Population Genetic Analysis of Modern and Ancient DNA Variations Yields New Insights Into the Formation, Genetic Structure, and Phylogenetic Relationship of Northern Han Chinese

Abstract

Modern East Asians derived from the admixture of aborigines and incoming farmers expanding from Yellow and Yangtze River Basins. Distinct genetic differentiation and subsequent admixture between Northeast Asians and Southeast Asians subsequently evidenced by the mitochondrial DNA, Y-chromosomal variations, and autosomal SNPs. Recently, population geneticists have paid more attention to the genetic polymorphisms and background of southern-Han Chinese and southern native populations. The genetic legacy of northern-Han remains uncharacterized. Thus, we performed this comprehensive population genetic analyses of modern and ancient genetic variations aiming to yield new insight into the formation of modern Han, and the genetic ancestry and phylogenetic relationship of the northern-Han Chinese population. We first genotyped 25 forensic associated markers in 3,089 northern-Han Chinese individuals using the new-generation of the Huaxia Platinum System. And then we performed the first meta-analysis focused on the genetic affinity between Asian Neolithic∼Iron Age ancients and modern northern-Han Chinese by combining mitochondrial variations in 417 ancient individuals from 13 different archeological sites and 812 modern individuals, as well as Y-chromosomal variations in 114 ancient individuals from 12 Neolithic∼Iron Age sites and 2,810 modern subjects. We finally genotyped 643,897 genome-wide nucleotide polymorphisms (SNPs) in 20 Shanxi Han individuals and combined with 1,927 modern humans and 40 Eurasian ancient genomes to explore the genetic structure and admixture of northern-Han Chinese. We addressed genetic legacy, population structure and phylogenetic relationship of northern-Han Chinese via various analyses. Our population genetic results from five different reference datasets indicated that Shanxi Han shares a closer phylogenetic relationship with northern-neighbors and southern ethnically close groups than with Uyghur and Tibetan. Genome-wide variations revealed that modern northern-Han derived their ancestry from Yakut-related population (25.2%) and She-related population (74.8%). Summarily, the genetic mixing that led to the emergence of a Han Chinese ethnicity occurred at a very early period, probably in Neolithic times, and this mixing involved an ancient Tibeto-Burman population and a local pre-Sinitic population, which may have been linguistically Altaic.

Peopling of Tibet Plateau and multiple waves of admixture of Tibetans inferred from both modern and ancient genome-wide data

“…Based on the farming/language dispersal hypothesis, and the similarities of material culture assemblage among TP, East Asia, South/Central Asia, and Siberia, the origin of modern and ancient Tibetans is still confused and unclear (Jeong, et al 2016). Shared ancestry revealed by our PCA, pairwise Fst genetic distance and outgroup-f3 values, ADMIXTURE, and f4-statistics among modern and ancient highlanders and northern East Asian lowlanders showed their close relationship among them, which is consistent with genetic similarities revealed by forensic low-density genetic markers and uniparental haplotype/haplogroup data Chen, Wu, et al 2019; Thus, our results in this meta-genomic analysis supported the main lineage of TP people was originated from the lower and middle Yellow River with the Neolithic expansion of millet farmer. Our Neolithic to present-day autosomal genome-based findings confirmed the origin, diversification, and expansion of the modern Sino-Tibetan population revealed by mitochondrial and Y-chromosome variations (Wang, Lu, et al 2018;Li, Tian, et al 2019b).…”

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

“…Strong associations between population genetic structure and linguistic similarity were subsequently evidenced among Afroasiatic, Nilo-Saharan, Niger-Congo, and Khoisan language families in Africa (Martin et al, 2018;Patin and Quintana-Murci, 2018;Gurdasani et al, 2019), as well as language families in Asia (Chen et al, 2019;He et al, 2020a,b,c). Recent genomewide modern and ancient DNA data have demonstrated that obvious population stratifications existed in East Asia with four regional dominant ancestries.…”

Combined Low-/High-Density Modern and Ancient Genome-Wide Data Document Genomic Admixture History of High-Altitude East Asians

“…However, the comprehensive genetic history of East Asia is poorly understood due to the lack of ancient DNA from a denser genetic sampling or sparse sampling of modern East Asians and combined analyses of spatiotemporally diverse East Asian populations ( Lu et al, 2016 ; Yao et al, 2017 ; Bai et al, 2018 ; He et al, 2020 ). Generally, patterns of genetic relatedness among present-day East Asians, especially for Han Chinese, run along a north-south cline ( Qin et al, 2014 ; Chiang et al, 2018 ; Chen et al, 2019b ; Gao et al, 2020b ). Recent ancient genome-wide data of 26 ancient northern and southern East Asians (including Shandong Houli and Fujian Tanshishan cultural backgrounds) spanning 9,500–300 years ago indicated human population shifts and admixture in northern and southern China and confirmed the genetic division between northern and southern East Asians since early Neolithic ( Yang et al, 2020 ).…”