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Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude
Open accessAbstract
No Genetic Vertigo: Peoples living in high altitudes have adapted to their situation (see the Perspective by Storz ). To identify gene regions that might have contributed to high-altitude adaptation in Tibetans, Simonson et al. (p. 72 , published online 13 May) conducted a genome scan of nucleotide polymorphism comparing Tibetans, Han Chinese, and Japanese, while Yi et al. (p. 75 ) performed comparable analyses on the coding regions of all genes—their exomes. Both studies converged on a gene, endothelial Per-Arnt-Sim domain protein 1 (also known as hypoxia-inducible factor 2 α), which has been linked to the regulation of red blood cell production. Other genes identified that were potentially under selection included adult and fetal hemoglobin and two functional candidate loci that were correlated with low hemoglobin concentration in Tibetans. Future detailed functional studies will now be required to examine the mechanistic underpinnings of physiological adaptation to high altitudes.
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“For example, by studying genes that show population-specific allele-frequency differences between Tibetans and Han Chinese, a signal of positive natural selection was detected in EPAS1, a transcription factor involved in the response to hypoxia, which most probably helps the Tibetans to live at high altitudes [40].”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [40]
In the citing paper
“Genome-wide searches for single-nucleotide polymorphisms (SNP), candidate gene approaches and exome sequencing have identified genetic variations in the HIF2A, PHD2 and PPARA genes that associate with lower hemoglobins in native Tibetans compared to Han Chinese and with high altitude adaptation in other populations.”
From Regulation of erythropoiesis by hypoxia-inducible factors (2013) · cites this paper as [173]
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MethodDifferent gene expressions between cattle and yak provide insights into high‐altitude adaptation
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Identifying loci under positive selection in complex population historiesPreprint
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HMOX2Functions as a Modifier Gene for High-Altitude Adaptation in Tibetans
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“Previous studies have reported a set of candidate genes exhibiting unusually large allelic divergence between Tibetan highlanders and Han Chinese lowlanders [Beall et al., 2010; Bigham et al., 2010; Simonson et al., 2010; Yi et al., 2010; Peng et al., 2011; Wang et al., 2011; Xu et al., 2011].”
ResultSelf-citationOkumiya, K., Sakamoto, R., Ishimoto, Y., Kimura, Y., Fukutomi, E., Ishikawa, M., Suwa, K., Imai, H., Chen, W., Kato, E., et al. (2016) · BMJ Open · doi:10.1136/bmjopen-2015-009728 · Cited by 53
“Polycythaemia may be a sign of maladaptation to hypoxia, which leads to glucose intolerance, because Tibetan people have acquired a hypoxic adaptation by preventing polycythaemia through a genetic response to hypoxia.20 21 69–73 Tibetans (mean age 34–35 years, BMI 18.4–18.5) compared with Andean highlanders (mean age…”
BackgroundInfluentialThin Air Resulting in High Pressure: Mountain Sickness and Hypoxia-Induced Pulmonary Hypertension
Grimminger, J., Richter, M. J., Tello, K., Sommer, N., Gall, H. J., & Ghofrani, H. A. (2017) · Canadian Respiratory Journal · doi:10.1155/2017/8381653 · Cited by 49
Cho, J. I., Basnyat, B., Jeong, C., Rienzo, A. D., Childs, G. H., Craig, S. R., Sun, J., & Beall, C. M. (2017) · Evolution Medicine and Public Health · doi:10.1093/emph/eox008 · Cited by 53
Genome-wide DNA methylation profiles in Tibetan and Yorkshire pigs under high-altitude hypoxia
Zhang, B., Ban, D., Gou, X., Zhang, Y., Yang, L., Chamba, Y., & Zhang, H. (2019) · Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology · doi:10.1186/s40104-019-0316-y · Cited by 47
Self-citationEvolution of affiliation: patterns of convergence from genomes to behaviour
Fischer, E. K., Nowicki, J. P., & O’Connell, L. A. (2019) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2018.0242 · Cited by 46
Wei, H., Hou, G., Fan, Q., Madsen, D. B., Qin, Z., Du, Y., Sun, Y., Gao, J., & Shan, F. (2019) · Progress in Physical Geography Earth and Environment · doi:10.1177/0309133319869596 · Cited by 47
“Consequently, the plateau has become one of the most important places to study human adaptation to cold environments (Moore et al., 1998; Yi et al., 2010), and investigations into the history and driving mechanisms of human habitation in the high-altitude regions of QTP are ongoing (Aldenderfer and…”
BackgroundWang, J., Xia, H., Yao, J., Shen, X., Cheng, T., Wang, Q., & Zhang, D. (2019) · Science China Earth Sciences · doi:10.1007/s11430-019-9519-8 · Cited by 47
Self-citationGenomic Analyses Reveal Genetic Adaptations to Tropical Climates in Chickens
Tian, S., Zhou, X., Phuntsok, T., Zhao, N., Zhang, D., Ning, C., Li, D., & Zhao, H. (2020) · iScience · doi:10.1016/j.isci.2020.101644 · Cited by 45
“It has been suggested that there is a close relationship between EPAS1 and the regulation of red blood cell production (Percy et al., 2008; Yi et al., 2010).”
BackgroundResultWorldwide genetic and cultural change in human evolution
Creanza, N., & Feldman, M. W. (2016) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2016.08.006 · Cited by 49
Ge, Q., Guo, Y., Zheng, W., Zhao, S., Cai, Y., & Qi, X. (2021) · Scientific Reports · doi:10.1038/s41598-021-87420-7 · Cited by 51
“Potential lncRNAs were identified from the assembled transcripts through the following highly stringent criterion: (1) transcript length is not less than 200 nt; (2) transcript expression is more than 3 reads; (3) transcripts with reads coverage of less than 5 were eliminated; (4) compared with the annotation file of…”
BackgroundMethodAlsmadi, O. A., John, S. E., Thareja, G., Hebbar, P., Antony, D., Behbehani, K., & Thanaraj, T. A. (2014) · PLoS ONE · doi:10.1371/journal.pone.0099069 · Cited by 48
“Apart from whole genome sequencing projects, population-scale exome sequencing projects (such as NHLBI Grand Opportunity Exome Sequencing Project (ESP) [20] that covers diverse and richly-phenotyped populations in United States of America) and large-scale exome sequencing projects conducted in individual countries (Ch…”
BackgroundDeciphering the Genetic Blueprint behind Holstein Milk Proteins and Production
Lee, H. J., Kim, J., Lee, T., Son, J.-K., Yoon, H., Baek, K., Jeong, J. Y., Cho, Y.-M., Lee, K., Yang, B., et al. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu102 · Cited by 46
“Because certain important cattle breeds are widely disseminated globally, defective genes are likely present in the Holstein population (Zenger et al. 2007).”
BackgroundXu, Q., Zhang, C., Zhang, D., Jiang, H., Peng, S., Liu, Y., Zhao, K. X., Wang, C., & Chen, L. (2016) · BMC Evolutionary Biology · doi:10.1186/s12862-015-0581-0 · Cited by 44
“Compared with people living at sea level, Tibetans possess several key adaptive features to cope with the hypoxic conditions.”
BackgroundInfluentialSelf-citationOxygen-Sensitive Remodeling of Central Carbon Metabolism by Archaic eIF5B
Ho, J. J. D., Balukoff, N. C., Jaramillo, G. C., Malcolm, P. D., Krieger, J. R., & Lee, S. (2018) · Cell Reports · doi:10.1016/j.celrep.2017.12.031 · Cited by 45
Thin Air, Thick Vessels: Historical and Current Perspectives on Hypoxic Pulmonary Hypertension
Young, J. M., Williams, D. R., & Thompson, A. A. R. (2019) · Frontiers in Medicine · doi:10.3389/fmed.2019.00093 · Cited by 46
Bergey, C. M., Lopez, M., Harrison, G. F., Patin, É., Cohen, J. A., Quintana‐Murci, L., Barreiro, L. B., & Perry, G. H. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1812135115 · Cited by 49
“To identify regions of the genome that may have been affected by positive selection in each of our test populations, we computed the population branch statistic (PBS) (29) for each exonic SNP identified among or between the Batwa and Bakiga and the Andamanese and Brahmin populations (SI Appendix, Figs.”
BackgroundMethodDistribution of local ancestry and evidence of adaptation in admixed populations
Secolin, R., Mas-Sandoval, À., Arauna, L. R., Torres, F. R., de Araujo, T. K., Santos, M. L., Rocha, C. S., Carvalho, B. S., Cendes, F., Lopes‐Cendes, Í., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-50362-2 · Cited by 51
Whole-Genome Sequence Data Suggest Environmental Adaptation of Ethiopian Sheep Populations
Wiener, P., Robert, C., Ahbara, A., Salavati, M., Abebe, A., Kebede, A., Wragg, D., Friedrich, J., Vasoya, D., Hume, D. A., et al. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab014 · Cited by 46
“Population differentiation The population-branch statistic (PBS) (Yi et al. 2010) is designed to identify population-specific allele frequency changes, in this case, to identify alleles associated with adaptation to high altitude.”
InfluentialA Population Genomic Assessment of Three Decades of Evolution in a Natural Drosophila Population
Lange, J. D., Bastide, H., Lack, J., & Pool, J. E. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab368 · Cited by 39
“The latter signal can be isolated by the Population Branch Statistic (PBS; Yi et al. 2010), which uses three population samples to quantify genetic differentiation on one population’s lineage.”
BackgroundSelf-citationRepeated genetic adaptation to altitude in two tropical butterflies
Montejo‐Kovacevich, G., Meier, J. I., Bacquet, C. N., Warren, I. A., Chan, Y. F., Kučka, M., Salazar, C. A., Rueda‐M, N., Montgomery, S. H., McMillan, W. O., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-32316-x · Cited by 47
Gu, M., Dong, X., Shi, L., Shi, L., Lin, K., Huang, X., & Chu, J. (2011) · Gene · doi:10.1016/j.gene.2011.12.016 · Cited by 47
Putra, A. C., Eguchi, H., Lee, K. L., Yamane, Y., Gustine, E., Isobe, T., Nishiyama, M., Hiyama, K., Poellinger, L., & Tanimoto, K. (2015) · PLoS ONE · doi:10.1371/journal.pone.0134496 · Cited by 45
Zhang, Q., Zhang, L., Zhao, T., Wang, J., Zhu, Q., Chen, J., & Yuan, M. (2017) · Gene · doi:10.1016/j.gene.2017.02.014 · Cited by 47
Self-citationThe genomic basis of adaptation to high‐altitude habitats in the eastern honey bee ( Apis cerana )
Montero‐Mendieta, S., Tan, K., Christmas, M. J., Olsson, A., Vilà, C., Wållberg, A., & Webster, M. T. (2018) · Molecular Ecology · doi:10.1111/mec.14986 · Cited by 46
Heinrich, E. C., Wu, L., Lawrence, E. S., Cole, A. M., Anza‐Ramirez, C., Villafuerte, F. C., & Simonson, T. S. (2019) · Annals of Human Genetics · doi:10.1111/ahg.12299 · Cited by 46
Metabolic adaptation to high altitude
O’Brien, K. A., Simonson, T. S., & Murray, A. J. (2019) · Current Opinion in Endocrine and Metabolic Research · doi:10.1016/j.coemr.2019.12.002 · Cited by 47
Effects of altitude on human oral microbes
Fang, L., Liang, T., Zhang, Z., Liu, L., Li, J., Dong, W., Zhang, H., Bai, S., Ma, L., & Kang, L. (2021) · AMB Express · doi:10.1186/s13568-021-01200-0 · Cited by 48
Self-citationQu, Y., Chen, C., Chen, X., Hao, Y., She, H., Wang, M., Ericson, P. G. P., Lin, H., Cai, T., Song, G., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2012398118 · Cited by 46
“This finding differs from what has been reported in previous genomic studies in the high-elevation animals, such as the Yak (Bos grunniens), Tibetan humans, ground tit (Parus humilis), and great tit (Parus major), as genes under positive selection have been rarely found to be shared across those species (5, 7, 41, 42).”
ResultSelf-citationPositive selection of AS3MT to arsenic water in Andean populations
Eichstaedt, C. A., Antão, T., Cardona, A., Pagani, L., Kivisild, T., & Mormina, M. (2015) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/j.mrfmmm.2015.07.007 · Cited by 46
“the signal can be due to extreme allele frequencies in either of the two populations), we also used the population branch statistic (PBS) to pinpoint allele differentiation to the population of interest [25,26].”
MethodArchaic adaptive introgression in TBX15/WARS2
Racimo, F., Gokhman, D., Fumagalli, M., Ko, A., Hansen, T., Moltke, I., Albrechtsen, A., Carmel, L., Huerta-Sánchez, E., & Nielsen, R. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw283 · Cited by 101
“ThealleleswithhighPBSvaluesandhighfrequencyinGIare almostabsentinAfrica,butpresentacrossEurasia.”
MethodInfluentialSelf-citationGarcia-Rojas, E. Y. L., Villanueva, C., & Bond, R. A. (2021) · Frontiers in Cardiovascular Medicine · doi:10.3389/fcvm.2021.709509 · Cited by 49
“This is translated as normal levels of hemoglobin despite the hypoxic conditions at high altitude (154, 161).”
BackgroundGlobal dispersal and adaptive evolution of domestic cattle: a genomic perspective
Xia, X., Qu, K., Wang, Y., Sinding, M. S., Wang, F., Hanif, Q., Ahmed, Z., Lenstra, J. A., Han, J., Lei, C., et al. (2023) · Stress Biology · doi:10.1007/s44154-023-00085-2 · Cited by 49
“EPAS1 encodes a subunit of the HIF transcription factor and is a key gene for hypoxia adaptation in Tibetans (Beall et al. 2010; Simonson et al. 2010; Yi et al. 2010).”
BackgroundSelf-citationSearching for molecular hypoxia sensors among oxygen-dependent enzymes
Li, L., Shen, S. Q., Bickler, P. E., Jacobson, M. P., Wu, L. F., & Altschuler, S. J. (2023) · eLife · doi:10.7554/elife.87705 · Cited by 43
“Tibetan PAOX (Simonson et al., 2010) Andean EGLN1 (Bigham et al., 2010; Bigham et al., 2009), EGLN2 (Bigham et al., 2009), NOS1 (Bigham et al., 2009), NOS2 (Bigham et al., 2010; Bigham et al., 2009; Crawford et al., 2017), DUOX2 (Jacovas et al., 2018), CYP39A1 (Eichstaedt et al., 2014), KDM2A (Eichstaedt et al., 2014)…”
BackgroundInfluentialLiang, X., Duan, Q., Li, B., Wang, Y., Bu, Y., Zhang, Y.-L., Kuang, Z., Mao, L., An, X., Wang, H.-H., et al. (2024) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.2322291121 · Cited by 44
Self-citation
Metadata
- Authors
- Yi, X., Liang, Y., Huerta-Sanchez, E., Jin, X., Cuo, Z. X. P., Pool, J. E., Xu, X., Jiang, H., Vinckenbosch, N., Korneliussen, T. S., Zheng, H., Liu, T., He, W., Li, K., Luo, R., Nie, X., Wu, H., Zhao, M., Cao, H., Zou, J., Shan, Y., Li, S., Yang, Q., Asan, Ni, P., Tian, G., Xu, J., Liu, X., Jiang, T., Wu, R., Zhou, G., Tang, M., Qin, J., Wang, T., Feng, S., Li, G., Huasang, Luosang, J., Wang, W., Chen, F., Wang, Y., Zheng, X., Li, Z., Bianba, Z., Yang, G., Wang, X., Tang, S., Gao, G., Chen, Y., Luo, Z., Gusang, L., Cao, Z., Zhang, Q., Ouyang, W., Ren, X., Liang, H., Zheng, H., Huang, Y., Li, J., Bolund, L., Kristiansen, K., Li, Y., Zhang, Y., Zhang, X., Li, R., Li, S., Yang, H., Nielsen, R., Wang, J., & Wang, J.
- Affiliations
- BGI Group (China) (CN)
- Department of Integrative Biology and Department of Statistics, University of California Berkeley, Berkeley, CA 94820, USA.
- Tibet Autonomous Region People's Hospital (CN)
- University of California, Davis (US)
- University of California, Berkeley (US)
- University of Copenhagen (DK)
- The Military General Hospital of Tibet, Lhasa, 850007, China.
- The hospital of XiShuangBanNa Dai Nationalities, Autonomous Jinghong 666100, Yunnan, China.
- Corresponding author
- Yi, Xin
- Liang, Yu
- Jin, Xin
- Cuo, Zha Xi Ping
- Pool, John E.
- ORCID
- Yi, Xin
- Liang, Yu
- Jin, Xin
- Pool, John E.
- Xu, Xun
- Jiang, Hui
- Korneliussen, Thorfinn Sand
- Zheng, Hancheng
- Liu, Tao
- He, Weiming
- Luo, Ruibang
- Wu, Honglong
- Cao, Hongzhi
- Zou, Jing
- Shan, Ying
- Yang, Qi
- Tian, Geng
- Xu, Junming
- Liu, Xiao
- Wu, Renhua
- Zhou, Guangyu
- Tang, Meifang
- Qin, Junjie
- Wang, Tong
- Wang, Wei
- Chen, Fang
- Li, Zhuo
- Yang, Ge
- Tang, Shuhui
- Gao, Guoyi
- Luo, Zhen
- Gusang, Lamu
- Zhang, Qinghui
- Liang, Huiqing
- Bolund, Lars
- Kristiansen, Karsten
- Li, Yingrui
- Zhang, Yong
- Zhang, Xiuqing
- Li, Ruiqiang
- Li, Songgang
- Yang, Huanming
- Nielsen, Rasmus
- Wang, Jun
- Wang, Jian
- Venue
- Science
- Published
- 2010-07-02
- Volume
- 329
- Issue
- 5987
- Pages
- 75-78
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC3711608
- OpenAlex
- W2147575903
- Cited by
- 1,611
- References
- 35
- Citations by year
- 2026: 92 · 2025: 95 · 2024: 90 · 2023: 123 · 2022: 113 · 2021: 123 · 2020: 101 · 2019: 106 · 2018: 84 · 2017: 88 · 2016: 105 · 2015: 111 · 2014: 95 · 2013: 97 · 2012: 90
- FWCI
- 50.78
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- The HKU Scholars Hub (University of Hong Kong) (submittedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
- Funders
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (124318)
- U.S. Public Health Service (R01-MHG084695)
- National Institute on Alcohol Abuse and Alcoholism (R21AA022707)
- National Institute of Mental Health (R01MH084695)
- National Human Genome Research Institute (R01HG003229)
- Topics
- Health Sciences › Medicine › Physiology (medical) › High Altitude and Hypoxia
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- high-altitude adaptation, Tibetan Plateau, EPAS1, natural selection, hypoxia response, allele frequency change, single nucleotide polymorphisms, Han Chinese, population genomics, exome sequencing
- MeSH terms
- Acclimatization, Endothelial PAS Domain-Containing Protein 1, Altitude, Bayes Theorem, China, Erythrocyte Count, Ethnicity, Exons, Female, Gene Frequency, Hemoglobins, Humans, Male, Oxygen, Selection, Genetic, Genome, Human, Sequence Analysis, DNA, Tibet, Polymorphism, Single Nucleotide, Asian People, Basic Helix-Loop-Helix Proteins, Basic Helix-Loop-Helix Transcription Factors, Genetic Association Studies
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