Fine-scale genetic structure and natural selection signatures of southwestern Hans inferred from patterns of genome-wide allele, haplotype, and haplogroup lineages
The evolutionary and admixture history of Han Chinese have been widely discussed via traditional autosomal and uniparental genetic markers [e.g., short tandem repeats, low-density single nucleotide polymorphisms). However, their fine-scale genetic landscapes (admixture scenarios and natural selectio...
| Main Authors: | , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | English |
| Published: |
2021
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| Online Access: | https://hdl.handle.net/10356/153524 |
| _version_ | 1811697696793165824 |
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| author | Wang, Mengge Yuan, Didi Zou, Xing Wang, Zheng Yeh, Hui-Yuan Liu, Jing Wei, Lan-Hai Wang, Chuan-Chao Zhu, Bofeng Liu, Chao He, Guanglin |
| author2 | School of Humanities |
| author_facet | School of Humanities Wang, Mengge Yuan, Didi Zou, Xing Wang, Zheng Yeh, Hui-Yuan Liu, Jing Wei, Lan-Hai Wang, Chuan-Chao Zhu, Bofeng Liu, Chao He, Guanglin |
| author_sort | Wang, Mengge |
| collection | NTU |
| description | The evolutionary and admixture history of Han Chinese have been widely discussed via traditional autosomal and uniparental genetic markers [e.g., short tandem repeats, low-density single nucleotide polymorphisms). However, their fine-scale genetic landscapes (admixture scenarios and natural selection signatures) based on the high-density allele/haplotype sharing patterns have not been deeply characterized. Here, we collected and generated genome-wide data of 50 Han Chinese individuals from four populations in Guizhou Province, one of the most ethnolinguistically diverse regions, and merged it with over 3,000 publicly available modern and ancient Eurasians to describe the genetic origin and population admixture history of Guizhou Hans and their neighbors. PCA and ADMIXTURE results showed that the studied four populations were homogeneous and grouped closely to central East Asians. Genetic homogeneity within Guizhou populations was further confirmed via the observed strong genetic affinity with inland Hmong-Mien people through the observed genetic clade in Fst and outgroup f 3 /f 4-statistics. qpGraph-based phylogenies and f 4-based demographic models illuminated that Guizhou Hans were well fitted via the admixture of ancient Yellow River Millet farmers related to Lajia people and southern Yangtze River farmers related to Hanben people. Further ChromoPainter-based chromosome painting profiles and GLOBETROTTER-based admixture signatures confirmed the two best source matches for southwestern Hans, respectively, from northern Shaanxi Hans and southern indigenes with variable mixture proportions in the historical period. Further three-way admixture models revealed larger genetic contributions from coastal southern East Asians into Guizhou Hans compared with the proposed inland ancient source from mainland Southeast Asia. We also identified candidate loci (e.g., MTUS2, NOTCH4, EDAR, ADH1B, and ABCG2) with strong natural selection signatures in Guizhou Hans via iHS, nSL, and ihh, which were associated with the susceptibility of the multiple complex diseases, morphology formation, alcohol and lipid metabolism. Generally, we provided a case and ideal strategy to reconstruct the detailed demographic evolutionary history of Guizhou Hans, which provided new insights into the fine-scale genomic formation of one ethnolinguistically specific targeted population from the comprehensive perspectives of the shared unlinked alleles, linked haplotypes, and paternal and maternal lineages. |
| first_indexed | 2024-10-01T07:59:22Z |
| format | Journal Article |
| id | ntu-10356/153524 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T07:59:22Z |
| publishDate | 2021 |
| record_format | dspace |
| spelling | ntu-10356/1535242023-03-11T20:06:53Z Fine-scale genetic structure and natural selection signatures of southwestern Hans inferred from patterns of genome-wide allele, haplotype, and haplogroup lineages Wang, Mengge Yuan, Didi Zou, Xing Wang, Zheng Yeh, Hui-Yuan Liu, Jing Wei, Lan-Hai Wang, Chuan-Chao Zhu, Bofeng Liu, Chao He, Guanglin School of Humanities Humanities::General Allele-Sharing Admixture History The evolutionary and admixture history of Han Chinese have been widely discussed via traditional autosomal and uniparental genetic markers [e.g., short tandem repeats, low-density single nucleotide polymorphisms). However, their fine-scale genetic landscapes (admixture scenarios and natural selection signatures) based on the high-density allele/haplotype sharing patterns have not been deeply characterized. Here, we collected and generated genome-wide data of 50 Han Chinese individuals from four populations in Guizhou Province, one of the most ethnolinguistically diverse regions, and merged it with over 3,000 publicly available modern and ancient Eurasians to describe the genetic origin and population admixture history of Guizhou Hans and their neighbors. PCA and ADMIXTURE results showed that the studied four populations were homogeneous and grouped closely to central East Asians. Genetic homogeneity within Guizhou populations was further confirmed via the observed strong genetic affinity with inland Hmong-Mien people through the observed genetic clade in Fst and outgroup f 3 /f 4-statistics. qpGraph-based phylogenies and f 4-based demographic models illuminated that Guizhou Hans were well fitted via the admixture of ancient Yellow River Millet farmers related to Lajia people and southern Yangtze River farmers related to Hanben people. Further ChromoPainter-based chromosome painting profiles and GLOBETROTTER-based admixture signatures confirmed the two best source matches for southwestern Hans, respectively, from northern Shaanxi Hans and southern indigenes with variable mixture proportions in the historical period. Further three-way admixture models revealed larger genetic contributions from coastal southern East Asians into Guizhou Hans compared with the proposed inland ancient source from mainland Southeast Asia. We also identified candidate loci (e.g., MTUS2, NOTCH4, EDAR, ADH1B, and ABCG2) with strong natural selection signatures in Guizhou Hans via iHS, nSL, and ihh, which were associated with the susceptibility of the multiple complex diseases, morphology formation, alcohol and lipid metabolism. Generally, we provided a case and ideal strategy to reconstruct the detailed demographic evolutionary history of Guizhou Hans, which provided new insights into the fine-scale genomic formation of one ethnolinguistically specific targeted population from the comprehensive perspectives of the shared unlinked alleles, linked haplotypes, and paternal and maternal lineages. Published version This study was supported by China Postdoctoral Science Foundation (2021M691879), the National Natural Science Foundation of China (31801040), Nanqiang Outstanding Young Talents Program of Xiamen University (X2123302), and Fundamental Research Funds for the Central Universities (2021M691879). 2021-12-06T12:06:52Z 2021-12-06T12:06:52Z 2021 Journal Article Wang, M., Yuan, D., Zou, X., Wang, Z., Yeh, H., Liu, J., Wei, L., Wang, C., Zhu, B., Liu, C. & He, G. (2021). Fine-scale genetic structure and natural selection signatures of southwestern Hans inferred from patterns of genome-wide allele, haplotype, and haplogroup lineages. Frontiers in Genetics, 12, 727821-. https://dx.doi.org/10.3389/fgene.2021.727821 1664-8021 https://hdl.handle.net/10356/153524 10.3389/fgene.2021.727821 34504517 2-s2.0-85114387619 12 727821 en Frontiers in Genetics Copyright © 2021 Wang, Yuan, Zou, Wang, Yeh, Liu, Wei, Wang, Zhu, Liu and He. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. application/pdf |
| spellingShingle | Humanities::General Allele-Sharing Admixture History Wang, Mengge Yuan, Didi Zou, Xing Wang, Zheng Yeh, Hui-Yuan Liu, Jing Wei, Lan-Hai Wang, Chuan-Chao Zhu, Bofeng Liu, Chao He, Guanglin Fine-scale genetic structure and natural selection signatures of southwestern Hans inferred from patterns of genome-wide allele, haplotype, and haplogroup lineages |
| title | Fine-scale genetic structure and natural selection signatures of southwestern Hans inferred from patterns of genome-wide allele, haplotype, and haplogroup lineages |
| title_full | Fine-scale genetic structure and natural selection signatures of southwestern Hans inferred from patterns of genome-wide allele, haplotype, and haplogroup lineages |
| title_fullStr | Fine-scale genetic structure and natural selection signatures of southwestern Hans inferred from patterns of genome-wide allele, haplotype, and haplogroup lineages |
| title_full_unstemmed | Fine-scale genetic structure and natural selection signatures of southwestern Hans inferred from patterns of genome-wide allele, haplotype, and haplogroup lineages |
| title_short | Fine-scale genetic structure and natural selection signatures of southwestern Hans inferred from patterns of genome-wide allele, haplotype, and haplogroup lineages |
| title_sort | fine scale genetic structure and natural selection signatures of southwestern hans inferred from patterns of genome wide allele haplotype and haplogroup lineages |
| topic | Humanities::General Allele-Sharing Admixture History |
| url | https://hdl.handle.net/10356/153524 |
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