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Wang Z, Wang M, Hu L, He G, Nie S. Evolutionary profiles and complex admixture landscape in East Asia: New insights from modern and ancient Y chromosome variation perspectives. Heliyon 2024; 10:e30067. [PMID: 38756579 PMCID: PMC11096704 DOI: 10.1016/j.heliyon.2024.e30067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/08/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Human Y-chromosomes are characterized by nonrecombination and uniparental inheritance, carrying traces of human history evolution and admixture. Large-scale population-specific genomic sources based on advanced sequencing technologies have revolutionized our understanding of human Y chromosome diversity and its anthropological and forensic applications. Here, we reviewed and meta-analyzed the Y chromosome genetic diversity of modern and ancient people from China and summarized the patterns of founding lineages of spatiotemporally different populations associated with their origin, expansion, and admixture. We emphasized the strong association between our identified founding lineages and language-related human dispersal events correlated with the Sino-Tibetan, Altaic, and southern Chinese multiple-language families related to the Hmong-Mien, Tai-Kadai, Austronesian, and Austro-Asiatic languages. We subsequently summarize the recent advances in translational applications in forensic and anthropological science, including paternal biogeographical ancestry inference (PBGAI), surname investigation, and paternal history reconstruction. Whole-Y sequencing or high-resolution panels with high coverage of terminal Y chromosome lineages are essential for capturing the genomic diversity of ethnolinguistically diverse East Asians. Generally, we emphasized the importance of including more ethnolinguistically diverse, underrepresented modern and spatiotemporally different ancient East Asians in human genetic research for a comprehensive understanding of the paternal genetic landscape of East Asians with a detailed time series and for the reconstruction of a reference database in the PBGAI, even including new technology innovations of Telomere-to-Telomere (T2T) for new genetic variation discovery.
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Affiliation(s)
- Zhiyong Wang
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510275, China
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
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Peng MS, Zhang YP. Sex-biased adaptation shapes uniparental gene pools in Tibetans. SCIENCE CHINA. LIFE SCIENCES 2024; 67:611-613. [PMID: 38324127 DOI: 10.1007/s11427-023-2506-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 12/08/2023] [Indexed: 02/08/2024]
Affiliation(s)
- Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China.
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China.
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Yao H, Wang K, Lu S, Cao F, Dai P. Development of an ARMS multiplex real-time PCR assay for the detection of HLA-B*13:01 genotype by detecting highly specific SNPs. Pharmacogenet Genomics 2024; 34:53-59. [PMID: 38050734 DOI: 10.1097/fpc.0000000000000517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
OBJECTIVES HLA-B*13:01 was strongly associated with Dapsone Hypersensitivity Syndrome (DHS). This study aimed to develop and validate a rapid and economical method for HLA-B*13:01 genotyping. METHODS Two tubes multiplex real-time PCR detection system comprising amplification refractory mutation system primers and TaqMan probes was established for HLA-B*13:01 genotyping. Sequence-based typing was applied to validate the accuracy of the assay. RESULTS The accuracy of the assay was 100% for HLA-B*13:01 genotyping. The detection limit of the new method was 0.025 ng DNA. The positive rate of HLA-B*13:01 in the Bouyei (20%, n = 50) populations was significantly higher than that in the Uighur population (4%, n = 100), Han (4.5%, n = 200), and Tibetan (1%, n = 100) ( P < 0.05). CONCLUSION The proposed method is rapid and reliable for HLA-B*13:01 screening in a clinical setting.
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Affiliation(s)
- Hao Yao
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an
| | - Kaixuan Wang
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an
| | - Sihai Lu
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an
| | - Fang Cao
- Department of Clinical Pharmacy, Shaanxi Provincial Cancer Hospital, Shaanxi Province, China
| | - Penggao Dai
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an
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He G, Wang P, Chen J, Liu Y, Sun Y, Hu R, Duan S, Sun Q, Tang R, Yang J, Wang Z, Yun L, Hu L, Yan J, Nie S, Wei L, Liu C, Wang M. Differentiated genomic footprints suggest isolation and long-distance migration of Hmong-Mien populations. BMC Biol 2024; 22:18. [PMID: 38273256 PMCID: PMC10809681 DOI: 10.1186/s12915-024-01828-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND The underrepresentation of Hmong-Mien (HM) people in Asian genomic studies has hindered our comprehensive understanding of the full landscape of their evolutionary history and complex trait architecture. South China is a multi-ethnic region and indigenously settled by ethnolinguistically diverse HM, Austroasiatic (AA), Tai-Kadai (TK), Austronesian (AN), and Sino-Tibetan (ST) people, which is regarded as East Asia's initial cradle of biodiversity. However, previous fragmented genetic studies have only presented a fraction of the landscape of genetic diversity in this region, especially the lack of haplotype-based genomic resources. The deep characterization of demographic history and natural-selection-relevant genetic architecture of HM people was necessary. RESULTS We reported one HM-specific genomic resource and comprehensively explored the fine-scale genetic structure and adaptative features inferred from the genome-wide SNP data of 440 HM individuals from 33 ethnolinguistic populations, including previously unreported She. We identified solid genetic differentiation between HM people and Han Chinese at 7.64‒15.86 years ago (kya) and split events between southern Chinese inland (Miao/Yao) and coastal (She) HM people in the middle Bronze Age period and the latter obtained more gene flow from Ancient Northern East Asians. Multiple admixture models further confirmed that extensive gene flow from surrounding ST, TK, and AN people entangled in forming the gene pool of Chinese coastal HM people. Genetic findings of isolated shared unique ancestral components based on the sharing alleles and haplotypes deconstructed that HM people from the Yungui Plateau carried the breadth of previously unknown genomic diversity. We identified a direct and recent genetic connection between Chinese inland and Southeast Asian HM people as they shared the most extended identity-by-descent fragments, supporting the long-distance migration hypothesis. Uniparental phylogenetic topology and network-based phylogenetic relationship reconstruction found ancient uniparental founding lineages in southwestern HM people. Finally, the population-specific biological adaptation study identified the shared and differentiated natural selection signatures among inland and coastal HM people associated with physical features and immune functions. The allele frequency spectrum of cancer susceptibility alleles and pharmacogenomic genes showed significant differences between HM and northern Chinese people. CONCLUSIONS Our extensive genetic evidence combined with the historical documents supported the view that ancient HM people originated from the Yungui regions associated with ancient "Three-Miao tribes" descended from the ancient Daxi-Qujialing-Shijiahe people. Then, some have recently migrated rapidly to Southeast Asia, and some have migrated eastward and mixed respectively with Southeast Asian indigenes, Liangzhu-related coastal ancient populations, and incoming southward ST people. Generally, complex population migration, admixture, and adaptation history contributed to the complicated patterns of population structure of geographically diverse HM people.
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Affiliation(s)
- Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China.
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China.
| | - Peixin Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Medical Information, Chongqing Medical University, Chongqing, 400331, China
| | - Jing Chen
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030001, China
| | - Yan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000, China
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
| | - Yuntao Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Rong Hu
- School of Sociology and Anthropology, Xiamen University, Xiamen, 361005, China
| | - Shuhan Duan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000, China
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
| | - Qiuxia Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Junbao Yang
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000, China
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
| | - Zhiyong Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Libing Yun
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Liping Hu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030001, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Lanhai Wei
- School of Ethnology and Anthropology, Inner Mongolia Normal University, Inner Mongolia, 010028, China
| | - Chao Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China.
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China.
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China.
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China.
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China.
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China.
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China.
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Song B, Fu J, Guo K, Qian J, He T, Yang L, Cheng J, Fu J. A Tibetan group from Ngawa Tibetan and Qiang Autonomous Prefecture, southwest China, is rich in genetic polymorphisms at 36 autosomal STR loci and shares a complex genetic structure with other Chinese populations. Heliyon 2023; 9:e23005. [PMID: 38125507 PMCID: PMC10731225 DOI: 10.1016/j.heliyon.2023.e23005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 11/14/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
The Tibetan people are ancient and populous, constituting the seventh-largest of the fifty-five ethnic minority groups in China. The Ngawa Tibetan and Qiang Autonomous Prefecture (NTQAP), situated on the border of northwest and southwest China, has its distinct group relationships. Short tandem repeat (STR) is extremely polymorphic and extensively used in the application of forensic medicine and population genetics. However, it is not clear the genetic information including linkage disequilibrium (LD) by 36 autosomal STR (A-STR) markers in the Tibetan group from NTQAP. The Tibetan population from NTQAP of southwest China was examined for 36 A-STR loci in the research. Every marker across the 36 A-STR loci was consistent with Hardy-Weinberg equilibrium (HWE). The results of the calculation revealed that the total discrimination power (TDP) is 1-2.2552 × 10-42 and the cumulative probability of exclusion (CPE) is 1-1.3031 × 10-16. Subsequently, a total of 345 alleles with allelic frequencies ranging from 0.00382 to 0.55343 were identified, and the allelic numbers varied from 5 in both the TH01 and TPOX markers to 28 in the SE33 locus. The Ngawa Tibetan population, along with other Chinese populations, exhibited influences from historical factors and regional distribution, as indicated by the results of population genetics analysis. We thus first explored the genetic characteristics and correlated forensic parameters of the 36 A-STR markers in NTQAP to fill the gap in the Tibetan population. It was discovered that these 36 autosomal STR markers supplemented forensic STR databases and offered extremely valuable polymorphisms for Chinese forensic applications, such as parentage testing and personal identification. Moreover, the study would contribute additional information regarding the substructure and diversity in the Chinese population.
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Affiliation(s)
- Binghui Song
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Laboratory of Precision Medicine and DNA Forensic Medicine, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Jiewen Fu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Laboratory of Precision Medicine and DNA Forensic Medicine, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Laboratory of Forensic DNA, the Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Kan Guo
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Jie Qian
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Ting He
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Lisha Yang
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Obstetrics and Center for Prenatal Diagnosis, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jingliang Cheng
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Laboratory of Precision Medicine and DNA Forensic Medicine, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Laboratory of Forensic DNA, the Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Laboratory of Precision Medicine and DNA Forensic Medicine, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Laboratory of Forensic DNA, the Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China
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Li X, Zhang X, Yu T, Ye L, Huang T, Chen Y, Liu S, Wen Y. Whole mitochondrial genome analysis in highland Tibetans: further matrilineal genetic structure exploration. Front Genet 2023; 14:1221388. [PMID: 38034496 PMCID: PMC10682103 DOI: 10.3389/fgene.2023.1221388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/21/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction: The Qinghai-Tibet Plateau is one of the last terrestrial environments conquered by modern humans. Tibetans are among the few high-altitude settlers in the world, and understanding the genetic profile of Tibetans plays a pivotal role in studies of anthropology, genetics, and archaeology. Methods: In this study, we investigated the maternal genetic landscape of Tibetans based on the whole mitochondrial genome collected from 145 unrelated native Lhasa Tibetans. Molecular diversity indices, haplotype diversity (HD), Tajima's D and Fu's Fs were calculated and the Bayesian Skyline Plot was obtained to determining the genetic profile and population fluctuation of Lhasa Tibetans. To further explore the genetic structure of Lhasa Tibetans, we collected 107 East Asian reference populations to perform principal component analysis (PCA), multidimensional scaling (MDS), calculated Fst values and constructed phylogenetic tree. Results: The maternal genetic landscape of Tibetans showed obvious East Asian characteristics, M9a (28.28%), R (11.03%), F1 (12.41%), D4 (9.66%), N (6.21%), and M62 (4.14%) were the dominant haplogroups. The results of PCA, MDS, Fst and phylogenetic tree were consistent: Lhasa Tibetans clustered with other highland Tibeto-Burman speakers, there was obvious genetic homogeneity of Tibetans in Xizang, and genetic similarity between Tibetans and northern Han people and geographically adjacent populations was found. In addition, specific maternal lineages of Tibetans also be determined in this study. Discussion: In general, this study further shed light on long-time matrilineal continuity on the Tibetan Plateau and the genetic connection between Tibetans and millet famers in the Yellow River Basin, and further revealed that multiple waves of population interaction and admixture during different historical periods between lowland and highland populations shaped the maternal genetic profile of Tibetans.
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Affiliation(s)
- Xin Li
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Xianpeng Zhang
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Ting Yu
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Liping Ye
- Department of Pathophysiology, Jinzhou Medical University, Jinzhou, China
| | - Ting Huang
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Ying Chen
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Shuhan Liu
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
| | - Youfeng Wen
- Institute of Biological Anthropology, Jinzhou Medical University, Jinzhou, China
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Zhao M, Cui W, Xu H, Zhang Y, Zhu B. Unveiling the genetic landscape of high-altitude adaptive ethnic groups with polymorphic markers: Implications of comprehensive forensic appraisals and population genetic investigations. Heliyon 2023; 9:e21229. [PMID: 38027587 PMCID: PMC10656254 DOI: 10.1016/j.heliyon.2023.e21229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 09/11/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Background Deletion/insertion polymorphisms (DIPs), a novel class of biomarker, have been widely utilized in forensic areas for individual identification, paternity tests, and ancestral origin inference due to its applicability to degraded samples and low mutation rates. Despite the availability of a well-established commercial kit, the Investigator® DIPplex kit (Qiagen), certain loci exhibit limited levels of polymorphisms in East Asian populations, particularly in Chinese populations. Objective This dissertation seeks to undertake a comprehensive evaluation about the forensic efficiency of a self-developed multiplex amplification system in high-altitude adaptive ethnic groups of China. Healthy unrelated Tibetan individuals residing in Tibet Autonomous Region and Qinghai Province were genotyped using previously reported 43 deletion/insertion polymorphism loci. Forensic statistical analyses including allele frequencies and forensic parameters were conducted in the two Tibetan groups, and the genetic relatedness of the studied groups with reference populations from the 1000 Genomes Project Phase 3 were investigated. Results Forensic statistical results showed that the polymorphism information content values of the 43 deletion/insertion polymorphism loci in the two Tibetan groups exceeded 0.35. Moreover, the combined power of discrimination using the 43 deletion/insertion polymorphism loci was calculated to be 0.9999999999999999984 in the Qinghai Tibetan group and 0.9999999999999999921 in the Tibet Tibetan group. The cumulative power of exclusion using the 43 deletion/insertion polymorphism loci was calculated to be 0.999782512 in the Qinghai Tibetan group and 0.999886205 in the Tibet Tibetan group. Analysis of population genetics demonstrated that the two studied Tibetan groups shared close genetic relationships with East Asia populations. Conclusion The set of 43 deletion/insertion polymorphism loci exhibited remarkable forensic efficacy, rendering it a promising tool for forensic practice. Population genetic analyses indicated that the two Tibetan groups had closer genetic affinities to East Asian populations.
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Affiliation(s)
- Ming Zhao
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 510515, Guangzhou, Guangdong, China
| | - Wei Cui
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 510515, Guangzhou, Guangdong, China
| | - Hui Xu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 510515, Guangzhou, Guangdong, China
| | - Yunying Zhang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 510515, Guangzhou, Guangdong, China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, 510515, Guangzhou, Guangdong, China
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8
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Zhao GB, Miao L, Wang M, Yuan JH, Wei LH, Feng YS, Zhao J, Kang KL, Zhang C, Ji AQ, He G, Wang L. Developmental validation of a high-resolution panel genotyping 639 Y-chromosome SNP and InDel markers and its evolutionary features in Chinese populations. BMC Genomics 2023; 24:611. [PMID: 37828453 PMCID: PMC10568895 DOI: 10.1186/s12864-023-09709-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023] Open
Abstract
Uniparental-inherited haploid genetic marker of Y-chromosome single nucleotide polymorphisms (Y-SNP) have the power to provide a deep understanding of the human evolutionary past, forensic pedigree, and bio-geographical ancestry information. Several international cross-continental or regional Y-panels instead of Y-whole sequencing have recently been developed to promote Y-tools in forensic practice. However, panels based on next-generation sequencing (NGS) explicitly developed for Chinese populations are insufficient to represent the Chinese Y-chromosome genetic diversity and complex population structures, especially for Chinese-predominant haplogroup O. We developed and validated a 639-plex panel including 633 Y-SNPs and 6 Y-Insertion/deletions, which covered 573 Y haplogroups on the Y-DNA haplogroup tree. In this panel, subgroups from haplogroup O accounted for 64.4% of total inferable haplogroups. We reported the sequencing metrics of 354 libraries sequenced with this panel, with the average sequencing depth among 226 individuals being 3,741×. We illuminated the high level of concordance, accuracy, reproducibility, and specificity of the 639-plex panel and found that 610 loci were genotyped with as little as 0.03 ng of genomic DNA in the sensitivity test. 94.05% of the 639 loci were detectable in male-female mixed DNA samples with a mix ratio of 1:500. Nearly all of the loci were genotyped correctly when no more than 25 ng/μL tannic acid, 20 ng/μL humic acid, or 37.5 μM hematin was added to the amplification mixture. More than 80% of genotypes were obtained from degraded DNA samples with a degradation index of 11.76. Individuals from the same pedigree shared identical genotypes in 11 male pedigrees. Finally, we presented the complex evolutionary history of 183 northern Chinese Hans and six other Chinese populations, and found multiple founding lineages that contributed to the northern Han Chinese gene pool. The 639-plex panel proved an efficient tool for Chinese paternal studies and forensic applications.
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Affiliation(s)
- Guang-Bin Zhao
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Lei Miao
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Mengge Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jia-Hui Yuan
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Lan-Hai Wei
- School of Ethnology and Anthropology, Inner Mongolia Normal University, Inner Mongolia, 010028, China
| | - Yao-Sen Feng
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Jie Zhao
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Ke-Lai Kang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Chi Zhang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - An-Quan Ji
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China.
| | - Le Wang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China.
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9
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He Y, Guo Y, Zheng W, Yue T, Zhang H, Wang B, Feng Z, Ouzhuluobu, Cui C, Liu K, Zhou B, Zeng X, Li L, Wang T, Wang Y, Zhang C, Xu S, Qi X, Su B. Polygenic adaptation leads to a higher reproductive fitness of native Tibetans at high altitude. Curr Biol 2023; 33:4037-4051.e5. [PMID: 37643619 DOI: 10.1016/j.cub.2023.08.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 06/01/2023] [Accepted: 08/04/2023] [Indexed: 08/31/2023]
Abstract
The adaptation of Tibetans to high-altitude environments has been studied extensively. However, the direct assessment of evolutionary adaptation, i.e., the reproductive fitness of Tibetans and its genetic basis, remains elusive. Here, we conduct systematic phenotyping and genome-wide association analysis of 2,252 mother-newborn pairs of indigenous Tibetans, covering 12 reproductive traits and 76 maternal physiological traits. Compared with the lowland immigrants living at high altitudes, indigenous Tibetans show better reproductive outcomes, reflected by their lower abortion rate, higher birth weight, and better fetal development. The results of genome-wide association analyses indicate a polygenic adaptation of reproduction in Tibetans, attributed to the genomic backgrounds of both the mothers and the newborns. Furthermore, the EPAS1-edited mice display higher reproductive fitness under chronic hypoxia, mirroring the situation in Tibetans. Collectively, these results shed new light on the phenotypic pattern and the genetic mechanism of human reproductive fitness in extreme environments.
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Affiliation(s)
- Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
| | - Yongbo Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Wangshan Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Tian Yue
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650000, China
| | - Bin Wang
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa 850000, China
| | - Zhanying Feng
- CEMS, NCMIS, MDIS, Academy of Mathematics & Systems Science, Chinese Academy of Sciences, Beijing 100080, China
| | - Ouzhuluobu
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa 850000, China; High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa 850000, China
| | - Chaoying Cui
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa 850000, China; High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa 850000, China
| | - Kai Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Bin Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Xuerui Zeng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Liya Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Tianyun Wang
- Department of Medical Genetics, Center for Medical Genetics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yong Wang
- CEMS, NCMIS, MDIS, Academy of Mathematics & Systems Science, Chinese Academy of Sciences, Beijing 100080, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Chao Zhang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China; Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa 850000, China; State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650000, China.
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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10
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Zhang G, Cui C, Wangdue S, Lu H, Chen H, Xi L, He W, Yuan H, Tsring T, Chen Z, Yang F, Tsering T, Li S, Tashi N, Yang T, Tong Y, Wu X, Li L, He Y, Cao P, Dai Q, Liu F, Feng X, Wang T, Yang R, Ping W, Zhang M, Gao X, Liu Y, Wang W, Fu Q. Maternal genetic history of ancient Tibetans over the past 4000 years. J Genet Genomics 2023; 50:765-775. [PMID: 36933795 DOI: 10.1016/j.jgg.2023.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/14/2023] [Accepted: 03/14/2023] [Indexed: 03/17/2023]
Abstract
The settlement of the Tibetan Plateau epitomizes human adaptation to a high-altitude environment that poses great challenges to human activity. Here, we reconstruct a 4000-year maternal genetic history of Tibetans using 128 ancient mitochondrial genome data from 37 sites in Tibet. The phylogeny of haplotypes M9a1a, M9a1b, D4g2, G2a'c, and D4i show that ancient Tibetans share the most recent common ancestor with ancient Middle and Upper Yellow River populations around the Early and Middle Holocene. In addition, the connections between Tibetans and Northeastern Asians vary over the past 4000 years, with a stronger matrilineal connection between the two during 4000 BP-3000 BP, and a weakened connection after 3000 BP, that are coincident with climate change, followed by a reinforced connection after the Tubo period (1400 BP-1100 BP). Besides, an over 4000-year matrilineal continuity is observed in some of the maternal lineages. We also find the maternal genetic structure of ancient Tibetans is correlated to the geography and interactions between ancient Tibetans and ancient Nepal and Pakistan populations. Overall, the maternal genetic history of Tibetans can be characterized as a long-term matrilineal continuity with frequent internal and external population interactions that are dynamically shaped by geography, climate changes, as well as historical events.
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Affiliation(s)
- Ganyu Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Can Cui
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shargan Wangdue
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Hongliang Lu
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Honghai Chen
- School of Cultural Heritage, Northwest University, Xi'an, Shaanxi 710069, China
| | - Lin Xi
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Wei He
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Haibing Yuan
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Tinley Tsring
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Zujun Chen
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Feng Yang
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Tashi Tsering
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Shuai Li
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Norbu Tashi
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Tsho Yang
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Yan Tong
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Xiaohong Wu
- School of Archaeology and Museology, Peking University, Beijing 100871, China
| | - Linhui Li
- Tibet Institute for Conservation and Research of Cultural Relics, Lhasa, Tibet 850000, China
| | - Yuanhong He
- Center for Archaeological Science, School of Archaeology and Museology, Sichuan University, Chengdu, Sichuan 610064, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Tianyi Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Wanjing Ping
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Ming Zhang
- School of Cultural Heritage, Northwest University, Xi'an, Shaanxi 710069, China
| | - Xing Gao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.
| | - Wenjun Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; Science and Technology Archaeology, National Centre for Archaeology, Beijing 100013, China.
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shanghai Qi Zhi Institute, Shanghai 200232, China.
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11
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He Y, Zheng W, Guo Y, Yue T, Cui C, Ouzhuluobu, Zhang H, Liu K, Yang Z, Wu T, Qu J, Jin ZB, Yang J, Lu F, Qi X, Su B. Deep phenotyping of 11,880 highlanders reveals novel adaptive traits in native Tibetans. iScience 2023; 26:107677. [PMID: 37680474 PMCID: PMC10481350 DOI: 10.1016/j.isci.2023.107677] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 06/26/2023] [Accepted: 08/14/2023] [Indexed: 09/09/2023] Open
Abstract
Tibetans are the ideal population to study genetic adaptation in extreme environments. Here, we performed systematic phenotyping of 11,880 highlanders, covering 133 quantitative traits of 13 organ systems. We provided a comprehensive phenotypic atlas by comparing altitude adaptation and altitude acclimatization. We found the differences between adaptation and acclimatization are quantitative rather than qualitative, with a whole-system "blunted effect" seen in the adapted Tibetans. We characterized twelve different functional changes between adaptation and acclimatization. More importantly, we established a landscape of adaptive phenotypes of indigenous Tibetans, including 45 newly identified Tibetan adaptation-nominated traits, involving specific changes of Tibetans in internal organ state, metabolism, eye morphology, and skin pigmentation. In addition, we observed a sex-biased pattern between altitude acclimatization and adaptation. The generated atlas of phenotypic landscape provides new insights into understanding of human adaptation to high-altitude environments, and it serves as a valuable blueprint for future medical and physiological studies.
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Affiliation(s)
- Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Wangshan Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Yongbo Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Tian Yue
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | | | - Ouzhuluobu
- Tibetan Fukang Hospital, Lhasa 850000, China
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650000, China
| | - Kai Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Zhaohui Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Academy of Medicine Science, Zhengzhou University, Zhengzhou 450052, China
| | - Tianyi Wu
- National Key Laboratory of High Altitude Medicine, High Altitude Medical Research Institute, Xining 810012, China
| | - Jia Qu
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Zi-Bing Jin
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing 100730, China
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Fan Lu
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Tibetan Fukang Hospital, Lhasa 850000, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650000, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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12
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Jiang Y, Ping J, Lu H, Zhang H, Liu M, Li Y, Zhou G. Associations between high-altitude adaptation and risk of cardiovascular diseases: a bidirectional Mendelian randomization study. Mol Genet Genomics 2023; 298:1007-1021. [PMID: 37233799 DOI: 10.1007/s00438-023-02035-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023]
Abstract
High-altitude adaptation (HAA) was reported to be significantly associated with reduced risks for multiple cardiovascular diseases (CVDs). However, the causality and direction of the associations are largely uncharacterized. We aimed to examine the potential causal relationships between HAA and six types of CVD, including coronary artery disease (CAD), cerebral aneurysm, ischemic stroke, peripheral artery disease, arrhythmia and atrial fibrillation. We obtained the summary data from largest available genome-wide association study of HAA and six types of CVD. Two-sample bidirectional Mendelian randomization (MR) analyses were performed to infer the causality between them. In the sensitivity analyses, MR-Egger regression analyses and MR-Pleiotropy RESidual Sum and Outlier (MR-PRESSO) global analyses were used to assess the pleiotropic effects; Cochran's Q tests were used to test the heterogeneity by inverse variance-weighted (IVW) and MR-Egger methods; and the leave-one-out analyses were used to examine whether some single nucleotide polymorphisms (SNPs) could influence the results independently. The MR main analyses showed that the genetically instrumented HAA was significantly causally associated with the reduced risks of CAD (odds ratio [OR] = 0.029; 95% confidence interval [CI] = 0.004-0.234; P = 8.64 × 10-4). In contrast, there was no statistically significant relationship between CVDs and HAA. Our findings provide evidence for the causal effects of HAA on the reduced risks of CAD. However, there is no causality of CVDs on HAA. These findings might be helpful in developing the prevention and intervention strategies for CAD.
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Affiliation(s)
- Yuqing Jiang
- Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing City, Jiangsu Province, 211166, People's Republic of China
| | - Jie Ping
- Department of Genetics and Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China
| | - Hao Lu
- Department of Genetics and Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China
| | - Haoxiang Zhang
- The No. 954 Hospital of PLA, Shannan City, 856100, People's Republic of China
| | - Mengyu Liu
- Department of Genetics and Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China
| | - Yuanfeng Li
- Department of Genetics and Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China.
| | - Gangqiao Zhou
- Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing City, Jiangsu Province, 211166, People's Republic of China.
- Department of Genetics and Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China.
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13
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Li L, Shen S, Bickler P, Jacobson MP, Wu LF, Altschuler SJ. Searching for molecular hypoxia sensors among oxygen-dependent enzymes. eLife 2023; 12:e87705. [PMID: 37494095 PMCID: PMC10371230 DOI: 10.7554/elife.87705] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/09/2023] [Indexed: 07/27/2023] Open
Abstract
The ability to sense and respond to changes in cellular oxygen levels is critical for aerobic organisms and requires a molecular oxygen sensor. The prototypical sensor is the oxygen-dependent enzyme PHD: hypoxia inhibits its ability to hydroxylate the transcription factor HIF, causing HIF to accumulate and trigger the classic HIF-dependent hypoxia response. A small handful of other oxygen sensors are known, all of which are oxygen-dependent enzymes. However, hundreds of oxygen-dependent enzymes exist among aerobic organisms, raising the possibility that additional sensors remain to be discovered. This review summarizes known and potential hypoxia sensors among human O2-dependent enzymes and highlights their possible roles in hypoxia-related adaptation and diseases.
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Affiliation(s)
- Li Li
- Department of Pharmaceutical Chemistry, University of California San Francisco, San FranciscoSan FranciscoUnited States
| | - Susan Shen
- Department of Pharmaceutical Chemistry, University of California San Francisco, San FranciscoSan FranciscoUnited States
- Department of Psychiatry, University of California, San FranciscoSan FranciscoUnited States
| | - Philip Bickler
- Hypoxia Research Laboratory, University of California San Francisco, San FranciscoSan FranciscoUnited States
- Center for Health Equity in Surgery and Anesthesia, University of California San Francisco, San FranciscoSan FranciscoUnited States
- Anesthesia and Perioperative Care, University of California San Francisco, San FranciscoSan FranciscoUnited States
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San FranciscoSan FranciscoUnited States
| | - Lani F Wu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San FranciscoSan FranciscoUnited States
| | - Steven J Altschuler
- Department of Pharmaceutical Chemistry, University of California San Francisco, San FranciscoSan FranciscoUnited States
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14
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Zheng W, He Y, Guo Y, Yue T, Zhang H, Li J, Zhou B, Zeng X, Li L, Wang B, Cao J, Chen L, Li C, Li H, Cui C, Bai C, Qi X, Su B. Large-scale genome sequencing redefines the genetic footprints of high-altitude adaptation in Tibetans. Genome Biol 2023; 24:73. [PMID: 37055782 PMCID: PMC10099689 DOI: 10.1186/s13059-023-02912-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/29/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND Tibetans are genetically adapted to high-altitude environments. Though many studies have been conducted, the genetic basis of the adaptation remains elusive due to the poor reproducibility for detecting selective signatures in the Tibetan genomes. RESULTS Here, we present whole-genome sequencing (WGS) data of 1001 indigenous Tibetans, covering the major populated areas of the Qinghai-Tibetan Plateau in China. We identify 35 million variants, and more than one-third of them are novel variants. Utilizing the large-scale WGS data, we construct a comprehensive map of allele frequency and linkage disequilibrium and provide a population-specific genome reference panel, referred to as 1KTGP. Moreover, with the use of a combined approach, we redefine the signatures of Darwinian-positive selection in the Tibetan genomes, and we characterize a high-confidence list of 4320 variants and 192 genes that have undergone selection in Tibetans. In particular, we discover four new genes, TMEM132C, ATP13A3, SANBR, and KHDRBS2, with strong signals of selection, and they may account for the adaptation of cardio-pulmonary functions in Tibetans. Functional annotation and enrichment analysis indicate that the 192 genes with selective signatures are likely involved in multiple organs and physiological systems, suggesting polygenic and pleiotropic effects. CONCLUSIONS Overall, the large-scale Tibetan WGS data and the identified adaptive variants/genes can serve as a valuable resource for future genetic and medical studies of high-altitude populations.
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Affiliation(s)
- Wangshan Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Yongbo Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Tian Yue
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Jun Li
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa, 850000, China
| | - Bin Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Xuerui Zeng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Liya Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Bin Wang
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa, 850000, China
| | - Jingxin Cao
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa, 850000, China
| | - Li Chen
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa, 850000, China
| | - Chunxia Li
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa, 850000, China
| | - Hongyan Li
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa, 850000, China
| | - Chaoying Cui
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, 850000, China
| | - Caijuan Bai
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa, 850000, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- Fukang Obstetrics, Gynecology and Children Branch Hospital, Tibetan Fukang Hospital, Lhasa, 850000, China.
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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15
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The matrilineal ancestry of Nepali populations. Hum Genet 2023; 142:167-180. [PMID: 36242641 DOI: 10.1007/s00439-022-02488-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/17/2022] [Indexed: 11/04/2022]
Abstract
The Tibetan plateau and high mountain ranges of Nepal are one of the challenging geographical regions inhabited by modern humans. While much of the ethnographic and population-based genetic studies were carried out to investigate the Tibetan and Sherpa highlanders, little is known about the demographic processes that enabled the colonization of the hilly areas of Nepal. Thus, the present study aimed to investigate the past demographic events that shaped the extant Nepalese genetic diversity using mitochondrial DNA (mtDNA) variations from ethnic Nepalese groups. We have analyzed mtDNA sequences of 999 Nepalese and compared data with 38,622 published mtDNA sequences from rest of the world. Our analysis revealed that the genomic landscapes of prehistoric Himalayan settlers of Nepal were similar to that of the low-altitude extant Nepalese (LAN), especially Newar and Magar population groups, but differ from contemporary high-altitude Sherpas. LAN might have derived their East Eurasian ancestry mainly from low-altitude Tibeto-Burmans, who likely have migrated from East Asia and assimilated across the Eastern Himalayas extended from the Eastern Nepal to the North-East of India, Bhutan, Tibet and Northern Myanmar. We also identified a clear genetic sub-structure across different ethnic groups of Nepal based on mtDNA haplogroups and ectodysplasin-A receptor (EDAR) gene polymorphism. Our comprehensive high-resolution mtDNA-based genetic study of Tibeto-Burman communities reconstructs the maternal origins of prehistoric Himalayan populations and sheds light on migration events that have brought most of the East Eurasian ancestry to the present-day Nepalese population.
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16
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Wang F, Li W, Wang X, Luo X, Dai P. A single-tube multiplex real-time PCR for HLA-B*38:02 genotype by detecting highly specific SNPs. Pharmacogenomics 2023; 24:5-14. [PMID: 36661044 DOI: 10.2217/pgs-2022-0132] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Purpose: HLA-B*38:02 is closely related to carbimazole/methimazole-induced agranulocytosis. This study aimed to develop and validate a rapid and economical method for HLA-B*38:02 genotyping. Methods: A single-tube multiplex real-time PCR detection system comprising amplification refractory mutation system primers and TaqMan probes was established for HLA-B*38:02 genotyping. Sequence-based typing was applied to validate the accuracy of the assay. Results: The accuracy of the assay was 100% for HLA-B*38:02 genotyping. The detection limit of the new method was 0.05 ng DNA. The positive rate of HLA-B*38:02 in the Han (8%, n = 100), Bouyei (17.8%, n = 90) and Tibetan (12.7%, n = 110) populations was significantly higher than that in the Uighur population (1%, n = 100) (p < 0.05). Conclusion: The proposed method is rapid and reliable for HLA-B*38:02 screening in a clinical setting.
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Affiliation(s)
- Fei Wang
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, Shaanxi Province, 710069, China
| | - Wenqi Li
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, Shaanxi Province, 710069, China
| | - Xuan Wang
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, Shaanxi Province, 710069, China
| | - Xiang Luo
- Department of Respiratory, Tongchuan People's Hospital Tongchuan, Shaanxi Province, People's Republic of China
| | - Penggao Dai
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University of Xi'an, Shaanxi Province, 710069, China.,Shaanxi Lifegen Co.,Ltd, Building 1, Collaborative Innovation Port, Fengdong New City, Xixian New Area, Xi'an, Shaanxi Province, 712000, China
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17
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Zhang L, Zhang R, Zhang F, Yin X, Liu Y, Guo Y, Sun P. Comparison of Cardiorespiratory Fitness of Chinese Tibetan Adolescents with Their Han Counterparts: A Cross-Sectional Retrospective Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:16526. [PMID: 36554405 PMCID: PMC9779579 DOI: 10.3390/ijerph192416526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/04/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Cardiorespiratory fitness (CRF) is a core element of healthy physical fitness. Foreign attention to CRF in adolescents at different altitudes is high, while less research has been conducted on Chinese adolescents. In order to compare the CRF of Chinese Tibetan adolescents with their Han counterparts born and raised at high altitude and Chinese Han adolescents at sea level. A total of 2748 participants, including Chinese Tibetan adolescents, Chinese Han adolescents born and raised at high altitudes, and Chinese Han adolescents at sea level aged 12-18 years old, were obtained using convenience sampling and random cluster sampling. The method of the 20 m shuttle run test (20 m SRT) test was used to derive VO2max by equation. One-way ANOVA and LSD methods were conducted, and effect sizes were calculated to compare the CRF of the three types of adolescents. Regression analysis was used to analyze the relationship between altitude and VO2max. The VO2max scores of Chinese Tibetan adolescents and Chinese Han adolescents at sea level were higher than Chinese Han adolescents born and raised at high altitudes. For both boys and girls, the VO2max scores of Chinese Tibetan adolescents exceeded Chinese Han adolescents at sea level after the age of 16 years old. Regression analysis showed that altitude was inversely associated with VO2max. The pace of lung growth may distinguish Chinese Tibetan adolescents from Chinese Han adolescents born and raised at high altitudes. The results of the study suggest that we should focus on the changes in CRF in adolescents at different altitudes and should adopt different CRF interventions for adolescents at different altitudes.
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Affiliation(s)
- Li Zhang
- Department of Physical Education, China University of Mining and Technology, Beijing 100083, China
| | - Ruming Zhang
- Department of Physical Education, China University of Mining and Technology, Beijing 100083, China
| | - Feng Zhang
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of Education, East China Normal University, Shanghai 200241, China
- College of Physical Education and Health, East China Normal University, Shanghai 200241, China
| | - Xiaojian Yin
- College of Economics and Management, Shanghai Institute of Technology, Shanghai 201418, China
| | - Yuan Liu
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of Education, East China Normal University, Shanghai 200241, China
- College of Physical Education and Health, East China Normal University, Shanghai 200241, China
| | - Yaru Guo
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of Education, East China Normal University, Shanghai 200241, China
- College of Physical Education and Health, East China Normal University, Shanghai 200241, China
| | - Pengwei Sun
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of Education, East China Normal University, Shanghai 200241, China
- College of Physical Education and Health, East China Normal University, Shanghai 200241, China
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18
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Askapuli A, Vilar M, Garcia-Ortiz H, Zhabagin M, Sabitov Z, Akilzhanova A, Ramanculov E, Schamiloglu U, Martinez-Hernandez A, Contreras-Cubas C, Barajas-Olmos F, Schurr TG, Zhumadilov Z, Flores-Huacuja M, Orozco L, Hawks J, Saitou N. Kazak mitochondrial genomes provide insights into the human population history of Central Eurasia. PLoS One 2022; 17:e0277771. [PMID: 36445929 PMCID: PMC9707748 DOI: 10.1371/journal.pone.0277771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 11/03/2022] [Indexed: 11/30/2022] Open
Abstract
As a historical nomadic group in Central Asia, Kazaks have mainly inhabited the steppe zone from the Altay Mountains in the East to the Caspian Sea in the West. Fine scale characterization of the genetic profile and population structure of Kazaks would be invaluable for understanding their population history and modeling prehistoric human expansions across the Eurasian steppes. With this mind, we characterized the maternal lineages of 200 Kazaks from Jetisuu at mitochondrial genome level. Our results reveal that Jetisuu Kazaks have unique mtDNA haplotypes including those belonging to the basal branches of both West Eurasian (R0, H, HV) and East Eurasian (A, B, C, D) lineages. The great diversity observed in their maternal lineages may reflect pivotal geographic location of Kazaks in Eurasia and implies a complex history for this population. Comparative analyses of mitochondrial genomes of human populations in Central Eurasia reveal a common maternal genetic ancestry for Turko-Mongolian speakers and their expansion being responsible for the presence of East Eurasian maternal lineages in Central Eurasia. Our analyses further indicate maternal genetic affinity between the Sherpas from the Tibetan Plateau with the Turko-Mongolian speakers.
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Affiliation(s)
- Ayken Askapuli
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Miguel Vilar
- The Genographic Project, National Geographic Society, Washington, DC, United States of America
- Department of Anthropology, University of Maryland, College Park, Maryland, United States of America
| | - Humberto Garcia-Ortiz
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Maxat Zhabagin
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | | | - Ainur Akilzhanova
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Erlan Ramanculov
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
| | - Uli Schamiloglu
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
| | - Angelica Martinez-Hernandez
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Theodore G. Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Zhaxybay Zhumadilov
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Marlen Flores-Huacuja
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - John Hawks
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Anthropology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Naruya Saitou
- Population Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
- Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Okinawa Ken, Japan
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19
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Zhu K, Du P, Li J, Zhang J, Hu X, Meng H, Chen L, Zhou B, Yang X, Xiong J, Allen E, Ren X, Ding Y, Xu Y, Chang X, Yu Y, Han S, Dong G, Wang CC, Wen S. Cultural and demic co-diffusion of Tubo Empire on Tibetan Plateau. iScience 2022; 25:105636. [PMID: 36582485 PMCID: PMC9792914 DOI: 10.1016/j.isci.2022.105636] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/15/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
A high point of Tibetan Plateau (TP) civilization, the expansive Tubo Empire (618-842 AD) wielded great influence across ancient western China. However, whether the Tubo expansion was cultural or demic remains unclear due to sparse ancient DNA sampling. Here, we reported ten ancient genomes at 0.017- to 0.867-fold coverages from the Dulan site with typical Tubo archaeological culture dating to 1308-1130 BP. Nine individuals from three different grave types have close relationship with previously reported ancient highlanders from the southwestern Himalayas and modern core-Tibetan populations. A Dulan-related Tubo ancestry contributed overwhelmingly (95%-100%) to the formation of modern Tibetans. A genetic outlier with dominant Eurasian steppe-related ancestry suggesting a potential population movement into the Tubo-controlled regions from Central Asia. Together with archeological evidence from burial styles and customs, our study suggested the impact of the Tubo empire on the northeast edge of the TP involved both cultural and demic diffusion.
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Affiliation(s)
- Kongyang Zhu
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China,State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Panxin Du
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Jiyuan Li
- Qinghai Provincial Cultural Relics and Archaeology Institute, Xining 810007, China
| | | | - Xiaojun Hu
- Qinghai Provincial Cultural Relics and Archaeology Institute, Xining 810007, China
| | - Hailiang Meng
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Liang Chen
- China-Central Asia Human Environmental “the Belt and Road” Joint Laboratory, Northwest University, Xi’an 710127, China
| | - Boyan Zhou
- Division of Biostatistics, Department of Population Health, School of Medicine, New York University, New York, NY 10016, USA
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China
| | - Jianxue Xiong
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Edward Allen
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Xiaoying Ren
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Yi Ding
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Yiran Xu
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Xin Chang
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Yao Yu
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Sheng Han
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Guanghui Dong
- Key Laboratory of Western China’s Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China,Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China,Institute of Artificial Intelligence, Xiamen University, Xiamen 361005, China,Corresponding author
| | - Shaoqing Wen
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China,Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China,MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China,Center for the Belt and Road Archaeology and Ancient Civilizations, Shanghai 200433, China,Corresponding author
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20
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Abstract
Strong ultraviolet (UV) radiation at high altitude imposes a serious selective pressure, which may induce skin pigmentation adaptation of indigenous populations. We conducted skin pigmentation phenotyping and genome-wide analysis of Tibetans in order to understand the underlying mechanism of adaptation to UV radiation. We observe that Tibetans have darker baseline skin color compared with lowland Han Chinese, as well as an improved tanning ability, suggesting a two-level adaptation to boost their melanin production. A genome-wide search for the responsible genes identifies GNPAT showing strong signals of positive selection in Tibetans. An enhancer mutation (rs75356281) located in GNPAT intron 2 is enriched in Tibetans (58%) but rare in other world populations (0 to 18%). The adaptive allele of rs75356281 is associated with darker skin in Tibetans and, under UVB treatment, it displays higher enhancer activities compared with the wild-type allele in in vitro luciferase assays. Transcriptome analyses of gene-edited cells clearly show that with UVB treatment, the adaptive variant of GNPAT promotes melanin synthesis, likely through the interactions of CAT and ACAA1 in peroxisomes with other pigmentation genes, and they act synergistically, leading to an improved tanning ability in Tibetans for UV protection.
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21
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Ancient DNA from Tubo Kingdom-related tombs in northeastern Tibetan Plateau revealed their genetic affinity to both Tibeto-Burman and Altaic populations. Mol Genet Genomics 2022; 297:1755-1765. [PMID: 36152077 DOI: 10.1007/s00438-022-01955-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 08/27/2022] [Indexed: 10/14/2022]
Abstract
The rise of the Tubo Kingdom is considered as the key period for the formation of modern groups on the Tibetan Plateau. The ethnic origin of the residents of the Tubo Kingdom is quite complex, and their genetic structure remains unclear. The tombs of the Tubo Kingdom period in Dulan County, Qinghai Province, dating back to the seventh century, are considered to be the remains left by Tubo conquerors or the Tuyuhun people dominated by the Tubo Kingdom. The human remains of these tombs are ideal materials for studying the population dynamics in the Tubo Kingdom. In this paper, we analyzed the genome-wide data of eight remains from these tombs by shotgun sequencing and multiplex PCR panels and compared the results with data of available ancient and modern populations across East Asia. Genetic continuity between ancient Dulan people with ancient Xianbei tribes in Northeast Asia, ancient settlers on the Tibetan Plateau, and modern Tibeto-Burman populations was found. Surprisingly, one out of eight individuals showed typical genetic features of populations from Central Asia. In summary, the genetic diversity of ancient Dulan people and their affiliations with other populations provide an example of the complex origin of the residents in the Tubo Kingdom and their long-distance connection with populations in a vast geographic region across ancient Asia.
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22
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Ma L, Wang R, Feng S, Yang X, Li J, Zhang Z, Zhan H, Wang Y, Xia Z, Wang CC, Kang L. Genomic insight into the population history and biological adaptations of high-altitude Tibetan highlanders in Nagqu. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.930840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Tibetan, one of the largest indigenous populations living in the high-altitude region of the Tibetan Plateau (TP), has developed a suite of physiological adaptation strategies to cope with the extreme highland environment in TP. Here, we reported genome-wide SNP data from 48 Kham-speaking Nagqu Tibetans and analyzed it with published data from 1,067 individuals in 167 modern and ancient populations to characterize the detailed Tibetan subgroup history and population substructure. Overall, the patterns of allele sharing and haplotype sharing suggested (1) the relatively genetic homogeny between the studied Nagqu Tibetans and ancient Nepalese as well as present-day core Tibetans from Lhasa, Nagqu, and Shigatse; and (2) the close relationship between our studied Kham-speaking Nagqu Tibetans and Kham-speaking Chamdo Tibetans. The fitted qpAdm models showed that the studied Nagqu Tibetans could be fitted as having the main ancestry from late Neolithic upper Yellow River millet farmers and deeply diverged lineages from Southern East Asians (represented by Upper Paleolithic Guangxi_Longlin and Laos_Hoabinhian), and a non-neglectable western Steppe herder-related ancestry (∼3%). We further scanned the candidate genomic regions of natural selection for our newly generated Nagqu Tibetans and the published core Tibetans via FST, iHS, and XP-EHH tests. The genes overlapping with these regions were associated with essential human biological functions such as immune response, enzyme activity, signal transduction, skin development, and energy metabolism. Together, our results shed light on the admixture and evolutionary history of Nagqu Tibetan populations.
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23
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Yang Z, Chen H, Lu Y, Gao Y, Sun H, Wang J, Jin L, Chu J, Xu S. Genetic evidence of tri-genealogy hypothesis on the origin of ethnic minorities in Yunnan. BMC Biol 2022; 20:166. [PMID: 35864541 PMCID: PMC9306206 DOI: 10.1186/s12915-022-01367-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 07/05/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Yunnan is located in Southwest China and consists of great cultural, linguistic, and genetic diversity. However, the genomic diversity of ethnic minorities in Yunnan is largely under-investigated. To gain insights into population history and local adaptation of Yunnan minorities, we analyzed 242 whole-exome sequencing data with high coverage (~ 100-150 ×) of Yunnan minorities representing Achang, Jingpo, Dai, and Deang, who were linguistically assumed to be derived from three ancient lineages (the tri-genealogy hypothesis), i.e., Di-Qiang, Bai-Yue, and Bai-Pu. RESULTS Yunnan minorities show considerable genetic differences. Di-Qiang populations likely migrated from the Tibetan area about 6700 years ago. Genetic divergence between Bai-Yue and Di-Qiang was estimated to be 7000 years, and that between Bai-Yue and Bai-Pu was estimated to be 5500 years. Bai-Pu is relatively isolated, but gene flow from surrounding Di-Qiang and Bai-Yue populations was also found. Furthermore, we identified genetic variants that are differentiated within Yunnan minorities possibly due to the living circumstances and habits. Notably, we found that adaptive variants related to malaria and glucose metabolism suggest the adaptation to thalassemia and G6PD deficiency resulting from malaria resistance in the Dai population. CONCLUSIONS We provided genetic evidence of the tri-genealogy hypothesis as well as new insights into the genetic history and local adaptation of the Yunnan minorities.
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Affiliation(s)
- Zhaoqing Yang
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, 650118, China
| | - Hao Chen
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yang Gao
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, 201203, China
| | - Hao Sun
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, 650118, China
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, 201203, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, 201203, China
| | - Jiayou Chu
- Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, 650118, China.
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, 201203, China.
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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24
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Xiong J, Tao Y, Ben M, Yang Y, Du P, Allen E, Wang H, Xu Y, Yu Y, Meng H, Bao H, Zhou B, Chen G, Li H, Wen S. Uniparental Genetic Analyses Reveal Multi-Ethnic Background of Dunhuang Foyemiaowan Population (220–907 CE) With Typical Han Chinese Archaological Culture. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.901295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The relationship between archeological culture and ethnicity is invariably complex. This is especially the case for periods of national division and rapid inter-ethnic exchange, such as China’s Sixteen Kingdoms (304–439 CE) and Northern and Southern Dynasties (420–589 CE). Going by tomb shape and grave goods, the Foyemiaowan cemetery at Dunhuang exhibits a typical third–tenth century Han style. Despite this, the ethnic makeup of the Foyemiaowan population has remained unclear. We therefore analyzed 485 Y-chromosomal SNPs and entire mitochondrial genomes of 34 Foyemiaowan samples. Our study yielded the following discoveries: (1) principal component analysis revealed that the Foyemiaowan population was closely clustered with Tibeto-Burman populations on the paternal side and close to Mongolic-speaking populations on the maternal side; (2) lineage comparisons at the individual level showed that the Foyemiaowan population consisted of primarily Tibeto-Burman and Han Chinese related lineages (Oα-M117, 25%;Oβ-F46, 18.75%), partially Altaic speaking North Eurasian lineages (N-F1206, 18.75%) and a slight admixture of southern East Asian lineages (O1b1a2-Page59, 6.25%; O1b1a1-PK4, 3.13%). Similarly, the maternal gene pool of Foyemiaowan contained northern East Asian (A, 4.17%; CZ, 16.67%; D, 20.83%; G, 4.17%; M9, 4.17%), southern East Asian (B, 12.51%; F, 20.83%) and western Eurasian (H, 4.17%; J, 4.17%) related lineages; (3) we discovered a relatively high genetic diversity among the Foyemiaowan population (0.891) in our ancient reference populations, indicating a complex history of population admixture. Archeological findings, stable isotope analysis and historical documents further corroborated our results. Although in this period China’s central government had relinquished control of the Hexi Corridor and regional non-Han regimes became the dominant regional power, Foyemiaowan’s inhabitants remained strongly influenced by Han culture.
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25
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Ma X, La Y, Bao P, Chu M, Guo X, Wu X, Pei J, Ding X, Liang C, Yan P. Regulatory Role of N6-Methyladenosine in Longissimus Dorsi Development in Yak. Front Vet Sci 2022; 9:757115. [PMID: 35498742 PMCID: PMC9043854 DOI: 10.3389/fvets.2022.757115] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
N6-methyladenine (m6A) RNA undergoes epigenetic modification, which is the most extensive intermediate chemical modification in mRNA. Although this modification occurs in all living organisms, it is the most widely studied among mammals. However, to date, no study has investigated the m6A transcriptome-wide map of yak and its potential biological functions in muscle development. In this study, the differences of m6A methylation and gene expression in yak muscle development belonging to three age groups, namely 3 years (group A), 6 months (group M), and 90-day-old fetuses (group E), were determined by using methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and RNA sequencing (RNA-Seq). In these three groups, a total of 6,278 (A), 9,298 (E), and 9,584 (M) m6A peaks were identified, with average densities between 1.02 and 2.01. m6A peaks were mostly enriched in the stop codon, 3′ untranslated region (UTR) region, and inner long exon region with consensus motifs of UGACA. In all the three stages, the m6A peak enrichment level was significantly negatively correlated with mRNA abundance (Pearson's correlation coefficient r = −0.22 to −0.32, p < 10−16). The functional enrichment of genes consistently modified by m6A methylation, particularly those genes that regulate cell differentiation as well as muscle growth and development, was observed at all three stages. Moreover, m6A abundance was negatively associated with gene expression levels, indicating that m6A might play a vital role in modulating gene expression during yak muscle development. This comprehensive map thus provides a solid foundation for determining the potential functional role of m6A RNA modification in yak muscle growth.
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Affiliation(s)
- Xiaoming Ma
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yongfu La
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Pengjia Bao
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Min Chu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xian Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiaoyun Wu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jie Pei
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xuezhi Ding
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chunnian Liang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
- *Correspondence: Chunnian Liang
| | - Ping Yan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Ping Yan
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Liu CC, Witonsky D, Gosling A, Lee JH, Ringbauer H, Hagan R, Patel N, Stahl R, Novembre J, Aldenderfer M, Warinner C, Di Rienzo A, Jeong C. Ancient genomes from the Himalayas illuminate the genetic history of Tibetans and their Tibeto-Burman speaking neighbors. Nat Commun 2022; 13:1203. [PMID: 35260549 PMCID: PMC8904508 DOI: 10.1038/s41467-022-28827-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 02/14/2022] [Indexed: 12/12/2022] Open
Abstract
Present-day Tibetans have adapted both genetically and culturally to the high altitude environment of the Tibetan Plateau, but fundamental questions about their origins remain unanswered. Recent archaeological and genetic research suggests the presence of an early population on the Plateau within the past 40 thousand years, followed by the arrival of subsequent groups within the past 10 thousand years. Here, we obtain new genome-wide data for 33 ancient individuals from high elevation sites on the southern fringe of the Tibetan Plateau in Nepal, who we show are most closely related to present-day Tibetans. They derive most of their ancestry from groups related to Late Neolithic populations at the northeastern edge of the Tibetan Plateau but also harbor a minor genetic component from a distinct and deep Paleolithic Eurasian ancestry. In contrast to their Tibetan neighbors, present-day non-Tibetan Tibeto-Burman speakers living at mid-elevations along the southern and eastern margins of the Plateau form a genetic cline that reflects a distinct genetic history. Finally, a comparison between ancient and present-day highlanders confirms ongoing positive selection of high altitude adaptive alleles.
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Affiliation(s)
- Chi-Chun Liu
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - David Witonsky
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Anna Gosling
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.,Department of Anatomy, University of Otago, Dunedin, 9054, New Zealand
| | - Ju Hyeon Lee
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Harald Ringbauer
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Richard Hagan
- Department of Anthropology, University of Oklahoma, Norman, OK, 73019, USA.,Department of Archaeology, University of York, York, YO10 5DD, UK
| | - Nisha Patel
- Department of Plant and Microbiology, University of Oklahoma, Norman, OK, 73019, USA.,Kintai Therapeutics, Cambridge, MA, 02139, USA
| | - Raphaela Stahl
- Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Mark Aldenderfer
- Department of Anthropology and Heritage Studies, University of California, Merced, CA, 95343, USA.
| | - Christina Warinner
- Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany. .,Department of Anthropology, Harvard University, Cambridge, MA, 02138, USA.
| | - Anna Di Rienzo
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
| | - Choongwon Jeong
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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27
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Zhang P, Zhang X, Zhang X, Gao X, Huerta-Sanchez E, Zwyns N. Denisovans and Homo sapiens on the Tibetan Plateau: dispersals and adaptations. Trends Ecol Evol 2022; 37:257-267. [PMID: 34863581 PMCID: PMC9140327 DOI: 10.1016/j.tree.2021.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/31/2021] [Accepted: 11/01/2021] [Indexed: 10/19/2022]
Abstract
Recent archaeological discoveries suggest that both archaic Denisovans and Homo sapiens occupied the Tibetan Plateau earlier than expected. Genetic studies show that a pulse of Denisovan introgression was involved in the adaptation of Tibetan populations to high-altitude hypoxia. These findings challenge the traditional view that the plateau was one of the last places on earth colonized by H. sapiens and warrant a reappraisal of the population history of this highland. Here, we integrate archaeological and genomic evidence relevant to human dispersal, settlement, and adaptation in the region. We propose two testable models to address the peopling of the plateau in the broader context of H. sapiens dispersal and their encounters with Denisovans in Asia.
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Affiliation(s)
- Peiqi Zhang
- Department of Anthropology, University of California, Davis, CA 95616, USA.
| | - Xinjun Zhang
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Xiaoling Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; CAS Center for Excellence in Life and Paleoenvironment, Beijing 10044, China
| | - Xing Gao
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China; CAS Center for Excellence in Life and Paleoenvironment, Beijing 10044, China
| | - Emilia Huerta-Sanchez
- Department of Ecology and Evolutionary Biology and Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
| | - Nicolas Zwyns
- Department of Anthropology, University of California, Davis, CA 95616, USA; Department of Human Evolution, Max Planck Insititute for Evolutionary Anthropology, Leipzig 04103, Germany
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28
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Gu B, Wang S, Liu F, Song Y, Li J, Ni Y, Chen M, Hu J, Ouzhu L, Li Z, Liu L, Li X, Liu X. Same total normal forms sperm counts of males from Lhasa and Shanghai, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:18820-18831. [PMID: 34704224 DOI: 10.1007/s11356-021-17083-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
Male infertility may be caused by genetic and/or environmental factors that impair spermatogenesis and sperm maturation. High-altitude (HA) hypoxic environments represent one of the most serious challenges faced by humans that reside in these areas. To assess the influence of the plateau environment on semen parameters, 2,798 males, including 1,111 native Tibetans and 1,687 Han Chinese individuals living in the plains (HCILP) who underwent pre-pregnancy checkups, were enrolled in this study. The semen samples of males were evaluated to determine conventional sperm parameters, sperm morphology, and sperm movement. Reproductive endocrine hormones (REHs) were detected in 474 males, including 221 Tibetans and 253 HCILP. Due to recurrent abortions in partners, the DNA fragmentation index (DFI) of 133 native Tibetans and 393 HCILP individuals was further compared. Luteinizing hormone (LH) (4.94 ± 2.12 vs. 3.29 ± 1.43 U/L), prolactin (11.34 ± 3.87 vs. 8.97 ± 3.48 nmol/L), E2/T (0.22 ± 0.11 vs 0.11 ± 0.05), median total sperm motility (61.20% vs. 51.56%), and DFI (23.11% vs. 7.22%) were higher in males from plateau areas while median progressive motility (PR) (35.60% vs. 41.12%), total number of PR sperms (51.61 vs. 59.63 mil/ejaculate), percentage of normal form sperms (3.70% vs. 6.00%), curvilinear velocity (36.10 vs. 48.97 μm/s), straight-line (rectilinear) velocity (14.70 vs. 31.52 μm/s), estradiol (103.82 ± 45.92 vs. 146.01 ± 39.73 pmol/L), progesterone (0.29 ± 0.27 vs. 2.22 ± 0.84 nmol/L), testosterone (4.90 ± 1.96 vs. 14.36 ± 5.24 nmol/L), and testosterone secretion index (ratio of testosterone to LH) (33.45 ± 22.86 vs 145.78 ± 73.41) were lower than those in males from the plains. There was no difference in median total sperm number (157.76 vs. 151.65 mil/mL), sperm concentration (52.40 vs. 51.79 mil/mL), volume (3.10 vs. 3.10 mL), total normal form sperms (5.91 vs. 6.58 mil/ejaculate, p50), and follicle-stimulating hormone (FSH) levels (4.13 ± 2.55 U/L vs 3.82 ± 2.35 U/L) between the two groups of males. The REH and sperm parameters of males from HA hypoxic environments were adaptively altered. Although the total number of PR sperm decreased and DFI increased, the Tibetan population that lives at HAs has been found to grown continuously and rapidly. These results supplement prior findings regarding the impact of HA on male reproductive function.
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Affiliation(s)
- Benhong Gu
- Department of Urology, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China
- Department of Urology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, China
| | - Shangren Wang
- Department of Urology, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China
| | - Feng Liu
- Department of Andrology, Center of Urologic Medicine, Shanghai General Hospital Affiliated To Shanghai Jiao Tong University, Shanghai, 200080, China
- Reproductive Medicine Center, Fokind Maternity and Children's Hospital, Tibet, Lhasa, 850000, China
| | - Yuxuan Song
- Department of Urology, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China
| | - Jun Li
- Reproductive Medicine Center, Fokind Maternity and Children's Hospital, Tibet, Lhasa, 850000, China
| | - Yongtao Ni
- Reproductive Medicine Center, Fokind Maternity and Children's Hospital, Tibet, Lhasa, 850000, China
| | - Min Chen
- Reproductive Medicine Center, Fokind Maternity and Children's Hospital, Tibet, Lhasa, 850000, China
| | - Jianlin Hu
- Department of Andrology, Center of Urologic Medicine, Shanghai General Hospital Affiliated To Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Luobu Ouzhu
- Reproductive Medicine Center, Fokind Maternity and Children's Hospital, Tibet, Lhasa, 850000, China
| | - Zheng Li
- Department of Andrology, Center of Urologic Medicine, Shanghai General Hospital Affiliated To Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Li Liu
- Department of Urology, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China.
| | - Xia Li
- Department of Urology, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China.
| | - Xiaoqiang Liu
- Department of Urology, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin, 300052, China.
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Li XN, Adnan A, Hadi S, Al-Qahtani WS, Alwaili MA, Alshaya DS, Jalal AS, Amer SAM, Jin F. Genetic characterization of the highlander Tibetan population from Qinghai-Tibet Plateau revealed by X chromosomal STRs. PLoS One 2022; 17:e0271769. [PMID: 35926061 PMCID: PMC9352086 DOI: 10.1371/journal.pone.0271769] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/17/2022] [Indexed: 01/20/2023] Open
Abstract
Tibetans are considered an East Asian ethnic group and primarily live in the high Tibetan plateau, the western Sichuan and Yunnan mountains of central and southern China, and areas throughout the Himalayas and around the Tibetan plateau. These people exhibit rare molecular machinery that allows them to adapt to hypoxic environments in the Qinghai-Tibet Plateau and make them a potential candidate for providing insights related to medical genetic, molecular medicine and human population studies. In the current study, we have genotyped 549 individuals with Investigator Argus X-12 Kit. For 12 X-STRs, a total of 174 unique alleles were found, among them DXS10134 and DXS10135 were the most polymorphic loci. All of the loci were in Hardy-Weinberg Equilibrium (HWE). The numbers of observed haplotypes in Highlander Tibetans males were 161,112, 96 and 108, respectively, whereas haplotype diversities (HD) were 0.9959, 0.9880, 0.9809 and 0.9873, respectively. The combined discrimination power for males (PDm) was 0.999 999 99701 and for females (PDf) was 0.999 999 999 999 9958. This study represents an extensive report on X chromosomal STR markers variation in the Highlander Tibetans population for forensic applications and population genetic studies.
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Affiliation(s)
- Xiao-na Li
- School of Fundamental Sciences, China Medical University, Shenyang, Liaoning, P.R. China
| | - Atif Adnan
- Department of Forensic Sciences, College of Criminal Justice, Naif Universsity of Security Sciences, Riyadh, Kingdom of Saudi Arabia
- * E-mail: (FJ); (AA)
| | - Sibte Hadi
- Department of Forensic Sciences, College of Criminal Justice, Naif Universsity of Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Wedad Saeed Al-Qahtani
- Department of Forensic Sciences, College of Criminal Justice, Naif Universsity of Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Maha Abdullah Alwaili
- Department of Biology, Collage of Sciences, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Dalal S. Alshaya
- Department of Biology, Collage of Sciences, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Areej S. Jalal
- Department of Biology, Collage of Sciences, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Sayed A. M. Amer
- Department of Forensic Sciences, College of Criminal Justice, Naif Universsity of Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Feng Jin
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, P.R. China
- * E-mail: (FJ); (AA)
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30
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Improving the regional Y-STR haplotype resolution utilizing haplogroup-determining Y-SNPs and the application of machine learning in Y-SNP haplogroup prediction in a forensic Y-STR database: A pilot study on male Chinese Yunnan Zhaoyang Han population. Forensic Sci Int Genet 2021; 57:102659. [PMID: 35007855 DOI: 10.1016/j.fsigen.2021.102659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 12/14/2021] [Accepted: 12/27/2021] [Indexed: 11/23/2022]
Abstract
Improving the resolution of the current widely used Y-chromosomal short tandem repeat (Y-STR) dataset is of great importance for forensic investigators, and the current approach is limited, except for the addition of more Y-STR loci. In this research, a regional Y-DNA database was investigated to improve the Y-STR haplotype resolution utilizing a Y-SNP Pedigree Tagging System that includes 24 Y-chromosomal single nucleotide polymorphism (Y-SNP) loci. This pilot study was conducted in the Chinese Yunnan Zhaoyang Han population, and 3473 unrelated male individuals were enrolled. Based on data on the male haplogroups under different panels, the matched or near-matching (NM) Y-STR haplotype pairs from different haplogroups indicated the critical roles of haplogroups in improving the regional Y-STR haplotype resolution. A classic median-joining network analysis was performed using Y-STR or Y-STR/Y-SNP data to reconstruct population substructures, which revealed the ability of Y-SNPs to correct misclassifications from Y-STRs. Additionally, population substructures were reconstructed using multiple unsupervised or supervised dimensionality reduction methods, which indicated the potential of Y-STR haplotypes in predicting Y-SNP haplogroups. Haplogroup prediction models were built based on nine publicly accessible machine-learning (ML) approaches. The results showed that the best prediction accuracy score could reach 99.71% for major haplogroups and 98.54% for detailed haplogroups. Potential influences on prediction accuracy were assessed by adjusting the Y-STR locus numbers, selecting Y-STR loci with various mutabilities, and performing data processing. ML-based predictors generally presented a better prediction accuracy than two available predictors (Nevgen and EA-YPredictor). Three tree models were developed based on the Yfiler Plus panel with unprocessed input data, which showed their strong generalization ability in classifying various Chinese Han subgroups (validation dataset). In conclusion, this study revealed the significance and application prospects of Y-SNP haplogroups in improving regional Y-STR databases. Y-SNP haplogroups can be used to discriminate NM Y-STR haplotype pairs, and it is important for forensic Y-STR databases to develop haplogroup prediction tools to improve the accuracy of biogeographic ancestry inferences.
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31
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The impact of prehistoric human dispersals on the presence of tobacco-related oral cancer in Northeast India. Gene 2021; 813:146098. [PMID: 34952175 DOI: 10.1016/j.gene.2021.146098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/20/2021] [Accepted: 11/16/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Northeast (NE) India is a subject of debate for predicting its involvement in prehistoric anatomically modern human (AMH) dispersal. The unique lifestyle and genetic characteristics of native ethnic groups in this region are believed to be responsible for their susceptibility to tobacco-related oral cancer (TrOC). The present study assessed mitochondrial macro-haplogroup (mHG) diversity and TrOC susceptibility autosomal loci to evaluate the impact of prehistoric AMH dispersal on the present day's high TrOC prevalence in major NE Indian ethnics. METHODS We considered 175 unrelated individuals from 35 ethnic groups and previously published 374 sequences for sequencing-based assessment of mtDNA-based marker by subsequent analyses like haplogroup diversity, phylogenetic, genetic structure by AMOVA, and MDS, descriptive statistics of demographic parameters, and migration analysis. Besides, we selected prolonged tobacco-chewing 124 case-control individuals from similar ethnic backgrounds for genotyping 115 autosomal loci in Sequenom iPLEX MassARRAY™ platform and mined 1000genome data (n = 398) for consequent global admixture and ancestry-specific allele frequencies-based analyses. RESULTS Our mtDNA-based findings suggested that NE populations were distinct from other Indian populations, owing to the first wave of migration from ancient southern China (∼54kya) and two successive spatial expansion events at ∼45kya and ∼43kya. Consequently, it probably acted as another source for prehistoric AMH dispersal in N/NE Asia. Besides, the second wave of back-migration from SE Asia (∼40kya) probably replaced the mitochondrial footprints of survivors from the first migrants and introduced the TrOC susceptibility traits in this region. Afterward, the autosomal marker-based observations on the transition of the disease-associated admixture component 'K6' from SE Asia reconfirmed these results. Moreover, we also observed that the mitochondrial mHG 'R' is significantly associated with the risk of TrOC (OR > 9.5) in NE India. Furthermore, the possible onset of the phenotypic expression of those traits was predicted at ∼4kya, thus, contributing to present-day's TrOC prevalence. CONCLUSIONS This study reflects its uniqueness by revealing an updated AMH dispersal route for the peopling in and out of NE India, which probably introduced the disease-causing traits in the ancestral NE Indian population. Those traits were then imprinted in their genome to get transferred through their respective generations, forming the present-day's TrOC-prevalent NE Indian population.
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32
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Basak N, Thangaraj K. High-altitude adaptation: Role of genetic and epigenetic factors. J Biosci 2021. [DOI: 10.1007/s12038-021-00228-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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33
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Guo J, Wang W, Zhao K, Li G, He G, Zhao J, Yang X, Chen J, Zhu K, Wang R, Ma H, Xu B, Wang C. Genomic insights into
Neolithic
farming‐related migrations in the junction of east and southeast
Asia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021. [DOI: 10.1002/ajpa.24434] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Weitao Wang
- Yunnan Modern Forensic Institute Kunming China
| | - Kai Zhao
- Yunnan Modern Forensic Institute Kunming China
| | | | - Guanglin He
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Jing Zhao
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Jinwen Chen
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Kongyang Zhu
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Rui Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Hao Ma
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
| | - Bingying Xu
- Research Center of Biomedical Engineering Kunming Medical University Kunming China
| | - Chuan‐Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, State Key Laboratory of Marine Environmental Science Xiamen University Xiamen China
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34
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Ge Q, Guo Y, Zheng W, Cai Y, Qi X, Zhao S. A comparative analysis of differentially expressed mRNAs, miRNAs and circRNAs provides insights into the key genes involved in the high-altitude adaptation of yaks. BMC Genomics 2021; 22:744. [PMID: 34654374 PMCID: PMC8518315 DOI: 10.1186/s12864-021-08044-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 09/29/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Yaks that inhabit the Tibetan Plateau exhibit striking phenotypic and physiological differences from cattle and have adapted well to the extreme conditions on the plateau. However, the mechanisms used by these animals for the regulation of gene expression at high altitude are not fully understood. RESULTS Here, we sequenced nine lung transcriptomes of yaks at altitudes of 3400, 4200 and 5000 m, and low-altitude Zaosheng cattle, which is a closely related species, served as controls. The analysis identified 21,764 mRNAs, 1377 circRNAs and 1209 miRNAs. By comparing yaks and cattle, 4975 mRNAs, 252 circRNAs and 75 miRNAs were identified differentially expressed. By comparing yaks at different altitudes, we identified 756 mRNAs, 64 circRNAs and 83 miRNAs that were differentially expressed (fold change ≥2 and P-value < 0.05). The pathways enriched in the mRNAs, circRNAs and miRNAs identified from the comparison of yaks and cattle were mainly associated with metabolism, including 'glycosaminoglycan degradation', 'pentose and glucuronate interconversions' and 'flavone and flavonol biosynthesis', and the mRNAs, circRNAs and miRNAs identified from the comparison of yaks at different altitude gradients were significantly enriched in metabolic pathways and immune and genetic information processing pathways. The core RNAs were identified from the mRNA-miRNA-circRNA networks constructed using the predominant differentially expressed RNAs. The core genes specific to the difference between yaks and cattle were associated with the endoplasmic reticulum and fat deposition, but those identified from the comparison among yaks at different altitude gradients were associated with maintenance of the normal biological functions of cells. CONCLUSIONS This study enhances our understanding of the molecular mechanisms involved in hypoxic adaptation in yaks and might contribute to improvements in the understanding and prevention of hypoxia-related diseases.
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Affiliation(s)
- Qianyun Ge
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yongbo Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Wangshan Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Yuan Cai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Shengguo Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
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35
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Wang M, Yuan D, Zou X, Wang Z, Yeh HY, Liu J, Wei LH, Wang CC, Zhu B, Liu C, He G. Fine-Scale Genetic Structure and Natural Selection Signatures of Southwestern Hans Inferred From Patterns of Genome-Wide Allele, Haplotype, and Haplogroup Lineages. Front Genet 2021; 12:727821. [PMID: 34504517 PMCID: PMC8421688 DOI: 10.3389/fgene.2021.727821] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 07/29/2021] [Indexed: 12/15/2022] Open
Abstract
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 f3/f4-statistics. qpGraph-based phylogenies and f4-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.
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Affiliation(s)
- Mengge Wang
- Guangzhou Forensic Science Institute, Guangzhou, China.,Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Didi Yuan
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Xing Zou
- College of Basic Medicine, Chongqing University, Chongqing, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Hui-Yuan Yeh
- School of Humanities, Nanyang Technological University, Singapore, Singapore
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Lan-Hai Wei
- State Key Laboratory of Marine Environmental Science, State Key Laboratory of Cellular Stress Biology, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
| | - Chuan-Chao Wang
- State Key Laboratory of Marine Environmental Science, State Key Laboratory of Cellular Stress Biology, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
| | - Bofeng Zhu
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Chao Liu
- Guangzhou Forensic Science Institute, Guangzhou, China.,Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Guanglin He
- School of Humanities, Nanyang Technological University, Singapore, Singapore.,State Key Laboratory of Marine Environmental Science, State Key Laboratory of Cellular Stress Biology, Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
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He G, Wang M, Zou X, Chen P, Wang Z, Liu Y, Yao H, Wei LH, Tang R, Wang CC, Yeh HY. Peopling History of the Tibetan Plateau and Multiple Waves of Admixture of Tibetans Inferred From Both Ancient and Modern Genome-Wide Data. Front Genet 2021; 12:725243. [PMID: 34650596 PMCID: PMC8506211 DOI: 10.3389/fgene.2021.725243] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/12/2021] [Indexed: 12/15/2022] Open
Abstract
Archeologically attested human occupation on the Tibetan Plateau (TP) can be traced back to 160 thousand years ago (kya) via the archaic Xiahe people and 30∼40 kya via the Nwya Devu anatomically modern human. However, the history of the Tibetan populations and their migration inferred from the ancient and modern DNA remains unclear. Here, we performed the first ancient and modern genomic meta-analysis among 3,017 Paleolithic to present-day Eastern Eurasian genomes (2,444 modern individuals from 183 populations and 573 ancient individuals). We identified a close genetic connection between the ancient-modern highland Tibetans and lowland island/coastal Neolithic Northern East Asians (NEA). This observed genetic affinity reflected the primary ancestry of high-altitude Tibeto-Burman speakers originated from the Neolithic farming populations in the Yellow River Basin. The identified pattern was consistent with the proposed common north-China origin hypothesis of the Sino-Tibetan languages and dispersal patterns of the northern millet farmers. We also observed the genetic differentiation between the highlanders and lowland NEAs. The former harbored more deeply diverged Hoabinhian/Onge-related ancestry and the latter possessed more Neolithic southern East Asian (SEA) or Siberian-related ancestry. Our reconstructed qpAdm and qpGraph models suggested the co-existence of Paleolithic and Neolithic ancestries in the Neolithic to modern East Asian highlanders. Additionally, we found that Tibetans from Ü-Tsang/Ando/Kham regions showed a strong population stratification consistent with their cultural background and geographic terrain. Ü-Tsang Tibetans possessed a stronger Chokhopani-affinity, Ando Tibetans had more Western Eurasian related ancestry and Kham Tibetans harbored greater Neolithic southern EA ancestry. Generally, ancient and modern genomes documented multiple waves of human migrations in the TP's past. The first layer of local hunter-gatherers mixed with incoming millet farmers and arose the Chokhopani-associated Proto-Tibetan-Burman highlanders, which further respectively mixed with additional genetic contributors from the western Eurasian Steppe, Yellow River and Yangtze River and finally gave rise to the modern Ando, Ü-Tsang and Kham Tibetans.
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Affiliation(s)
- Guanglin He
- School of Humanities, Nanyang Technological University, Singapore, Singapore
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
- Guangzhou Forensic Science Institute, Guangzhou, China
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xing Zou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
- School of Medicine, Chongqing University, Chongqing, China
| | - Pengyu Chen
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yan Liu
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, China
| | - Hongbin Yao
- Key Laboratory of Evidence Science of Gansu Province, Gansu Institute of Political Science and Law, Lanzhou, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, National Institute for Data Science in Health and Medicine, School of Life Sciences, Xiamen University, Xiamen, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Hui-Yuan Yeh
- School of Humanities, Nanyang Technological University, Singapore, Singapore
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Genetic insights into the paternal admixture history of Chinese Mongolians via high-resolution customized Y-SNP SNaPshot panels. Forensic Sci Int Genet 2021; 54:102565. [PMID: 34332322 DOI: 10.1016/j.fsigen.2021.102565] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/10/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022]
Abstract
The Mongolian people, one of the Mongolic-speaking populations, are native to the Mongolian Plateau in North China and southern Siberia. Many ancient DNA studies recently reported extensive population transformations during the Paleolithic to historic periods in this region, while little is known about the paternal genetic legacy of modern geographically different Mongolians. Here, we genotyped 215 Y-chromosomal single nucleotide polymorphisms (Y-SNPs) and 37 Y-chromosomal short tandem repeats (Y-STRs) among 679 Mongolian individuals from Hohhot, Hulunbuir, and Ordos in North China using the AGCU Y37 kit and our developed eight Y-SNP SNaPshot panels (including two panels first reported herein). The C-M130 Y-SNP SNaPshot panel defines 28 subhaplogroups, and the N/O/Q complementary Y-SNP SNaPshot panel defines 30 subhaplogroups of N1b-F2930, N1a1a1a1a3-B197, Q-M242, and O2a2b1a1a1a4a-CTS4658, which improved the resolution our developed Y-SNP SNaPshot panel set and could be applied for dissecting the finer-scale paternal lineages of Mongolic speakers. We found a strong association between Mongolian-prevailing haplogroups and some observed microvariants among the newly generated Y-STR haplotype data, suggesting the possibility of haplogroup prediction based on the distribution of Y-STR haplotypes. We identified three main ancestral sources of the observed Mongolian-dominant haplogroups, including the local lineage of C2*-M217 and incoming lineages from other regions of southern East Asia (O2*-M122, O1b*-P31, and N1*-CTS3750) and western Eurasia (R1*-M173). We also observed DE-M145, D1*-M174, C1*-F3393, G*-M201, I-M170, J*-M304, L-M20, O1a*-M119, and Q*-M242 at relatively low frequencies (< 5.00%), suggesting a complex admixture history between Mongolians and other incoming Eurasians from surrounding regions. Genetic clustering analyses indicated that the studied Mongolians showed close genetic affinities with other Altaic-speaking populations and Sinitic-speaking Hui people. The Y-SNP haplotype/haplogroup-based genetic legacy not only revealed that the stratification among geographically/linguistically/ethnically different Chinese populations was highly consistent with the geographical division and language classification, but also demonstrated that patrilineal genetic materials could provide fine-scale genetic structures among geographically different Mongolian people, suggesting that our developed high-resolution Y-SNP SNaPshot panels have the potential for forensic pedigree searches and biogeographical ancestry inference.
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The History and Driving Force for Prehistoric Human Expansion Upward to the Hinterland of the Tibetan Plateau Post–Last Glacial Maximum. SUSTAINABILITY 2021. [DOI: 10.3390/su13137065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The timing and motivation of prehistoric human expansion into the hinterland of the Tibetan Plateau (TP) is a widely debated scientific issue. Recent archaeological studies have brought forward predictions of the earliest human occupation of the TP to the late–Middle Pleistocene. However, massive human occupation of the TP did not appear until the termination of the Last Glacial Maximum (LGM). The spatio-temporal distribution of prehistoric hunter-gatherers on the TP varies significantly before the permanent occupation after 3600 BP (before present). Here, we report on environmental-archaeological evidence from the Canxionggashuo (CXGS) site in Yushu Prefecture, which provides information that is key to understanding the dynamics of post-LGM human occupation on the TP. Radiocarbon dating has revealed two occupation periods of the CXGS site at 8600–7100 cal (calibrated years) BP and 2400–2100 cal BP. The charcoal concentration in cultural layers correlates well with paleo–human activities. Hunter-gatherers expanded westwards from the northeastern margin of the TP to the hinterland of the TP during the warming period of the early–middle Holocene (~11,500–6000 BP). However, these groups retreated during the middle–late Holocene (~6000–3600 BP) under a cooling-drying climate. Prehistoric humans finally occupied the hinterland of the TP permanently after 3600 BP, with an enhanced cold-adaptive lifestyle, although the climate was still deteriorating.
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Quan C, Li Y, Liu X, Wang Y, Ping J, Lu Y, Zhou G. Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression. Genome Biol 2021; 22:159. [PMID: 34034800 PMCID: PMC8146648 DOI: 10.1186/s13059-021-02382-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/14/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Structural variation (SV) acts as an essential mutational force shaping the evolution and function of the human genome. However, few studies have examined the role of SVs in high-altitude adaptation and little is known of adaptive introgressed SVs in Tibetans so far. RESULTS Here, we generate a comprehensive catalog of SVs in a Chinese Tibetan (n = 15) and Han (n = 10) population using nanopore sequencing technology. Among a total of 38,216 unique SVs in the catalog, 27% are sequence-resolved for the first time. We systematically assess the distribution of these SVs across repeat sequences and functional genomic regions. Through genotyping in additional 276 genomes, we identify 69 Tibetan-Han stratified SVs and 80 candidate adaptive genes. We also discover a few adaptive introgressed SV candidates and provide evidence for a deletion of 335 base pairs at 1p36.32. CONCLUSIONS Overall, our results highlight the important role of SVs in the evolutionary processes of Tibetans' adaptation to the Qinghai-Tibet Plateau and provide a valuable resource for future high-altitude adaptation studies.
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Affiliation(s)
- Cheng Quan
- Department of Genetics & Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 People’s Republic of China
| | - Yuanfeng Li
- Department of Genetics & Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 People’s Republic of China
| | - Xinyi Liu
- Department of Genetics & Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 People’s Republic of China
| | - Yahui Wang
- Department of Genetics & Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 People’s Republic of China
| | - Jie Ping
- Department of Genetics & Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 People’s Republic of China
| | - Yiming Lu
- Department of Genetics & Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 People’s Republic of China
- Hebei University, Baoding, Hebei Province 071002 People’s Republic of China
| | - Gangqiao Zhou
- Department of Genetics & Integrative Omics, State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing, 100850 People’s Republic of China
- Hebei University, Baoding, Hebei Province 071002 People’s Republic of China
- Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu Province 211166 People’s Republic of China
- Medical College of Guizhou University, Guiyang, Guizhou Province 550025 People’s Republic of China
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Local adaptation of Mycobacterium tuberculosis on the Tibetan Plateau. Proc Natl Acad Sci U S A 2021; 118:2017831118. [PMID: 33879609 DOI: 10.1073/pnas.2017831118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
During its global dispersal, Mycobacterium tuberculosis (Mtb) has encountered varied geographic environments and host populations. Although local adaptation seems to be a plausible model for describing long-term host-pathogen interactions, genetic evidence for this model is lacking. Here, we analyzed 576 whole-genome sequences of Mtb strains sampled from different regions of high-altitude Tibet. Our results show that, after sequential introduction of a few ancestral strains, the Tibetan Mtb population diversified locally while maintaining strict separation from the Mtb populations on the lower altitude plain regions of China. The current population structure and estimated past population dynamics suggest that the modern Beijing sublineage strains, which expanded over most of China and other global regions, did not show an expansion advantage in Tibet. The mutations in the Tibetan strains showed a higher proportion of A > G/T > C transitions than strains from the plain regions, and genes encoding DNA repair enzymes showed evidence of positive selection. Moreover, the long-term Tibetan exclusive selection for truncating mutations in the thiol-oxidoreductase encoding sseA gene suggests that Mtb was subjected to local selective pressures associated with oxidative stress. Collectively, the population genomics of Mtb strains in the relatively isolated population of Tibet provides genetic evidence that Mtb has adapted to local environments.
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Liu Y, Wang M, Chen P, Wang Z, Liu J, Yao L, Wang F, Tang R, Zou X, He G. Combined Low-/High-Density Modern and Ancient Genome-Wide Data Document Genomic Admixture History of High-Altitude East Asians. Front Genet 2021; 12:582357. [PMID: 33643377 PMCID: PMC7905318 DOI: 10.3389/fgene.2021.582357] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 01/05/2021] [Indexed: 01/26/2023] Open
Abstract
The Tibetan Plateau (TP) is considered to be one of the last terrestrial environments conquered by the anatomically modern human. Understanding of the genetic background of highland Tibetans plays a pivotal role in archeology, anthropology, genetics, and forensic investigations. Here, we genotyped 22 forensic genetic markers in 1,089 Tibetans residing in Nagqu Prefecture and collected 1,233,013 single nucleotide polymorphisms (SNPs) in the highland East Asians (Sherpa and Tibetan) from the Simons Genome Diversity Project and ancient Tibetans from Nepal and Neolithic farmers from northeastern Qinghai-Tibetan Plateau from public databases. We subsequently merged our two datasets with other worldwide reference populations or eastern ancient Eurasians to gain new insights into the genetic diversity, population movements, and admixtures of high-altitude East Asians via comprehensive population genetic statistical tools [principal component analysis (PCA), multidimensional scaling plot (MDS), STRUCTURE/ADMIXTURE, f3 , f4 , qpWave/qpAdm, and qpGraph]. Besides, we also explored their forensic characteristics and extended the Chinese National Database based on STR data. We identified 231 alleles with the corresponding allele frequencies spanning from 0.0005 to 0.5624 in the forensic low-density dataset, in which the combined powers of discrimination and the probability of exclusion were 1-1.22E-24 and 0.999999998, respectively. Additionally, comprehensive population comparisons in our low-density data among 57 worldwide populations via the Nei's genetic distance, PCA, MDS, NJ tree, and STRUCTURE analysis indicated that the highland Tibeto-Burman speakers kept the close genetic relationship with ethnically close populations. Findings from the 1240K high-density dataset not only confirmed the close genetic connection between modern Highlanders, Nepal ancients (Samdzong, Mebrak, and Chokhopani), and the upper Yellow River Qijia people, suggesting the northeastern edge of the TP served as a geographical corridor for ancient population migrations and interactions between highland and lowland regions, but also evidenced that late Neolithic farmers permanently colonized into the TP by adopting cold-tolerant barley agriculture that was mediated via the acculturation of idea via the millet farmer and not via the movement of barley agriculturalist as no obvious western Eurasian admixture signals were identified in our analyzed modern and ancient populations. Besides, results from the qpAdm-based admixture proportion estimation and qpGraph-based phylogenetic relationship reconstruction consistently demonstrated that all ancient and modern highland East Asians harbored and shared the deeply diverged Onge/Hoabinhian-related eastern Eurasian lineage, suggesting a common Paleolithic genetic legacy existed in high-altitude East Asians as the first layer of their gene pool.
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Affiliation(s)
- Yan Liu
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Pengyu Chen
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Lilan Yao
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Center of Forensic Expertise, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Fei Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Xing Zou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Guanglin He
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
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Sun J, Li YX, Ma PC, Yan S, Cheng HZ, Fan ZQ, Deng XH, Ru K, Wang CC, Chen G, Wei LH. Shared paternal ancestry of Han, Tai-Kadai-speaking, and Austronesian-speaking populations as revealed by the high resolution phylogeny of O1a-M119 and distribution of its sub-lineages within China. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 174:686-700. [PMID: 33555039 DOI: 10.1002/ajpa.24240] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 12/27/2022]
Abstract
OBJECTIVES The aim of this research was to explore the origin, diversification, and demographic history of O1a-M119 over the past 10,000 years, as well as its role during the formation of East Asian and Southeast Asian populations, particularly the Han, Tai-Kadai-speaking, and Austronesian-speaking populations. MATERIALS AND METHODS Y-chromosome sequences (n = 141) of the O1a-M119 lineage, including 17 newly generated in this study, were used to reconstruct a revised phylogenetic tree with age estimates, and identify sub-lineages. The geographic distribution of 12 O1a-M119 sub-lineages was summarized, based on 7325 O1a-M119 individuals identified among 60,009 Chinese males. RESULTS A revised phylogenetic tree, age estimation, and distribution maps indicated continuous expansion of haplogroup O1a-M119 over the past 10,000 years, and differences in demographic history across geographic regions. We propose several sub-lineages of O1a-M119 as founding paternal lineages of Han, Tai-Kadai-speaking, and Austronesian-speaking populations. The sharing of several young O1a-M119 sub-lineages with expansion times less than 6000 years between these three population groups supports a partial common ancestry for them in the Neolithic Age; however, the paternal genetic divergence pattern is much more complex than previous hypotheses based on ethnology, archeology, and linguistics. DISCUSSION Our analyses contribute to a better understanding of the demographic history of O1a-M119 sub-lineages over the past 10,000 years during the emergence of Han, Austronesians, Tai-Kadai-speaking populations. The data described in this study will assist in understanding of the history of Han, Tai-Kadai-speaking, and Austronesian-speaking populations from ethnology, archeology, and linguistic perspectives in the future.
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Affiliation(s)
- Jin Sun
- Xingyi Normal University for Nationalities, Xingyi, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Ying-Xiang Li
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Peng-Cheng Ma
- School of Life Sciences, Jilin University, Changchun, China
| | - Shi Yan
- School of Ethnology and Sociology, Minzu University of China, Beijing, China
| | - Hui-Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Zhi-Quan Fan
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Xiao-Hua Deng
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- Center for collation and studies of Fujian local literature, Fujian University of Technology, Fuzhou, China
| | - Kai Ru
- Enlighten Co., Ltd., Shanghai, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Gang Chen
- Hunan Key Lab of Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
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43
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Zhang H, Ji T, Pagel M, Mace R. Dated phylogeny suggests early Neolithic origin of Sino-Tibetan languages. Sci Rep 2020; 10:20792. [PMID: 33247154 PMCID: PMC7695722 DOI: 10.1038/s41598-020-77404-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/09/2020] [Indexed: 11/21/2022] Open
Abstract
An accurate reconstruction of Sino-Tibetan language evolution would greatly advance our understanding of East Asian population history. Two recent phylogenetic studies attempted to do so but several of their conclusions are different from each other. Here we reconstruct the phylogeny of the Sino-Tibetan language family, using Bayesian computational methods applied to a larger and linguistically more diverse sample. Our results confirm previous work in finding that the ancestral Sino-Tibetans first split into Sinitic and Tibeto-Burman clades, and support the existence of key internal relationships. But we find that the initial divergence of this group occurred earlier than previously suggested, at approximately 8000 years before the present, coinciding with the onset of millet-based agriculture and significant environmental changes in the Yellow River region. Our findings illustrate that key aspects of phylogenetic history can be replicated in this complex language family, and calls for a more nuanced understanding of the first Sino-Tibetan speakers in relation to the "early farming dispersal" theory of language evolution.
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Affiliation(s)
- Hanzhi Zhang
- Department of Anthropology, University College London, London, WC1H 0BW, UK.
| | - Ting Ji
- Key Laboratory of Animal Ecology and Conservation Biology, Centre for Computational and Evolutionary Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mark Pagel
- School of Biological Sciences, University of Reading, Reading, RG6 6UR, UK
- Santa Fe Institute, Santa Fe, NM, 87501, USA
| | - Ruth Mace
- Department of Anthropology, University College London, London, WC1H 0BW, UK.
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Ding J, Fan H, Zhou Y, Wang Z, Wang X, Song X, Zhu B, Qiu P. Genetic polymorphisms and phylogenetic analyses of the Ü-Tsang Tibetan from Lhasa based on 30 slowly and moderately mutated Y-STR loci. Forensic Sci Res 2020; 7:181-188. [PMID: 35784414 PMCID: PMC9245999 DOI: 10.1080/20961790.2020.1810882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
As a result of the expansion of old Tibet on the Qinghai-Tibet Plateau, Tibetans diverged into three main branches, Ü-Tsang, Amdo, and Kham Tibetan. Ü-Tsang Tibetans are geographically distributed across the wide central and western portions of the Qinghai-Tibet Plateau while Lhasa is the central gathering place for Tibetan culture. The AGCU Y30, a 6-dye fluorescence kit including 30 slowly and moderately mutated Y-STR loci, has been validated for its stability and sensitivity in different biomaterials and diverse Chinese populations (Han and other minorities), and widely used in the practical work of forensic science. However, the 30 Y-STR profiling of Tibetan, especially for Ü-Tsang Tibetan, were insufficient. We utilized the AGCU Y30 to genotype 577 Ü-Tsang Tibetan unrelated males from Lhasa in the Tibet Autonomous Region of China to fill up the full and accurate Y-STR profiles. A total of 552 haplotypes were observed, 536 (97.10%) of which were unique. One hundred and ninety-four alleles were observed at 26 single copy loci and the allelic frequencies ranged from 0.0017 to 0.8180. For the two multi-copy loci DYS385a/b and DYS527a/b, 64 and 36 allelic combinations were observed, respectively. The gene diversity (GD) values ranged from 0.3079 at DYS391 to 0.9142 at DYS385a/b and the overall haplotype diversity (HD) was 0.9998, and its discrimination capacity (DC) was 0.9567. The population genetic analyses demonstrated that Lhasa Ü-Tsang Tibetan had close relationships with other Tibetan populations from Tibet and Qinghai, especially with Ü-Tsang Tibetan. From the perspective of Y haplogroups, the admixture of the southward Qiang people with dominant haplogroup O-M122 and the northward migrations of the initial settlers of East Asia with haplogroup D-M175 hinted the Sino-Tibetan homologous, thus, we could not ignore the gene flows with other Sino-Tibetan populations, especially for Han Chinese, to characterize the forensic genetic landscape of Tibetan.
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Affiliation(s)
- Jiuyang Ding
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Shanghai, China
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Haoliang Fan
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
- School of Basic Medicine and Life Science, Hainan Medical University, Haikou, China
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Yongsong Zhou
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Zhuo Wang
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xiao Wang
- Department of Psychiatry, The First Clinical Medical College, Shanxi Medical University, Taiyuan, China
| | - Xuheng Song
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Bofeng Zhu
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
| | - Pingming Qiu
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
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Xin J, Zhang H, He Y, Duren Z, Bai C, Chen L, Luo X, Yan DS, Zhang C, Zhu X, Yuan Q, Feng Z, Cui C, Qi X, Ouzhuluobu, Wong WH, Wang Y, Su B. Chromatin accessibility landscape and regulatory network of high-altitude hypoxia adaptation. Nat Commun 2020; 11:4928. [PMID: 33004791 PMCID: PMC7529806 DOI: 10.1038/s41467-020-18638-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/03/2020] [Indexed: 12/27/2022] Open
Abstract
High-altitude adaptation of Tibetans represents a remarkable case of natural selection during recent human evolution. Previous genome-wide scans found many non-coding variants under selection, suggesting a pressing need to understand the functional role of non-coding regulatory elements (REs). Here, we generate time courses of paired ATAC-seq and RNA-seq data on cultured HUVECs under hypoxic and normoxic conditions. We further develop a variant interpretation methodology (vPECA) to identify active selected REs (ASREs) and associated regulatory network. We discover three causal SNPs of EPAS1, the key adaptive gene for Tibetans. These SNPs decrease the accessibility of ASREs with weakened binding strength of relevant TFs, and cooperatively down-regulate EPAS1 expression. We further construct the downstream network of EPAS1, elucidating its roles in hypoxic response and angiogenesis. Collectively, we provide a systematic approach to interpret phenotype-associated noncoding variants in proper cell types and relevant dynamic conditions, to model their impact on gene regulation.
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Affiliation(s)
- Jingxue Xin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China
- Bio-X Program, Stanford University, Stanford, CA, 94305, USA
- University of Chinese Academy of Sciences, 100101, Beijing, China
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China
| | - Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China
- University of Chinese Academy of Sciences, 100101, Beijing, China
| | - Zhana Duren
- Departments of Statistics, Stanford University, Stanford, CA, 94305, USA
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, Greenwood, SC, 29646, USA
| | - Caijuan Bai
- High Altitude Medical Research Center, School of Medicine, Tibetan University, 850000, Lhasa, China
| | - Lang Chen
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China
- University of Chinese Academy of Sciences, 100101, Beijing, China
| | - Xin Luo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China
- University of Chinese Academy of Sciences, 100101, Beijing, China
| | - Dong-Sheng Yan
- School of Mathematical Science, Inner Mongolia University, 010021, Huhhot, China
| | - Chaoyu Zhang
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China
- University of Chinese Academy of Sciences, 100101, Beijing, China
| | - Xiang Zhu
- Departments of Statistics, Stanford University, Stanford, CA, 94305, USA
| | - Qiuyue Yuan
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China
- University of Chinese Academy of Sciences, 100101, Beijing, China
| | - Zhanying Feng
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China
- University of Chinese Academy of Sciences, 100101, Beijing, China
| | - Chaoying Cui
- High Altitude Medical Research Center, School of Medicine, Tibetan University, 850000, Lhasa, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China
| | - Ouzhuluobu
- High Altitude Medical Research Center, School of Medicine, Tibetan University, 850000, Lhasa, China
| | - Wing Hung Wong
- Bio-X Program, Stanford University, Stanford, CA, 94305, USA.
- Departments of Statistics, Stanford University, Stanford, CA, 94305, USA.
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Yong Wang
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China.
- University of Chinese Academy of Sciences, 100101, Beijing, China.
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 330106, Hangzhou, China.
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China.
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Zhang K, Lenstra JA, Zhang S, Liu W, Liu J. Evolution and domestication of the Bovini species. Anim Genet 2020; 51:637-657. [PMID: 32716565 DOI: 10.1111/age.12974] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2020] [Indexed: 12/17/2022]
Abstract
Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species - taurine cattle, zebu and yak - and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y-chromosomal DNA. The high diversity of European breeds has been shaped through isolation-by-distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.
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Affiliation(s)
- K Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht Yalelaan 104, Utrecht, 3584 CM, The Netherlands
| | - S Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - W Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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Haptoglobin polymorphisms in Latin American populations. Sci Rep 2020; 10:13780. [PMID: 32792581 PMCID: PMC7426911 DOI: 10.1038/s41598-020-70755-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/03/2020] [Indexed: 11/16/2022] Open
Abstract
Several genetic polymorphisms of the haptoglobin gene (HP) or haptoglobin-related gene (HPR) were reported to show a population-specific distribution and to be associated with not only serum haptoglobin (HP) but also cholesterol levels. For such association studies, it is important to know the distribution of polymorphisms or their haplotypes in the populations concerned. However, no comprehensive genetic studies have explored this in Latin Americans, and not every human variation or genotype is available in a database. In this study, we determined the genotypes of common HP (HP1 and HP2), HPdel, rs5471, rs5472, and rs2000999 in several Latin American populations. Haplotypes of rs5472-common HP-rs2000999 polymorphisms were estimated. We did not encounter any HPdel, and the frequencies of rs5471 A, rs5472 A, HP1, and rs2000999 G were higher than their counterpart alleles in studied populations. All of the alleles with higher frequency in the Latin Americans are associated with higher serum HP and lower cholesterol levels. Both A-1-G (probably HP1S) and G-1-G (probably HP1F) haplotypes were higher in Latin American populations than those in other geographic regions. In addition, the genetic influx from populations of other continents into Peruvians seems to be relatively lower than that into other Latin Americans.
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Pamenter ME, Hall JE, Tanabe Y, Simonson TS. Cross-Species Insights Into Genomic Adaptations to Hypoxia. Front Genet 2020; 11:743. [PMID: 32849780 PMCID: PMC7387696 DOI: 10.3389/fgene.2020.00743] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Over millions of years, vertebrate species populated vast environments spanning the globe. Among the most challenging habitats encountered were those with limited availability of oxygen, yet many animal and human populations inhabit and perform life cycle functions and/or daily activities in varying degrees of hypoxia today. Of particular interest are species that inhabit high-altitude niches, which experience chronic hypobaric hypoxia throughout their lives. Physiological and molecular aspects of adaptation to hypoxia have long been the focus of high-altitude populations and, within the past decade, genomic information has become increasingly accessible. These data provide an opportunity to search for common genetic signatures of selection across uniquely informative populations and thereby augment our understanding of the mechanisms underlying adaptations to hypoxia. In this review, we synthesize the available genomic findings across hypoxia-tolerant species to provide a comprehensive view of putatively hypoxia-adaptive genes and pathways. In many cases, adaptive signatures across species converge on the same genetic pathways or on genes themselves [i.e., the hypoxia inducible factor (HIF) pathway). However, specific variants thought to underlie function are distinct between species and populations, and, in most cases, the precise functional role of these genomic differences remains unknown. Efforts to standardize these findings and explore relationships between genotype and phenotype will provide important clues into the evolutionary and mechanistic bases of physiological adaptations to environmental hypoxia.
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Affiliation(s)
- Matthew E. Pamenter
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Brain and Mind Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - James E. Hall
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Yuuka Tanabe
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Tatum S. Simonson
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, San Diego, CA, United States
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50
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Segurel L, Guarino-Vignon P, Marchi N, Lafosse S, Laurent R, Bon C, Fabre A, Hegay T, Heyer E. Why and when was lactase persistence selected for? Insights from Central Asian herders and ancient DNA. PLoS Biol 2020; 18:e3000742. [PMID: 32511234 PMCID: PMC7302802 DOI: 10.1371/journal.pbio.3000742] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/18/2020] [Indexed: 01/22/2023] Open
Abstract
The genetic adaptation of humans to the consumption of milk from dairying animals is one of the most emblematic cases of recent human evolution. While the phenotypic change under selection, lactase persistence (LP), is known, the evolutionary advantage conferred to persistent individuals remains obscure. One informative but underappreciated observation is that not all populations whose ancestors had access to milk genetically adapted to become lactase persistent. Indeed, Central Asian herders are mostly lactase nonpersistent, despite their significant dietary reliance on dairy products. Investigating the temporal dynamic of the -13.910:C>T Eurasian mutation associated with LP, we found that, after its emergence in Ukraine 5,960 before present (BP), the T allele spread between 4,000 BP and 3,500 BP throughout Eurasia, from Spain to Kazakhstan. The timing and geographical progression of the mutation coincides well with the migration of steppe populations across and outside of Europe. After 3,000 BP, the mutation strongly increased in frequency in Europe, but not in Asia. We propose that Central Asian herders have adapted to milk consumption culturally, by fermentation, and/or by colonic adaptation, rather than genetically. Given the possibility of a nongenetic adaptation to avoid intestinal symptoms when consuming dairy products, the puzzle then becomes this: why has LP been selected for at all?
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Affiliation(s)
- Laure Segurel
- Eco-anthropologie, Muséum national d’Histoire naturelle, CNRS, Université de Paris, Paris, France
- * E-mail:
| | - Perle Guarino-Vignon
- Eco-anthropologie, Muséum national d’Histoire naturelle, CNRS, Université de Paris, Paris, France
| | - Nina Marchi
- Eco-anthropologie, Muséum national d’Histoire naturelle, CNRS, Université de Paris, Paris, France
| | - Sophie Lafosse
- Eco-anthropologie, Muséum national d’Histoire naturelle, CNRS, Université de Paris, Paris, France
| | - Romain Laurent
- Eco-anthropologie, Muséum national d’Histoire naturelle, CNRS, Université de Paris, Paris, France
| | - Céline Bon
- Eco-anthropologie, Muséum national d’Histoire naturelle, CNRS, Université de Paris, Paris, France
| | - Alexandre Fabre
- Aix Marseille University, INSERM, MMG, Marseille, France
- APHM, Hôpital de la Timone Enfant, Service de Pédiatrie Multidisciplinaire, Marseille, France
| | - Tatyana Hegay
- Institute of Immunology and Human Genomics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan
| | - Evelyne Heyer
- Eco-anthropologie, Muséum national d’Histoire naturelle, CNRS, Université de Paris, Paris, France
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