The genetic assimilation in language borrowing inferred from Jing People

Differentiated adaptative genetic architecture and language-related demographical history in South China inferred from 619 genomes from 56 populations

BACKGROUND

The underrepresentation of human genomic resources from Southern Chinese populations limited their health equality in the precision medicine era and complete understanding of their genetic formation, admixture, and adaptive features. Besides, linguistical and genetic evidence supported the controversial hypothesis of their origin processes. One hotspot case was from the Chinese Guangxi Pinghua Han people (GPH), whose language was significantly similar to Southern Chinese dialects but whose uniparental gene pool was phylogenetically associated with the indigenous Tai-Kadai (TK) people. Here, we analyzed genome-wide SNP data in 619 people from four language families and 56 geographically different populations, in which 261 people from 21 geographically distinct populations were first reported here.

RESULTS

We identified significant population stratification among ethnolinguistically diverse Guangxi populations, suggesting their differentiated genetic origin and admixture processes. GPH shared more alleles related to Zhuang than Southern Han Chinese but received more northern ancestry relative to Zhuang. Admixture models and estimates of genetic distances showed that GPH had a close genetic relationship with geographically close TK compared to Northern Han Chinese, supporting their admixture origin hypothesis. Further admixture time and demographic history reconstruction supported GPH was formed via admixture between Northern Han Chinese and Southern TK people. We identified robust signatures associated with lipid metabolisms, such as fatty acid desaturases (FADS) and medically relevant loci associated with Mendelian disorder (GJB2) and complex diseases. We also explored the shared and unique selection signatures of ethnically different but linguistically related Guangxi lineages and found some shared signals related to immune and malaria resistance.

CONCLUSIONS

Our genetic analysis illuminated the language-related fine-scale genetic structure and provided robust genetic evidence to support the admixture hypothesis that can explain the pattern of observed genetic diversity and formation of GPH. This work presented one comprehensive analysis focused on the population history and demographical adaptative process, which provided genetic evidence for personal health management and disease risk prediction models from Guangxi people. Further large-scale whole-genome sequencing projects would provide the entire landscape of southern Chinese genomic diversity and their contributions to human health and disease traits.

Systematic selection of ancestry informative SNPs for differentiating Han, Japanese, Dai, and Kinh populations

Biogeographical origin inferences of different populations can provide valuable clues in the forensic investigation by narrowing down the detection scope. However, much research mainly focuses on forensic ancestral origin analyses of major continental populations, which may provide limited information in forensic practice. To improve the ancestral resolution of East Asian populations, we systematically selected ancestry informative single-nucleotide polymorphisms (AISNPs) for differentiating Han, Dai, Japanese, and Kinh populations. In addition, we evaluated the performance of the selected AISNPs to differentiate these populations via multiple methods. Totally 116 AISNPs were selected from the genome-wide data to infer the population origins of these four populations. Results of principle component analysis and population genetic structure of these populations indicated that the selected 116 AISNPs could achieve ancestral resolution of most individuals. Furthermore, the machine learning model built by 116 AISNPs unveiled that most individuals from these four populations could be assigned to correct population origins. To sum up, the selected 116 SNPs could be available for ancestral origin predictions of Han, Dai, Japanese, and Kinh populations, which could provide valuable information for forensic research and genome-wide association study in East Asian populations to some extent.

Insight into forensic efficiency and genetic structure of the Guizhou Dong group via a 64-plex panel

Insertion/deletion polymorphisms (InDels) show great application values in forensic research because they own superiorities of short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs). Whereas, InDels commonly display low genetic diversities in comparison to STRs. Therefore, they may provide limited genetic information in forensic kinship testing. Here, we evaluated forensic application efficiency of a novel multiplex amplification system including two STRs, 59 InDels, and three sex-determination loci in the Guizhou Dong group. In addition, we explored the genetic background of the Guizhou Dong group in comparison to other reported populations based on 59 InDels. We found that 59 InDels displayed relatively high genetic diversities in the Guizhou Dong group. Moreover, the cumulative forensic efficiency of two STRs and 59 InDels could meet the requirement of individual identification and paternity testing in the Guizhou Dong group. For these 59 InDels, we observed that some loci exhibited relatively high genetic differentiations among different continental populations, especially for African and Non-African populations, which could be viewed as candidate ancestry informative markers in the future. Genetic structure results indicated that the Dong group had close genetic relationships with East Asian and some Southern Chinese Han populations. To sum up, we stated that the 64-plex panel could be performed for forensic application of the Guizhou Dong group.

Genomic Insights Into the Demographic History of the Southern Chinese

Southern China is the birthplace of rice-cultivating agriculture and different language families and has also witnessed various human migrations that facilitated cultural diffusions. The fine-scale demographic history in situ that forms present-day local populations, however, remains unclear. To comprehensively cover the genetic diversity in East and Southeast Asia, we generated genome-wide SNP data from 211 present-day Southern Chinese and co-analyzed them with ∼1,200 ancient and modern genomes. In Southern China, language classification is significantly associated with genetic variation but with a different extent of predictability, and there is strong evidence for recent shared genetic history particularly in Hmong–Mien and Austronesian speakers. A geography-related genetic sub-structure that represents the major genetic variation in Southern East Asians is established pre-Holocene and its extremes are represented by Neolithic Fujianese and First Farmers in Mainland Southeast Asia. This sub-structure is largely reduced by admixture in ancient Southern Chinese since > ∼2,000 BP, which forms a “Southern Chinese Cluster” with a high level of genetic homogeneity. Further admixture characterizes the demographic history of the majority of Hmong–Mien speakers and some Kra-Dai speakers in Southwest China happened ∼1,500–1,000 BP, coeval to the reigns of local chiefdoms. In Yellow River Basin, we identify a connection of local populations to genetic sub-structure in Southern China with geographical correspondence appearing > ∼9,000 BP, while the gene flow likely closely related to “Southern Chinese Cluster” since the Longshan period (∼5,000–4,000 BP) forms ancestry profile of Han Chinese Cline.

Genomic Insights Into the Unique Demographic History and Genetic Structure of Five Hmong-Mien-Speaking Miao and Yao Populations in Southwest China

Southern China was the original center of multiple ancestral populations related to modern Hmong-Mien, Tai-Kadai, Austroasiatic, and Austronesian people. More recent genetic surveys have focused on the fine-scale genetic structure and admixture history of southern Chinese populations, but the genetic formation and diversification of Hmong-Mien speakers are far from clear due to the sparse genetic sampling. Here, we reported nearly 700,000 single-nucleotide polymorphisms (SNPs) data from 130 Guizhou Miao and Yao individuals. We used principal component analysis, ADMIXTURE, f-statistics, qpAdm, phylogenetic tree, fineSTRUCTURE, and ALDER to explore the fine-scale population genetic structure and admixture pattern of Hmong-Mien people. The sharing allele patterns showed that our studied populations had a strong genetic affinity with ancient and modern groups from southern and southeastern East Asia. We identified one unique ancestry component maximized in Yao people, which widely existed in other Hmong-Mien-speaking populations in southern China and Southeast Asia and ancient samples of Guangxi. Guizhou Hmong-Mien speakers harbored the dominant proportions of ancestry related to southern indigenous East Asians and minor proportions of northern ancestry related to Yellow River farmers, suggesting the possibility of genetic admixture between Hmong-Mien people and recent southward Sino-Tibetan-related populations. Furthermore, we found a genetic substructure among geographically different Miao and Yao people in Leishan and Songtao. The Yao and Miao people in Leishan harbored more southern East Asian ancestry, but Miao in Songtao received more northern East Asian genetic influence. We observed high mtDNA but low Y-chromosome diversity in studied Hmong-Mien groups, supporting the role of sex-specific residence in influencing human genetic variation. Our data provide valuable clues for further exploring population dynamics in southern China.

Genomic Insight Into the Population Structure and Admixture History of Tai-Kadai-Speaking Sui People in Southwest China

Sui people, which belong to the Tai-Kadai-speaking family, remain poorly characterized due to a lack of genome-wide data. To infer the fine-scale population genetic structure and putative genetic sources of the Sui people, we genotyped 498,655 genome-wide single-nucleotide polymorphisms (SNPs) using SNP arrays in 68 Sui individuals from seven indigenous populations in Guizhou province and Guangxi Zhuang Autonomous Region in Southwest China and co-analyzed with available East Asians via a series of population genetic methods including principal component analysis (PCA), ADMIXTURE, pairwise Fst genetic distance, f-statistics, qpWave, and qpAdm. Our results revealed that Guangxi and Guizhou Sui people showed a strong genetic affinity with populations from southern China and Southeast Asia, especially Tai-Kadai- and Hmong-Mien-speaking populations as well as ancient Iron Age Taiwan Hanben, Gongguan individuals supporting the hypothesis that Sui people came from southern China originally. The indigenous Tai-Kadai-related ancestry (represented by Li), Northern East Asian-related ancestry, and Hmong-Mien-related lineage contributed to the formation processes of the Sui people. We identified the genetic substructure within Sui groups: Guizhou Sui people were relatively homogeneous and possessed similar genetic profiles with neighboring Tai-Kadai-related populations, such as Maonan. While Sui people in Yizhou and Huanjiang of Guangxi might receive unique, additional gene flow from Hmong-Mien-speaking populations and Northern East Asians, respectively, after the divergence within other Sui populations. Sui people could be modeled as the admixture of ancient Yellow River Basin farmer-related ancestry (36.2-54.7%) and ancient coastal Southeast Asian-related ancestry (45.3-63.8%). We also identified the potential positive selection signals related to the disease susceptibility in Sui people via integrated haplotype score (iHS) and number of segregating sites by length (nSL) scores. These genomic findings provided new insights into the demographic history of Tai-Kadai-speaking Sui people and their interaction with neighboring populations in Southern China.

Inferring the population history of Tai-Kadai-speaking people and southernmost Han Chinese on Hainan Island by genome-wide array genotyping

Hainan Island, located between East Asia and Southeast Asia, represents an ideal region for the study of the genetic architecture of geographically isolated populations. However, the genetic structure and demographic history of the indigenous Tai-Kadai-speaking Hlai people and recent expanded southernmost Han Chinese on this island are poorly characterized due to a lack of genetic data. Thus, we collected and genotyped 36 Qiongzhong Hlai and 48 Haikou Han individuals at 497,637 single nucleotide polymorphisms (SNPs). We applied principal component analysis, ADMIXTURE, symmetrical D-statistics, admixture-f₃ statistics, qpWave, and qpAdm analysis to infer the population history. Our results revealed the East Asian populations are characterized by a north-south genetic cline with Hlai at the southernmost end. We have not detected recent gene flow from neighboring populations into Hlai, therefore, we used Hlai as an unadmixed proxy to model the admixture history of mainland Tai-Kadai-speaking populations and southern Han Chinese. The mainland Tai-Kadai-speaking populations are suggested deriving a larger number of their ancestry from Hlai-related lineage, but also having admixture from South Asian-related or other neighboring populations. The Hlai group is also suggested to contribute about half of the ancestry to Han Chinese in Hainan. The complex patterns of genetic structure in East Asia were shaped via language categories, geographical boundaries, and large southward population movements with language dispersal and agriculture propagation.

Paternal Y chromosomal genotyping reveals multiple large-scale admixtures in the formation of Lolo-Burmese-speaking populations in southwest China

Background: Bai and Yi people are two Tibeto-Burman speaking ethnic groups in Yunnan, southwest China. The genetic structure and history of these two groups are largely unknown due to a lack of available genetic data.Aim: To investigate the paternal genetic structure and population relationship of the Yi and Bai people.Subjects and methods: We collected samples from 278 Bai individuals and 283 Yi individuals from Yunnan and subsequently genotyped 43 phylogenetically relevant Y-SNPs in those samples. We estimated haplogroup frequencies and merged our data with a reference database including 46 representative worldwide populations to infer genetic relationships.Results: Y chromosomal haplogroup O-M175 is the dominant lineage in both Bai and Yi people. The Bai and Yi show a close genetic relationship with other Tibeto-Burman-speaking populations with high frequencies of haplogroup O2a2b1a1-Page23, which is also confirmed by PCA. The frequencies of the Tai-Kadai specific lineage O1a-M119, the southern China widespread lineage O1b-P31 and the eastern China enriched lineage O2a1b-002611, are also relatively high in our studied populations.Conclusions: The paternal Y chromosomal affinity of the Bai and Yi with Tibeto-Burman groups is consistent with the language classification. During the formation of the Bai and Yi populations, there were multiple large-scale admixtures, including the expansion of Neolithic farming populations from northern China, the assimilation of Tai-Kadai-speaking populations in southwest China, the demographic expansion driven by Neolithic agricultural revolution from southern China, and the admixture with populations of military immigration from northern and eastern China.