Genetic Origins and Sex-Biased Admixture of the Huis

Abstract

The Hui people are unique among Chinese ethnic minorities in that they speak the same language as Han Chinese (HAN) but practice Islam. However, as the second-largest minority group in China numbering well over 10 million, the Huis are under-represented in both global and regional genomic studies. Here, we present the first whole-genome sequencing effort of 234 Hui individuals (NXH) aged over 60 who have been living in Ningxia, where the Huis are mostly concentrated. NXH are genetically more similar to East Asian than to any other global populations. In particular, the genetic differentiation between NXH and HAN (FST = 0.0015) is only slightly larger than that between northern and southern HAN (FST = 0.0010), largely attributed to the western ancestry in NXH (∼10%). Highly differentiated functional variants between NXH and HAN were identified in genes associated with skin pigmentation (e.g., SLC24A5), facial morphology (e.g., EDAR), and lipid metabolism (e.g., ABCG8). The Huis are also distinct from other Muslim groups such as the Uyghurs (FST = 0.0187), especially, NXH derived much less western ancestry (∼10%) compared with the Uyghurs (∼50%). Modeling admixture history indicated that NXH experienced an episode of two-wave admixture. An ancient admixture occurred ∼1,025 years ago, reflecting the intensive west-east contacts during the late Tang Dynasty, and the Five Dynasties and Ten Kingdoms period. A recent admixture occurred ∼500 years ago, corresponding to the Ming Dynasty. Notably, we identified considerable sex-biased admixture, i.e., excess of western males and eastern females contributing to the NXH gene pool. The origins and the genomic diversity of the Hui people imply the complex history of contacts between western and eastern Eurasians.

The Genetic Structure and East-West Population Admixture in Northwest China Inferred From Genome-Wide Array Genotyping

“…The close genetic affinity among Chinese Turkic speakers, Tungusic, and Mongolic populations indicated the probability of common ancestor of Altaic speakers. Our results showed that both West and East Eurasian contributed the genetic formation of Altaic populations in Northwest China, which coinciding with previous studies suggested the east-west admixture in Alatic populations and Hui population ( Xu and Jin, 2008 ; Bai et al, 2018 ; Jeong et al, 2019 ; Zhao et al, 2020 ; Ma et al, 2021 ). The closer genetic relationship between our studied population and Sino-Tibetan populations and the results of qpAdm and GLOBETROTTER suggested the majority contributing East Eurasian ancestry might derived from millet farmers in Yellow River Basin related population.…”

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

“…The most natural selection marker was SNP rs11966200 located in SLC44A4 in chromosome 6, which was associated with susceptibility of postlingual non-syndromic mid-frequency hearing loss ( Ma et al, 2017 ). SNP rs4148211 located in ABCG8 (iHS: –0.1227 and nSL: 0.0538 in Guizhou Hans) was also one identified SNP that possessed high genetic differentiation between Huis and Hans ( Ma et al, 2021 ), but which is not significant in our studied Hans. Among 83 SNPs, we identified 15 SNPs with the natural selection signals (iHS < –1) located in ABCG1 or ABCG2 associated with the regulation lipid metabolism, especially for SNP rs3788008 (iHS: –2.1567).…”

“…All of them except SNP rs72939934 harbored nSL values ranging from 1.1930 to 1.4646. SNP rs3827760, one variation being recently evidenced harboring greater genetic differentiation between Gansu Huis and Hans ( Ma et al, 2021 ), also had relatively high natural selection signals in Guizhou Hans (iHS: 1.1139 and nSL: 1.2567). Among 3,133 SNPs located in the Solute Carrier Family (SLC) genes, we identified 70 loci that had large iHS values larger than 1 and 527 SNPs less than –1.…”

Tracing Bai-Yue Ancestry in Aboriginal Li People on Hainan Island

“…To construct a paternal and maternal genealogy of HNL, we classified NRY haplogroups using Y-LineageTracker v1.3.0 ( Chen et al 2021 ) based on the ISOGG Y-DNA tree v2019-2020 ( https://isogg.org/tree ), and mtDNA haplogroups using HaploGrep v2.1.16 ( Weissensteiner et al 2016 ) based on a PhyloTree mtDNA tree v17 ( https://www.phylotree.org/tree ; Van Oven 2015 ). To investigate the population structure at paternal and maternal levels more comprehensively, we also collected NRY and mtDNA haplogroup data of East Asian and Southeast Asian populations from published research ( Kong et al 2003 ; Wen et al 2005 ; Hammer et al 2006 ; Hill et al 2007 ; Li, Cai, et al 2007 ; Li, Zhong, et al 2007 ; Jin et al 2009 ; Li et al 2010 ; Zhao et al 2010 ; Delfin et al 2012 , 2014 ; Ko et al 2014 ; Trejaut et al 2014 ; 1000 Genomes Project Consortium 2015 ; Lu et al 2016 ; Poznik et al 2016 ; Song et al 2019 ; Gao et al 2020 ; He et al 2020 ; Ma et al 2021 ) for comparison ( supplementary tables S4 and S5, Supplementary Material online) and performed PCA based on haplogroup frequency. We also calculated the haplogroup diversity for each population following the formula: , where n is the sample size of each population and x is the frequency of each haplogroup in each population.…”