Genomic Scan Reveals Loci under Altitude Adaptation in Tibetan and Dahe Pigs

High altitude environments are of particular interest in the studies of local adaptation as well as their implications in physiology and clinical medicine in human. Some Chinese pig breeds, such as Tibetan pig (TBP) that is well adapted to the high altitude and Dahe pig (DHP) that dwells at the moderate altitude, provide ideal materials to study local adaptation to altitudes. Yet, it is still short of in-depth analysis and understanding of the genetic adaptation to high altitude in the two pig populations. In this study we conducted a genomic scan for selective sweeps using F_ST to identify genes showing evidence of local adaptations in TBP and DHP, with Wuzhishan pig (WZSP) as the low-altitude reference. Totally, we identified 12 specific selective genes (CCBE1, F2RL1, AGGF1, ZFPM2, IL2, FGF5, PLA2G4A, ADAMTS9, NRBF2, JMJD1C, VEGFC and ADAM19) for TBP and six (OGG1, FOXM, FLT3, RTEL1, CRELD1 and RHOG) for DHP. In addition, six selective genes (VPS13A, GNA14, GDAP1, PARP8, FGF10 and ADAMTS16) were shared by the two pig breeds. Among these selective genes, three (VEGFC, FGF10 and ADAMTS9) were previously reported to be linked to the local adaptation to high altitudes in pigs, while many others were newly identified by this study. Further bioinformatics analysis demonstrated that majority of these selective signatures have some biological functions relevant to the altitude adaptation, for examples, response to hypoxia, development of blood vessels, DNA repair and several hematological involvements. These results suggest that the local adaptation to high altitude environments is sophisticated, involving numerous genes and multiple biological processes, and the shared selective signatures by the two pig breeds may provide an effective avenue to identify the common adaptive mechanisms to different altitudes.     

Genetic variations in Tibetan populations and high-altitude adaptation at the Himalayas

Modern humans have occupied almost all possible environments globally since exiting Africa about 100,000 years ago. Both behavioral and biological adaptations have contributed to their success in surviving the rigors of climatic extremes, including cold, strong ultraviolet radiation, and high altitude. Among these environmental stresses, high-altitude hypoxia is the only condition in which traditional technology is incapable of mediating its effects. Inhabiting at >3,000-m high plateau, the Tibetan population provides a widely studied example of high-altitude adaptation. Yet, the genetic mechanisms underpinning long-term survival in this environmental extreme remain unknown. We performed an analysis of genome-wide sequence variations in Tibetans. In combination with the reported data, we identified strong signals of selective sweep in two hypoxia-related genes, EPAS1 and EGLN1. For these two genes, Tibetans show unusually high divergence from the non-Tibetan lowlanders (Han Chinese and Japanese) and possess high frequencies of many linked sequence variations as reflected by the Tibetan-specific haplotypes. Further analysis in seven Tibetan populations (1,334 individuals) indicates the prevalence of selective sweep across the Himalayan region. The observed indicators of natural selection on EPAS1 and EGLN1 suggest that during the long-term occupation of high-altitude areas, the functional sequence variations for acquiring biological adaptation to high-altitude hypoxia have been enriched in Tibetan populations.     

A proposed classification of environmental adaptation: the example of high altitude

Extreme environments are defined as the opposite of usual environments where the evoked physiological responses are unperceivable, repeatable and adjusted to the constraint. Adaptation strategies to a given environment show three levels: cultural or technological, where a buffer space is built to protect the organism from the hostile milieu, physiological, where temporary adaptive mechanisms are developed, and genetic, where full adaptation is possible with normal life and reproduction. The cost of adaptation increases from the genetic level (minimal cost) to the technological level. These concepts are illustrated by the example of adaptation to altitude hypoxia. The technological level is given by the use of oxygen bottles by high altitude climbers. The physiological level involves various physiological and biological systems (increase in heart rate, ventilation, erythropoiesis, expression of hypoxia-inducible factors, etc.). The genetic level has been reached by some animal species such as Yaks, Llamas, Pikas but has not yet been demonstrated in humans. Diseases developed during exposure to acute or chronic hypoxia may be considered as “adaptive crises” that mimic the transition to a lower energy level of adaptation.     

藏族的高原适应——西藏藏族生物人类学研究回顾

藏族生活在具有世界屋脊之称的青藏高原, 特殊的生态环境和特殊的文化背景造就了藏族特殊的适应高原缺氧机制, 引起了国内外学者的广泛关注和浓厚的研究兴趣。本文根据国内外数据库的文献并结合我们的研究工作, 从高原适应的角度回顾了30多年藏族人类学研究。回顾显示, 藏族由于长期生活在高原缺氧的环境中, 不仅形态和机能发生了适应性变化, 而且体成分也表现出相应的变化, 体现了形态、机能和体成分的统一。这些变化是长期进化形成的, 与安第斯山人等有明显不同, 就是在同一高原生活的西藏、青海、四川、甘肃和云南的藏族乃至尼泊尔和印度藏族的体质也表现出地域差异, 这些差异的产生是多种因素所致, 两个关键性的基因是导致两大高原人口高原适应机制不同的最主要的原因。     

Predicted structural change in erythropoietin of plateau zokors--adaptation to high altitude

Erythropoietin (EPO) is a glycoprotein hormone, expressed mainly in fetus liver and adult kidneys. EPO plays an important role in enhancing red blood cell formation in bone marrow under hypoxia. Plateau zokor (Myospalax baileyi), an subterranean burrowing endemic rodent inhabiting areas of 2 800-4 200 m above sea level on Qinghai-Tibet Plateau, is a typical high hypoxia tolerant mammal with high ratio of oxygen utilization in adaptation to the harsh plateau environment. To investigate the possible mechanisms of adaptation of plateau zokor EPO to high altitude, the complete cDNA and amino acid sequences of plateau zokor EPO have been described. Phylogenetic tree of Epo showed the convergence of the Spalax and Myospalax, indicating that, the convergent evolution was driven by similar hypoxic ecological niches. Our results showed that some common sites under positive selection in zokor (116M and 144A) and Spalax (102R, 116M, 144A and 152P) are the important sites for Epo biological activity. This study thus reports a gene level observation which may be involved in adaptation to underground life at high altitude.     

Altitude, migration, and fertility in the Andes

In order to examine the relationship between hypoxia and reduced fertility of high Andean populations, a sample of 241 females living in the low-altitude Tambo Valley of Peru was studied. 63 of the subjects were born in the low-altitude valley, 121 were migrants from high altitudes, and 57 were migrants born in low altitudes. The rate of abortion was low among high-altitude subjects before they migrated, but became greater after migrating. It was found that the high-altitude populations had almost twice as long parity intervals than the low-altitude populations. Compared to migrants born at low altitudes, the high-altitude-born subjects who migrated to low altitudes had higher fertility rates. The results of the study are consistent with the hypothesis that high altitudes, through anoxia, have a lowering effect on fertility. Of the several possible explanations which might account for the increase in fertility of downward migrants on migration from high to low altitude (migration, socioeconomic factors, acculturation, seasonal male emigration from high altitude, and removal of hypoxia stress), altitude appears to be the most significant.     

Altitudinal gradients,plant hybrid zones and evolutionary novelty

Altitudinal gradients are characterized by steep changes of the physical and biotic environment that present challenges to plant adaptation throughout large parts of the world. Hybrid zones may form where related species inhabit different neighbouring altitudes and can facilitate interspecific gene flow and potentially the breakdown of species barriers. Studies of such hybrid zones can reveal much about the genetic basis of adaptation to environmental differences stemming from changes in altitude and the maintenance of species divergence in the face of gene flow. Furthermore, owing to recombination and transgressive effects, such hybrid zones can be sources of evolutionary novelty. We document plant hybrid zones associated with altitudinal gradients and emphasize similarities and differences in their structure. We then focus on recent studies of a hybrid zone between two Senecio species that occur at high and low altitude on Mount Etna, Sicily, showing how adaptation to local environments and intrinsic selection against hybrids act to maintain it. Finally, we consider the potential of altitudinal hybrid zones for generating evolutionary novelty through adaptive introgression and hybrid speciation. Examples of homoploid hybrid species of Senecio and Pinus that originated from altitudinal hybrid zones are discussed.     

Altitudinal variation in life cycle syndromes of California populations of the grasshopper,Melanoplus sanguinipes (F.)

Summary Life cycles of California populations of the grasshopper, Melanoplus sanguinipes, varied along an altitudinal gradient. Temperature records indicate a longer season at low altitude on the coast, based on computation of degree days available for development, even though summer air temperatures are cooler than at high altitude; this is a result of warm soil temperatures. At high and low altitudes there was a high proportion of diapause eggs oviposited, while intermediate proportions of diapause eggs occurred at mid altitudes. The low altitude, and especially sea level, populations diapaused at all stages of embryonic development, while at high altitudes most diapause occurred in the late stages just before hatch. Diapause was more intense at high altitudes. One result of diapause differences was delayed hatching in the sea level population. Nymphal development and development of adults to age at first reproduction were both accelerated at high altitude relative to sea level. At lower temperatures (27° C) there was a tendency for short days to accelerate development of sea level nymphs, but not high altitude nymphs. In both sea level and high altitude grasshoppers, short days accelerated maturation of adults to onset of oviposition at warm temperature (33° C); there was little reproduction at 27° C. Population differences for all traits studied appear to be largely genetic with some maternal effects possible. We interpret diapause variation at low and mid altitudes to be responses to environmental uncertainty and variations in development rates to be adaptations to prevailing season lengths.     

Neonatal tolerance to hypoxia: a comparative-physiological approach.

Newborn mammals exhibit a number of physiological reactions which differ from normal adult physiology and are often regarded as signs of immaturity. However, when looked upon from a comparative point of view, it becomes obvious that some of these 'physiological peculiarities' bear striking similarity to adaptation mechanisms known from hypoxia-tolerant animals and may thus contribute to the well-established, yet poorly understood, phenomenon of neonatal hypoxia tolerance. As the mammalian fetus lives at oxygen partial pressures corresponding to 8000 m altitude, the first line of perinatal hypoxia defense consists of long-term adaptations to limited intrauterine oxygen supply: (1) improved O2 transport by fetal acclimatization to high altitude, (2) reduced metabolic rate by hibernation-like deviation from metabolic size allometry, (3) diminished cerebral vulnerability by functional analogies to diving turtle brain, and (4) enhanced metabolic flexibility by optional repartitioning of energy supply from growth to maintenance metabolism. In the case of birth asphyxia, these background mechanisms are complemented by short-term responses to acute oxygen lack: (1) reduction of body temperature as in natural torpor, (2) reduction of heart rate and redistribution of circulation as in diving mammals, (3) reduction of respiration rate typical of 'hypoxic hypometabolism', and (4) reduction of blood pH according to the concept of 'acidotic torpidity'. Although anaerobic metabolism is improved in neonatal mammals by increased glycogen stores, reduced metabolic demands, and sustained wash-out of acid metabolites, neonatal hypoxia tolerance seems to be primarily based on the ability to maintain tissue aerobiosis as long as possible. This is even reflected by isoenzyme patterns which do not consistently favour anaerobic glycolysis and, thus, are reminiscent of the 'lactate paradox' found in high altitude adaptation. Altogether, from a biological point of view, the perinatal period appears as a source of adaptive mechanisms that can be refound, in varying combinations, in many survival strategies. From a clinical point of view, the interplay of long- and short-term mechanisms offers a novel approach to estimation of the newborn's ability to withstand temporary oxygen lack. However, most of these mechanisms are not unambiguous and, above all, not unlimited in their protective effect so that they do not release obstetricians or neonatologists from their obligation to counteract fetal or neonatal hypoxia without delay.     

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.     

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.     

BIOCHEMICAL ADAPTATION AND LOSS OF GENETIC CAPACITY IN HELMINTH PARASITES

1. Adaptation and loss of genetic capacity differ chiefly in that adaptation is goal- directed whereas loss of genetic capacity is not. Given sufficient information about an individual organism and its environment, adaptations are recognizable without reference to historical events extending beyond a single generation. This is not true of loss of genetic capacity, which requires a preliminary judgement that genetic information now absent was present in ancestral organisms. Together, adaptation and loss of genetic capacity are the major contributors to overall reproductive fitness. Accidental selection is genetically associated with adaptation, but is not goal-directed. 2. Adaptations arevariant or invariant; invariant adaptations comprising biochemical unity, and variant adaptations contributing to biochemical diversity. Variant adaptations may be either exploitive or epigenetic. Exploitive adaptations are a measure of thegenetic capacity for phenotypic response to an altered environment, which the individual may not in fact encounter. Epigenetic adaptations are more rigidly programmed and are responsive to altered environments only insofar as these are a constant feature of the life cycle. 3. Selected observations in the biochemistry of helminth parasites are examined with respect to their interpretation in terms of adaptation, loss of genetic capacity and accidental selection. Secure judgements concerning adaptation are often possible at the most general level, i.e. when the physicochemical properties of the environment, such as temperature or oxygen supply, are clearly defined. I t is more difficult to make judgements concerning the specific mechanisms used in achieving these goals. Conclusions concerning loss of genetic capacity require knowledge of the specific function through-out the life cycle. In many cases loss of genetic capacity is only apparent, as the function appears in another part of the life cycle. Such apparent losses are in reality epigenetic adaptations. These concepts are helpful in interpreting past work and in devising new experiments. 4. Development in helminth parasites includes a pronounced capacity for the orderly release of information to be used in the next stage. As each stage may require a radically different environment, programming for it may lead to phenomena which are superficially puzzling, such as the existence of aerobic electron transport systems in a stage whose energy metabolism is fermentative. The concept of epigenetic adaptation is especially useful for interpreting such observations. 5. Although possible adaptations are most readily apparent in biochemically complex mechanisms, these mechanisms are an expression of the orderly effects of many different primary gene products which have not been much studied. There are indications that organisms possessing relatively complex life cycles may provide opportunities for relating primary gene products, such as isozymes, to their physiological functions.     

Developmental plasticity in aerobic performance in deer mice (Peromyscus maniculatus)

While several studies have examined the abiotic effects of altitude (low ambient temperatures and hypoxia) on the aerobic performance of small mammals, few have explored the effects of development and maturation at different altitudes on aerobic performance as adults. We examined the basal metabolism and aerobic performance of deer mice (Peromyscus maniculatus) under four different developmental and testing regimes: (1) reared (gestation through weaning) and tested at high altitude; (2) reared and tested at low altitude; (3) reared at low altitude and tested at high altitude after acclimation; and (4) reared at low altitude and tested in hypoxia without acclimation. We found that mice that developed and were tested at low altitudes had a higher aerobic capacity (both aerobic performance and basal metabolic rate) than those that developed, or were acclimated as adults, at high altitudes. In addition, we found that mice that developed at high altitude did not have a higher aerobic capacity than those that developed at low altitude and were acclimated to high altitude as adults. Both groups tested at high altitudes had higher hematocrits (% red blood cells) and hemoglobin than mice tested at low altitudes. Surprisingly, mice acclimated to low altitudes and given an instantaneous exposure to hypoxia did not suffer a depression in aerobic performance.     

Mitogenomic analysis of Chinese snub-nosed monkeys: Evidence of positive selection in NADH dehydrogenase genes in high-altitude adaptation

Chinese snub-nosed monkeys belong to the genus Rhinopithecus and are limited in distribution to six isolated mountainous areas in the temperate regions of Central and Southwest China. Compared to the other members of the subfamily Colobinae (or leaf-eating monkeys), these endangered primates are unique in being adapted to a high altitude environment and display a remarkable ability to tolerate low temperatures and hypoxia. They thus offer an interesting organismal model of adaptation to extreme environmental stress. Mitochondria generate energy by oxidative phosphorylation (OXPHOS) and play important roles in oxygen usage and energy metabolism. We analyzed the mitochondrial genomes of two Chinese snub-nosed monkey species and eight other colobines in the first attempt to understand the genetic basis of high altitude adaptation in non-human primates. We found significant evidence of positive selection in one Chinese snub-nosed monkey, Rhinopithecus roxellana, which is suggestive of adaptive change related to high altitude and cold weather stress. In addition, our study identified two potentially important adaptive amino acid residues (533 and 3307) in the NADH2 and NADH6 genes, respectively. Surprisingly, no evidence for positive selection was found in Rhinopithecus bieti (the other Chinese snub-nosed monkey analyzed). This finding is intriguing, especially considering that R. bieti inhabits a higher altitudinal distribution than R. roxellana. We hypothesize that a different adaptive genetic basis to high altitude survival exists in R. bieti from those seen in other mammals, and that positive selection and functionally associated mutations in this species may be detected in nuclear genes related to energy and oxygen metabolism. More information on the structure, function, and evolution of mitochondrial and nuclear genomes in Chinese snub-nosed monkeys is required to reveal the molecular mechanisms that underlie adaptations to high altitude survival in non-human primates.     

Mitochondrial OXPHOS genes provides insights into genetics basis of hypoxia adaptation in anchialine cave shrimps

Cave shrimps from the genera Typhlatya, Stygiocaris and Typhlopatsa (TST complex) comprises twenty cave-adapted taxa, which mainly occur in the anchialine environment. Anchialine habitats may undergo drastic environmental fluctuations, including spatial and temporal changes in salinity, temperature, and dissolved oxygen content. Previous studies of crustaceans from anchialine caves suggest that they have possessed morphological, behavioral, and physiological adaptations to cope with the extreme conditions, similar to other cave-dwelling crustaceans. However, the genetic basis has not been thoroughly explored in crustaceans from anchialine habitats, which can experience hypoxic regimes. To test whether the TST shrimp-complex hypoxia adaptations matched adaptive evolution of mitochondrial OXPHOS genes. The 13 OXPHOS genes from mitochondrial genomes of 98 shrimps and 1 outgroup were examined. For each of these genes was investigated and compared to orthologous sequences using both gene (i.e. branch-site and Datamonkey) and protein (i.e. TreeSAAP) level approaches. Positive selection was detected in 11 of the 13 candidate genes, and the radical amino acid changes sites scattered throughout the entire TST complex phylogeny. Additionally, a series of parallel/convergent amino acid substitutions were identified in mitochondrial OXPHOS genes of TST complex shrimps, which reflect functional convergence or similar genetic mechanisms of cave adaptation. The extensive occurrence of positive selection is suggestive of their essential role in adaptation to hypoxic anchialine environment, and further implying that TST complex shrimps might have acquired a finely capacity for energy metabolism. These results provided some new insights into the genetic basis of anchialine hypoxia adaptation.     

Leptin cDNA cloning and its mRNA expression in plateau pikas (Ochotona curzoniae) from different altitudes on Qinghai-Tibet Plateau

Leptin, an adipocyte-derived hormone, plays an important role in body energy homeostasis. Plateau pika (Ochotona curzoniae), an endemic and keystone species living only at 3000-5000 m above sea level on Qinghai-Tibet Plateau, is a typically high hypoxia and low temperature tolerant mammal with high resting metabolic rate (RMR), non-shivering thermogenesis (NST), and high ratio of oxygen utilization to cope with harsh plateau environment. To explore the molecular mechanism of ecological acclimation in plateau pika, we first cloned pika leptin cDNA and compared its mRNA expression in different altitudes (3200 and 3900 m) using real-time RT-PCR (Taqman probe) technology. The full-length pika leptin cDNA was 3015 with 504 bp open-reading frame encoding the precursor peptide of 167 amino acids including 21 residues of signal peptide. Pika leptin was 70-72% homologous to that of other species and was of similarly structural characteristics with other species. The pika-specific genetic diversity in leptin sequence occurred at twenty sites. With the increase in altitude, there were larger fat store and high level of ob gene expression in plateau pika. Our results indicated that leptin is sensitive to cold and hypoxia plateau environment and may play one of important roles in pika's ecological adaptation to harsh plateau environment.     

Larval development and poor trophic resource availability: Local adaptations and plasticity in a widespread amphibian species

Theory predicts that, in organisms with complex life cycles, if the earlier-stage limiting factor induces weak later-stage phenotypes, the development of the later-stage trait should evolve to reduce carry-over effects. Local adaptations could thus favour decoupling of later stages. However, decoupling is not always possible. In this study, we used a widespread amphibian, the European fire salamander (Salamandra salamandra), to assess the role of local adaptations to environmental stressful conditions experienced at the larval stage. We exposed 150 larvae from different altitudes to two conditions: rich food and poor food condition. Conditions in early life stages can affect an individual's traits, either as a direct effect or mediated through outcomes in successive life stages. To distinguish between effects of rearing conditions and local adaptation, we searched for a causal model. The causal model detected effects of both food treatment and population origin (altitude) on all life stages. Larvae reared under rich food condition metamorphosed earlier, had higher growth rates and reached smaller size at metamorphosis. Significant differences occurred between larvae of different origin: low-altitude individuals performed poorly under the poor food treatment. Moreover, larvae from higher altitudes were slower with rich food and faster with poor food compared to those from lower altitudes. Our results underline that environmental conditions and local adaptation can interplay in determining the plasticity of larval stages, still adaptations can maximize the growth efficiency of early stages in oligotrophic environments, leading to divergent pathways across populations and environmental conditions.