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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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“The gene encoding HIF-2α (Epas1) in particular has experienced a history of natural selection in human populations from the Qinghai–Tibet Plateau and in many animals native to high altitude (Ai et al., 2014; Beall et al., 2010; Buroker et al., 2012; Gou et al., 2014; Graham & McCracken, 2019; Li et al., 2013, 2014; Pe…”
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“The rs4953354 is located near the EPAS1 gene encoding HIF-2α which stimulates production of erythrocytes and levels of haemoglobin (Beall et al., 2010; Yi et al., 2010).”
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“In 2010, a hypoxia pathway gene, EPAS1 was identified (Yi et al., 2010) as having the most extreme signature of positive selection in Tibetans and was shown to be associated with differences in haemoglobin concentration at high altitude.”
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“The latter also stabilizes and enhances the activity of HIF1A, the hypoxia- inducible factor that has been identified in the adaptation to altitude of several species (Bigham et al., 2009; Li et al., 2013; Qu et al., 2013; Yi et al., 2010).”
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Self-citationAn Indian lineage of Histoplasma with strong signatures of differentiation and selection
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Self-citationThe immunogenetic impact of European colonization in the Americas
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MethodThe genetic and evolutionary basis of gene expression variation in East Africans
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Transcriptomic analysis provides insight into high-altitude acclimation in domestic goats
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“To identify these SNPs, we used a combination of a statistical test robust to the small effects of sample size together with an Fst statistic; the latter has been successfully applied to identify missense SNPs for adaptation to altitude in Tibetans [6] and disease SNPs in individuals of Aboriginal ancestry in array ge…”
BackgroundMethodHyperuricemia cosegregating with osteogenesis imperfecta is associated with a mutation in GPATCH8
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“For the RIL population, RealSFS (Yi et al., 2010) was used for SNP calling based on the Bayesian estimation of locus frequency.”
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“With PBS we compared FST between our NM dataset, an ingroup composed by Peruvian samples with predominant NatAm ancestry, and an outgroup of Han Chinese samples.”
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Responses of Han Migrants Compared to Tibetans at High Altitude
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“…significant differences from low altitude Han samples have been noted for SNPs in the EPAS1 and ELGN1 loci (Bigham et al., 2010; Peng et al., 2011; Yi et al., 2010), as well as for haplotypes based on a number of SNPs in the most differentiated EPAS and ELGN1 regions (Xu et al., 2011); but only…”
BackgroundPhenotype and Genotype Analysis of Chinese Patients with Osteogenesis Imperfecta Type V
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“The low-quality variations were filtered out using the following criteria: (i) quality score 520 (Q20); (ii) average copy number at the allele site 42; (iii) distance of two adjacent SNPs 55 bp; and (iv) sequencing depth 54 and 4500 [31].”
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“Interestingly, a single nucleotide polymorphism in Hif2a was recently demonstrated to be highly associated with adaptability to high altitude hypoxia in ethnic Tibetans [50].”
BackgroundA large‐scale replication study for the association of rs17039192 in HIF‐2α with knee osteoarthritis
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High-Altitude Andean H194R HIF2A Allele Is a Hypomorphic Allele
Jorgensen, K. C., Song, D., Weinstein, J. B., Garcia, O. A., Pearson, L. N., Inclán, M., Rivera, M. C., Lèon‐Velarde, F., Kiyamu, M., Brutsaert, T. D., et al. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad162 · Cited by 18
“We identified 32 significant SNVs for PBS ranging from PBS = 0.07 to PBS = 0.14 (supplementary table S2 and fig.”
BackgroundMethodResultInfluentialOxygen‐sensing pathways and the pulmonary circulation
Slingo, M. (2023) · The Journal of Physiology · doi:10.1113/jp284591 · Cited by 16
“Relationships between this haemoglobin phenotype and candidate genes exhibiting signals of selection, including those within the HIF pathway (EGLN1/PHD2 and EPAS1/HIF-2 α ), have now been demonstrated (Beall et al., 2010; Simonson et al., 2010; Yi et al., 2010).”
Identifying adaptive alleles in the human genome: from selection mapping to functional validation
Werren, E. A., Garcia, O. A., & Bigham, A. W. (2020) · Human Genetics · doi:10.1007/s00439-020-02206-7 · Cited by 17
Lim, M., Bi, K., Witt, C. C., Graham, C. H., & Dávalos, L. M. (2021) · Journal of Heredity · doi:10.1093/jhered/esab008 · Cited by 16
The Counteracting Effects of Demography on Functional Genomic Variation: The Roma Paradigm
Font‐Porterias, N., Caro-Consuegra, R., Lucas-Sánchez, M., Lopez, M., Giménez, A., Carballo-Mesa, A., Bosch, E., Calafell, F., Quintana‐Murci, L., & Comas, D. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab070 · Cited by 18
“PBS was then obtained as previously described (Yi et al. 2010): PBS 1⁄4 ðT þ T TÞ=2; T 1⁄4 logð1 FstÞ, where Y represents YRI, X either European or South Asian group populations, and W the target population (Roma, Europe, or South Asia).”
MethodThe demographic and ecological factors shaping diversification among rareAstragalusspecies
Jones, M. R., Winkler, D. E., & Massatti, R. T. (2021) · Diversity and Distributions · doi:10.1111/ddi.13288 · Cited by 16
“We then calculated expected PBS distributions for each population as PBS_Pop1 = (−log(1 − FST (Pop1_ Pop2)) + (−log(1 − FST(Pop1_Pop3)) − (−log(1 − FST(Pop2_Pop3)))/2 according to Yi et al. (2010).”
BackgroundMethodHigh-altitude adaptation: Role of genetic and epigenetic factors
Basak, N., & Kumarasamy Thangaraj, K. (2021) · Journal of Biosciences · doi:10.1007/s12038-021-00228-5 · Cited by 16
Stepwise colonization of the Andes by Ruddy Ducks and the evolution of novel β‐globin variants
Muñoz‐Fuentes, V., Cortázar‐Chinarro, M., Lozano-Jaramillo, M., & McCracken, K. G. (2013) · Molecular Ecology · doi:10.1111/mec.12151 · Cited by 16
“2007), and numerous studies have revealed examples of genetic adaptations in high-altitude species (Storz et al. 2007; Simonson et al. 2010; Yi et al. 2010; Scott et al. 2011).”
BackgroundChang, C. L., Cai, J. J., Cheng, P. J., Chueh, H. Y., & Hsu, S. Y. (2011) · Diabetes · doi:10.2337/db10-1331 · Cited by 16
“, the adaptation to environmental oxygen levels and altitude) (5,39).”
BackgroundMolecular evolution of globin genes in Gymnotiform electric fishes: relation to hypoxia tolerance
Tian, R., Losilla, M., Lu, Y. C., Yang, G. Z., & Zakon, H. H. (2017) · BMC Evolutionary Biology · doi:10.1186/s12862-017-0893-3 · Cited by 15
“Recent studies have shown strong evidence for positive selection in hypoxia tolerant species, like yak [47], hummingbirds [48], and cetaceans [49], when compared with their hypoxia intolerant relatives, as well as hypoxiatolerant populations of humans such as Tibetans [50].”
BackgroundSelf-citationHuang, H.-R., Liu, J., Xu, Y., Lascoux, M., Ge, X., & Wright, S. (2018) · New Phytologist · doi:10.1111/nph.15299 · Cited by 16
Pan, W., Liu, C., Zhang, J., Gao, X., Yu, S., Tan, H., Yu, J., Qian, D., Li, J., Bian, S., et al. (2019) · Frontiers in Physiology · doi:10.3389/fphys.2019.00059 · Cited by 16
“[12C > G; 380G > C] PHD2 variant and PKLR gene (Yi et al., 2010; Xiang et al., 2013).”
Self-citationNew advances in the study of prehistoric human activity on the Tibetan Plateau
Zhang, D., Shen, X., Cheng, T., Xia, H., Liu, W., Gao, X., & Chen, F. (2020) · Chinese Science Bulletin (Chinese Version) · doi:10.1360/tb-2019-0382 · Cited by 17
Self-citationGenome scans for selection and introgression based on k ‐nearest neighbour techniques
Pfeifer, B., Alachiotis, N., Pavlidis, P., & Schimek, M. G. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13221 · Cited by 16
“The underlying idea of our approach is influenced by the population branch length statistics (PBS) method (Yi et al., 2010), but supports an arbitrary number of branches.”
Human Evolution: Genomic Gifts from Archaic Hominins
Vernot, B., & Akey, J. M. (2014) · Current Biology · doi:10.1016/j.cub.2014.07.079 · Cited by 13
“Consistent with previous studies [4], they found that many EPAS1 variants exhibited substantial allele frequency differences between Tibetan and non-Tibetan populations, as would be expected for a gene influenced by geographically restricted selection.”
InfluentialShpak, M., Lawrence, K. N., & Pool, J. E. (2025) · Genome Biology and Evolution · doi:10.1093/gbe/evaf080 · Cited by 19
“Among these is the population branch statistic (PBS), first proposed in Yi et al. (2010) as an estimate of the branch length of the focal population.”
Self-citationLin, Y., Li, B., Shi, X., Chen, Y., Pan, S., Lin, Z., Gu, Z., Hailer, F., Hu, L., & Zhan, X. (2025) · Nature Communications · doi:10.1038/s41467-025-64110-w · Cited by 15
Self-citationHigh altitude medicine in China in the 21st century: opportunities and challenges
Huang, L. (2014) · Military Medical Research · doi:10.1186/2054-9369-1-17 · Cited by 15
“Overall, much research on the molecular basis and clinical efficacy was well-established after decades of exploration [7,8].”
BackgroundGesang, L., Gusang, L., Dawa, C., Gesang, G., & Li, K. (2019) · Disease Markers · doi:10.1155/2019/5946461 · Cited by 17
Self-citationHigh‐altitude adaptations mitigate risk for hypertension and diabetes‐associated anemia
Wander, K., Su, M., Mattison, P. M., Sum, C., Witt, C. C., Shenk, M. K., Blumenfield, T., Li, H., & Mattison, S. M. (2020) · American Journal of Physical Anthropology · doi:10.1002/ajpa.24032 · Cited by 17
“…rapidly, particularly with regard to their genetic bases (Beall et al., 2010; Bigham et al., 2010; Bigham & Lee, 2014; Erzurum et al., 2007; Gilbert-Kawai et al., 2017; Guo, He, & Cui, 2017; He et al., 2018; Peng et al., 2010; Simonson et al., 2010; Yi et al., 2010; Zheng, He, & Cui, 2017).”
BackgroundZhao, F., Cheng, W., Wang, Y., Gao, X., Huang, D., Kong, J., Antwi-Boasiako, A., Zheng, L., Yan, W., Chang, F., et al. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23042113 · Cited by 15
“The SNP calling was performed using Real SFS software [46] on the basis of the Bayesian estimation.”
MethodSelf-citationZila-Velasque, J. P., Soriano‐Moreno, D. R., Medina-Ramírez, S. A., Ccami‐Bernal, F., Castro-Díaz, S. D., Cortez-Soto, A. G., Esparza–Varas, A. L., Fernandez-Morales, J., Olortegui-Rodriguez, J. J., Pelayo-Luis, I. P., et al. (2023) · PLoS ONE · doi:10.1371/journal.pone.0292111 · Cited by 15
“The tendency to a higher prevalence of hypertension in the Tibetan population could be due to the physiological changes, such as improved levels of hypoxic ventilation response, blood saturation, pulmonary function, maximal cardiac output, lower levels of pulmonary vasoconstriction, and higher hemoglobin concentration…”
BackgroundJiang, W., Liu, Y., Zhang, C., Pan, L., Wang, W. J., Zhao, C., Zhao, T., & Li, Y. (2024) · Journal of Experimental Botany · doi:10.1093/jxb/erad483 · Cited by 15
Self-citationSong, J., Han, S., Amaru, R., Lanikova, L., Quispe, T., Kim, D., Crawford, J. E., Kim, S. J., Lee, Y., & Prchal, J. T. (2025) · Nature Communications · doi:10.1038/s41467-025-56848-0 · Cited by 15
“Whole-genome-sequencing (WGS) analysis of high altitudepopulationsincludingTibetans 12 – 14 ,Ethiopians 1 ,andQuechuas 15 have identi fi ed signals of natural selection: strong single nucleotide polymorphisms (SNPs)selection signalsin EPAS1 and ELGN1 in Tibetans and SENP1 and ANP32D genesinQuechuas.”
An horizon scan of biogeography
Dawson, M. N., Algar, A. C., Antonelli, A., Dávalos, L. M., Davis, E., Early, R., Guisan, A., Jansson, R., Lessard, J.-P., Marske, K. A., et al. (2013) · Frontiers of Biogeography · doi:10.21425/f5fbg18854 · Cited by 15
“…include detailed genotype and phenotype databases for diverse populations coupled with an extensive historical and fossil re ‐ cord (e.g., Homo; Thomas et al. 1998) with ana ‐ logues in other taxa and/or environments (e.g., Yi et al. 2010, Huerta ‐ Sanchez et al. 2013 c.f. Mirceta et al. 2013).”
The origin of chow chows in the light of the East Asian breeds
Yang, H., Wang, G., Wang, M., Ma, Y., Yin, T., Fan, R., Wu, H., Li, Z., Irwin, D. M., Zhai, W., et al. (2017) · BMC Genomics · doi:10.1186/s12864-017-3525-9 · Cited by 16
“The top panel is for the PBS statistic and the bottom panel is for the SweepFinder.”
MethodInfluentialSelf-citationKovalaskas, S. A., Rilling, J. K., & Lindo, J. (2020) · Genes Brain & Behavior · doi:10.1111/gbb.12715 · Cited by 15
Introgressive Hybridization and Hypoxia Adaptation in High-Altitude Vertebrates
Storz, J. F., & Signore, A. V. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.696484 · Cited by 16
Yang, Y., Wang, Y., Qi, Y., Du, Y., Ma, L., Ga, Q., & Ge, R. (2013) · Wilderness and Environmental Medicine · doi:10.1016/j.wem.2013.05.006 · Cited by 15
“In contrast, the incidence of the G allele and the genotype distribution of GG in the HLT group were significantly more prevalent among the HLT group, suggesting a dominant effect of the G allele and the genotypic distribution of CC in the Tibetans.”
BackgroundResultInfluentialSelf-citationPelster, B., & Burggren, W. W. (2018) · Springer eBooks · doi:10.1007/978-3-319-75935-7_5 · Cited by 15
UNVEILing connections between genotype, phenotype, and fitness in natural populations
Nelson, T. C., Jones, M. R., Velotta, J. P., Dhawanjewar, A. S., & Schweizer, R. M. (2019) · Molecular Ecology · doi:10.1111/mec.15067 · Cited by 15
“…target of natural selection in several high‐altitude species, including high‐altitude human populations, defying the theoretical predictions outlined above (Beall et al., 2010; Huerta‐ Sánchez et al., 2014; Li et al., 2014; Newman et al., 2014; Xu et al., 2011; Yi et al., 2010; Zhang et al., 2014).”
BackgroundZhou, X., Bao, Q., Cui, Y., Li, X., Cheng-zhong, Y., Yi-dong, Y., Gao, Y., Chen, D., & Huang, J. V. (2025) · Frontiers in Genetics · doi:10.3389/fgene.2025.1528935 · Cited by 14
Hypoxia and Tissue Regeneration: Adaptive Mechanisms and Therapeutic Opportunities
Vélez, I. C. V., Domínguez, C. M. C., Sánchez, M. J. F., & Garavito-Aguilar, Z. V. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26199272 · Cited by 18
“Genetic adaptations involve pathways regulating oxygen sensing, erythropoiesis, and mitochondrial metabolism [32,33].”
Kristan, A., Debeljak, N., & Kunej, T. (2019) · European Journal Of Haematology · doi:10.1111/ejh.13304 · Cited by 14
Yan, W., Karikari, B., Chang, F., Zhao, F., Zhang, Y., Li, D., Zhao, T., & Jiang, H. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.715529 · Cited by 14
Self-citationWinters, N., Wafula, E. K., Knollenberg, B. J., Hämälä, T., Timilsena, P. R., Perryman, M. G., Zhang, D., Sheaffer, L. L., Praul, C. A., Ralph, P. E., et al. (2024) · BMC Biology · doi:10.1186/s12915-024-01831-2 · Cited by 14
Adaptations to water stress and pastoralism in the Turkana of northwest Kenya
Lea, A. J., Caldas, I. V., Garske, K. M., Gerlinger, E. R., Arroyo, J. P., John, E., Gurven, M., Handley, C., Kahumbu, J. C., Kamau, J., et al. (2025) · Science · doi:10.1126/science.adv2467 · Cited by 14
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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