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.     

Identifying Signatures of Natural Selection in Tibetan and Andean Populations Using Dense Genome Scan Data

High-altitude hypoxia (reduced inspired oxygen tension due to decreased barometric pressure) exerts severe physiological stress on the human body. Two high-altitude regions where humans have lived for millennia are the Andean Altiplano and the Tibetan Plateau. Populations living in these regions exhibit unique circulatory, respiratory, and hematological adaptations to life at high altitude. Although these responses have been well characterized physiologically, their underlying genetic basis remains unknown. We performed a genome scan to identify genes showing evidence of adaptation to hypoxia. We looked across each chromosome to identify genomic regions with previously unknown function with respect to altitude phenotypes. In addition, groups of genes functioning in oxygen metabolism and sensing were examined to test the hypothesis that particular pathways have been involved in genetic adaptation to altitude. Applying four population genetic statistics commonly used for detecting signatures of natural selection, we identified selection-nominated candidate genes and gene regions in these two populations (Andeans and Tibetans) separately. The Tibetan and Andean patterns of genetic adaptation are largely distinct from one another, with both populations showing evidence of positive natural selection in different genes or gene regions. Interestingly, one gene previously known to be important in cellular oxygen sensing, EGLN1 (also known as PHD2), shows evidence of positive selection in both Tibetans and Andeans. However, the pattern of variation for this gene differs between the two populations. Our results indicate that several key HIF-regulatory and targeted genes are responsible for adaptation to high altitude in Andeans and Tibetans, and several different chromosomal regions are implicated in the putative response to selection. These data suggest a genetic role in high-altitude adaption and provide a basis for future genotype/phenotype association studies necessary to confirm the role of selection-nominated candidate genes and gene regions in adaptation to altitude.     

The genomic basis of adaptation to high‐altitude habitats in the eastern honey bee (Apis cerana)

The eastern honey bee (Apis cerana) is of central importance for agriculture in Asia. It has adapted to a wide variety of environmental conditions across its native range in southern and eastern Asia, which includes high‐altitude regions. eastern honey bees inhabiting mountains differ morphologically from neighbouring lowland populations and may also exhibit differences in physiology and behaviour. We compared the genomes of 60 eastern honey bees collected from high and low altitudes in Yunnan and Gansu provinces, China, to infer their evolutionary history and to identify candidate genes that may underlie adaptation to high altitude. Using a combination of F_ST‐based statistics, long‐range haplotype tests and population branch statistics, we identified several regions of the genome that appear to have been under positive selection. These candidate regions were strongly enriched for coding sequences and had high haplotype homozygosity and increased divergence specifically in highland bee populations, suggesting they have been subjected to recent selection in high‐altitude habitats. Candidate loci in these genomic regions included genes related to reproduction and feeding behaviour in honey bees. Functional investigation of these candidate loci is necessary to fully understand the mechanisms of adaptation to high‐altitude habitats in the eastern honey bee.     

Genomic Analysis of Natural Selection and Phenotypic Variation in High-Altitude Mongolians

Deedu (DU) Mongolians, who migrated from the Mongolian steppes to the Qinghai-Tibetan Plateau approximately 500 years ago, are challenged by environmental conditions similar to native Tibetan highlanders. Identification of adaptive genetic factors in this population could provide insight into coordinated physiological responses to this environment. Here we examine genomic and phenotypic variation in this unique population and present the first complete analysis of a Mongolian whole-genome sequence. High-density SNP array data demonstrate that DU Mongolians share genetic ancestry with other Mongolian as well as Tibetan populations, specifically in genomic regions related with adaptation to high altitude. Several selection candidate genes identified in DU Mongolians are shared with other Asian groups (e.g., EDAR), neighboring Tibetan populations (including high-altitude candidates EPAS1, PKLR, and CYP2E1), as well as genes previously hypothesized to be associated with metabolic adaptation (e.g., PPARG). Hemoglobin concentration, a trait associated with high-altitude adaptation in Tibetans, is at an intermediate level in DU Mongolians compared to Tibetans and Han Chinese at comparable altitude. Whole-genome sequence from a DU Mongolian (Tianjiao1) shows that about 2% of the genomic variants, including more than 300 protein-coding changes, are specific to this individual. Our analyses of DU Mongolians and the first Mongolian genome provide valuable insight into genetic adaptation to extreme environments.     

Genomic and phenotypic differentiation of Arabidopsis thaliana along altitudinal gradients in the North Italian Alps

Altitudinal gradients in mountain regions are short‐range clines of different environmental parameters such as temperature or radiation. We investigated genomic and phenotypic signatures of adaptation to such gradients in five Arabidopsis thaliana populations from the North Italian Alps that originated from 580 to 2350 m altitude by resequencing pools of 19–29 individuals from each population. The sample includes two pairs of low‐ and high‐altitude populations from two different valleys. High‐altitude populations showed a lower nucleotide diversity and negative Tajima's D values and were more closely related to each other than to low‐altitude populations from the same valley. Despite their close geographic proximity, demographic analysis revealed that low‐ and high‐altitude populations split between 260 000 and 15 000 years before present. Single nucleotide polymorphisms whose allele frequencies were highly differentiated between low‐ and high‐altitude populations identified genomic regions of up to 50 kb length where patterns of genetic diversity are consistent with signatures of local selective sweeps. These regions harbour multiple genes involved in stress response. Variation among populations in two putative adaptive phenotypic traits, frost tolerance and response to light/UV stress was not correlated with altitude. Taken together, the spatial distribution of genetic diversity reflects a potentially adaptive differentiation between low‐ and high‐altitude populations, whereas the phenotypic differentiation in the two traits investigated does not. It may resemble an interaction between adaptation to the local microhabitat and demographic history influenced by historical glaciation cycles, recent seed dispersal and genetic drift in local populations.     

High altitude adaptation in Daghestani populations from the Caucasus

We have surveyed 15 high-altitude adaptation candidate genes for signals of positive selection in North Caucasian highlanders using targeted re-sequencing. A total of 49 unrelated Daghestani from three ethnic groups (Avars, Kubachians, and Laks) living in ancient villages located at around 2,000 m above sea level were chosen as the study population. Caucasian (Adygei living at sea level, N = 20) and CEU (CEPH Utah residents with ancestry from northern and western Europe; N = 20) were used as controls. Candidate genes were compared with 20 putatively neutral control regions resequenced in the same individuals. The regions of interest were amplified by long-PCR, pooled according to individual, indexed by adding an eight-nucleotide tag, and sequenced using the Illumina GAII platform. 1,066 SNPs were called using false discovery and false negative thresholds of ~6%. The neutral regions provided an empirical null distribution to compare with the candidate genes for signals of selection. Two genes stood out. In Laks, a non-synonymous variant within HIF1A already known to be associated with improvement in oxygen metabolism was rediscovered, and in Kubachians a cluster of 13 SNPs located in a conserved intronic region within EGLN1 showing high population differentiation was found. These variants illustrate both the common pathways of adaptation to high altitude in different populations and features specific to the Daghestani populations, showing how even a mildly hypoxic environment can lead to genetic adaptation.     

High altitude adaptation of the schizothoracine fishes (Cyprinidae) revealed by the mitochondrial genome analyses

The schizothoracine fishes, also known as “mountain carps” are widely distributed in the Qinghai-Tibetan Plateau and its peripheral regions. Although they provide a prime example of high altitude adaptation, the phylogenetic relationships and the divergence times among these carp lineages are still controversial. Moreover, the genetic basis for high altitude adaptation is also poorly understood. In this study, we determined the mitochondrial genomes from two species of the schizothoracine fishes, representing a “morphologically primitive” clade and “morphologically specialized” clade, respectively. The phylogenetic tree and the divergence times were estimated within the evolutionary framework of the entire order Cypriniformes. Our results indicate a polyphylyetic relationship of the schizothoracine fishes and suggest two independent migration events into the Qinghai-Tibetan Plateau: one by the “morphologically primitive” clade in the Late Miocene and another by the “morphologically specialized” clade in the Eocene. Rapid speciation events of each clade from the Late Miocene to the Pliocene correspond to the timing of the geologic acceleration of the Qinghai-Tibetan Plateau. Interestingly, we found evidence for positive selection acting on the protein coding genes in the mitochondrial genomes of the “morphologically specialized” clade, implying a possible genetic basis for high altitude adaptation in this derived lineage of cypriniform fishes.     

Increased affinity to substrate in sarcolemmal ATPases from hearts acclimatized to high altitude hypoxia

It has been well documented that acclimatization to chronic high altitude hypoxia involves a complex of adaptation changes which are capable of protecting the myocardium in diverse situations such as in acute hypoxia, coronary occlusion-induced ischaemia or isoprenaline-induced calcium overload. Since many of the former changes concern membrane functions, namely those of the sarcolemma, the activities and kinetic properties of sarcolemmal Mg2+-, Ca2+- and (Na+ + K+)-ATPase were investigated in right heart ventricles of rats acclimatized to intermittent high altitude hypoxia simulated in a barochamber. In the course of the experiment, the ventricles were subjected to a special anoxic test in vitro. The high altitude induced increase in cardiac tolerance to anoxia was not accompanied by any preservation of the sarcolemmal ATPase activities. On the contrary, membrane preparations obtained from the right ventricles of hearts acclimatized to high altitude exhibited significantly lower ATPase activities in comparison to non-acclimatized controls. The significant diminution in Km values of ATPases established in acclimatized hearts points to an increase in the affinity of their active sites to ATP. The latter effect is in agreement with the lowered rate of both the decrease in ATPase activities and the reduction of contractility in acclimatized hearts during the anoxic test, as well as with the considerably improved postanoxic reparability of contractions as compared to the controls. It is being concluded that the sarcolemmal changes at the level of ATPases involved in ionic transport processes represent an integral part of the adaptation complex to chronic high altitude hypoxia.     

Hypoxia and the CNS: Maturation and adaptation at high altitude

The well known circulatory, including hemopoetic, and respiratory adjustments to high altitude often serve as classic examples of adaptation to specific environmental conditions. Less extensively studied are the contributions of the nervous and endocrine systems to such adaptive mechanisms even though their involvement in humans and animals is indisputed. Observations from our and other laboratories have identified in the rat a number of neurologic and endocrine responses to acute and prolonged exposure to high altitude attributable primarily to its hypoxic component. These responses include general retardation in maturation and function of the central nervous system as manifested by alterations in spontaneous and evoked electrical activity particularly in the limbic structures and involving selectively the synapse and are associated with impairment of brain protein and lipid metabolism, myelinogenesis and neurotransmission. Together with these neurologic disturbances, endocrine dysfunctions lead to alterations in growth, fertility and metabolism. Thus hypoxia, even of moderate severity, would affect profoundly the biochemical and functional maturation and activity of the brain and endocrines, and, reciprocally, prevention and treatment of these neuroendocrine imbalances might strengthen the adaptive competence of the individual.     

Widespread Signals of Convergent Adaptation to High Altitude in Asia and America

Living at high altitude is one of the most difficult challenges that humans had to cope with during their evolution. Whereas several genomic studies have revealed some of the genetic bases of adaptations in Tibetan, Andean, and Ethiopian populations, relatively little evidence of convergent evolution to altitude in different continents has accumulated. This lack of evidence can be due to truly different evolutionary responses, but it can also be due to the low power of former studies that have mainly focused on populations from a single geographical region or performed separate analyses on multiple pairs of populations to avoid problems linked to shared histories between some populations. We introduce here a hierarchical Bayesian method to detect local adaptation that can deal with complex demographic histories. Our method can identify selection occurring at different scales, as well as convergent adaptation in different regions. We apply our approach to the analysis of a large SNP data set from low- and high-altitude human populations from America and Asia. The simultaneous analysis of these two geographic areas allows us to identify several candidate genome regions for altitudinal selection, and we show that convergent evolution among continents has been quite common. In addition to identifying several genes and biological processes involved in high-altitude adaptation, we identify two specific biological pathways that could have evolved in both continents to counter toxic effects induced by hypoxia.     

Genotypic and environmental variation in specific leaf area in a widespread Alpine plant after transplantation to different altitudes

Specific leaf area (SLA) is an important plant functional trait as it is an indicator of ecophysiological characteristics like relative growth rate, stress tolerance and leaf longevity. Substantial intraspecific variation in SLA is common and usually correlates with environmental conditions. For instance, SLA decreases with increasing altitude, which is understood as adjustment to temperature. It is generally assumed that intraspecific variation is mostly the result of environmentally induced phenotypic plasticity, but genetic effects may also be present, due to local adaptation or genetic drift. In this study, genotypic and environmental effects on SLA were experimentally separated for the widespread Alpine bell flower Campanula thyrsoides by transplanting plants to three common gardens at contrasting altitudes (600, 1,235 and 1,850 m a.s.l.). Seeds were sampled from 18 populations in four phylogeographic regions within the European Alps. A strong plastic response was observed: SLA decreased with increasing altitude of the common gardens (22.0% of variation). The phylogeographic regions were differentiated in SLA in the common gardens (10.1% of variation), indicating that SLA is at least partly genetically determined. Plants from the six easternmost populations experienced a submediterranean climate and showed decreased SLA values in the three common gardens compared to populations to the west, which may be explained as adaptation to drought. Within these submediterranean populations, SLA decreased with altitude of origin in two out of three common gardens. Concluding, SLA shows strong phenotypic plasticity as well as substantial genetic effects, the latter probably being the result of adaptation to local conditions rather than genetic drift.     

Neutral and functionally important genes shed light on phylogeography and the history of high‐altitude colonization in a widespread New World duck

Phylogeographic studies often infer historical demographic processes underlying species distributions based on patterns of neutral genetic variation, but spatial variation in functionally important genes can provide additional insights about biogeographic history allowing for inferences about the potential role of adaptation in geographic range evolution. Integrating data from neutral markers and genes involved in oxygen (O₂)‐transport physiology, we test historical hypotheses about colonization and gene flow across low‐ and high‐altitude regions in the Ruddy Duck (Oxyura jamaicensis), a widely distributed species in the New World. Using multilocus analyses that for the first time include populations from the Colombian Andes, we also examined the hypothesis that Ruddy Duck populations from northern South America are of hybrid origin. We found that neutral and functional genes appear to have moved into the Colombian Andes from both North America and southern South America, and that high‐altitude Colombian populations do not exhibit evidence of adaptation to hypoxia in hemoglobin genes. Therefore, the biogeographic history of Ruddy Ducks is likely more complex than previously inferred. Our new data raise questions about the hypothesis that adaptation via natural selection to high‐altitude conditions through amino acid replacements in the hemoglobin protein allowed Ruddy Ducks to disperse south along the high Andes into southern South America. The existence of shared genetic variation with populations from both North America and southern South America as well as private alleles suggests that the Colombian population of Ruddy Ducks may be of old hybrid origin. This study illustrates the breadth of inferences one can make by combining data from nuclear and functionally important loci in phylogeography, and underscores the importance of complete range‐wide sampling to study species history in complex landscapes.     

The impact of elevated UV-B (280–320 nm) radiation levels on the reproduction biology of a highland and a lowland population of Silene vulgaris

A highland (altitude 1600 m) and a lowland (altitude –2 m) population of the perennial herb Silene vulgaris were tested on the effects of elevated levels of UV-B radiation on their reproductivity. Highland populations receive higher natural UV-B doses than lowland populations. Therefore adaptation to high UV-B levels of the highland population is to be expected. The lowland population showed a decrease in the number of seed producing flowers and the number of seeds produced per plant under elevated UV-B levels. The highland population increased the number of seeds per plant under elevated UV-B levels. In both populations individual seed mass as well as seed germination percentages were unaffected by the UV-B flux received by the parental plant. Possible effects of UV-B induced alterations in reproductivity on the geographical distribution of the different populations are discussed.     

不同海拔地区高原鼠兔热中性区及静止代谢率的差异

高原地区动物面临一系列严峻的生存考验,随着海拔的变化,动物栖息地的食物资源等差异大,温度、氧分压等环境因子都将发生变化.环境差异可能会影响动物种群的生活史对策.在生理功能适应中,动物的能量代谢适应扮演着重要的角色.为探究高原鼠兔(Ochotona curzoniae)在不同海拔地区的能量代谢适应与热中性区范围,分别选取...     

Altitude adaptation. V. (conclusion). Morbidity and mortality. Literature]

The ability to adapt to extreme conditions is a continously working principle of man's evolution, in a permanent orientation to an optimal equilibrium between man and environment. A paradigm of biological adaptation is the condition of hypoxia at high altitudes, as one of the few environment constellations to which a pure biological and thus genetically based answer could be possible. The majority of adaptations are influenced by technological actions, which partially modify the environment in compensating unfavourable constellations (heating, clothing, housing, etc.). It is discussed, how far the adaptation to high altitudes produces transitory or permanent alterations with reference to constitution, perseverance, cold-sensitivity, diseases, duration of life, fertility, course of pregnancy, adaptations at the organ- and tissue-level, blood-composition, fluid-equilibrium of the body etc., which guarantee the survival of the individual and its successful reproduction with regard to the continuance of a mendel population. The elucidation of the question on genetic determination of features characteristic for high altitude inhabitants is difficult because we know next to nothing about the genetic determination of physiologic parameters. Studies on ethnic marker-genes (Ethiopia, South-America) give no reference to population differences. Remarkable is a striking prevalence of the blood-group O for all populations of high altitudes, but one must consider the effects of isolation in terms of the increase in the homozygote recessive alleles. We can propose, that in the primary settlement at high altitudes a "hard selection" was working, a kind of biological assortation-process from the beginning, which eliminated those individuals, who proved to be (for genetic reasons?) not adaptable. A good example for this are observations of cattle, from which 50% do not develop pulmonary hypertension when exposed to altitude, that means they already have a higher initial fitness. The non-adaptable animals have to be returned to the lowlands. In the F1-generation only 2% of the animals remaining at high altitude, develop "brisket disease". Possibly that means a sort of "out-mendeling" of "pulmonary-hypertension-genes", which may manifest themselves in the condition of hypoxia. Also the good adaptation of llamas is partially due to the fact that the camelids per se possess an outstanding O2 affinity and morphologically different red blood cells, which predispose this species to inhabit high altitudes. Parallel to considerations like these it could be imaginable, that e.g. the indianids of mongoloids in general, are genetically composed as fit to inhabit lowlands as well as highlands, in contrast to caucasoids and negroids. The largest mountain areas of the world (the Andes: 12 X 10(6)), the Himalayas 12 X 10(6)) are inhabited by populations of mongoloid ancestry, for about 10,000 years, a period, which ought to be long enough to make possible genetic specialisation, although it is not yet possible to prove it...     

Functional changes in hematopoiesis in healthy subjects during adaptation to a high altitude hypoxia

In the article, findings of the studies of white blood in healthy subjects during a short-term adaptation to high altitude (per. Tuya-Ashu, 3200 m), are discussed. A 40-day adaptation of healthy people has led to positive shifts: an increase of the number of leukocytes with prevalence of the absolute count of neutrophiles and lymphocytes, as well as an activation of the latter during the first days of stay at high altitude. An effect of the high-altitude hypoxia resulted in intensification of erythropoiesis that manifests itself in an improvement of red cell hemoglobinization and a decrease of the degree of non-effective erythropoiesis. The data obtained support the data of the myelograms demonstrating an improvement of differentiation of white hematopoiesis.     

Sex-related patterns of body tolerance to repeated acute hypobaric hypoxia

The individual differences in the response of male and female rats to repeated exposure to acute hypobaric hypoxia were experimentally studied. The time of attitudinal reflex maintenance and recovery in a rotating decompression chamber as well as the value of hypoxic hypothermia after decompression to a simulated altitude of 11200 m were used to evaluate the tolerance to hypoxia. Males demonstrated a slightly higher reactivity than females. At the same time, a more efficient adaptation to hypoxia conserved the body’s compensatory capacity and rapidly restored the functions affected by repeated exposure to the extreme factor. Such long-term adaptation was observed in initially low-resistant females, which could increase their resistance to repeated exposures to the stress factor.     

Chromosomal Q-heterochromatin regions in native highlanders of Pamir and Tien-Shan and in newcomers

The variability of human chromosomal Q-heterochromatin regions (Q-HR) was studied in 385 newcomers well adapted to the extreme environmental conditions of Pamir and Tien-Shan, as well as in 284 representatives of the native population of these regions. Newcomers were found to represent a highly homogeneous group as regards all the quantitative characteristics of Q-HR variability, but at the same time they differed significantly from both native residents and individuals of similar nationality (Russians) living permanently at low altitude. Differences between these three groups in the amount of Q-HRs in their genome are discussed as evidence in favour of the hypothesis of the possible selective value of chromosomal Q-heterochromatin material in human adaptation to extreme environmental high-altitude conditions.     

Study of the respiratory sensation on high-altitude andeans

The respiratory sensation and some routine cardiorespiratory parameters were studied on native Highlanders from the Argentine Andes and on Lowlanders from Europe, already tested during previous high altitude expeditions. The tests were performed at various altitude levels from 2688m e.i., the village altitude for Highlanders, to 5600m during an expedition to Mt. Aconcagua (6990m). At rest, the perception of 4 external inspiratory resistive loads (ranged between 2.5 and 13 cm.H2O.L-1.s) can allow us to fix by discrimination the sensitivity index P(A) independently of response bias (B) according to Sensory Decision Theory (SDT). The Andean highlanders did not experience the respiratory sensation at the same limits as the European lowlanders well adaptated to high altitude. At higher altitudes than their village altitude, their respiratory sensation presented a lower threshold of perception and a weaker discrimination which might be partly explained by the evolution of some parameters of their cardio-respiratory function when altitude increased. Indeed, in response to high altitude hypoxia (5600m), they increased their respiratory frequency and not their minuteventilation or mouth pressure. This chosen ventilatory pattern was opposite to the one chosen by the Lowlanders and did not allow for sufficient adaptation to a more important altitude hypoxia than that of their village altitude. In conclusion, the Andean highlanders wellbeing adapted to their village altitude, exhibited a difficult acclimatization to higher altitudes which might be due to the characteristics of their respiratory sensation. These results might explain their weak physical performances during ascent to the Mt. Aconcagua summit in spite of special training.     

Molecular cloning and characterization of hemoglobin alpha and beta chains from plateau pika (Ochotona curzoniae) living at high altitude

Hemoglobin (Hb) plays an important role in oxygen transfer from lung to tissues. Possession of a Hb with high oxygen affinity helps highland animals to adapt to high altitude, has been studied profoundly. Plateau pika (Ochotona curzoniae), a native species living at 3,000-5,000 m above sea level on Qinghai-Tibet Plateau, is a typical hypoxia and low temperature tolerant mammal. To investigate the possible mechanisms of plateau pika Hb in adaptation to high altitude, the complete cDNA and amino acid sequences of plateau pika hemoglobin alpha and beta chains have been described. Compared with human Hb, alterations in important regions can be noted: alpha111 Ala-->Asn, beta35 Tyr-->Phe, beta112 Cys-->Val, beta115 Ala-->Ser, and beta125 Pro-->Gln. Phylogenetic analysis of alpha and beta chains shows that plateau pika is closer to rabbit than to other species. This study provides essential information for elucidating the possible roles of hemoglobin in adaptation to extremely high altitude in plateau pika.