Demographic model and biological adaptation inferred from the genome‐wide single nucleotide polymorphism data reveal tripartite origins of southernmost Chinese Huis

Abstract

Objectives The culturally unique Sanya Hui (SYH) people are considered descendants of ancient Cham people in Central Vietnam and exhibit a scenario of complex migration and admixture history. We aimed to characterize the genetic structure, origin, and admixture history of SYH people and explore the effect of the cultural admixture from Central/South Asia and East Asia on their genetic admixture. Materials and Methods We sampled 94 Hui individuals from Hainan and genotyped these samples using the Infinium Global Screening Array version 2 with over 717K SNPs. We then investigated the demographic history of SYH people by combining currently available modern and ancient genome‐wide SNP data and leveraging shared allele‐ and haplotype‐based strategies. Results Patterns of genetic differentiation showed that SYH people were genetically different from the northern Hui but harbored a close genomic affinity with indigenous Vietnamese. SYH had a relatively distant relationship with the Cham, which confirmed the hypothesis of the documented recent historical migration from Central Vietnam and assimilation with the Hainan indigenous people. The fitted three‐way admixture models and the reconstructed demographic frameworks showed that SYH was the admixture result with primary ancestry from East Asia and mainland Southeast Asia and minor ancestry related to Central/South Asia. GLOBETTRTER and ALDER‐based admixture time estimation revealed that genetic contact with Central Asia occurred around 28 generations ago. Our model was consistent with the frequent cultural communication along the Southern Maritime Silk Road and extensive interaction with East Asia. Besides, analyses focused on natural‐selected signatures of SYH people revealed some candidate loci associated with metabolism and immune function. Discussion The SYH people are considered to be Cham refugees' descendants. A long‐standing hypothesis posits that SYH derives from different genetic and cultural origins, which hypothesizes that the genetically attested admixture history of SYH people is different from northern Hui people possessing prominent Han‐related ancestry and minor western Eurasian ancestry. We found that the genetic structure of SYH people was different from Vietnam Cham and geographically diverse Hui people. Generally, three genetically attested genealogies from Central Vietnam, East Asia, and Central/South Asia in modern SYH people supported their tripartite model of genomic origins.

Malaria resistance-related biological adaptation and complex evolutionary footprints inferred from one integrative Tai-Kadai-related genomic resource

“…Therefore, the genetic origin and phylogenetic relationships within TK-speaking populations remain to be further characterized [ 34 , [46] , [47] , [48] ]. We collected and genotyped 24 BBN individuals and merged newly generated data with previously published data to produce three datasets—a low-density merged HO dataset [ 28 , 29 ], a middle-density merged 1240K dataset, and a high-density merged WGS dataset [ [49] , [50] , [51] , [52] , [53] , [54] , [55] ] to provide new insights into the demographic history, population structure, and human genetic diversity of TK-speaking individuals. The ADMIXTURE result based on a high-density dataset identified a unique genetic component that was greatest in TK-speaking Bouyei, indicating that the Bouyei populations possessed a unique genetic structure ( Fig.…”

“…In addition, to explore the genetic relationship between TK people and other modern and ancient eastern Eurasians, we merged our genome-wide data with previously published modern and ancient people from the Allen Ancient DNA Resource (AADR), which formed a low-density merged HO dataset [ 28 , 29 ], including 56,814 SNPs, and a middle-density merged 1240K dataset, including 146,802 SNPs. To explore the fine-scale genetic structure and obtain phased genomes to illuminate the biological adaptation mechanisms, we combined our data with previously published Illumina data [ [49] , [50] , [51] , [52] , [53] , [54] , [55] , 62 ], 54 worldwide populations included in the HGDP [ 28 ], and 20 populations from Taiwan Island, SEA Island, and Oceania included in the Oceanian genomic resources [ 29 ], which formed the high-density merged WGS dataset and included 460,678 SNPs.…”

Malaria resistance-related biological adaptation and complex evolutionary footprints of Tai-Kadai people inferred from 796 genomes

“…Therefore, the genetic origin and phylogenetic relationship within TK-speaking populations remained to be further characterized (32,(40)(41)(42). We collected and genotyped 24 Bouyei individuals from Guizhou Bannong and merged newly-generated data with previously published data to produce three datasets: low-density merged HO dataset (26,27); middle-density merged 1240K dataset, and high-density merged WGS dataset (43)(44)(45)(46)(47)(48)(49) to provide new insights into the demographic history, population structure and human genetic diversity of TK-speaking. The ADMIXTURE result based on a high-density dataset identified a unique genetic component maximised in TK-speaking Bouyei, indicating that Bouyei populations possessed a unique genetic structure (Figure 1A).…”

“…Besides, to explore the genetic relationship between TK-speaking people and other modern and ancient eastern Eurasians, we merged our genome-wide data with the previously publicly modern and ancient people from Allen Ancient DNA Resource (AADR), which formed low-density merged HO dataset (26,27), including 56814 SNPs; and middle-density merged 1240K dataset, including 146,802 SNPs. To explore the fine-scale genetic structure and obtain phased genomes to illuminate the biological adaptation mechanisms, we combined our data with previously published Illumina data (43)(44)(45)(46)(47)(48)(49), 54 worldwide populations included in the Human genetic diversity project (HGDP) (26), 20 populations from Taiwan Island, SEA Island, and Oceania included in the Oceanian genomic resources (27), which formed the high-density merged WGS dataset and included 460,678 SNPs.…”

Multiple Human Population Movements and Cultural Dispersal Events Shaped the Landscape of Chinese Paternal Heritage

“…Numerous studies have sought to bridge the knowledge gap regarding the genetic diversity of Chinese populations by examining their evolutionary histories and the genetics of complex traits and diseases. Recent research utilized genome-wide SNP microarrays to analyze the genomic diversity and population history of various Sino-Tibetan, Mongolic, Tungusic, Turkic, Tai-Kadai, and Hmong-Mien groups ( Feng et al 2017 ; He et al 2022 ; Wang et al 2022 ; He et al 2023b ; Sun et al 2023 ; Li et al 2024 ). Additionally, the rise of whole-genome sequencing studies has expanded, featuring projects, such as the Westlake BioBank for Chinese, the NyuWa genome resource, the China Metabolic Analytics Project, and the 10K Chinese People Genomic Diversity Project (10K_CPGDP; Cao et al 2020 ; Zhang et al 2021a ; Cong et al 2022 ; Cheng et al 2023 ; He et al 2023c ).…”