Genetic signatures reveal high-altitude adaptation in a set of ethiopian populations

Whole-genome sequencing reveals genomic diversity and selection signatures in Xia'nan cattle

BACKGROUND

The crossbreeding of specialized beef cattle breeds with Chinese indigenous cattle is a common method of genetic improvement. Xia'nan cattle, a crossbreed of Charolais and Nanyang cattle, is China's first specialized beef cattle breed with independent intellectual property rights. After more than two decades of selective breeding, Xia'nan cattle exhibit a robust physique, good environmental adaptability, good tolerance to coarse feed, and high meat production rates. This study analyzed the population genetic structure, genetic diversity, and genomic variations of Xia'nan cattle using whole-genome sequencing data from 30 Xia'nan cattle and 178 published cattle genomic data.

RESULT

The ancestry estimating composition analysis showed that the ancestry proportions for Xia'nan cattle were mainly Charolais with a small amount of Nanyang cattle. Through the genetic diversity studies (nucleotide diversity and linkage disequilibrium decay), we found that the genomic diversity of Xia'nan cattle is higher than that of specialized beef cattle breeds in Europe but lower than that of Chinese native cattle. Then, we used four methods to detect genome candidate regions influencing the excellent traits of Xia'nan cattle. Among the detected results, 42 genes (θπ and CLR) and 131 genes (FST and XP-EHH) were detected by two different detection strategies. In addition, we found a region in BTA8 with strong selection signals. Finally, we conducted functional annotation on the detected genes and found that these genes may influence body development (NR6A1), meat quality traits (MCCC1), growth traits (WSCD1, TMEM68, MFN1, NCKAP5), and immunity (IL11RA, CNTFR, CCL27, SLAMF1, SLAMF7, NAA35, and GOLM1).

CONCLUSION

We elucidated the genomic features and population structure of Xia'nan cattle and detected some selection signals in genomic regions potentially associated with crucial economic traits in Xia'nan cattle. This research provided a basis for further breeding improvements in Xia'nan cattle and served as a reference for genetic enhancements in other crossbreed cattle.

Positive selection in the genomes of two Papua New Guinean populations at distinct altitude levels

Highlanders and lowlanders of Papua New Guinea have faced distinct environmental stress, such as hypoxia and environment-specific pathogen exposure, respectively. In this study, we explored the top genomics regions and the candidate driver SNPs for selection in these two populations using newly sequenced whole-genomes of 54 highlanders and 74 lowlanders. We identified two candidate SNPs under selection - one in highlanders, associated with red blood cell traits and another in lowlanders, which is associated with white blood cell count - both potentially influencing the heart rate of Papua New Guineans in opposite directions. We also observed four candidate driver SNPs that exhibit linkage disequilibrium with an introgressed haplotype, highlighting the need to explore the possibility of adaptive introgression within these populations. This study reveals that the signatures of positive selection in highlanders and lowlanders of Papua New Guinea align closely with the challenges they face, which are specific to their environments.

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.

Genomic structural variation is associated with hypoxia adaptation in high-altitude zokors

Zokors, an Asiatic group of subterranean rodents, originated in lowlands and colonized high-elevational zones following the uplift of the Qinghai-Tibet plateau about 3.6 million years ago. Zokors live at high elevation in subterranean burrows and experience hypobaric hypoxia, including both hypoxia (low oxygen concentration) and hypercapnia (elevated partial pressure of CO2). Here we report a genomic analysis of six zokor species (genus Eospalax) with different elevational ranges to identify structural variants (deletions and inversions) that may have contributed to high-elevation adaptation. Based on an assembly of a chromosome-level genome of the high-elevation species, Eospalax baileyi, we identified 18 large inversions that distinguished this species from congeners native to lower elevations. Small-scale structural variants in the introns of EGLN1, HIF1A, HSF1 and SFTPD of E. baileyi were associated with the upregulated expression of those genes. A rearrangement on chromosome 1 was associated with altered chromatin accessibility, leading to modified gene expression profiles of key genes involved in the physiological response to hypoxia. Multigene families that underwent copy-number expansions in E. baileyi were enriched for autophagy, HIF1 signalling and immune response. E. baileyi show a significantly larger lung mass than those of other Eospalax species. These findings highlight the key role of structural variants underlying hypoxia adaptation of high-elevation species in Eospalax.

Tensor Decomposition-based Feature Extraction and Classification to Detect Natural Selection from Genomic Data

Inferences of adaptive events are important for learning about traits, such as human digestion of lactose after infancy and the rapid spread of viral variants. Early efforts toward identifying footprints of natural selection from genomic data involved development of summary statistic and likelihood methods. However, such techniques are grounded in simple patterns or theoretical models that limit the complexity of settings they can explore. Due to the renaissance in artificial intelligence, machine learning methods have taken center stage in recent efforts to detect natural selection, with strategies such as convolutional neural networks applied to images of haplotypes. Yet, limitations of such techniques include estimation of large numbers of model parameters under nonconvex settings and feature identification without regard to location within an image. An alternative approach is to use tensor decomposition to extract features from multidimensional data although preserving the latent structure of the data, and to feed these features to machine learning models. Here, we adopt this framework and present a novel approach termed T-REx, which extracts features from images of haplotypes across sampled individuals using tensor decomposition, and then makes predictions from these features using classical machine learning methods. As a proof of concept, we explore the performance of T-REx on simulated neutral and selective sweep scenarios and find that it has high power and accuracy to discriminate sweeps from neutrality, robustness to common technical hurdles, and easy visualization of feature importance. Therefore, T-REx is a powerful addition to the toolkit for detecting adaptive processes from genomic data.

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.

Oxygen stress on age-stage, two-sex life tables and transcriptomic response of diamondback moth (Plutella xylostella)

Elucidating the genetic basis of local adaption is one of the important tasks in evolutionary biology. The Qinghai-Tibet Plateau has the highest biodiversity for an extreme environment worldwide, and provides an ideal natural laboratory to study adaptive evolution. The diamondback moth (DBM), Plutella xylostella, is one of the most devastating pests of the global Brassica industry. A highly heterozygous genome of this pest has facilitated its adaptation to a variety of complex environments, and so provides an ideal model to study fast adaptation. We conducted a pilot study combining RNA-seq with an age-stage, two-sex life table to study the effects of oxygen deprivation on DBM. The developmental periods of all instars were significantly shorter in the hypoxic environment. We compared the transcriptomes of DBM from Fuzhou, Fujian (low-altitude) and Lhasa, Tibet (high-altitude) under hypoxia treatment in a hypoxic chamber. Some DEGs are enriched in pathways associated with DNA replication, such as DNA repair, nucleotide excision repair, base excision repair, mismatch repair and homologous recombination. The pathways with significant changes were associated with metabolism process and cell development. Thus, we assumed that insects could adapt to different environments by regulating their metabolism. Our findings indicated that although adaptive mechanisms to hypoxia in different DBM strains could be similar, DBM individuals from Tibet had superior tolerance to hypoxia compared with those of Fuzhou. Local adaptation of the Tibetan colony was assumed to be responsible for this difference. Our research suggests novel mechanisms of insect responses to hypoxia stress.

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

BACKGROUND

Tibetans are genetically adapted to high-altitude environments. Though many studies have been conducted, the genetic basis of the adaptation remains elusive due to the poor reproducibility for detecting selective signatures in the Tibetan genomes.

RESULTS

Here, we present whole-genome sequencing (WGS) data of 1001 indigenous Tibetans, covering the major populated areas of the Qinghai-Tibetan Plateau in China. We identify 35 million variants, and more than one-third of them are novel variants. Utilizing the large-scale WGS data, we construct a comprehensive map of allele frequency and linkage disequilibrium and provide a population-specific genome reference panel, referred to as 1KTGP. Moreover, with the use of a combined approach, we redefine the signatures of Darwinian-positive selection in the Tibetan genomes, and we characterize a high-confidence list of 4320 variants and 192 genes that have undergone selection in Tibetans. In particular, we discover four new genes, TMEM132C, ATP13A3, SANBR, and KHDRBS2, with strong signals of selection, and they may account for the adaptation of cardio-pulmonary functions in Tibetans. Functional annotation and enrichment analysis indicate that the 192 genes with selective signatures are likely involved in multiple organs and physiological systems, suggesting polygenic and pleiotropic effects.

CONCLUSIONS

Overall, the large-scale Tibetan WGS data and the identified adaptive variants/genes can serve as a valuable resource for future genetic and medical studies of high-altitude populations.

Tensor decomposition based feature extraction and classification to detect natural selection from genomic data

Inferences of adaptive events are important for learning about traits, such as human digestion of lactose after infancy and the rapid spread of viral variants. Early efforts toward identifying footprints of natural selection from genomic data involved development of summary statistic and likelihood methods. However, such techniques are grounded in simple patterns or theoretical models that limit the complexity of settings they can explore. Due to the renaissance in artificial intelligence, machine learning methods have taken center stage in recent efforts to detect natural selection, with strategies such as convolutional neural networks applied to images of haplotypes. Yet, limitations of such techniques include estimation of large numbers of model parameters under non-convex settings and feature identification without regard to location within an image. An alternative approach is to use tensor decomposition to extract features from multidimensional data while preserving the latent structure of the data, and to feed these features to machine learning models. Here, we adopt this framework and present a novel approach termed T-REx , which extracts features from images of haplotypes across sampled individuals using tensor decomposition, and then makes predictions from these features using classical machine learning methods. As a proof of concept, we explore the performance of T-REx on simulated neutral and selective sweep scenarios and find that it has high power and accuracy to discriminate sweeps from neutrality, robustness to common technical hurdles, and easy visualization of feature importance. Therefore, T-REx is a powerful addition to the toolkit for detecting adaptive processes from genomic data.

Genomic evidence for adaptation to tuberculosis in the Andes before European contact

Most studies focusing on human high-altitude adaptation in the Andean highlands have thus far been focused on Peruvian populations. We present high-coverage whole genomes from Indigenous people living in the Ecuadorian highlands and perform multi-method scans to detect positive natural selection. We identified regions of the genome that show signals of strong selection to both cardiovascular and hypoxia pathways, which are distinct from those uncovered in Peruvian populations. However, the strongest signals of selection were related to regions of the genome that are involved in immune function related to tuberculosis. Given our estimated timing of this selection event, the Indigenous people of Ecuador may have adapted to Mycobacterium tuberculosis thousands of years before the arrival of Europeans. Furthermore, we detect a population collapse that coincides with the arrival of Europeans, which is more severe than other regions of the Andes, suggesting differing effects of contact across high-altitude populations.

Genomic adaptation of Ethiopian indigenous cattle to high altitude

The mountainous areas of Ethiopia represent one of the most extreme environmental challenges in Africa faced by humans and other inhabitants. Selection for high-altitude adaptation is expected to have imprinted the genomes of livestock living in these areas. Here we assess the genomic signatures of positive selection for high altitude adaptation in three cattle populations from the Ethiopian mountainous areas (Semien, Choke, and Bale mountains) compared to three Ethiopian lowland cattle populations (Afar, Ogaden, and Boran), using whole-genome resequencing and three genome scan approaches for signature of selection (iHS, XP-CLR, and PBS). We identified several candidate selection signature regions and several high-altitude adaptation genes. These include genes such as ITPR2, MB, and ARNT previously reported in the human population inhabiting the Ethiopian highlands. Furthermore, we present evidence of strong selection and high divergence between Ethiopian high- and low-altitude cattle populations at three new candidate genes (CLCA2, SLC26A2, and CBFA2T3), putatively linked to high-altitude adaptation in cattle. Our findings provide possible examples of convergent selection between cattle and humans as well as unique African cattle signature to the challenges of living in the Ethiopian mountainous regions.

The association between altitude and the prevalence of hypertension among permanent highlanders

Hypertension (HTN) is a growing contributor to the global disease burden, and it is prevalent among people living at high altitudes (H-ALTs). This study aimed to explore the relationship between altitude and the prevalence of HTN among inhabitants living at H-ALTs. We searched electronic databases, including PubMed, Embase, and Web of Science, up to April 30, 2022. The quality of included studies was assessed using the Joanna Briggs Institute (JBI) checklist for prevalence studies. A total of 1273 articles were screened, and 32 studies (86,487 participants) were eligible for further analyses. The pooled prevalence among highlanders was 28.7%. General additive model (GAM)-based meta-regression analysis was conducted to explore the association between altitude and the prevalence of HTN. A curve-shaped line was found between altitude and the prevalence of HTN (β = 0.998, p = 0.039) after adjusting for factors including publication year, sample size, age, sex, ethnic group, body mass index (BMI), smoking and alcohol consumption. The turning point was observed at 3300 m. The predictive parameter indicated that the smoothness and goodness of model fit were good (GCV = 0.014, R² = 0.60, respectively). The findings may provide clues for further mechanistic studies that can improve HTN prevention among highlanders.

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.

Genetic differentiation in East African ethnicities and its relationship with endurance running success

Since the 1960s, East African athletes, mainly from Kenya and Ethiopia, have dominated long-distance running events in both the male and female categories. Further demographic studies have shown that two ethnic groups are overrepresented among elite endurance runners in each of these countries: the Kalenjin, from Kenya, and the Oromo, from Ethiopia, raising the possibility that this dominance results from genetic or/and cultural factors. However, looking at the life history of these athletes or at loci previously associated with endurance athletic performance, no compelling explanation has emerged. Here, we used a population approach to identify peaks of genetic differentiation for these two ethnicities and compared the list of genes close to these regions with a list, manually curated by us, of genes that have been associated with traits possibly relevant to endurance running in GWAS studies, and found a significant enrichment in both populations (Kalenjin, P = 0.048, and Oromo, P = 1.6x10^-5). Those traits are mainly related to anthropometry, circulatory and respiratory systems, energy metabolism, and calcium homeostasis. Our results reinforce the notion that endurance running is a systemic activity with a complex genetic architecture, and indicate new candidate genes for future studies. Finally, we argue that a deterministic relationship between genetics and sports must be avoided, as it is both scientifically incorrect and prone to reinforcing population (racial) stereotyping.

The genomic signatures of natural selection in admixed human populations

Admixture has been a pervasive phenomenon in human history, extensively shaping the patterns of population genetic diversity. There is increasing evidence to suggest that admixture can also facilitate genetic adaptation to local environments, i.e., admixed populations acquire beneficial mutations from source populations, a process that we refer to as "adaptive admixture." However, the role of adaptive admixture in human evolution and the power to detect it remain poorly characterized. Here, we use extensive computer simulations to evaluate the power of several neutrality statistics to detect natural selection in the admixed population, assuming multiple admixture scenarios. We show that statistics based on admixture proportions, F_adm and LAD, show high power to detect mutations that are beneficial in the admixed population, whereas other statistics, including iHS and F_ST, falsely detect neutral mutations that have been selected in the source populations only. By combining F_adm and LAD into a single, powerful statistic, we scanned the genomes of 15 worldwide, admixed populations for signatures of adaptive admixture. We confirm that lactase persistence and resistance to malaria have been under adaptive admixture in West Africans and in Malagasy, North Africans, and South Asians, respectively. Our approach also uncovers other cases of adaptive admixture, including APOL1 in Fulani nomads and PKN2 in East Indonesians, involved in resistance to infection and metabolism, respectively. Collectively, our study provides evidence that adaptive admixture has occurred in human populations whose genetic history is characterized by periods of isolation and spatial expansions resulting in increased gene flow.

The evolution of larger size in high-altitude Drosophila melanogaster has a variable genetic architecture

Important uncertainties persist regarding the genetic architecture of adaptive trait evolution in natural populations, including the number of genetic variants involved, whether they are drawn from standing genetic variation, and whether directional selection drives them to complete fixation. Here, we take advantage of a unique natural population of Drosophila melanogaster from the Ethiopian highlands, which has evolved larger body size than any other known population of this species. We apply a bulk segregant quantitative trait locus mapping approach to 4 unique crosses between highland Ethiopian and lowland Zambian populations for both thorax length and wing length. Results indicated a persistently variable genetic basis for these evolved traits (with largely distinct sets of quantitative trait loci for each cross), and at least a moderately polygenic architecture with relatively strong effects present. We complemented these mapping experiments with population genetic analyses of quantitative trait locus regions and gene ontology enrichment analysis, generating strong hypotheses for specific genes and functional processes that may have contributed to these adaptive trait changes. Finally, we find that the genetic architectures indicated by our quantitative trait locus mapping results for size traits mirror those from similar experiments on other recently evolved traits in this species. Collectively, these studies suggest a recurring pattern of polygenic adaptation in this species, in which causative variants do not approach fixation and moderately strong effect loci are present.

Molecular regulations of circadian rhythm and implications for physiology and diseases

The term “circadian rhythms” describes endogenous oscillations with ca. 24-h period associated with the earth’s daily rotation and light/dark cycle. Such rhythms reflect the existence of an intrinsic circadian clock that temporally orchestrates physiological processes to adapt the internal environment with the external cues. At the molecular level, the circadian clock consists of multiple sets of transcription factors resulting in autoregulatory transcription-translation feedback loops. Notably, in addition to their primary role as generator of circadian rhythm, the biological clock plays a key role in controlling physiological functions of almost all tissues and organs. It regulates several intracellular signaling pathways, ranging from cell proliferation, DNA damage repair and response, angiogenesis, metabolic and redox homeostasis, to inflammatory and immune response. In this review, we summarize findings showing the crosstalk between the circadian molecular clock and some key intracellular pathways, describing a scenario wherein their reciprocal regulation impinges upon several aspects of mammalian physiology. Moreover, based on evidence indicating that circadian rhythms can be challenged by environmental factors, social behaviors, as well as pre-existing pathological conditions, we discuss implications of circadian misalignment in human pathologies, such as cancer and inflammatory diseases. Accordingly, disruption of circadian rhythm has been reported to affect several physiological processes that are relevant to human diseases. Expanding our understanding of this field represents an intriguing and transversal medicine challenge in order to establish a circadian precision medicine.

Role of mitochondrial genetic interactions in determining adaptation to high altitude human population

Physiological and haplogroup studies performed to understand high-altitude adaptation in humans are limited to individual genes and polymorphic sites. Due to stochastic evolutionary forces, the frequency of a polymorphism is affected by changes in the frequency of a near-by polymorphism on the same DNA sample making them connected in terms of evolution. Here, first, we provide a method to model these mitochondrial polymorphisms as "co-mutation networks" for three high-altitude populations, Tibetan, Ethiopian and Andean. Then, by transforming these co-mutation networks into weighted and undirected gene-gene interaction (GGI) networks, we were able to identify functionally enriched genetic interactions of CYB and CO3 genes in Tibetan and Andean populations, while NADH dehydrogenase genes in the Ethiopian population playing a significant role in high altitude adaptation. These co-mutation based genetic networks provide insights into the role of different set of genes in high-altitude adaptation in human sub-populations.

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.

Adaptation of mammals to hypoxia

Oxygen plays a pivotal role in the metabolism and activities of mammals. However, oxygen is restricted in some environments-subterranean burrow systems or habitats at high altitude or deep in the ocean-and this could exert hypoxic stresses such as oxidative damage on organisms living in these environments. In order to cope with these stresses, organisms have evolved specific strategies to adapt to hypoxia, including changes in physiology, gene expression regulation, and genetic mutations. Here, we review how mammals have adapted to the three high-altitude plateaus of the world, the limited oxygen dissolved in deep water habitats, and underground tunnels, with the aim of better understanding the adaptation of mammals to hypoxia.

Yak miR-2285o-3p attenuates hypoxia-induced apoptosis by targeting caspase-3

miRNAs are a class of hairpin‐derived RNAs, 21–24 nucleotides in length, which are involved in a range of biological processes. The bta‐miR‐2285 family has over 40 members spanning the entire bovine genome. We previously found that bta‐miR‐2285o‐3p was highly expressed in yak heart and lung when compared with cattle, which prompted us to investigate its potential function in high‐altitude adaptation of yaks. In this study, we detected wide‐spread high expression of bta‐miR‐2285o‐3p in yak tissues. Further experiments revealed that the protein tyrosine phosphatase receptor type M (PTPRM) gene was the host gene of bta‐miR‐2285o‐3p and that two linked SNPs in bta‐mir‐2285o precursor affected the biogenesis of mature miRNA (bta‐miR‐2285o‐3p). Functional analysis in vitro indicated that bta‐miR‐2285o‐3p attenuated hypoxia‐induced apoptosis by targeting very low‐density lipoprotein receptor (VLDLR), phosphatase and tensin homolog (PTEN) and caspase‐3. Expression level analysis in vivo revealed the high negative Pearson’s correlation between bta‐miR‐2285o‐3p and caspase3 in yak, highlighting the potential important roles of bta‐miR‐2285o‐3p in yak high‐altitude adaptation. Our study provides a typical model for deciphering the function of miRNAs in environmental adaptation.

A comparative analysis of differentially expressed mRNAs, miRNAs and circRNAs provides insights into the key genes involved in the high-altitude adaptation of yaks

BACKGROUND

Yaks that inhabit the Tibetan Plateau exhibit striking phenotypic and physiological differences from cattle and have adapted well to the extreme conditions on the plateau. However, the mechanisms used by these animals for the regulation of gene expression at high altitude are not fully understood.

RESULTS

Here, we sequenced nine lung transcriptomes of yaks at altitudes of 3400, 4200 and 5000 m, and low-altitude Zaosheng cattle, which is a closely related species, served as controls. The analysis identified 21,764 mRNAs, 1377 circRNAs and 1209 miRNAs. By comparing yaks and cattle, 4975 mRNAs, 252 circRNAs and 75 miRNAs were identified differentially expressed. By comparing yaks at different altitudes, we identified 756 mRNAs, 64 circRNAs and 83 miRNAs that were differentially expressed (fold change ≥2 and P-value < 0.05). The pathways enriched in the mRNAs, circRNAs and miRNAs identified from the comparison of yaks and cattle were mainly associated with metabolism, including 'glycosaminoglycan degradation', 'pentose and glucuronate interconversions' and 'flavone and flavonol biosynthesis', and the mRNAs, circRNAs and miRNAs identified from the comparison of yaks at different altitude gradients were significantly enriched in metabolic pathways and immune and genetic information processing pathways. The core RNAs were identified from the mRNA-miRNA-circRNA networks constructed using the predominant differentially expressed RNAs. The core genes specific to the difference between yaks and cattle were associated with the endoplasmic reticulum and fat deposition, but those identified from the comparison among yaks at different altitude gradients were associated with maintenance of the normal biological functions of cells.

CONCLUSIONS

This study enhances our understanding of the molecular mechanisms involved in hypoxic adaptation in yaks and might contribute to improvements in the understanding and prevention of hypoxia-related diseases.

Whole genome sequencing reveals a complex introgression history and the basis of adaptation to subarctic climate in wild sheep

To predict species responses to anthropogenic disturbances and climate change, it is reasonable to use species with high sensitivity to such factors. Snow sheep (Ovis nivicola) could represent a good candidate for this; as the only large herbivore species adapted to the cold and alpine habitats of northeastern Siberia, it plays a crucial role in its ecosystem. Despite having an extensive geographical distribution among all ovine species, it is one of the least studied. In this study, we sequenced and analysed six genomes of snow sheep in combination with all other wild sheep species to infer key aspects of their evolutionary history and unveil the genetic basis of their adaptation to subarctic environments. Despite their large census population size, snow sheep genomes showed remarkably low heterozygosity, which could reflect the effect of isolation and historical bottlenecks that we inferred using the pairwise sequential Markovian coalescent and runs of homozygosity. F₄ -statistics indicated instances of introgression involving snow sheep with argali (Ovis ammon) and Dall (Ovis dalli) sheep, suggesting that these species might have been more widespread during the Pleistocene. Furthermore, the introgressed segments, which were identified using mainly minimum relative node depth, covered genes associated with immunity, adipogenesis and morphology-related traits, representing potential targets of adaptive introgression. Genes related to mitochondrial functions and thermogenesis associated with adipose tissue were identified to be under selection. Overall, our data suggest introgression as a mechanism facilitating adaptation in wild sheep species and provide insights into the genetic mechanisms underlying cold adaptation in snow sheep.

Genomic and functional evidence reveals convergent evolution in fishes on the Tibetan Plateau

High-altitude environments are strong drivers of adaptive evolution in endemic organisms. However, little is known about the genetic mechanisms of convergent adaptation among different lineages, especially in fishes. There are three independent fish groups on the Tibetan Plateau: Tibetan Loaches, Schizothoracine fishes and Glyptosternoid fishes; all are well adapted to the harsh environmental conditions. They represent an excellent example of convergent evolution but with an unclear genetic basis. We used comparative genomic analyses between Tibetan fishes and fishes from low altitudes and detected genomic signatures of convergent evolution in fishes on the Tibetan Plateau. The Tibetan fishes exhibited genome-wide accelerated evolution in comparison with a control set of fishes from low altitudes. A total of 368 positively selected genes were identified in Tibetan fishes, which were enriched in functional categories related to energy metabolism and hypoxia response. Widespread parallel amino acid substitutions were detected among the Tibetan fishes and a subset of these substitutions occurred in positively selected genes associated with high-altitude adaptation. Functional assays suggested that von Hippel-Lindau (VHL) tumour suppressor genes from Tibetan fishes enhance hypoxia-inducible factor (HIF) activity convergently under hypoxia compared to low-altitude fishes. The results provide genomic and functional evidence supporting convergent genetic mechanisms for high-altitude adaptation in fishes on the Tibetan Plateau.

Selection pressure at altitude for genes related to alcohol metabolism: A role for endogenous enteric ethanol synthesis?

NEW FINDINGS

What is the topic of this review? Highland natives have undergone natural selection for genetic variants advantageous in adaptation to the hypobaric hypoxia experienced at high altitude. Why genes related to alcohol metabolism appear consistently selected for has not been greatly considered. We hypothesize that altitude-related changes in the gut microbiome offer one possible explanation. What advances does it highlight? Low intestinal oxygen tension might favour the production of ethanol through anaerobic fermentation by the gut microbiome. Subsequent increases in endogenous ethanol absorption could therefore provide a selection pressure for gene variants favouring its increased degradation, or perhaps reduced degradation if endogenously synthesized ethanol acts as a metabolic signalling molecule.

ABSTRACT

Reduced tissue availability of oxygen results from ascent to high altitude, where atmospheric pressure, and thus the partial pressure of inspired oxygen, fall (hypobaric hypoxia). In humans, adaptation to such hypoxia is necessary for survival. These functional changes remain incompletely characterized, although metabolic adaptation (rather than simple increases in convective oxygen delivery) appears to play a fundamental role. Those populations that have remained native to high altitude have undergone natural selection for genetic variants associated with advantageous phenotypic traits. Interestingly, a consistent genetic signal has implicated alcohol metabolism in the human adaptive response to hypobaric hypoxia. The reasons for this remain unclear. One possibility is that increased alcohol synthesis occurs through fermentation by gut bacteria in response to enteric hypoxia. There is growing evidence that anaerobes capable of producing ethanol become increasingly prevalent with high-altitude exposure. We hypothesize that: (1) ascent to high altitude renders the gut luminal environment increasingly hypoxic, favouring (2) an increase in the population of enteric fermenting anaerobes, hence (3) the synthesis of alcohol which, through systemic absorption, leads to (4) selection pressure on genes relating to alcohol metabolism. In theory, alcohol could be viewed as a toxic product, leading to selection of gene variants favouring its metabolism. On the contrary, alcohol is a metabolic substrate that might be beneficial. This mechanism could also account for some of the interindividual differences of lowlanders in acclimatization to altitude. Future research should be aimed at determining any shifts to favour ethanol-producing anaerobes after ascent to altitude.

Oxygen in Metabolic Dysfunction and Its Therapeutic Relevance

Significance: In recent years, a number of studies have shown altered oxygen partial pressure at a tissue level in metabolic disorders, and some researchers have considered oxygen to be a (macro) nutrient. Oxygen availability may be compromised in obesity and several other metabolism-related pathological conditions, including sleep apnea-hypopnea syndrome, the metabolic syndrome (which is a set of conditions), type 2 diabetes, cardiovascular disease, and cancer. Recent Advances: Strategies designed to reduce adiposity and its accompanying disorders have been mainly centered on nutritional interventions and physical activity programs. However, novel therapies are needed since these approaches have not been sufficient to counteract the worldwide increasing rates of metabolic disorders. In this regard, intermittent hypoxia training and hyperoxia could be potential treatments through oxygen-related adaptations. Moreover, living at a high altitude may have a protective effect against the development of abnormal metabolic conditions. In addition, oxygen delivery systems may be of therapeutic value for supplying the tissue-specific oxygen requirements. Critical Issues: Precise in vivo methods to measure oxygenation are vital to disentangle some of the controversies related to this research area. Further, it is evident that there is a growing need for novel in vitro models to study the potential pathways involved in metabolic dysfunction to find appropriate therapeutic targets. Future Directions: Based on the existing evidence, it is suggested that oxygen availability has a key role in obesity and its related comorbidities. Oxygen should be considered in relation to potential therapeutic strategies in the treatment and prevention of metabolic disorders. Antioxid. Redox Signal. 35, 642-687.

Phenotypic differences between highlanders and lowlanders in Papua New Guinea

OBJECTIVES

Altitude is one of the most demanding environmental pressures for human populations. Highlanders from Asia, America and Africa have been shown to exhibit different biological adaptations, but Oceanian populations remain understudied [Woolcock et al., 1972; Cotes et al., 1974; Senn et al., 2010]. We tested the hypothesis that highlanders phenotypically differ from lowlanders in Papua New Guinea, as a result of inhabiting the highest mountains in Oceania for at least 20,000 years.

MATERIALS AND METHODS

We collected data for 13 different phenotypes related to altitude for 162 Papua New Guineans living at high altitude (Mont Wilhelm, 2,300-2,700 m above sea level (a.s.l.) and low altitude (Daru, <100m a.s.l.). Multilinear regressions were performed to detect differences between highlanders and lowlanders for phenotypic measurements related to body proportions, pulmonary function, and the circulatory system.

RESULTS

Six phenotypes were significantly different between Papua New Guinean highlanders and lowlanders. Highlanders show shorter height (p-value = 0.001), smaller waist circumference (p-value = 0.002), larger Forced Vital Capacity (FVC) (p-value = 0.008), larger maximal (p-value = 3.20e -4) and minimal chest depth (p-value = 2.37e -5) and higher haemoglobin concentration (p-value = 3.36e -4).

DISCUSSION

Our study reports specific phenotypes in Papua New Guinean highlanders potentially related to altitude adaptation. Similar to other human groups adapted to high altitude, the evolutionary history of Papua New Guineans appears to have also followed an adaptive biological strategy for altitude.

Evidence of the interplay of genetics and culture in Ethiopia

The rich linguistic, ethnic and cultural diversity of Ethiopia provides an unprecedented opportunity to understand the level to which cultural factors correlate with-and shape-genetic structure in human populations. Using primarily new genetic variation data covering 1,214 Ethiopians representing 68 different ethnic groups, together with information on individuals' birthplaces, linguistic/religious practices and 31 cultural practices, we disentangle the effects of geographic distance, elevation, and social factors on the genetic structure of Ethiopians today. We provide evidence of associations between social behaviours and genetic differences among present-day peoples. We show that genetic similarity is broadly associated with linguistic affiliation, but also identify pronounced genetic similarity among groups from disparate language classifications that may in part be attributable to recent intermixing. We also illustrate how groups reporting the same culture traits are more genetically similar on average and show evidence of recent intermixing, suggesting that shared cultural traits may promote admixture. In addition to providing insights into the genetic structure and history of Ethiopia, we identify the most important cultural and geographic predictors of genetic differentiation and provide a resource for designing sampling protocols for future genetic studies involving Ethiopians.

Application of a novel haplotype-based scan for local adaptation to study high-altitude adaptation in rhesus macaques

When natural populations split and migrate to different environments, they may experience different selection pressures that can lead to local adaptation. To capture the genomic patterns of a local selective sweep, we develop XP-nSL, a genomic scan for local adaptation that compares haplotype patterns between two populations. We show that XP-nSL has power to detect ongoing and recently completed hard and soft sweeps, and we then apply this statistic to search for evidence of adaptation to high altitude in rhesus macaques. We analyze the whole genomes of 23 wild rhesus macaques captured at high altitude (mean altitude > 4000 m above sea level) to 22 wild rhesus macaques captured at low altitude (mean altitude < 500 m above sea level) and find evidence of local adaptation in the high-altitude population at or near 303 known genes and several unannotated regions. We find the strongest signal for adaptation at EGLN1, a classic target for convergent evolution in several species living in low oxygen environments. Furthermore, many of the 303 genes are involved in processes related to hypoxia, regulation of ROS, DNA damage repair, synaptic signaling, and metabolism. These results suggest that, beyond adapting via a beneficial mutation in one single gene, adaptation to high altitude in rhesus macaques is polygenic and spread across numerous important biological systems.

Structure and ancestry patterns of Ethiopians in genome-wide autosomal DNA

We review some of the current insights derived from the analyses of new large-scale, genome-wide autosomal variation data studies incorporating Ethiopians. Consistent with their substantial degree of cultural and linguistic diversity, genetic diversity among Ethiopians is higher than that seen across much larger geographic regions worldwide. This genetic variation is associated in part with ethnic identity, geography and linguistic classification. Numerous and varied admixture events have been inferred in Ethiopian groups, for example, involving sources related to present-day groups in West Eurasia and North Africa, with inferred dates spanning a few hundred to more than 4500 years ago. These disparate inferred ancestry patterns are correlated in part with groups' broad linguistic classifications, though with some notable exceptions. While deciphering these complex genetic signals remains challenging with available data, these studies and other projects focused on resolving competing hypotheses on the origins of specific ethnolinguistic groups demonstrate how genetic analyses can complement findings from anthropological and linguistic studies on Ethiopians.

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.

Understanding the Adaptive Evolutionary Histories of South American Ancient and Present-Day Populations via Genomics

The South American continent is remarkably diverse in its ecological zones, spanning the Amazon rainforest, the high-altitude Andes, and Tierra del Fuego. Yet the original human populations of the continent successfully inhabited all these zones, well before the buffering effects of modern technology. Therefore, it is likely that the various cultures were successful, in part, due to positive natural selection that allowed them to successfully establish populations for thousands of years. Detecting positive selection in these populations is still in its infancy, as the ongoing effects of European contact have decimated many of these populations and introduced gene flow from outside of the continent. In this review, we explore hypotheses of possible human biological adaptation, methods to identify positive selection, the utilization of ancient DNA, and the integration of modern genomes through the identification of genomic tracts that reflect the ancestry of the first populations of the Americas.

Scanning the human genome for "signatures" of positive selection: Transformative opportunities and ethical obligations

The relationship history of evolutionary anthropology and genetics is complex. At best, genetics is a beautifully integrative part of the discipline. Yet this integration has also been fraught, with punctuated, disruptive challenges to dogma, periodic reluctance by some members of the field to embrace results from analyses of genetic data, and occasional over-assertions of genetic definitiveness by geneticists. At worst, evolutionary genetics has been a tool for reinforcing racism and colonialism. While a number of genetics/genomics papers have disproportionately impacted evolutionary anthropology, here we highlight the 2002 presentation of an elegantly powerful approach for identifying "signatures" of past positive selection from haplotype-based patterns of genetic variation. Together with technological advances in genotyping methods, this article transformed our field by facilitating genome-wide "scans" for signatures of past positive selection in human populations. This approach helped researchers test longstanding evolutionary anthropology hypotheses while simultaneously providing opportunities to develop entirely new ones. Genome-wide scans for signatures of positive selection have since been conducted in diverse worldwide populations, with striking findings of local adaptation and convergent evolution. Yet there are ethical considerations with respect to the ubiquity of these studies and the cross-application of the genome-wide scan approach to existing datasets, which we also discuss.

Improving Selection Detection with Population Branch Statistic on Admixed Populations

Detecting natural selection signals in admixed populations can be problematic since the source of the signal typically dates back prior to the admixture event. On one hand, it is now possible to study various source populations before a particular admixture thanks to the developments in ancient DNA (aDNA) in the last decade. However, aDNA availability is limited to certain geographical regions and the sample sizes and quality of the data might not be sufficient for selection analysis in many cases. In this study, we explore possible ways to improve detection of pre-admixture signals in admixed populations using a local ancestry inference approach. We used masked haplotypes for population branch statistic (PBS) and full haplotypes constructed following our approach from Yelmen et al. (2019) for cross-population extended haplotype homozygosity (XP-EHH), utilizing forward simulations to test the power of our analysis. The PBS results on simulated data showed that using masked haplotypes obtained from ancestry deconvolution instead of the admixed population might improve detection quality. On the other hand, XP-EHH results using the admixed population were better compared with the local ancestry method. We additionally report correlation for XP-EHH scores between source and admixed populations, suggesting that haplotype-based approaches must be used cautiously for recently admixed populations. Additionally, we performed PBS on real South Asian populations masked with local ancestry deconvolution and report here the first possible selection signals on the autochthonous South Asian component of contemporary South Asian populations.

Pervasive Genomic Signatures of Local Adaptation to Altitude Across Highland Specialist Andean Hummingbird Populations

Populations along steep environmental gradients are subject to differentiating selection that can result in local adaptation, despite countervailing gene flow, and genetic drift. In montane systems, where species are often restricted to narrow ranges of elevation, it is unclear whether the selection is strong enough to influence functional differentiation of subpopulations differing by a few hundred meters in elevation. We used targeted capture of 12 501 exons from across the genome, including 271 genes previously implicated in altitude adaptation, to test for adaptation to local elevations for 2 highland hummingbird species, Coeligena violifer (n = 62) and Colibri coruscans (n = 101). For each species, we described population genetic structure across the complex geography of the Peruvian Andes and, while accounting for this structure, we tested whether elevational allele frequency clines in single nucleotide polymorphisms (SNPs) showed evidence for local adaptation to elevation. Although the 2 species exhibited contrasting population genetic structures, we found signatures of clinal genetic variation with shifts in elevation in both. The genes with SNP-elevation associations included candidate genes previously discovered for high-elevation adaptation as well as others not previously identified, with cellular functions related to hypoxia response, energy metabolism, and immune function, among others. Despite the homogenizing effects of gene flow and genetic drift, natural selection on parts of the genome evidently optimizes elevation-specific cellular function even within elevation range-restricted montane populations. Consequently, our results suggest local adaptation occurring in narrow elevation bands in tropical mountains, such as the Andes, may effectively make them "taller" biogeographic barriers.

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.

Adaptive selection drives TRPP3 loss-of-function in an Ethiopian population

TRPP3 (also called PKD2L1) is a nonselective, cation-permeable channel activated by multiple stimuli, including extracellular pH changes. TRPP3 had been considered a candidate for sour sensor in humans, due to its high expression in a subset of tongue receptor cells detecting sour, along with its membership to the TRP channel family known to function as sensory receptors. Here, we describe the functional consequences of two non-synonymous genetic variants (R278Q and R378W) found to be under strong positive selection in an Ethiopian population, the Gumuz. Electrophysiological studies and 3D modelling reveal TRPP3 loss-of-functions produced by both substitutions. R278Q impairs TRPP3 activation after alkalinisation by mislocation of H⁺ binding residues at the extracellular polycystin mucolipin domain. R378W dramatically reduces channel activity by altering conformation of the voltage sensor domain and hampering channel transition from closed to open state. Sour sensitivity tests in R278Q/R378W carriers argue against both any involvement of TRPP3 in sour detection and the role of such physiological process in the reported evolutionary positive selection past event.

Genomic Analyses Reveal Genetic Adaptations to Tropical Climates in Chickens

The genetic footprints of adaptations to naturally occurring tropical stress along with domestication are poorly reported in chickens. Here, by conducting population genomic analyses of 67 chickens inhabiting distinct climates, we found signals of gene flow from Tibetan chickens to Sri Lankan and Saudi Arabian breeds and identified 12 positively selected genes that are likely involved in genetic adaptations to both tropical desert and tropical monsoon island climates. Notably, in tropical desert climate, advantageous alleles of TLR7 and ZC3HAV1, which could inhibit replication of viruses in cells, suggest immune adaptation to the defense against zoonotic diseases in chickens. Furthermore, comparative genomic analysis showed that four genes (OC90, PLA2G12B, GPR17 and TNFRSF11A) involved in arachidonic acid metabolism have undergone convergent adaptation to tropical desert climate between birds and mammals. Our study offers insights into the genetic mechanisms of adaptations to tropical climates in birds and other animals and provides practical value for breeding design and medical research on avian viruses.

Positive selection in admixed populations from Ethiopia

BACKGROUND

In the process of adaptation of humans to their environment, positive or adaptive selection has played a main role. Positive selection has, however, been under-studied in African populations, despite their diversity and importance for understanding human history.

RESULTS

Here, we have used 119 available whole-genome sequences from five Ethiopian populations (Amhara, Oromo, Somali, Wolayta and Gumuz) to investigate the modes and targets of positive selection in this part of the world. The site frequency spectrum-based test SFselect was applied to idfentify a wide range of events of selection (old and recent), and the haplotype-based statistic integrated haplotype score to detect more recent events, in each case with evaluation of the significance of candidate signals by extensive simulations. Additional insights were provided by considering admixture proportions and functional categories of genes. We identified both individual loci that are likely targets of classic sweeps and groups of genes that may have experienced polygenic adaptation. We found population-specific as well as shared signals of selection, with folate metabolism and the related ultraviolet response and skin pigmentation standing out as a shared pathway, perhaps as a response to the high levels of ultraviolet irradiation, and in addition strong signals in genes such as IFNA, MRC1, immunoglobulins and T-cell receptors which contribute to defend against pathogens.

CONCLUSIONS

Signals of positive selection were detected in Ethiopian populations revealing novel adaptations in East Africa, and abundant targets for functional follow-up.

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.

Out of breath, out of time: interactions between HIF and circadian rhythms

Humans have internal circadian clocks that ensure that important physiological functions occur at specific times of the day. These molecular clocks are regulated at the genomic level and exist in most cells of the body. Multiple circadian resetting cues have been identified, including light, temperature, and food. Recently, oxygen has been identified as a resetting cue, and emerging science indicates that this occurs through interactions at the cellular level between the circadian transcription-translation feedback loop and the hypoxia-inducible pathway (hypoxia-inducible factor; subject of the 2019 Nobel Prize in Physiology or Medicine). This review will cover recently identified relationships between HIF and proteins of the circadian clock. Interactions between the circadian clock and hypoxia could have wide-reaching implications for human diseases, and understanding the molecular mechanisms regulating these overlapping pathways may open up new strategies for drug discovery.

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.

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.

Adaptation to Extreme Environments in an Admixed Human Population from the Atacama Desert

Inorganic arsenic (As) is a toxic xenobiotic and carcinogen associated with severe health conditions. The urban population from the Atacama Desert in northern Chile was exposed to extremely high As levels (up to 600 µg/l) in drinking water between 1958 and 1971, leading to increased incidence of urinary bladder cancer (BC), skin cancer, kidney cancer, and coronary thrombosis decades later. Besides, the Andean Native-American ancestors of the Atacama population were previously exposed for millennia to elevated As levels in water (∼120 µg/l) for at least 5,000 years, suggesting adaptation to this selective pressure. Here, we performed two genome-wide selection tests—PBS_n1 and an ancestry-enrichment test—in an admixed population from Atacama, to identify adaptation signatures to As exposure acquired before and after admixture with Europeans, respectively. The top second variant selected by PBS_n1 was associated with LCE4A-C1orf68, a gene that may be involved in the immune barrier of the epithelium during BC. We performed association tests between the top PBS_n1 hits and BC occurrence in our population. The strongest association (P = 0.012) was achieved by the LCE4A-C1orf68 variant. The ancestry-enrichment test detected highly significant signals (P = 1.3 × 10⁻⁹) mapping MAK16, a gene with important roles in ribosome biogenesis during the G1 phase of the cell cycle. Our results contribute to a better understanding of the genetic factors involved in adaptation to the pathophysiological consequences of As exposure.

Selection signatures for high-altitude adaptation in ruminants

High-altitude areas are important socio-economical habitats with ruminants serving as a major source of food and commodities for humans. Living at high altitude, however, is extremely challenging, predominantly due to the exposure to hypoxic conditions, but also because of cold temperatures and limited feed for livestock. To survive in high-altitude environments over the long term, ruminants have evolved adaptation strategies, e.g. physiological and morphological modifications, which allow them to cope with these harsh conditions. Identification of such selection signatures in ruminants may contribute to more informed breeding decisions, and thus improved productivity. Moreover, studying the genetic background of altitude adaptation in ruminants provides insights into a common molecular basis across species and thus a better understanding of the physiological basis of this adaptation. In this paper, we review the major effects of high altitude on the mammalian body and highlight some of the most important short-term (coping) and genetically evolved (adaptation) physiological modifications. We then discuss the genetic architecture of altitude adaptation and target genes that show evidence of being under selection based on recent studies in various species, with a focus on ruminants. The yak is presented as an interesting native species that has adapted to the high-altitude regions of Tibet. Finally, we conclude with implications and challenges of selection signature studies on altitude adaptation in general. We found that the number of studies on genetic mechanisms that enable altitude adaptation in ruminants is growing, with a strong focus on identifying selection signatures, and hypothesise that the investigation of genetic data from multiple species and regions will contribute greatly to the understanding of the genetic basis of altitude adaptation.