Genomic Insights Into the Admixture History of Mongolic- and Tungusic-Speaking Populations From Southwestern East Asia

Abstract

As a major part of the modern Trans-Eurasian or Altaic language family, most of the Mongolic and Tungusic languages were mainly spoken in northern China, Mongolia, and southern Siberia, but some were also found in southern China. Previous genetic surveys only focused on the dissection of genetic structure of northern Altaic-speaking populations; however, the ancestral origin and genomic diversification of Mongolic and Tungusic–speaking populations from southwestern East Asia remain poorly understood because of the paucity of high-density sampling and genome-wide data. Here, we generated genome-wide data at nearly 700,000 single-nucleotide polymorphisms (SNPs) in 26 Mongolians and 55 Manchus collected from Guizhou province in southwestern China. We applied principal component analysis (PCA), ADMIXTURE, f statistics, qpWave/qpAdm analysis, qpGraph, TreeMix, Fst, and ALDER to infer the fine-scale population genetic structure and admixture history. We found significant genetic differentiation between northern and southern Mongolic and Tungusic speakers, as one specific genetic cline of Manchu and Mongolian was identified in Guizhou province. Further results from ADMIXTURE and f statistics showed that the studied Guizhou Mongolians and Manchus had a strong genetic affinity with southern East Asians, especially for inland southern East Asians. The qpAdm-based estimates of ancestry admixture proportion demonstrated that Guizhou Mongolians and Manchus people could be modeled as the admixtures of one northern ancestry related to northern Tungusic/Mongolic speakers or Yellow River farmers and one southern ancestry associated with Austronesian, Tai-Kadai, and Austroasiatic speakers. The qpGraph-based phylogeny and neighbor-joining tree further confirmed that Guizhou Manchus and Mongolians derived approximately half of the ancestry from their northern ancestors and the other half from southern Indigenous East Asians. The estimated admixture time ranged from 600 to 1,000 years ago, which further confirmed the admixture events were mediated via the Mongolians Empire expansion during the formation of the Yuan dynasty.

Fine-Scale Genetic Structure and Natural Selection Signatures of Southwestern Hans Inferred From Patterns of Genome-Wide Allele, Haplotype, and Haplogroup Lineages

“…Genetic analysis based on the unlinked SNPs can only capture the major information of population history encoded in the genomes. Thus, to further identify, date, and describe the fine-scale admixture events and decode more detailed information of population demographic history of Guizhou Hans, we merged population data with previous published East Asians genotyped using the same array (700K), including 11 Han populations from Shaanxi Province ( He G.-L. et al, 2020 ), Lanzhou Hans from Gansu Province ( Yao et al, 2021 ), Boshu Huis and Nanchong Hans ( Liu et al, 2021b ) from Sichuan Province, officially unrecognized populations [Chuanqings, Gejias, Dongjias, and Xijias ( Lu et al, 2020 )], and Manchus and Mongolians from Guizhou Province ( Chen et al, 2021 ). We used SHAPEIT to phase the genome-wide data and obtain the phased SNPs.…”

“…Genetic origins and admixture history of four geographically different Guizhou Hans and the finer-scale substructure among Han Chinese based on the genome-wide data were the main studied focus. We also included minorities (Geijia, Dongjia, Xijia, Manchu, and Mongolian) residing in Guizhou Province and other Hans from the surrounding provinces as our references ( Lu et al, 2020 ; Chen et al, 2021 ; Liu et al, 2021b ). PCA and ADMIXTURE results clustered Guizhou Hans in the intermediated position between northern East Asians and southern East Asians, consistent with the clustering patterns in the TreeMix-based phylogeny and the geographical location.…”

“…There are also important studies focused on the genetic relationships between central Hans and their neighbors (e.g., Han, Manchu, Mongolian, and Tujia). However, all of these studies mainly focused on the patterns from the shared alleles and sample frequency spectrum of independent SNPs ( Chen et al, 2021 ; He et al, 2021 ) and lacked evidence from a fine-scale genetic structure based on the shared haplotype chunks (successive linked SNP fragments) and uniparental haplogroup lineages.…”

The genomic formation of Tanka people, an isolated 'Gypsies in water' in the coastal region of Southeast China

“…We subsequently explored the genetic similarities and differences within and between Tanka people and their adjacent East Asians(Chen et al, 2021; He et al, 2021; Y. Liu et al, 2021; Lu et al, 2020; Jin Sun et al, 2020; Q.…”

“…Missing SNPs and missing individuals were checked using the Plink 1.9 (Purcell et al, 2007) with the two parameters (mind: 0.01 and geno: 0.01). We then merged the quality-controlled data with previously published modern and ancient Eurasian populations included in the Human Origin dataset or 1240K dataset publicly shared from Reich Lab and other published genetic studies (Chen et al, 2021; Guanglin He et al, 2020; He et al, 2021; Lipson et al, 2018; D. Liu et al, 2020; Y.…”