Evolutionary history of Tibetans inferred from whole-genome sequencing

Cardiovascular Plasticity and Adaptation of High-Altitude Birds and Mammals

Exposure to a hypoxic environment at high altitudes imposes severe pressure on animals living there, which utilize substantial cardiovascular and respiratory responses to meet the physiological challenge of oxygen requirement. These responses may result from phenotypic plasticity through short-term exposure (i.e., within a generation) to a new environment or shaped by adaptation (i.e., many generations) through long-term evolution. For example, plasticity triggers a sympathetic-mediated adrenergic response, resulting in an elevation of heart rate and hypoxia-induced pulmonary vasoconstriction that eventually contributes to pulmonary hypertension in some animals. Adaptation to high altitudes can drive an increase in muscular capillarization and adaptive cardiac growth, which promote oxygen diffusion and transportation. Exposure to a high-altitude hypoxic environment stimulates excessive erythropoiesis, which has maladaptive effects and contributes to chronic mountain sickness. Maladaptation caused by plasticity at early stages can be reversed during adaptation. Despite extensive research on high-altitude adaptation, the phenotypic changes and genetic variations in cardiovascular systems responding to high-altitude hypoxia remain insufficiently integrated across taxa. While genomic and transcriptomic studies have advanced our understanding, a cross-taxa comparison of cardiovascular adaptations is still incomplete. We here review recent literature on phenotypic plasticity, adaptations, and genetic and transcriptional basis of cardiovascular systems of mammals and birds living in high altitudes with respect to their duration of exposure at high altitudes. By integrating and comparing data across mammalian and avian species, we aim to provide a framework for understanding the plasticity and adaptation of the cardiovascular system in high-altitude environments.

Flores S, Esquivel E, Ding Y, Peitzsch M, Robles-Guirado JÁ, Regojo Zapata RM, Pozo-Kreilinger JJ, Iglesias C, Dwight T, Muir CA, Oleaga A, Garrido-Lestache Rodríguez-Monte ME, Del Cerro MJ, Martínez-Bendayán I, Álvarez-González E, Cubiella T, Lourenço DM, A. Pereira MA, Burnichon N, Buffet A, Broberg C, Dickson PV, Fraga MF, Llorente Pendás JL, Rueda Soriano J, Buendía Fuentes F, Toledo SP, Clifton-Bligh R, Dienstmann R, Villanueva J, Capdevila J, Gimenez-Roqueplo AP, Favier J, Nuciforo P, Young WF, Bechmann N, Opotowsky AR, Vaidya A, Bancos I, Weghorn D, Robledo M, Casteràs A, Dos-Subirà L, Adameyko I, Chiara MD, Dahia PL, Toledo RA. Convergent Genetic Adaptation in Human Tumors Developed Under Systemic Hypoxia and in Populations Living at High Altitudes

SIGNIFICANCE

This study reveals a broad convergence in genetic adaptation to hypoxia between natural populations and tumors, suggesting that insights from natural populations could enhance our understanding of cancer biology and identify novel therapeutic targets. See related commentary by Lee, p. 875.

Population genomics advances in frontier ethnic minorities in China

China, with its large geographic span, possesses rich genetic diversity across vast frontier regions in addition to the Han Chinese majority. Importantly, demographic events and various natural and cultural environments in Chinese frontier regions have shaped the genomic diversity of ethnic minorities via local adaptations. Thus, insights into the genetic diversity and adaptive evolution of these under-represented ethnic groups are crucial for understanding evolutionary scenarios and biomedical implications in East Asian populations. Here, we focus on ethnic minorities in Chinese frontier regions and review research advances regarding genomic diversity, genetic structure, population history, genetic admixture, and local adaptation. We first provide an overview of the extensive genetic diversity across populations in different Chinese frontier regions. Next, we summarize research progress regarding genetic ancestry, demographic history, the adaptive process, and the archaic identification of multiple ethnic minorities in different Chinese frontier regions. Finally, we discuss the gaps and opportunities in genomic studies of Chinese populations and the need for a more comprehensive understanding of genomic diversity and the evolution of populations of East Asian ancestry in the post-genomic era.

Genetic Associations with the Susceptibility to High-Altitude Pulmonary Edema in the Japanese Population

Yunden Droma, Masao Ota, Nobumitsu Kobayashi, Michiko Ito, Toshio Kobayashi, and Masayuki Hanaoka. Genetic Associations with the Susceptibility to High-Altitude Pulmonary Edema in the Japanese Population. High Alt Med Biol. 00:00-00, 2025.-High-altitude pulmonary edema (HAPE) is a life-threatening, noncardiogenic pulmonary condition that may occur in individuals rapidly ascending to altitudes higher than 2,500 m above sea level. Exaggerated hypoxia-induced pulmonary hypertension plays a critical role in its pathophysiological mechanism. In addition to environmental factors such as hypoxia and hypobaria at high altitudes, individual genetic predisposition significantly influences HAPE occurrence. Several candidate genes have been proposed based on the pathophysiology of HAPE, particularly involving the hypoxia-induced factor pathway and vasodilators/vasoconstrictors. Over the past two decades, we have investigated the associations between susceptibility to HAPE and these candidate genes, including genes EPAS1 (endothelial Per-ARNT-Sim [PAS] domain protein 1), EGLN1 (egl-9 family hypoxia inducible factor 1), eNOS (endothelial nitric oxide synthase), ACE (angiotensin-converting enzyme), and TIMP3 (tissue inhibitor of metalloproteinase 3) in the Japanese population. This review summarizes the major findings of these studies, shedding light on genetic associations with HAPE in the Japanese population.

Convergent evolution of complex adaptive traits modulates angiogenesis in high-altitude Andean and Himalayan human populations

Convergent adaptations represent paradigmatic examples of the capacity of natural selection to influence organisms' biology. However, the possibility to investigate the genetic determinants underpinning convergent complex adaptive traits has been offered only recently by methods for inferring polygenic adaptations from genomic data. Relying on this approach, we demonstrate how high-altitude Andean human groups experienced pervasive selective events at angiogenic pathways, which resemble those previously attested for Himalayan populations despite partial convergence at the single-gene level was observed. This provides additional evidence for the drivers of convergent evolution of enhanced blood perfusion in populations exposed to hypobaric hypoxia for thousands of years.

Alternatively spliced NFKB1 transcripts enriched in Andean Aymara modulate inflammation, HIF and hemoglobin

The molecular basis of increased hemoglobin in Andean Aymara highlanders is unknown. We conducted an integrative analysis of whole-genome-sequencing and granulocytes transcriptomics from Aymara and Europeans in Bolivia to explore genetic basis of the Aymara high hemoglobin. Differentially expressed and spliced genes in Aymaras were associated with inflammatory and hypoxia-related pathways. We identified transcripts with 4th or 5th exon skipping of NFKB1 (AS-NFKB1), key part of NF-kB complex, and their splicing quantitative trait loci; these were increased in Aymaras. AS-NFKB1 transcripts correlated with both transcripts and protein levels of inflammatory and HIF-regulated genes, including hemoglobin. While overexpression of the AS-NFKB1 variant led to increased expression of inflammatory and HIF-targeted genes; under inflammatory stress, NF-kB protein translocation to the nucleus was attenuated, resulting in reduced expression of these genes. Our study reveals AS-NFKB1 splicing events correlating with increased hemoglobin in Aymara and their possible protective mechanisms against excessive inflammation.

Effect of epigenetic changes in hypoxia induced factor (HIF) gene across cancer types

Cancer hypoxia, a crucial characteristic of malignancy, ranging from practically non-hypoxic to severe, impacts gene expression, metabolism and mechanisms associated with tumor formation serves as a key obstacle in cancer therapy. It triggers a complex network of cell signaling pathways, such as the NF-κB, PI3K, mTOR/AKT,MAPK, HIF and their associated genes regulating the effects of the same. The onset and advancement of cancer are attributed to genetic and epigenetic modifications which are intrinsically related. Off late, it has been observed that in disease progression, the epigenetic modifications lead to gene mutations that in turn alter the epigenome, presenting a major hurdle in fabricating treatment strategies. However, theprogress in science and technology has led to the emergence of various surfacing omics and multi-view clustering algorithms, which offer unparalleled prospects for further subtyping cancers, enhancing the prognosis and treatment results of these subtypes, and comprehending crucial pathophysiological mechanisms across diverse molecular strata. Multi-omics has allowed scientists to gain a more comprehensive understanding of the various ways that cellular malfunction can lead to cancer. So, it becomes of utmost importance to firstly understand the epigenetic changes taking place in tumor hypoxia at gene level. This review sheds light on the role of HIF gene in hypoxic milieu and its relationship with mechanisms of cancer epigenetics. It further glances as to how omics approach can be used to study the oncogenic cellular changes and how bioinformatic tools aid in identification of complex gene networks involved in disease progression. Lastly, it glimpses through the benefits and shortcomings of the existing epi drug therapy and how it can be used in developing novel treatment options.

Validation of new predictors of mortality and BODE index variants in patients with COPD at moderate altitude

Background

COPD ranks as the third leading global cause of mortality. Despite the widespread use of the BODE index and its variants for mortality prediction, their accuracy may be affected by factors like ethnicity, altitude and regional disparities. This study aimed to assess a new altitude-adapted prognostic index in COPD patients at moderate altitudes compared with the BODE and other mortality predictors.

Methods

We evaluated the performance of BODE and other standard prognostic indexes in an exploratory cohort of COPD patients using Cox proportional hazards models. Additionally, we developed a new risk-weighted prognostics model. We assessed its performance utilising receiver operating characteristic curves and compared it with BODE index variants. The indices were validated in a second cohort. The mean follow-up period in both cohorts was 7 years.

Results

In the exploratory cohort (n=416), COPD patients had a 77% 5-year survival rate. eBODE exhibited superior predictive capacity (HR 1.22, 95% CI 1.11-1.34, p<0.05). Prognostic models included oxygen saturation measured by pulse oximetry <90%, body mass index, 6-min walk test (6MWT) and current smoking as primary relevant risks (BOSEA-90), with the second model excluding 6MWT (BOSA-90). BOSEA-90 predicted a major risk per point (HR 1.41, 95% CI 1.31-1.51, p<0.001) and superior discrimination (area under the curve (AUC) >0.75) compared to other indices (AUC <0.70, p<0.001). The validation cohort (n=436) confirmed effectiveness in differentiating mild and very severe cases.

Conclusions

The BODE prognostic index and its variants effectively predicted mortality, and the newly proposed BOSEA-90 and BOSA-90 indices demonstrated appropriate performance for a group of COPD patients at moderate altitude.

A chromosome-scale reference genome assembly for Triplophysa lixianensis

In this study, we constructed a chromosome-scale reference genome assembly for Lixian plateau loach, Triplophysa lixianensis, by integration of MGI short-read, PacBio HiFi long-read and Hi-C sequencing technologies. A 668-Mb haplotypic genome assembly was obtained for a female T. lixianensis, and 98.91% of the assembled sequences were anchored into 25 chromosomes. This assembly owned a moderate repeat content (35.63%) and an annotation of 23,774 protein-coding genes, among them 94.15% were predicted with functions. The assembled genome of T. lixianensis shared a good syntenic relationship with previously published data of its relative T. dalaica. Taken together, our genome data presented here provide a valuable genetic resource for in-depth evolutionary and functional studies, as well as molecular breeding and conservation of this valuable fish species to elevate its ecological and economical values.

Archaic introgression contributed to shape the adaptive modulation of angiogenesis and cardiovascular traits in human high-altitude populations from the Himalayas

It is well established that several Homo sapiens populations experienced admixture with extinct human species during their evolutionary history. Sometimes, such a gene flow could have played a role in modulating their capability to cope with a variety of selective pressures, thus resulting in archaic adaptive introgression events. A paradigmatic example of this evolutionary mechanism is offered by the EPAS1 gene, whose most frequent haplotype in Himalayan highlanders was proved to reduce their susceptibility to chronic mountain sickness and to be introduced in the gene pool of their ancestors by admixture with Denisovans. In this study, we aimed at further expanding the investigation of the impact of archaic introgression on more complex adaptive responses to hypobaric hypoxia evolved by populations of Tibetan/Sherpa ancestry, which have been plausibly mediated by soft selective sweeps and/or polygenic adaptations rather than by hard selective sweeps. For this purpose, we used a combination of composite-likelihood and gene network-based methods to detect adaptive loci in introgressed chromosomal segments from Tibetan WGS data and to shortlist those presenting Denisovan-like derived alleles that participate to the same functional pathways and are absent in populations of African ancestry, which are supposed to do not have experienced Denisovan admixture. According to this approach, we identified multiple genes putatively involved in archaic introgression events and that, especially as regards TBC1D1, RASGRF2, PRKAG2, and KRAS, have plausibly contributed to shape the adaptive modulation of angiogenesis and of certain cardiovascular traits in high-altitude Himalayan peoples. These findings provided unprecedented evidence about the complexity of the adaptive phenotype evolved by these human groups to cope with challenges imposed by hypobaric hypoxia, offering new insights into the tangled interplay of genetic determinants that mediates the physiological adjustments crucial for human adaptation to the high-altitude environment.

Higher oxygen content and transport characterize high-altitude ethnic Tibetan women with the highest lifetime reproductive success

We chose the "natural laboratory" provided by high-altitude native ethnic Tibetan women who had completed childbearing to examine the hypothesis that multiple oxygen delivery traits were associated with lifetime reproductive success and had genomic associations. Four hundred seventeen (417) women aged 46 to 86 y residing at ≥3,500 m in Upper Mustang, Nepal, provided information on reproductive histories, sociocultural factors, physiological measurements, and DNA samples for this observational cohort study. Simultaneously assessing multiple traits identified combinations associated with lifetime reproductive success measured as the number of livebirths. Women with the most livebirths had distinctive hematological and cardiovascular traits. A hemoglobin concentration near the sample mode and a high percent of oxygen saturation of hemoglobin raised arterial oxygen concentration without risking elevated blood viscosity. We propose ongoing stabilizing selection on hemoglobin concentration because extreme values predicted fewer livebirths and directional selection favoring higher oxygen saturation because higher values had more predicted livebirths. EPAS1, an oxygen homeostasis locus with strong signals of positive natural selection and a high frequency of variants occurring only among populations indigenous to the Tibetan Plateau, associated with hemoglobin concentration. High blood flow into the lungs, wide left ventricles, and low hypoxic heart rate responses aided effective convective oxygen transport to tissues. Women with physiologies closer to unstressed, low altitude values had the highest lifetime reproductive success. This example of ethnic Tibetan women residing at high altitudes in Nepal links reproductive fitness with trait combinations increasing oxygen delivery under severe hypoxic stress and demonstrates ongoing natural selection.

Ancestral origins and post-admixture adaptive evolution of highland Tajiks

It remains debatable how many genes and how various the mechanisms are behind human adaptation to extreme environments, such as high altitudes. Despite extensive studies on Tibetans, Andeans and Ethiopians, new insights are expected to be provided with careful analysis of underrepresented highlanders living in a different geographical region, such as the Tajiks, who reside on the Pamir Plateau at an average altitude exceeding 4000 meters. Moreover, genetic admixture, as we observed in the current whole-genome deep-sequencing study of Xinjiang Tajiks (XJT), offers a unique opportunity to explore how admixture may facilitate adaptation to high-altitude environments. Compared with other extensively studied highlanders, XJT showed pronounced admixture patterns: most of their ancestry are derived from West Eurasians (34.5%-48.3%) and South Asians (21.4%-40.0%), and some minor ancestry from East Asians and Siberians (3.62%-17.5%). The greater genetic diversity in XJT than in their ancestral source populations provides a genetic basis for their adaptation to high-altitude environments. The admixture gain of functional adaptive components from ancestral populations could facilitate adaptation to high-altitude environments. Specifically, admixture-facilitated adaptation was strongly associated with skin-related candidate genes that respond to UV radiation (e.g. HERC2 and BNC2) and cardiovascular-system-related genes (e.g. MPI and BEST1). Notably, no adaptive variants of genes showing outstanding natural selection signatures in the Tibetan or Andean highlanders were identified in XJT, including EPAS1 and EGLN1, indicating that a different set of genes contributed to XJT's survival on the Pamir Plateau, although some genes underlying natural selection in XJT have been previously reported in other highlanders. Our results highlight the unique genetic adaptations in XJT and propose that admixture may play a vital role in facilitating high-altitude adaptation. By introducing and elevating diversity, admixture likely induces novel genetic factors that contribute to the survival of populations in extreme environments like the highlands.

Polymorphic transposable elements provide new insights on high-altitude adaptation in the Tibetan Plateau

Several studies demonstrated that populations living in the Tibetan plateau are genetically and physiologically adapted to high-altitude conditions, showing genomic signatures ascribable to the action of natural selection. However, so far most of them relied solely on inferences drawn from the analysis of coding variants and point mutations. To fill this gap, we focused on the possible role of polymorphic transposable elements in influencing the adaptation of Tibetan and Sherpa highlanders. To do so, we compared high-altitude and middle/low-lander individuals of East Asian ancestry by performing in silico analyses and differentiation tests on 118 modern and ancient samples. We detected several transposable elements associated with high altitude, which map genes involved in cardiovascular, hematological, chem-dependent and respiratory conditions, suggesting that metabolic and signaling pathways taking part in these functions are disproportionately impacted by the effect of environmental stressors in high-altitude individuals. To our knowledge, our study is the first hinting to a possible role of transposable elements in the adaptation of Tibetan and Sherpa highlanders.

Hypobaric hypoxia drives selection of altitude-associated adaptative alleles in the Himalayan population

Genetic variants play a crucial role in shaping the adaptive phenotypes associated with high-altitude populations. Nevertheless, a comprehensive understanding of the specific impacts of different environments associated with increasing altitudes on the natural selection of these genetic variants remains undetermined. Hence, this study aimed to identify genetic markers responsible for high-altitude adaptation with specific reference to different altitudes, majorly focussing on an altitude elevation range of ∼1500 m and a corresponding decrease of ≥5 % in ambient oxygen availability. We conducted a comprehensive genome-wide investigation (n = 192) followed by a validation study (n = 514) in low-altitude and three high-altitude populations (>2400 m) of Nubra village (NU) (3048 m), Sakti village (SKT) (3812 m), and Tso Moriri village (TK) (4522 m). Extensive genetic analysis identified 86 SNPs that showed significant associations with high-altitude adaptation. Frequency mapping of these SNPs revealed 38 adaptive alleles and specific haplotypes that exhibited a strong linear correlation with increasing altitude. Notably, these SNPs spanned crucial genes, such as ADH6 and NAPG along with the vastly studied genes like EGLN1 and EPAS1, involved in oxygen sensing, metabolism, and vascular homeostasis. Correlation analyses between these adaptive alleles and relevant clinical and biochemical markers provided evidence of their functional relevance in physiological adaptation to hypobaric hypoxia. High-altitude population showed a significant increase in plasma 8-isoPGF2α levels as compared to low-altitude population. Similar observation showcased increased blood pressure in NU as compared to TK (P < 0.0001). In silico analyses further confirmed that these alleles regulate gene expression of EGLN1, EPAS1, COQ7, NAPG, ADH6, DUOXA1 etc. This study provides genetic insights into the effects of hypobaric-hypoxia on the clinico-physiological characteristics of natives living in increasing high-altitude regions. Overall, our findings highlight the synergistic relationship between environment and evolutionary processes, showcasing physiological implications of genetic variants in oxygen sensing and metabolic pathway genes in increasing high-altitude environments.

Functional EPAS1/HIF2A missense variant is associated with hematocrit in Andean highlanders

Hypoxia-inducible factor pathway genes are linked to adaptation in both human and nonhuman highland species. EPAS1, a notable target of hypoxia adaptation, is associated with relatively lower hemoglobin concentration in Tibetans. We provide evidence for an association between an adaptive EPAS1 variant (rs570553380) and the same phenotype of relatively low hematocrit in Andean highlanders. This Andean-specific missense variant is present at a modest frequency in Andeans and absent in other human populations and vertebrate species except the coelacanth. CRISPR-base-edited human cells with this variant exhibit shifts in hypoxia-regulated gene expression, while metabolomic analyses reveal both genotype and phenotype associations and validation in a lowland population. Although this genocopy of relatively lower hematocrit in Andean highlanders parallels well-replicated findings in Tibetans, it likely involves distinct pathway responses based on a protein-coding versus noncoding variants, respectively. These findings illuminate how unique variants at EPAS1 contribute to the same phenotype in Tibetans and a subset of Andean highlanders despite distinct evolutionary trajectories.

Hypoxia Inducible Factor pathway proteins in high-altitude mammals

Humans and other mammals inhabit hypoxic high-altitude locales. In many of these species, genes under positive selection include ones in the Hypoxia Inducible Factor (HIF) pathway. One is PHD2 (EGLN1), which encodes for a key oxygen sensor. Another is HIF2A (EPAS1), which encodes for a PHD2-regulated transcription factor. Recent studies have provided insights into mechanisms for these high-altitude alleles. These studies have (i) shown that selection can occur on nonconserved, unstructured regions of proteins, (ii) revealed that high altitude-associated amino acid substitutions can have differential effects on protein-protein interactions, (iii) provided evidence for convergent evolution by different molecular mechanisms, and (iv) suggested that mutations in different genes can complement one another to produce a set of adaptive phenotypes.

Genomic Variation, Population History, and Long-Term Genetic Adaptation to High Altitudes in Tibetan Partridge (Perdix hodgsoniae)

Species residing across elevational gradients display adaptations in response to environmental changes such as oxygen availability, ultraviolet radiation, and temperature. Here, we study genomic variation, gene expression, and long-term adaptation in Tibetan Partridge (Perdix hodgsoniae) populations residing across the elevational gradient of the Tibetan Plateau. We generated a high-quality draft genome and used it to carry out downstream population genomic and transcriptomic analysis. The P. hodgsoniae populations residing across various elevations were genetically distinct, and their phylogenetic clustering was consistent with their geographic distribution. We identified possible evidence of gene flow between populations residing in <3,000 and >4,200 m elevation that is consistent with known habitat expansion of high-altitude populations of P. hodgsoniae to a lower elevation. We identified a 60 kb haplotype encompassing the Estrogen Receptor 1 (ESR1) gene, showing strong genetic divergence between populations of P. hodgsoniae. We identified six single nucleotide polymorphisms within the ESR1 gene fixed for derived alleles in high-altitude populations that are strongly conserved across vertebrates. We also compared blood transcriptome profiles and identified differentially expressed genes (such as GAPDH, LDHA, and ALDOC) that correlated with differences in altitude among populations of P. hodgsoniae. These candidate genes from population genomics and transcriptomics analysis were enriched for neutrophil degranulation and glycolysis pathways, which are known to respond to hypoxia and hence may contribute to long-term adaptation to high altitudes in P. hodgsoniae. Our results highlight Tibetan Partridges as a useful model to study molecular mechanisms underlying long-term adaptation to high altitudes.

Tissue Perfusion and Diffusion and Cellular Respiration: Transport and Utilization of Oxygen

This article provides an overview of the journey of inspired oxygen after its uptake across the alveolar-capillary interface, and the interplay among tissue perfusion, diffusion, and cellular respiration in the transport and utilization of oxygen. The critical interactions between oxygen and its facilitative carriers (hemoglobin in red blood cells and myoglobin in muscle cells), and with other respiratory and vasoactive molecules (carbon dioxide, nitric oxide, and carbon monoxide), are emphasized to illustrate how this versatile system dynamically optimizes regional convective transport and diffusive gas exchange. The rates of reciprocal gas exchange in the lung and the periphery must be well-matched and sufficient for meeting the range of energy demands from rest to maximal stress but not excessive as to become toxic. The mobile red blood cells play a vital role in matching tissue perfusion and gas exchange by dynamically regulating the controlled uptake of oxygen and communicating regional metabolic signals across different organs. Intracellular oxygen diffusion and facilitation via myoglobin into the mitochondria, and utilization via electron transport chain and oxidative phosphorylation, are summarized. Physiological and pathophysiological adaptations are briefly described. Dysfunction of any component across this integrated system affects all other components and elicits corresponding structural and functional adaptation aimed at matching the capacities across the entire system and restoring equilibrium under normal and pathological conditions.

To the extreme! How biological anthropology can inform exercise physiology in extreme environments

The fields of biological anthropology and exercise physiology are closely related and can provide mutually beneficial insights into human performance. These fields often use similar methods and are both interested in how humans function, perform, and respond in extreme environments. However, these two fields have different perspectives, ask different questions, and work within different theoretical frameworks and timescales. Biological anthropologists and exercise physiologists can greatly benefit from working together when examining human adaptation, acclimatization, and athletic performance in the extremes of heat, cold, and high-altitude. Here we review the adaptations and acclimatizations in these three different extreme environments. We then examine how this work has informed and built upon exercise physiology research on human performance. Finally, we present an agenda for moving forward, hopefully, with these two fields working more closely together to produce innovative research that improves our holistic understanding of human performance capacities informed by evolutionary theory, modern human acclimatization, and the desire to produce immediate and direct benefits.

Massively parallel sequencing of 74 microhaplotypes and forensic characteristics in three Chinese Sino-Tibetan populations

Microhaplotype (MH), as an emerging type of forensic genetic marker in recent years, has the potential to support multiple forensic applications, especially for mixture deconvolution and biogeographic ancestry inference. Herein, we investigated the genotype data of 74 MHs included in a novel MH panel, the Ion AmpliSeq MH-74 Plex Microhaplotype Research Panel, in three Chinese Sino-Tibetan populations (Han, Tibetan, and Yi) using the Ion Torrent semiconductor sequencing. The sequencing performance, allele frequencies, effective number of alleles (Ae), informativeness (In), and forensic parameters were subsequently estimated and calculated. In addition, principal component analysis (PCA) and structure analysis were performed to explore the population relationships among the three populations and the ancestry component distribution. Overall, this novel MH panel is robust and reliable, and has an excellent sequencing performance. The Ae values ranged from 1.0126 to 7.0855 across all samples, and 75.68 % of MHs had Ae values >2.0000. Allele frequencies at some loci varied considerably among the three studied populations, and the mean In value was 0.0195. Moreover, the genetic affinity between Tibetans and Yis was closer than that between Tibetans and Hans. The aforementioned results suggest that the Ion AmpliSeq MH-74 Plex Microhaplotype Research Panel is highly polymorphic in three investigated populations and could be used as an effective tool for human forensics. Although these 74 MHs have demonstrated the competency in continental population stratification, a higher resolution for distinguishing intracontinental subpopulations and a more comprehensive database with sufficient reference population data still remain to be accomplished.

Disruption of sirtuin 7 in zebrafish facilitates hypoxia tolerance

SIRT7 is a member of the sirtuin family proteins with nicotinamide adenine dinucleotide (NAD+)-dependent histone deacetylase activity, which can inhibit the activity of hypoxia-inducible factors independently of its enzymatic activity. However, the role of SIRT7 in affecting hypoxia signaling in vivo is still elusive. Here, we find that sirt7-null zebrafish are more resistant to hypoxic conditions, along with an increase of hypoxia-responsive gene expression and erythrocyte numbers, compared with their wildtype siblings. Overexpression of sirt7 suppresses the expression of hypoxia-responsive genes. Further assays indicate that sirt7 interacts with zebrafish hif-1αa, hif-1αb, hif-2αa, and hif-2αb to inhibit their transcriptional activity and mediate their protein degradation. In addition, sirt7 not only binds to the hypoxia responsive element of hypoxia-inducible gene promoters but also causes a reduction of H3K18Ac on these promoters. Sirt7 may regulate hypoxia-responsive gene expression through its enzymatic and nonenzymatic activities. This study provides novel insights into sirt7 function and sheds new light on the regulation of hypoxia signaling by sirt7.

"What We Know and What We Do Not Know about Evolutionary Genetic Adaptation to High Altitude Hypoxia in Andean Aymaras"

Three well-studied populations living at high altitudes are Tibetans, Andeans (Aymaras and Quechuas), and Ethiopians. Unlike Tibetans and Ethiopians who have similar hemoglobin (Hb) levels as individuals living at sea level, Aymara Hb levels increase when living at higher altitudes. Our previous whole genome study of Aymara people revealed several selected genes that are involved in cardiovascular functions, but their relationship with Hb levels was not elucidated. Here, we studied the frequencies of known evolutionary-selected variants in Tibetan and Aymara populations and their correlation with high Hb levels in Aymara. We genotyped 177 Aymaras at three different altitudes: 400 m (Santa Cruz), 4000 m (La Paz), and 5000 m (Chorolque), and correlated the results with the elevation of residence. Some of the Tibetan-selected variants also exist in Aymaras, but at a lower prevalence. Two of 10 Tibetan selected variants of EPAS1 were found (rs13005507 and rs142764723) and these variants did not correlate with Hb levels. Allele frequencies of 5 Aymara selected SNPs (heterozygous and homozygous) at 4000 m (rs11578671_BRINP3, rs34913965_NOS2, rs12448902_SH2B1, rs10744822_TBX5, and rs487105_PYGM) were higher compared to Europeans. The allelic frequencies of rs11578671_BRINP3, rs34913965_NOS2, and rs10744822_SH2B1 were significantly higher for Aymaras living at 5000 m than those at 400 m elevation. Variant rs11578671, close to the BRINP3 coding region, correlated with Hb levels in females. Variant rs34913965 (NOS2) correlated with leukocyte counts. Variants rs12448902 (SH2B1) and rs34913965 (NOS2) associated with higher platelet levels. The correlation of these SNPs with blood cell counts demonstrates that the selected genetic variants in Aymara influence hematopoiesis and cardiovascular effects.

Adaptation and altitude sickness: A 40-year bibliometric analysis and collaborative networks

Introduction

We analyze the scientific production and collaboration networks of studies based on adaptation and altitude diseases in the period 1980-2020.

Methods

The publications were extracted from journals indexed in Scopus. The bibliometric analysis was used to analyze the scientific production, including the number of annual publications, the documents, and the characteristics of the publications. With the VOSviewer software, the analysis of collaborative networks, productivity of the countries, as well as the analysis of the co-occurrence of keywords were visualized.

Results

15,240 documents were registered, of which 3,985 documents were analyzed. A significant trend was observed in the number of publications (R ²: 0.9847; P: < 0.001), with annual growth of 4.6%. The largest number of publications were original articles (77.8%), these published more frequently in the journal "Altitude Medicine and Biology". The largest number of countries were from Europe and Asia; however, the largest collaboration network was with the United States. Of the countries with high altitudes, China and Peru ranked first in scientific productivity. The research priorities were on the adaptation mechanism (37.1%), mainly anoxia and respiratory function. Acute mountain sickness (18.4%) and pulmonary edema (14.7%) were the most reported diseases. Of the top 10 institutions, "University of Colorado" and "Universidad Peruana Cayetano Heredia" contributed more than 100 publications.

Conclusions

Scientific production on adaptation and altitude illnesses continues to grow. The United States and United Kingdom present collaborative networks with high-altitude countries. The research is aimed at studying the mechanisms of adaptation to altitude and acute mountain sickness.

Markhor-derived Introgression of a Genomic Region Encompassing PAPSS2 Confers High-altitude Adaptability in Tibetan Goats

Understanding the genetic mechanism of how animals adapt to extreme conditions is fundamental to determine the relationship between molecular evolution and changing environments. Goat is one of the first domesticated species and has evolved rapidly to adapt to diverse environments, including harsh high-altitude conditions with low temperature and poor oxygen supply but strong ultraviolet radiation. Here, we analyzed 331 genomes of domestic goats and wild caprid species living at varying altitudes (high > 3000 m above sea level and low < 1200 m), along with a reference-guided chromosome-scale assembly (contig-N50: 90.4 Mb) of a female Tibetan goat genome based on PacBio HiFi long reads, to dissect the genetic determinants underlying their adaptation to harsh conditions on the Qinghai-Tibetan Plateau (QTP). Population genomic analyses combined with genome-wide association studies (GWAS) revealed a genomic region harboring the 3'-phosphoadenosine 5'-phosphosulfate synthase 2 (PAPSS2) gene showing strong association with high-altitude adaptability (PGWAS = 3.62 × 10-25) in Tibetan goats. Transcriptomic data from 13 tissues revealed that PAPSS2 was implicated in hypoxia-related pathways in Tibetan goats. We further verified potential functional role of PAPSS2 in response to hypoxia in PAPSS2-deficient cells. Introgression analyses suggested that the PAPSS2 haplotype conferring the high-altitude adaptability in Tibetan goats originated from a recent hybridization between goats and a wild caprid species, the markhor (Capra falconeri). In conclusion, our results uncover a hitherto unknown contribution of PAPSS2 to high-altitude adaptability in Tibetan goats on QTP, following interspecific introgression and natural selection.

Genetic adaptation of skin pigmentation in highland Tibetans

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.

Insight into the Effects of High-Altitude Hypoxic Exposure on Learning and Memory

The earth land area is heterogeneous in terms of elevation; about 45% of its land area belongs to higher elevation with altitude above 500 meters compared to sea level. In most cases, oxygen concentration decreases as altitude increases. Thus, high-altitude hypoxic stress is commonly faced by residents in areas with an average elevation exceeding 2500 meters and those who have just entered the plateau. High-altitude hypoxia significantly affects advanced neurobehaviors including learning and memory (L&M). Hippocampus, the integration center of L&M, could be the most crucial target affected by high-altitude hypoxia exposure. Based on these points, this review thoroughly discussed the relationship between high-altitude hypoxia and L&M impairment, in terms of hippocampal neuron apoptosis and dysfunction, neuronal oxidative stress disorder, neurotransmitters and related receptors, and nerve cell energy metabolism disorder, which is of great significance to find potential targets for medical intervention. Studies illustrate that the mechanism of L&M damaged by high-altitude hypoxia should be further investigated based on the entire review of issues related to this topic.

Time Domains of Hypoxia Responses and -Omics Insights

The ability to respond rapidly to changes in oxygen tension is critical for many forms of life. Challenges to oxygen homeostasis, specifically in the contexts of evolutionary biology and biomedicine, provide important insights into mechanisms of hypoxia adaptation and tolerance. Here we synthesize findings across varying time domains of hypoxia in terms of oxygen delivery, ranging from early animal to modern human evolution and examine the potential impacts of environmental and clinical challenges through emerging multi-omics approaches. We discuss how diverse animal species have adapted to hypoxic environments, how humans vary in their responses to hypoxia (i.e., in the context of high-altitude exposure, cardiopulmonary disease, and sleep apnea), and how findings from each of these fields inform the other and lead to promising new directions in basic and clinical hypoxia research.

Human adaptation to high altitude: a review of convergence between genomic and proteomic signatures

Both genomics- and proteomics-based investigations have identified several essential genes, proteins, and pathways that may facilitate human adaptive genotype/phenotype in a population-specific manner. This comprehensive review provides an up-to-date list of genes and proteins identified for human adaptive responses to high altitudes. Genomics studies for indigenous high-altitude populations like Tibetans, Andeans, Ethiopians, and Sherpas have identified 169 genes under positive natural selection. Similarly, global proteomics studies have identified 258 proteins (± 1.2-fold or more) for Tibetan, Sherpa, and Ladakhi highlanders. The primary biological processes identified for genetic signatures include hypoxia-inducible factor (HIF)-mediated oxygen sensing, angiogenesis, and erythropoiesis. In contrast, major biological processes identified for proteomics signatures include 14–3-3 mediated sirtuin signaling, integrin-linked kinase (ILK), phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT), and integrin signaling. Comparing genetic and protein signatures, we identified 7 common genes/proteins (HBB/hemoglobin subunit beta, TF/serotransferrin, ANGPTL4/angiopoietin-related protein 4, CDC42/cell division control protein 42 homolog, GC/vitamin D-binding protein, IGFBP1/insulin-like growth factor-binding protein 1, and IGFBP2/insulin-like growth factor-binding protein 2) involved in crucial molecular functions like IGF-1 signaling, LXR/RXR activation, ferroptosis signaling, iron homeostasis signaling and regulation of cell cycle. Our combined multi-omics analysis identifies common molecular targets and pathways for human adaptation to high altitude. These observations further corroborate convergent positive selection of hypoxia-responsive molecular pathways in humans and advocate using multi-omics techniques for deciphering human adaptive responses to high altitude.

High-Altitude Erythrocytosis: Mechanisms of Adaptive and Maladaptive Responses

Erythrocytosis, or increased production of red blood cells, is one of the most well-documented physiological traits that varies within and among in high-altitude populations. Although a modest increase in blood O2-carrying capacity may be beneficial for life in highland environments, erythrocytosis can also become excessive and lead to maladaptive syndromes such as chronic mountain sickness (CMS).

Forensic Efficiency Estimation of a Homemade Six-Color Fluorescence Multiplex Panel and In-Depth Anatomy of the Population Genetic Architecture in Two Tibetan Groups

The genetic information of the Chinese Tibetan group has been a long-standing research hotspot among population geneticists and archaeologists. Herein, 309 unrelated individuals from two Tibetan groups living in Qinghai Province, China (CTQ), and Tibet Autonomous Region, China (CTT), were successfully genotyped using a new homemade six-color fluorescence multiplex panel, which contained 59 autosomal deletion/insertion polymorphisms (au-DIPs), two mini short tandem repeats (miniSTRs), two Y-chromosomal DIPs, and one Amelogenin. The cumulative probability of matching and combined power of exclusion values for this new panel in CTQ and CTT groups were 1.9253E-27 and 0.99999729, as well as 1.5061E-26 and 0.99999895, respectively. Subsequently, comprehensive population genetic analyses of Tibetan groups and reference populations were carried out based on the 59 au-DIPs. The multitudinous statistical analysis results supported that Tibetan groups have close genetic affinities with East Asian populations. These findings showed that this homemade system would be a powerful tool for forensic individual identification and paternity testing in Chinese Tibetan groups and give us an important insight for further perfecting the genetic landscape of Tibetan groups.

Ancient genomes from the Himalayas illuminate the genetic history of Tibetans and their Tibeto-Burman speaking neighbors

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.

Denisovans and Homo sapiens on the Tibetan Plateau: dispersals and adaptations

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.

The genomic basis of high-elevation adaptation in wild house mice (Mus musculus domesticus) from South America

Understanding the genetic basis of environmental adaptation in natural populations is a central goal in evolutionary biology. The conditions at high elevation, particularly the low oxygen available in the ambient air, impose a significant and chronic environmental challenge to metabolically active animals with lowland ancestry. To understand the process of adaptation to these novel conditions and to assess the repeatability of evolution over short timescales, we examined the signature of selection from complete exome sequences of house mice (Mus musculus domesticus) sampled across two elevational transects in the Andes of South America. Using phylogenetic analysis, we show that house mice colonized high elevations independently in Ecuador and Bolivia. Overall, we found distinct responses to selection in each transect and largely nonoverlapping sets of candidate genes, consistent with the complex nature of traits that underlie adaptation to low oxygen availability (hypoxia) in other species. Nonetheless, we also identified a small subset of the genome that appears to be under parallel selection at the gene and SNP levels. In particular, three genes (Col22a1, Fgf14, and srGAP1) bore strong signatures of selection in both transects. Finally, we observed several patterns that were common to both transects, including an excess of derived alleles at high elevation, and a number of hypoxia-associated genes exhibiting a threshold effect, with a large allele frequency change only at the highest elevations. This threshold effect suggests that selection pressures may increase disproportionately at high elevations in mammals, consistent with observations of some high-elevation diseases in humans.

Functional and HRE motifs count analysis of induction of selected hypoxia-responsive genes by HIF-1 and HIF-2 in human umbilical endothelial cells

We analyzed the effects of selective knockdown of either HIF-1α or HIF-2α on the transcriptional response to hypoxia of human umbilical endothelial cells at two time-points (2 h and 8 h) of hypoxia. We focused on 13 previously identified hypoxia-responsive genes, pre-selected to have different activation kinetics and different proportions of HRE motifs annotated to either HIF-1 or HIF-2 in open promoters - open chromatin DNase-hypersensitive sites (DHS) regions within ±1 kb of the gene start. We report that genes activated by both HIF-1 and 2 tend to be activated earlier than genes activated by HIF-1 only, which, in turn, tend to be activated earlier than genes activated by HIF-2 only. Moreover, for the 13 analyzed genes, we found that the effect of silencing HIF1A on the gene induction by hypoxia is greater for the genes with more HRE motifs annotated to HIF-1 in their promoter open chromatin DHS regions within ±1 kb and also within ±10 kb of the gene start. We corroborated and extended this finding by showing that among 232 genes previously identified as activated by hypoxia, the genes with ChIP-seq peak(s) for HIF-1α within a ±10 kb flank of the gene start contain more HRE motifs annotated to HIF-1 in the DHS regions within this flank than the genes with no ChIP-seq peaks. Also in the whole genome, the DHS regions intersecting ChIP-seq peaks for HIF-1α contain more HRE motifs annotated to HIF-1 than the DHS regions not intersecting the ChIP-seq peaks. This suggests a mechanism, by which higher promoter content of HRE motifs in DHS regions increases HIF-1 binding, which in turn increases gene induction by hypoxia.

Introgressive Hybridization and Hypoxia Adaptation in High-Altitude Vertebrates

In natural populations of animals, a growing body of evidence suggests that introgressive hybridization may often serve as an important source of adaptive genetic variation. Population genomic studies of high-altitude vertebrates have provided strong evidence of positive selection on introgressed allelic variants, typically involving a long-term highland species as the donor and a more recently arrived colonizing species as the recipient. In high-altitude humans and canids from the Tibetan Plateau, case studies of adaptive introgression involving the HIF transcription factor, EPAS1, have provided insights into complex histories of ancient introgression, including examples of admixture from now-extinct source populations. In Tibetan canids and Andean waterfowl, directed mutagenesis experiments involving introgressed hemoglobin variants successfully identified causative amino acid mutations and characterized their phenotypic effects, thereby providing insights into the functional properties of selectively introgressed alleles. We review case studies of adaptive introgression in high-altitude vertebrates and we highlight findings that may be of general significance for understanding mechanisms of environmental adaptation involving different sources of genetic variation.

The history and evolution of the Denisovan-EPAS1 haplotype in Tibetans

Recent studies suggest that admixture with archaic hominins played an important role in facilitating biological adaptations to new environments. For example, interbreeding with Denisovans facilitated the adaptation to high-altitude environments on the Tibetan Plateau. Specifically, the EPAS1 gene, a transcription factor that regulates the response to hypoxia, exhibits strong signatures of both positive selection and introgression from Denisovans in Tibetan individuals. Interestingly, despite being geographically closer to the Denisova Cave, East Asian populations do not harbor as much Denisovan ancestry as populations from Melanesia. Recently, two studies have suggested two independent waves of Denisovan admixture into East Asians, one of which is shared with South Asians and Oceanians. Here, we leverage data from EPAS1 in 78 Tibetan individuals to interrogate which of these two introgression events introduced the EPAS1 beneficial sequence into the ancestral population of Tibetans, and we use the distribution of introgressed segment lengths at this locus to infer the timing of the introgression and selection event. We find that the introgression event unique to East Asians most likely introduced the beneficial haplotype into the ancestral population of Tibetans around 48,700 (16,000-59,500) y ago, and selection started around 9,000 (2,500-42,000) y ago. Our estimates suggest that one of the most convincing examples of adaptive introgression is in fact selection acting on standing archaic variation.

Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression

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.

Inferring archaic introgression from hominin genetic data

Questions surrounding the timing, extent, and evolutionary consequences of archaic admixture into human populations have a long history in evolutionary anthropology. More recently, advances in human genetics, particularly in the field of ancient DNA, have shed new light on the question of whether or not Homo sapiens interbred with other hominin groups. By the late 1990s, published genetic work had largely concluded that archaic groups made no lasting genetic contribution to modern humans; less than a decade later, this conclusion was reversed following the successful DNA sequencing of an ancient Neanderthal. This reversal of consensus is noteworthy, but the reasoning behind it is not widely understood across all academic communities. There remains a communication gap between population geneticists and paleoanthropologists. In this review, we endeavor to bridge this gap by outlining how technological advancements, new statistical methods, and notable controversies ultimately led to the current consensus.

A Likelihood Approach for Uncovering Selective Sweep Signatures from Haplotype Data

Selective sweeps are frequent and varied signatures in the genomes of natural populations, and detecting them is consequently important in understanding mechanisms of adaptation by natural selection. Following a selective sweep, haplotypic diversity surrounding the site under selection decreases, and this deviation from the background pattern of variation can be applied to identify sweeps. Multiple methods exist to locate selective sweeps in the genome from haplotype data, but none leverages the power of a model-based approach to make their inference. Here, we propose a likelihood ratio test statistic T to probe whole-genome polymorphism data sets for selective sweep signatures. Our framework uses a simple but powerful model of haplotype frequency spectrum distortion to find sweeps and additionally make an inference on the number of presently sweeping haplotypes in a population. We found that the T statistic is suitable for detecting both hard and soft sweeps across a variety of demographic models, selection strengths, and ages of the beneficial allele. Accordingly, we applied the T statistic to variant calls from European and sub-Saharan African human populations, yielding primarily literature-supported candidates, including LCT, RSPH3, and ZNF211 in CEU, SYT1, RGS18, and NNT in YRI, and HLA genes in both populations. We also searched for sweep signatures in Drosophila melanogaster, finding expected candidates at Ace, Uhg1, and Pimet. Finally, we provide open-source software to compute the T statistic and the inferred number of presently sweeping haplotypes from whole-genome data.

High-Altitude Adaptation: Mechanistic Insights from Integrated Genomics and Physiology

Population genomic analyses of high-altitude humans and other vertebrates have identified numerous candidate genes for hypoxia adaptation, and the physiological pathways implicated by such analyses suggest testable hypotheses about underlying mechanisms. Studies of highland natives that integrate genomic data with experimental measures of physiological performance capacities and subordinate traits are revealing associations between genotypes (e.g., hypoxia-inducible factor gene variants) and hypoxia-responsive phenotypes. The subsequent search for causal mechanisms is complicated by the fact that observed genotypic associations with hypoxia-induced phenotypes may reflect second-order consequences of selection-mediated changes in other (unmeasured) traits that are coupled with the focal trait via feedback regulation. Manipulative experiments to decipher circuits of feedback control and patterns of phenotypic integration can help identify causal relationships that underlie observed genotype–phenotype associations. Such experiments are critical for correct inferences about phenotypic targets of selection and mechanisms of adaptation.

Physiological Genomics of Adaptation to High-Altitude Hypoxia

Population genomic studies of humans and other animals at high altitude have generated many hypotheses about the genes and pathways that may have contributed to hypoxia adaptation. Future advances require experimental tests of such hypotheses to identify causal mechanisms. Studies to date illustrate the challenge of moving from lists of candidate genes to the identification of phenotypic targets of selection, as it can be difficult to determine whether observed genotype-phenotype associations reflect causal effects or secondary consequences of changes in other traits that are linked via homeostatic regulation. Recent work on high-altitude models such as deer mice has revealed both plastic and evolved changes in respiratory, cardiovascular, and metabolic traits that contribute to aerobic performance capacity in hypoxia, and analyses of tissue-specific transcriptomes have identified changes in regulatory networks that mediate adaptive changes in physiological phenotype. Here we synthesize recent results and discuss lessons learned from studies of high-altitude adaptation that lie at the intersection of genomics and physiology.

[Adaption to chronic hypoxaemia by populations living at high altitude]

Permanent life at high altitude induces important physiological stresses linked to the exposure to chronic hypoxia. Various strategies have been adopted by diverse populations living in the Andes, Tibet or East Africa. The main mechanism is an increase in red blood cell production, more marked in Andeans than in Tibetans or Ethiopians. Other changes are observed in the cardiovascular or respiratory systems, as well as in the utero-placental circulation. Sometimes, a de-adaptation process to hypoxia develops, when erythrocytosis becomes excessive and leads to haematological, vascular and cerebral complications (Monge's disease or chronic mountain sickness). Pulmonary hypertension may also appear. Therapeutic options are available but not sufficiently used. Genetic studies have recently been undertaken to try to better understand the evolution of the human genome in populations living in various high altitude regions of the world, as well as the genetic risk factors for chronic diseases. A new model has appeared, intermittent chronic hypoxia, due to the development of economic activities (mainly mining) in desert regions of the Altiplano.

The oxygen cascade in patients treated with hemodialysis and native high-altitude dwellers: lessons from extreme physiology to benefit patients with end-stage renal disease

Patients treated with hemodialysis (HD) repeatedly undergo intradialytic low arterial oxygen saturation and low central venous oxygen saturation, reflecting an imbalance between upper body systemic oxygen supply and demand, which are associated with increased mortality. Abnormalities along the entire oxygen cascade, with impaired diffusive and convective oxygen transport, contribute to the reduced tissue oxygen supply. HD treatment impairs pulmonary gas exchange and reduces ventilatory drive, whereas ultrafiltration can reduce tissue perfusion due to a decline in cardiac output. In addition to these factors, capillary rarefaction and reduced mitochondrial efficacy can further affect the balance between cellular oxygen supply and demand. Whereas it has been convincingly demonstrated that a reduced perfusion of heart and brain during HD contributes to organ damage, the significance of systemic hypoxia remains uncertain, although it may contribute to oxidative stress, systemic inflammation, and accelerated senescence. These abnormalities along the oxygen cascade of patients treated with HD appear to be diametrically opposite to the situation in Tibetan highlanders and Sherpa, whose physiology adapted to the inescapable hypobaric hypoxia of their living environment over many generations. Their adaptation includes pulmonary, vascular, and metabolic alterations with enhanced capillary density, nitric oxide production, and mitochondrial efficacy without oxidative stress. Improving the tissue oxygen supply in patients treated with HD depends primarily on preventing hemodynamic instability by increasing dialysis time/frequency or prescribing cool dialysis. Whether dietary or pharmacological interventions, such as the administration of L-arginine, fermented food, nitrate, nuclear factor erythroid 2-related factor 2 agonists, or prolyl hydroxylase 2 inhibitors, improve clinical outcome in patients treated with HD warrants future research.

Cross-Species Insights Into Genomic Adaptations to Hypoxia

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.

Tibetan PHD2, an allele with loss-of-function properties

Tibetans have adapted to the chronic hypoxia of high altitude and display a distinctive suite of physiologic adaptations, including augmented hypoxic ventilatory response and resistance to pulmonary hypertension. Genome-wide studies have consistently identified compelling genetic signatures of natural selection in two genes of the Hypoxia Inducible Factor pathway, PHD2 and HIF2A The product of the former induces the degradation of the product of the latter. Key issues regarding Tibetan PHD2 are whether it is a gain-of-function or loss-of-function allele, and how it might contribute to high-altitude adaptation. Tibetan PHD2 possesses two amino acid changes, D4E and C127S. We previously showed that in vitro, Tibetan PHD2 is defective in its interaction with p23, a cochaperone of the HSP90 pathway, and we proposed that Tibetan PHD2 is a loss-of-function allele. Here, we report that additional PHD2 mutations at or near Asp-4 or Cys-127 impair interaction with p23 in vitro. We find that mice with the Tibetan Phd2 allele display augmented hypoxic ventilatory response, supporting this loss-of-function proposal. This is phenocopied by mice with a mutation in p23 that abrogates the PHD2:p23 interaction. Hif2a haploinsufficiency, but not the Tibetan Phd2 allele, ameliorates hypoxia-induced increases in right ventricular systolic pressure. The Tibetan Phd2 allele is not associated with hemoglobin levels in mice. We propose that Tibetans possess genetic alterations that both activate and inhibit selective outputs of the HIF pathway to facilitate successful adaptation to the chronic hypoxia of high altitude.

Seq-ing Higher Ground: Functional Investigation of Adaptive Variation Associated With High-Altitude Adaptation

Human populations at high altitude exhibit both unique physiological responses and strong genetic signatures of selection thought to compensate for the decreased availability of oxygen in each breath of air. With the increased availability of genomic information from Tibetans, Andeans, and Ethiopians, much progress has been made to elucidate genetic adaptations to chronic hypoxia that have occurred throughout hundreds of generations in these populations. In this perspectives piece, we discuss specific hypoxia-pathway variants that have been identified in high-altitude populations and methods for functional investigation, which may be used to determine the underlying causal factors that afford adaptation to high altitude.

The origin of domestication genes in goats

Goat domestication was critical for agriculture and civilization, but its underlying genetic changes and selection regimes remain unclear. Here, we analyze the genomes of worldwide domestic goats, wild caprid species, and historical remains, providing evidence of an ancient introgression event from a West Caucasian tur-like species to the ancestor of domestic goats. One introgressed locus with a strong signature of selection harbors the MUC6 gene, which encodes a gastrointestinally secreted mucin. Experiments revealed that the nearly fixed introgressed haplotype confers enhanced immune resistance to gastrointestinal pathogens. Another locus with a strong signal of selection may be related to behavior. The selected alleles at these two loci emerged in domestic goats at least 7200 and 8100 years ago, respectively, and increased to high frequencies concurrent with the expansion of the ubiquitous modern mitochondrial haplogroup A. Tracking these archaeologically cryptic evolutionary transformations provides new insights into the mechanisms of animal domestication.

Neural network correlates of high-altitude adaptive genetic variants in Tibetans: A pilot, exploratory study

Although substantial progress has been made in the identification of genetic substrates underlying physiology, neuropsychology, and brain organization, the genotype–phenotype associations remain largely unknown in the context of high‐altitude (HA) adaptation. Here, we related HA adaptive genetic variants in three gene loci (EGLN1, EPAS1, and PPARA) to interindividual variance in a set of physiological characteristics, neuropsychological tests, and topological attributes of large‐scale structural and functional brain networks in 135 indigenous Tibetan highlanders. Analyses of individual HA adaptive single‐nucleotide polymorphisms (SNPs) revealed that specific SNPs selectively modulated physiological characteristics (erythrocyte level, ratio between forced expiratory volume in the first second to forced vital capacity, arterial oxygen saturation, and heart rate) and structural network centrality (the left anterior orbital gyrus) with no effects on neuropsychology or functional brain networks. Further analyses of genetic adaptive scores, which summarized the overall degree of genetic adaptation to HA, revealed significant correlations only with structural brain networks with respect to local interconnectivity of the whole networks, intermodule communication between the right frontal and parietal module and the left occipital module, nodal centrality in several frontal regions, and connectivity strength of a subnetwork predominantly involving in intramodule edges in the right temporal and occipital module. Moreover, the associations were dependent on gene loci, weight types, or topological scales. Together, these findings shed new light on genotype–phenotype interactions under HA hypoxia and have important implications for developing new strategies to optimize organism and tissue responses to chronic hypoxia induced by extreme environments or diseases.

Prioritizing natural-selection signals from the deep-sequencing genomic data suggests multi-variant adaptation in Tibetan highlanders

Human genetic adaptation to high altitudes (>2500 m) has been extensively studied over the last few years, but few functional adaptive genetic variants have been identified, largely owing to the lack of deep-genome sequencing data available to previous studies. Here, we build a list of putative adaptive variants, including 63 missense, 7 loss-of-function, 1,298 evolutionarily conserved variants and 509 expression quantitative traits loci. Notably, the top signal of selection is located in TMEM247, a transmembrane protein-coding gene. The Tibetan version of TMEM247 harbors one high-frequency (76.3%) missense variant, rs116983452 (c.248C > T; p.Ala83Val), with the T allele derived from archaic ancestry and carried by >94% of Tibetans but absent or in low frequencies (<3%) in non-Tibetan populations. The rs116983452-T is strongly and positively correlated with altitude and significantly associated with reduced hemoglobin concentration (p = 5.78 × 10-5), red blood cell count (p = 5.72 × 10-7) and hematocrit (p = 2.57 × 10-6). In particular, TMEM247-rs116983452 shows greater effect size and better predicts the phenotypic outcome than any EPAS1 variants in association with adaptive traits in Tibetans. Modeling the interaction between TMEM247-rs116983452 and EPAS1 variants indicates weak but statistically significant epistatic effects. Our results support that multiple variants may jointly deliver the fitness of the Tibetans on the plateau, where a complex model is needed to elucidate the adaptive evolution mechanism.