Genomic history and forensic characteristics of Sherpa highlanders on the Tibetan Plateau inferred from high-resolution InDel panel and genome-wide SNPs
Sherpa people, one of the high-altitude hypoxic adaptive populations, mainly reside in Nepal and the southern Tibet Autonomous Region. The genetic origin and detailed evolutionary profiles of Sherpas remain to be further explored and comprehensively characterized. Here we analyzed the newly-generate...
| Main Authors: | , , , , , , , , , , , , , , , , , , |
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| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
2022
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10356/160173 |
| _version_ | 1811688012340264960 |
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| author | Wang, Mengge Du, Weian Tang, Renkuan Liu, Yan Zou, Xing Yuan, Didi Wang, Zheng Liu, Jing Guo, Jianxin Yang, Xiaomin Chen, Jing Yang, Meiqing Zhang, Xianpeng Wei, Lan-Hai Yuan, Haibing Yeh, Hui-Yuan Wang, Chuan-Chao Liu, Chao He, Guanglin |
| author2 | School of Humanities |
| author_facet | School of Humanities Wang, Mengge Du, Weian Tang, Renkuan Liu, Yan Zou, Xing Yuan, Didi Wang, Zheng Liu, Jing Guo, Jianxin Yang, Xiaomin Chen, Jing Yang, Meiqing Zhang, Xianpeng Wei, Lan-Hai Yuan, Haibing Yeh, Hui-Yuan Wang, Chuan-Chao Liu, Chao He, Guanglin |
| author_sort | Wang, Mengge |
| collection | NTU |
| description | Sherpa people, one of the high-altitude hypoxic adaptive populations, mainly reside in Nepal and the southern Tibet Autonomous Region. The genetic origin and detailed evolutionary profiles of Sherpas remain to be further explored and comprehensively characterized. Here we analyzed the newly-generated InDel genotype data from 628 Dingjie Sherpas by merging with 4222 worldwide InDel profiles and collected genome-wide SNP data (approximately 600K SNPs) from 1612 individuals in 191 modern and ancient populations to explore and reconstruct the fine-scale genetic structure of Sherpas and their relationships with nearby modern and ancient East Asians based on the shared alleles and haplotypes. The forensic parameters of 57 autosomal InDels (A-InDels) included in our used new-generation InDel amplification system showed that this focused InDel panel is informative and polymorphic in Dingjie Sherpas, suggesting that it can be used as the supplementary tool for forensic personal identification and parentage testing in Dingjie Sherpas. Descriptive findings from the PCA, ADMIXTURE, and TreeMix-based phylogenies suggested that studied Nepal Sherpas showed excess allele sharing with neighboring Tibeto-Burman Tibetans. Furthermore, patterns of allele sharing in f-statistics demonstrated that Nepal Sherpas had a different evolutionary history compared with their neighbors from Nepal (Newar and Gurung) but showed genetic similarity with 2700-year-old Chokhopani and modern Tibet Tibetans. QpAdm/qpGraph-based admixture sources and models further showed that Sherpas, core Tibetans, and Chokhopani formed one clade, which could be fitted as having the main ancestry from late Neolithic Qijia millet farmers and other deep ancestries from early Asians. Chromosome painting profiles and shared IBD fragments inferred from fineSTRUCTURE and ChromoPainter not only confirmed the abovementioned genomic affinity patterns but also revealed the fine-scale genetic microstructures among Sino-Tibetan speakers. Finally, natural-selection signals revealed via iHS, nSL and iHH12 showed natural selection signatures associated with disease susceptibility in Sherpas. Generally, we provided the comprehensive landscape of admixture and evolutionary history of Sherpa people based on the shared alleles and haplotypes from the InDel-based genotype data and high-density genome-wide SNP data. The more detailed genetic landscape of Sherpa people should be further confirmed and characterized via ancient genomes or single-molecule real-time sequencing technology. |
| first_indexed | 2024-10-01T05:25:26Z |
| format | Journal Article |
| id | ntu-10356/160173 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T05:25:26Z |
| publishDate | 2022 |
| record_format | dspace |
| spelling | ntu-10356/1601732022-07-14T03:33:10Z Genomic history and forensic characteristics of Sherpa highlanders on the Tibetan Plateau inferred from high-resolution InDel panel and genome-wide SNPs Wang, Mengge Du, Weian Tang, Renkuan Liu, Yan Zou, Xing Yuan, Didi Wang, Zheng Liu, Jing Guo, Jianxin Yang, Xiaomin Chen, Jing Yang, Meiqing Zhang, Xianpeng Wei, Lan-Hai Yuan, Haibing Yeh, Hui-Yuan Wang, Chuan-Chao Liu, Chao He, Guanglin School of Humanities Science::Biological sciences Forensic Genetics Genetic Admixture History Sherpa people, one of the high-altitude hypoxic adaptive populations, mainly reside in Nepal and the southern Tibet Autonomous Region. The genetic origin and detailed evolutionary profiles of Sherpas remain to be further explored and comprehensively characterized. Here we analyzed the newly-generated InDel genotype data from 628 Dingjie Sherpas by merging with 4222 worldwide InDel profiles and collected genome-wide SNP data (approximately 600K SNPs) from 1612 individuals in 191 modern and ancient populations to explore and reconstruct the fine-scale genetic structure of Sherpas and their relationships with nearby modern and ancient East Asians based on the shared alleles and haplotypes. The forensic parameters of 57 autosomal InDels (A-InDels) included in our used new-generation InDel amplification system showed that this focused InDel panel is informative and polymorphic in Dingjie Sherpas, suggesting that it can be used as the supplementary tool for forensic personal identification and parentage testing in Dingjie Sherpas. Descriptive findings from the PCA, ADMIXTURE, and TreeMix-based phylogenies suggested that studied Nepal Sherpas showed excess allele sharing with neighboring Tibeto-Burman Tibetans. Furthermore, patterns of allele sharing in f-statistics demonstrated that Nepal Sherpas had a different evolutionary history compared with their neighbors from Nepal (Newar and Gurung) but showed genetic similarity with 2700-year-old Chokhopani and modern Tibet Tibetans. QpAdm/qpGraph-based admixture sources and models further showed that Sherpas, core Tibetans, and Chokhopani formed one clade, which could be fitted as having the main ancestry from late Neolithic Qijia millet farmers and other deep ancestries from early Asians. Chromosome painting profiles and shared IBD fragments inferred from fineSTRUCTURE and ChromoPainter not only confirmed the abovementioned genomic affinity patterns but also revealed the fine-scale genetic microstructures among Sino-Tibetan speakers. Finally, natural-selection signals revealed via iHS, nSL and iHH12 showed natural selection signatures associated with disease susceptibility in Sherpas. Generally, we provided the comprehensive landscape of admixture and evolutionary history of Sherpa people based on the shared alleles and haplotypes from the InDel-based genotype data and high-density genome-wide SNP data. The more detailed genetic landscape of Sherpa people should be further confirmed and characterized via ancient genomes or single-molecule real-time sequencing technology. This study was supported by grants from the China Postdoctoral Science Foundation (2021M691879) , the Science and Technology Pro-gram of Guangzhou, China (2019030016) , the "Double First Class Uni-versity Plan" key construction project of Xiamen University (the origin and evolution of East Asian populations and the spread of Chinese civilization) , National Natural Science Foundation of China (NSFC 31801040) , Nanqiang Outstanding Young Talents Program of Xiamen University (X2123302) , the Major project of National Social Science Foundation of China (20&ZD248) , the European Research Council (ERC) grant to Dan Xu (ERC-2019-ADG-883700-TRAM). 2022-07-14T03:33:10Z 2022-07-14T03:33:10Z 2022 Journal Article Wang, M., Du, W., Tang, R., Liu, Y., Zou, X., Yuan, D., Wang, Z., Liu, J., Guo, J., Yang, X., Chen, J., Yang, M., Zhang, X., Wei, L., Yuan, H., Yeh, H., Wang, C., Liu, C. & He, G. (2022). Genomic history and forensic characteristics of Sherpa highlanders on the Tibetan Plateau inferred from high-resolution InDel panel and genome-wide SNPs. Forensic Science International: Genetics, 56, 102633-. https://dx.doi.org/10.1016/j.fsigen.2021.102633 1872-4973 https://hdl.handle.net/10356/160173 10.1016/j.fsigen.2021.102633 34826721 2-s2.0-85119611598 56 102633 en Forensic Science International: Genetics © 2021 Elsevier B.V. All rights reserved. |
| spellingShingle | Science::Biological sciences Forensic Genetics Genetic Admixture History Wang, Mengge Du, Weian Tang, Renkuan Liu, Yan Zou, Xing Yuan, Didi Wang, Zheng Liu, Jing Guo, Jianxin Yang, Xiaomin Chen, Jing Yang, Meiqing Zhang, Xianpeng Wei, Lan-Hai Yuan, Haibing Yeh, Hui-Yuan Wang, Chuan-Chao Liu, Chao He, Guanglin Genomic history and forensic characteristics of Sherpa highlanders on the Tibetan Plateau inferred from high-resolution InDel panel and genome-wide SNPs |
| title | Genomic history and forensic characteristics of Sherpa highlanders on the Tibetan Plateau inferred from high-resolution InDel panel and genome-wide SNPs |
| title_full | Genomic history and forensic characteristics of Sherpa highlanders on the Tibetan Plateau inferred from high-resolution InDel panel and genome-wide SNPs |
| title_fullStr | Genomic history and forensic characteristics of Sherpa highlanders on the Tibetan Plateau inferred from high-resolution InDel panel and genome-wide SNPs |
| title_full_unstemmed | Genomic history and forensic characteristics of Sherpa highlanders on the Tibetan Plateau inferred from high-resolution InDel panel and genome-wide SNPs |
| title_short | Genomic history and forensic characteristics of Sherpa highlanders on the Tibetan Plateau inferred from high-resolution InDel panel and genome-wide SNPs |
| title_sort | genomic history and forensic characteristics of sherpa highlanders on the tibetan plateau inferred from high resolution indel panel and genome wide snps |
| topic | Science::Biological sciences Forensic Genetics Genetic Admixture History |
| url | https://hdl.handle.net/10356/160173 |
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