTS335
ZZS7   Q1a1a1a1~/Y551   Q-Y37165, downstream of Q-Y551   

ZZS27   R1a1a1b2a2~/Z2121   R-Z2121 (low coverage, fail to be further classified)

ZZS951   R1a1a1b2a2b1d1~/F1019   R-F1019   
ZZS43   T1a1a/L208   T-L208 (low coverage, fail to be further classified)


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