Adaptation In Tibetans Research Articles

Polygenic adaptation leads to a higher reproductive fitness of native Tibetans at high altitude

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.

Identification of HMOX2 promoter variants linked to adaptation in Tibetans

Populations living at high altitude have been subjected to the selective pressure of hypoxia due to low atmospheric pressure for hundreds of generations. Adaptive genetic signals are apparent in the genomes of present-day populations, but the links to physiological changes and underlying mechanisms are not completely understood. Our recent physiological studies revealed that Tibetans residing at intermediate altitude (2200 m; 13,780 ft) have lower hemoglobin concentration ([Hb]) and elevated carbon monoxide (CO) relative to other populations resident at the same altitude. Our previous genetic studies revealed that Tibetans residing at 4200 m (13,780 ft) exhibit a haplotype (20 kilobases) encompassing the Heme Oxygenase 2 (HMOX2) gene region. Heme oxygenase 2 protein produces carbon monoxide (CO) as a byproduct of hemoglobin breakdown. We hypothesize that HMOX2 underlies the observed CO levels at high altitude. We further hypothesize that regulatory variants could be linked to elevated heme oxygenase activity and, therefore, elevated CO levels in people of Tibetan ancestry.We measured carboxyhemoglobin (COHb) in Tibetan (n = 10) and Han Chinese (n = 8) male residents of Xining (2,200 m; 7,218 ft), China, using a co-oximeter and Tibetan (13 women, 8 men) and Han Chinese (6 women, 10 men) residents of Salt Lake City, Utah (1,413 m/4,637 ft) with a finger pulse oximeter. In the Xining cohort, COHb levels were 97% higher in Tibetans (1.01 ± 0.59 %) compared to their Han Chinese counterparts (0.51 ± 0.39 %, p < 0.048). This result was replicated in Salt Lake City, where Tibetans exhibited significantly higher COHb (4.31 ± 0.48%) compared to Han Chinese (2.00 ± 0.6%, p = 0.004).We also examined localized signals of natural selection (Composite of Multiple Signals test, CMS) from 27 previously published Tibetan genomes and identified single nucleotide variants (SNVs) within the selected haplotype with potential functional impacts on heme-oxygenase expression. Eleven variants were located within the promoter region of the HMOX2 gene. These variants exhibit significant delta allele frequencies (DAF) between Tibetans and Han Chinese (DAF > 0.2, p < 0.005) and are in high linkage disequilibrium (R2 > 0.9) in both populations. Literature and in-silico prediction tools (CIS-BP, JASPAR) indicate some of these variants have a potential gain-of-function roles as transcription factor binding sites.These results suggest adaptive, regulatory variants in HMOX2 may contribute to the observed increased endogenous CO in highland Tibetans, conferring protection from the selective stresses of high-altitude hypoxia. This project is funded by NIH R01HL145470. This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Reduced Hypoxic Ventilatory and Heart Rate Responses to Hypoxia in Post- versus Pre-menopausal Tibetan Women in Mustang, Nepal

Populations living at high altitudes exhibit distinct cardiovascular and ventilatory responses to hypoxia, which may result from exposure to the selective pressure of chronic hypoxia throughout hundreds of generations at high altitude. Compared to Andean highlanders and some acclimatized lowlanders, many Tibetans show an increased hypoxic ventilatory response (HVR) and lower hemoglobin concentration ([Hb]). While the effects of menopause on [Hb] have been well studied, its effects on HVR and heart rate responses to hypoxia (HHRR) in Tibetan women residing at high altitude have not been elucidated. We hypothesized that hypoxic ventilatory and heart rate responses to hypoxia decrease with menopausal status in Tibetan women, suggesting a change of adaptation during post-reproductive years in women. We measured minute ventilation (V I ) and heart rate (HR) during room air and acute hypoxia in 376 Tibetan women (age range 46-86 years old) living in in Mustang, Nepal (>11,482ft / 3,500m) and compared responses between pre- and post-menopausal groups (mean ± SEM). Using a rebreathing system, we induced hypoxia to produce events of at least 10% desaturation (from 91 ± 0.2% to 78 ± 0.2%), expressed HVR and HRR as -ΔV I / ΔSpO 2 and -ΔHR / ΔSpO 2 , respectively, and tested for associations between HVR and HHRR with age and [Hb]. HVR, HHRR, and [Hb] associated negatively with age in the post- but not pre-menopausal group. During hypoxia, post-menopausal women had lower V I (14.2 ± 0.2 L/min) and HR (80 ± 1 BPM) when compared (p<0.01) to pre-menopausal women (16.9 ± 0.4 L/min for V I and 85 ± 1 BPM for HR). V I was also lower in room air conditions (p<0.01) for post-menopausal (11.5 ± 0.1 L/min) versus pre-menopausal women (12.6 ± 0.2 L/min). HVR and HHRR was lower in post- (0.21 ± 0.01 L/%O2 and 0.65 ± 0.02 BPM/%O2 respectively) versus pre-menopausal women (HVR: 0.34 ± 0.03 L/%O2 and HHRR: 0.92 ± 0.05 BPM/%O2). Pre-menopausal women also exhibited negative correlations with HVR and HHRR with increasing [Hb]; however, these correlations were not significant in the post-menopausal group. A non-blunted HVR is a hallmark of adaptation in Tibetans, and physiological changes observed in Tibetan women during later life stages may result in a loss of such traits. These data suggest a hypothesis of menopause-related loss, or change, of adaptation to high-altitude hypoxia among middle-aged to elderly Tibetan women. Supported by NSF award 1831530 to CMB and NIH 1R01HL145470 to TSS. This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Large-scale genome sequencing redefines the genetic footprints of high-altitude adaptation in Tibetans

BackgroundTibetans 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.ResultsHere, 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.ConclusionsOverall, 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.

High-altitude adaptation: Role of genetic and epigenetic factors

After the completion of the Human Genome Project in 2003, the field of genetics has witnessed massive progress that spanned research in high-altitude biology also. Especially the decade of 2010s witnessed the most of it and revealed various genetic signatures of high-altitude adaptation in Tibetans, Andeans and Ethiopians. High-altitude area, with its extreme environment, harbors a tremendous potential for gene-environment interaction, an aspect that could be explored by epigenetic studies. There are only four original articles till now which explore the epigenetic aspect of high-altitude adaptation or acclimatization. However, there is no comprehensive review to provide complete information on the genetic and epigenetic aspects of high-altitude adaptations. Hence, we have prepared this mini-review to summarize the genetic and epigenetic studies that have correlated the high-altitude adaptation or acclimatization, until recently.

Correlations Between Intestinal Microbial Community and Hematological Profile in Native Tibetans and Han Immigrants.

Hematological features are one of the best-known aspects of high-altitude adaptation in Tibetans. However, it is still unclear whether the intestinal microbiota is associated with the hematology profile. In this study, routine blood tests and 16S rRNA gene sequencing were used to investigate the differences in the intestinal microbiota and hematological parameters of native Tibetan herders and Han immigrants sampled at 3,900 m. The blood test results suggested that the platelet counts (PLTs) were significantly higher in native Tibetans than the Han immigrants. The feces of the native Tibetans had significantly greater microbial diversity (more different species: Simpson’s and Shannon’s indices) than that of the Han immigrants. The native Tibetans also had a different fecal microbial community structure than the Han immigrants. A Bray–Curtis distance-based redundancy analysis and envfit function test showed that body mass index (BMI) and PLT were significant explanatory variables that correlated with the fecal microbial community structure in native Tibetans. Spearman’s correlation analysis showed that Megamonas correlated positively with BMI, whereas Bifidobacterium correlated negatively with BMI. Alistipes and Parabacteroides correlated positively with the PLT. Succinivibrio correlated positively with SpO2. Intestinibacter correlated negatively with the red blood cell count, hemoglobin, and hematocrit (HCT). Romboutsia correlated negatively with HCT, whereas Phascolarctobacterium correlated positively with HCT. A functional analysis showed that the functional capacity of the gut microbial community in the native Tibetans was significantly related to carbohydrate metabolism. These findings suggest that the hematological profile is associated with the fecal microbial community, which may influence the high-altitude adaptation/acclimatization of Tibetans.

Chromatin accessibility landscape and regulatory network of high-altitude hypoxia adaptation

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.

Interbreeding between archaic human groups and anatomically modern humans commonly occurring in prehistory

A hominin bone fragment from Denisova Cave (Russia) was identified among very few archaic human specimens (i.e., Neanderthals and Denisovans) as being the first-generation offspring of a Neanderthal mother and a Denisovan father. The ancient genomic study of this individual, together with previous evidence of interbreeding, suggests that admixture between archaic and modern humans was common. Here, we review the evidence for hominin interbreeding and the impact of introgressed archaic human DNA on modern humans. As the recovery of human remains in the Pleistocene is extremely rare, a collagen fingerprinting method, often referred to as Zooarchaeology by Mass Spectrometry (ZooMS), was applied to identify over 2000 fragmented bones from Denisova Cave with one being of hominin origin. This individual, named Denisova 11, had her genome sequenced to an average coverage of 2.6-fold. Her mitochondrial DNA was found to be of the Neanderthal type and direct radiocarbon dating showed her to be more than 50000 years old. Approximately equal proportions of Neanderthal-like and Denisovan-like alleles were found in the Denisova 11 individual. This can be explained by her belonging to a population with mixed Neanderthal and Denisovan ancestry, or by her parents being from each one of these two groups. After excluding any accidental mixing of DNA in the laboratory or systematic errors in data processing, analysis of the individual’s alleles carried by two randomly drawn DNA fragments indicated that she had a Neanderthal mother and a Denisovan father. Interbreeding between archaic and modern humans outside Africa was confirmed by a series of studies since the draft sequence of the Neanderthal genome was published in 2010; non-Africans today are the products of this mixture. The proportion of Neanderthal ancestry is significantly higher in present-day East Asians (2.3%−2.6%) than in Western Eurasians (1.8%−2.4%). This has been explained by two independent Neanderthal gene flow events, a later out-of-Africa migration that diluted the proportion of Neanderthal ancestry in Western Eurasian ancestors, or by purifying selection in different population groups. A recent study found that African populations have more Neanderthal ancestry than previously thought, which can be explained by back-migration of Europeans carrying Neanderthal ancestry into Africa. Another widely-known archaic human group, the Denisovans, was identified by the ancient DNA extracted from a finger bone found in Denisova Cave. Along with the high proportion (~5%) of ancestry contributed to present-day Melanesians in Oceania, Denisovans also contributed ~0.2% to the ancestry of mainland Asian and Native American populations. Genes flow into Denisovans from Neanderthals and an unknown hominin (“super-archaic”) were also suggested by ancient DNA studies. Archaeological, ancient genomic, and ancient protein studies suggest Denisovans may have had a wide ecological and geographic distribution. Overall, frequent admixture among different human groups resulted in ~2% Neanderthal ancestry in all non-African humans and up to 5% Denisovan ancestry in some present-day Oceanians. The introgressed archaic human DNA in present-day humans have been affected by natural selection, and inferences about the functional, evolutionary, and phenotypic significance reveal both positive and negative effects. Functional regions of modern human genomes have fewer archaic alleles than expected under a neutral demographic model, which suggests a reduced fitness of some archaic alleles in modern humans. Many Neanderthal variants associated with phenotypes and susceptibility to diseases have been identified in present-day non-Africans, such as type 2 diabetes, lupus, biliary cirrhosis, etc. However, many of the introgressed tracts are also functionally important and possibly helped modern humans adapt to different environments, such as high altitude and latitude areas. For example, the EPAS1 and WARS2/TBX15 , are associated with a high-altitude and high-latitude adaptation in Tibetans and Greenlandic Inuits, respectively. These findings illustrate that admixture with archaic humans has provided genetic variation that helped humans adapt to new environments and has continued to shape our biology. We expect that in the future there will be more evidence of interbreeding between humans in different areas and time periods, adding more details to human genetic history.

Tibetan and Han Chinese oxygen transport at 2200 m and simulated 4200 m during peak exercise

Despite lower Hb concentration, Tibetans resident at 4200m exhibit greater exercise capacity than do Han Chinese also resident at 4200m. Whether these adaptations are maintained at intermediate altitude and/or acute hypobaric hypoxia are unknown.Thirty‐seven healthy, non‐smoking subjects, all resident for at least six months at ~2200 m, of Tibetan (NMale = 10; NFemale = 9) or Han Chinese (NMale = 8; NFemale = 10) ancestries were studied at 2200 m and then during acutely simulated altitude (4200 m in a hypobaric chamber). Subjects performed an incremental cycle test to exhaustion. At peak exercise, oxygen consumption (VO2max), cardiac output (QTmax), ventilation (VE), hemoglobin ([Hb]), blood oxygen saturation (SaO2), and arterial blood gases were measured and diffusing capacity in lung (DL) and muscle (DM) were calculated.At peak exercise at 2200 m, Tibetan males had 1.23 g/dL less [Hb] compared to their Han Chinese male counterparts (p = 0.03). Tibetan females had 1.05 g/dL less [Hb] then Han Chinese females, but the result is not statistically significant (p = 0.064)Compared to Han Chinese, Tibetan females tended to have 4.85 and 2.72 mLmin−1Kg−1 higher VO2max at 2200 m and 4200 m (both p = 0.03). For males, Tibetans tended to have 6.90 and 2.78 mLmin−1Kg−1 higher VO2max than Han Chinese. However, the difference in VO2max was not significant in males at 2200 m or 4200 m (p = 0.095, p = 0.306, respectively).Tibetan males, but not females, had a significantly higher lung O2 diffusing capacity (DL) compared to Han Chinese (p = 0.028 for males; p = 0.192 for females). Tibetans also tended to have increased muscle O2 diffusing capacity (DM), but the difference was not statistically significant.Tibetan compared to Han Chinese females exhibited higher VE during maximal exercise at both 2200 m and 4200 m (p < 0.03, p < 0.02, respectively). The differences were not significant in males (p > 0.54 for 2200 m, p > 0.20 for 4200 m).In addition, Tibetans had 0.53 g/dL higher carboxyhemoglobin compared to Han Chinese at 2200 m (p = 0.005) independent of sex. Considering Tibetans had lower [Hb] than Han Chinese, higher CO content might suggest increased red blood cell destruction in Tibetans.In summary, among Tibetans, who exhibit significantly lower [Hb] and elevated COHb, females exhibit increased exercise capacity and ventilation compared to Han Chinese females at 2200m, and similar trends were exhibited in males acutely exposed to simulated 4200 m. Male Tibetans exhibited greater DL than Han Chinese counterparts. Trends were further noted for greater QT and DM in Tibetans, which is consistent with our previous studies of Tibetans residents at 4200 m. Therefore, it is evident that unique traits of high‐altitude adaptation of Tibetans are retained at intermediate altitude. Such differences between hypoxic‐exercise responses of Tibetans and Han Chinese are likely innate and may be attributed to genetics.Table 1

Genetic variants at the EGLN1 locus associated with high-altitude adaptation in Tibetans are absent or found at low frequency in highland Andeans.

EGLN1 encodes the hypoxia-inducible factor (HIF) pathway prolyl hydroxylase 2 (PHD2) that serves as an oxygen-sensitive regulator of HIF activity. The EGLN1 locus exhibits a signature of positive selection in Tibetan and Andean populations and is associated with hemoglobin concentration in Tibetans. Recent reports provide evidence for functional roles of protein-coding variants within the first exon of EGLN1 (rs186996510, rs12097901) that are linked to an adaptive signal in Tibetans, yet whether these same variants are present and contribute to adaptation in Andean highlanders is unknown. We determined the frequencies of these adaptive Tibetan alleles in Quechua Andeans resident at high altitude (4,350m) in addition to individuals of Nepali ancestry resident at sea level. The rs186996510 C (minor) allele previously found at high frequency in Tibetans is absent in Andean (G: 100%) and rare among Nepali (C: 11.8%, G: 88.2%) cohorts. The minor G allele of rs12097901 is found at similarly low frequencies in Andeans (G: 12.7%, C: 87.3%) and Nepalis (G: 23.5%, C: 76.5%) compared to Tibetans. These results suggest that adaptation involving EGLN1 in Andeans involves different mechanisms than those described in Tibetans. The precise Andean adaptive variants remain to be determined.

Genetic Missense Variants at the EGLN1 Locus Associated with High‐Altitude Adaptation in Tibetans are Rare in Andeans

High‐altitude populations have been challenged by chronic hypoxia for many generations and demonstrate some of the most rapid evolution observed in humans. Genome‐wide scans have brought to light numerous hypoxic‐response candidate genes that are associated with distinct traits in these populations. One example is EGLN1, which shows signals of selection in Tibetan and Andean populations and has been linked to hemoglobin concentration in Tibetans living at high altitude. EGLN1 encodes the hypoxia‐inducible factor (HIF) prolyl hydroxylase 2 (PHD2) protein, which serves as an oxygen‐sensitive regulator of HIF transcription factor activity. We examined the frequencies of two single nucleotide polymorphisms (SNPs) (rs186996510, rs12097901) in the first exon of EGLN1, previously identified at high frequencies and having a gain‐of‐function effect in Tibetans, in a cohort of Quechua Andeans resident at high altitude and individuals of Himalayan (Tibetan, Nepali) ancestry resident at sea level. The minor C allele of rs186996510 is rare among Andeans (0.95%; 1/105) and Nepalese (5.9%; 1/17) but present in 50% (3/6) of Tibetans (X2=36.6, p<0.0001). The minor G allele of rs12097901 was found at 6.6% (7/106) in Andeans, 11.8% (2/17) in Nepalese, and 50% (3/6) in Tibetans (X2=12.8, p<0.002). Two female sea‐level, Tibetan participants with the minor C allele rs186996510 both had significantly lower hematocrit values than the other sea‐level women (F(1,7)=8.8, p=0.025). These genomic differences suggest that despite the identification of an adaptive genetic signal at this locus in both Andean and Tibetan populations, the EGLN1 variants previously reported in Tibetans are very rare in Andeans.Support or Funding InformationThis study was supported by an NIH NRSA Individual Postdoctoral Fellowship (Parent F32) to ECH (F32HL131218), NIH TL1TR001443 to LW, a University of California, San Diego Ledell Family Undergraduate Research Scholarship award for Science and Engineering to ESL, and NIH R00HL118215 and American Physiological Society Giles F. Filley Memorial Award to TSS. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. The UPCH team was supported by a Wellcome Trust PHTM grant (107544/Z/15/Z) to FCV.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Blunted nitric oxide regulation in Tibetans under high-altitude hypoxia

ABSTRACT Nitric oxide (NO) is an important molecule for vasomotor tone, and elevated NO signaling was previously hypothesized as a unique and adaptive physiological change in highland Tibetans. However, there has been lack of NO data from Tibetans living at low altitude and lowlander immigrants living at high altitude, which is crucial to test this hypothesis. Here, through cross-altitude (1990–5018 m) and cross-population (Tibetans and Han Chinese) analyses of serum NO metabolites (NOx) of 2086 individuals, we demonstrate that although Tibetans have a higher serum NOx level compared to lowlanders, Han Chinese immigrants living at high altitude show an even higher level than Tibetans. Consequently, our data contradict the previous proposal of increased NO signaling as the unique adaptive strategy in Tibetans. Instead, Tibetans have a relatively lower circulating NOx level at high altitude. This observation is further supported by data from the hypoxic experiments using human umbilical vein endothelial cells and gene knockout mice. No difference is detected between Tibetans and Han Chinese for endothelial nitric oxide synthase (eNOS), the key enzyme for circulating NO synthesis, suggesting that eNOS itself is unlikely to be the cause. We show that other NO synthesis-related genes (e.g. GCH1) carry Tibetan-enriched mutations significantly associated with the level of circulating NOx in Tibetans. Furthermore, gene network analysis revealed that the downregulation and upregulation of NOx is possibly achieved through distinct pathways. Collectively, our findings provide novel insights into the physiological and genetic mechanisms of the evolutionary adaptation of Tibetans to high-altitude hypoxia.

Regional cerebral blood flow in natives at high altitude: An arterial spin labeled MRI study.

It is known that a neurologic sequence occurs at high altitudes (HA); hence, cerebral blood flow (CBF) might vary by altitude. To use arterial spin labeled (ASL) MRI to evaluate absolute CBF differences between subjects who live at HA and lowlands. Cohort prospective trial. In all, 64 HA Tibetans, 19 lowland Tibetans, and 25 lowland Han subjects. CBF was measured with the pulsed ASL sequence at 3T. CBF was correlated with abode altitude in HA Tibetans; CBF differences among HA Tibetans, lowland Tibetans, and lowland Han subjects was assessed. Pearson correlation assessed the correlation. Independent t-tests analyzed group differences. In HA Tibetans, CBF decreased with altitude in the bilateral anterior and posterior cingulate gyri, fusiform gyrus, cerebellar tonsil and cortices, and thalamus as well as left middle and inferior temporal gyri and right insula (P < 0.05); HA Tibetans (vs. lowland Tibetans) had lower CBF in the left hemisphere (precuneus, anterior cingulate gyrus, fusiform gyrus, and lingual gyrus) and right hemisphere (superior parietal lobule, precuneus, posterior cingulate gyrus, and cerebellar tonsil), while they had higher CBF in the left inferior parietal lobule, lentiform nucleus, and inferior frontal gyrus (P < 0.05). The overlapping regions, in which CBF in HA Tibetans correlated with altitude and decreased (vs. lowland Tibetans), were selected for region of interest analysis, and the results showed lower CBF in HA Tibetans than lowland Han subjects (P < 0.05). HA adaptation in Tibetans is associated with a decrease of regional CBF. 2 Technical Efficacy: Stage 4 J. Magn. Reson. Imaging 2018.

Genetic signatures of high-altitude adaptation in Tibetans

Indigenous Tibetan people have lived on the Tibetan Plateau for millennia. There is a long-standing question about the genetic basis of high-altitude adaptation in Tibetans. We conduct a genome-wide study of 7.3 million genotyped and imputed SNPs of 3,008 Tibetans and 7,287 non-Tibetan individuals of Eastern Asian ancestry. Using this large dataset, we detect signals of high-altitude adaptation at nine genomic loci, of which seven are unique. The alleles under natural selection at two of these loci [methylenetetrahydrofolate reductase (MTHFR) and EPAS1] are strongly associated with blood-related phenotypes, such as hemoglobin, homocysteine, and folate in Tibetans. The folate-increasing allele of rs1801133 at the MTHFR locus has an increased frequency in Tibetans more than expected under a drift model, which is probably a consequence of adaptation to high UV radiation. These findings provide important insights into understanding the genomic consequences of high-altitude adaptation in Tibetans.

Down-Regulation of EPAS1 Transcription and Genetic Adaptation of Tibetans to High-Altitude Hypoxia.

Tibetans are well adapted to the hypoxic environments at high altitude, yet the molecular mechanism of this adaptation remains elusive. We reported comprehensive genetic and functional analyses of EPAS1, a gene encoding hypoxia inducible factor 2α (HIF-2α) with the strongest signal of selection in previous genome-wide scans of Tibetans. We showed that the Tibetan-enriched EPAS1 variants down-regulate expression in human umbilical endothelial cells and placentas. Heterozygous EPAS1 knockout mice display blunted physiological responses to chronic hypoxia, mirroring the situation in Tibetans. Furthermore, we found that the Tibetan version of EPAS1 is not only associated with the relatively low hemoglobin level as a polycythemia protectant, but also is associated with a low pulmonary vasoconstriction response in Tibetans. We propose that the down-regulation of EPAS1 contributes to the molecular basis of Tibetans’ adaption to high-altitude hypoxia.

EP300 contributes to high-altitude adaptation in Tibetans by regulating nitric oxide production.

The genetic adaptation of Tibetans to high altitude hypoxia likely involves a group of genes in the hypoxic pathway, as suggested by earlier studies. To test the adaptive role of the previously reported candidate gene EP300 (histone acetyltransferase p300), we conducted resequencing of a 108.9 kb gene region of EP300 in 80 unrelated Tibetans. The allele-frequency and haplotype-based neutrality tests detected signals of positive Darwinian selection on EP300 in Tibetans, with a group of variants showing allelic divergence between Tibetans and lowland reference populations, including Han Chinese, Europeans, and Africans. Functional prediction suggested the involvement of multiple EP300 variants in gene expression regulation. More importantly, genetic association tests in 226 Tibetans indicated significant correlation of the adaptive EP300 variants with blood nitric oxide (NO) concentration. Collectively, we propose that EP300 harbors adaptive variants in Tibetans, which might contribute to high-altitude adaptation through regulating NO production.

GCH1 plays a role in the high-altitude adaptation of Tibetans.

Tibetans are well adapted to high-altitude hypoxia. Previous genome-wide scans have reported many candidate genes for this adaptation, but only a few have been studied. Here we report on a hypoxia gene (GCH1, GTP-cyclohydrolase I), involved in maintaining nitric oxide synthetase (NOS) function and normal blood pressure, that harbors many potentially adaptive variants in Tibetans. We resequenced an 80.8 kb fragment covering the entire gene region of GCH1 in 50 unrelated Tibetans. Combined with previously published data, we demonstrated many GCH1 variants showing deep divergence between highlander Tibetans and lowlander Han Chinese. Neutrality tests confirmed a signal of positive Darwinian selection on GCH1 in Tibetans. Moreover, association analysis indicated that the Tibetan version of GCH1 was significantly associated with multiple physiological traits in Tibetans, including blood nitric oxide concentration, blood oxygen saturation, and hemoglobin concentration. Taken together, we propose that GCH1 plays a role in the genetic adaptation of Tibetans to high altitude hypoxia.

Four kinds of humans in past 100000 years and their relations

In the past 100000 years four kinds of humans coexisted. They are early modern humans, Neanderthals, Homo floresiensis , and Denisovans. Early modern humans are ancestors of extant humans and have fundmentally similar morphology to that of ours. Neanderthals are slightly shorter than modern humans. They have robust extremities and larger brain volume, Neanderthals inhabited widely in Europe and also distributed in West and Central Asia. They disappeared around 30000 year ago. Evidence of DNA analysis and morphology verified the gene flow between Neanderthals and early modern humans. The genes with Neanderthal ancestry in the genome of extant humans have definite influences on the physiology, morphology and risk for certain diseases in extant humans. Fossils of Homo floresiensis were unearthed only in Flores Island, Indonesia. This kind of humans is very short, with cranial capacity as small as one third of extant humans. They lived 100000–60000 years ago. The origin and their relation with other kinds of humans are mysteries. Fossils of Denisovans were unearthed only at Denisova Cave of Altai region, south Siberia of Russia and only a finger bone and two teeth were found. Denisovans are identified by DNA analysis and lived around 40000 years ago. In the genome of Melanesians 4.8%± 0.5% are derived from Denisovans. It is suggested that the gene flow with Denisovans was helpful for the adaptation of Tibetans to the high plateau environment. Paleo-DNA study also suggests that perhaps another kind of humans coexisted with our ancestor during this period.

Wide distribution and altitude correlation of an archaic high-altitude-adaptive EPAS1 haplotype in the Himalayas.

High-altitude adaptation in Tibetans is influenced by introgression of a 32.7-kb haplotype from the Denisovans, an extinct branch of archaic humans, lying within the endothelial PAS domain protein 1 (EPAS1), and has also been reported in Sherpa. We genotyped 19 variants in this genomic region in 1507 Eurasian individuals, including 1188 from Bhutan and Nepal residing at altitudes between 86 and 4550 m above sea level. Derived alleles for five SNPs characterizing the core Denisovan haplotype (AGGAA) were present at high frequency not only in Tibetans and Sherpa, but also among many populations from the Himalayas, showing a significant correlation with altitude (Spearman’s correlation coefficient = 0.75, p value 3.9 × 10−11). Seven East- and South-Asian 1000 Genomes Project individuals shared the Denisovan haplotype extending beyond the 32-kb region, enabling us to refine the haplotype structure and identify a candidate regulatory variant (rs370299814) that might be interacting in an additive manner with the derived G allele of rs150877473, the variant previously associated with high-altitude adaptation in Tibetans. Denisovan-derived alleles were also observed at frequencies of 3–14 % in the 1000 Genomes Project African samples. The closest African haplotype is, however, separated from the Asian high-altitude haplotype by 22 mutations whereas only three mutations, including rs150877473, separate the Asians from the Denisovan, consistent with distant shared ancestry for African and Asian haplotypes and Denisovan adaptive introgression.Electronic supplementary materialThe online version of this article (doi:10.1007/s00439-016-1641-2) contains supplementary material, which is available to authorized users.

HMOX2 Functions as a Modifier Gene for High-Altitude Adaptation in Tibetans.

Tibetans are well adapted to high-altitude environments. Among the adaptive traits in Tibetans, the relatively low hemoglobin level is considered a blunted erythropoietic response to hypoxic challenge. Previously, EPAS1 and EGLN1, the major upstream regulators in the hypoxic pathway, were reportedly involved in the hemoglobin regulation in Tibetans. In this study, we report a downstream gene (HMOX2) involved in heme catabolism, which harbors potentially adaptive variants in Tibetans. We first resequenced the entire genomic region (45.6 kb) of HMOX2 in Tibetans, which confirmed the previously suspected signal of positive selection on HMOX2 in Tibetans. Subsequent association analyses of hemoglobin levels in two independent Tibetan populations (a total of 1,250 individuals) showed a male-specific association between the HMOX2 variants and hemoglobin levels. Tibetan males with the derived C allele at rs4786504:T>C displayed lower hemoglobin level as compared with the T allele carriers. Furthermore, our in vitro experiments indicated that the C allele of rs4786504 could increase the expression of HMOX2, presumably leading to a more efficient breakdown of heme that may help maintain a relatively low hemoglobin level at high altitude. Collectively, we propose that HMOX2 contributes to high-altitude adaptation in Tibetans by functioning as a modifier in the regulation of hemoglobin metabolism.