Genetic trail for the early migrations of Aisin Gioro, the imperial house of the Qing dynasty

Abstract

The House of Aisin Gioro, the imperial clan of Qing dynasty (1644-1911), affected the history of China and the formation of Manchu ethnicity greatly. However, owing to the lack of historical records and archeological evidences, the origin of the House of Aisin Gioro remains ambiguous. To clarify the origin of Aisin Gioro clan, we conducted whole Y-chromosome sequencing on three samples and Y-single-nucleotide polymorphism (Y-SNP) genotyping on other four samples beside those reported in previous work. We confirmed that the paternal lineage of the Aisin Gioro clan belongs to haplogroup C3b1a3a2-F8951, a brother branch of C3*-Star Cluster (currently named as C3b1a3a1-F3796, once linked to Genghis Khan), which is quite different from the predominant lineage C3c-M48 in other Tungusic-speaking populations. We also determined a series of unique Y-SNP markers for the Aisin Gioro clan. Diversity analyses of haplogroup C3b1a3a2-F8951 revealed the early migration of the ancestors of the Aisin Gioro clan from the middle reaches of Amur River to their later settlement in southeastern Manchuria. Hence, our results suggest that the Aisin Gioro clan may be descendants of ancient populations in Transbaikal region and closely related to origin of current Daur populations. Our research indicated that detailed research of stemma and deep sequencing of Y chromosomes are helpful to explore the prehistoric activities of populations lacking historical records and archeological evidences.

Whole-sequence analysis indicates that the Y chromosome C2*-Star Cluster traces back to ordinary Mongols, rather than Genghis Khan

“…It is worth noting the distribution of haplogroup C2b1a3a2-F8951, the closest branch to C2*-ST. We defined this clade as C2*-Daur clade in our previous study [17]. The Y-STR C2b1a3a2-F8951 haplotype has been randomly detected in the Daur, Manchu, Mongolian, Mongolian Buryats, Oroqen, and Xibe populations [17].…”

“…The Y-STR C2b1a3a2-F8951 haplotype has been randomly detected in the Daur, Manchu, Mongolian, Mongolian Buryats, Oroqen, and Xibe populations [17]. This haplogroup is the founding paternal lineage of the Daur and Aisin Gioro clan in the Manchu populations [17]. We tended to detect C2b1a3a2-F8951 in populations in the eastern Greater Khingan Mountains, while we mainly detected C2b1a3a1-F3796 in populations in the western Greater Khingan Mountains, i.e., the Mongolia Plateau, Central Asia, western Asia, and Northern Caucasus region (Supplementary Table S2).…”

“…S1). Haplogroup C2-F8951, also called the "C3*-Daur clade" in our previous study [17], is the most closely related lineage to C2*-ST. A number of variants were determined after the analysis of Ychromosome sequences (see Supplementary Table S4, Supplementary Fig. S1, and Supplementary file 5,.vcf file).…”

“…Standard procedures (bwa + samtools) were followed to analyze the next-generation sequencing data [15,16]. Another 17 previously published Y-chromosome sequences were also used to construct a phylogeny of haplogroup C2*-ST, including one sequence from Yan et al [12], three from Wei et al [17], one from Karmin et al [18], and 11 from Lippold et al [19] The regulations proposed by the YCC were followed to revise the phylogenetic tree with respect to new variants in the non-recombining region of the Y chromosome [20]. According to recent phylogenetic studies, C1-M8, C2-M38, C4-M347, and C5-M356 now belong to the newly defined C1-F3393 haplogroup [18,21].…”

“…To obtain a confident data set for age estimation, a series of strict filters were applied to the file containing original variants. The age of haplogroup CT-M168 (71,760 years, 95% confidence interval [CI] = 69,777-73,799) [18] and the splitting time (470 ± 20 years ago) of samples (YCH508 and YCH1981) from the Aisin Gioro family [17] were used as calibration points to estimate the coalescent times of all samples in the study. The details of the filters and the selection of calibration points are described in the Supplementary Text.…”