Genetic determinants of Tibetan high-altitude adaptation

Some highland populations have genetic adaptations that enable their successful existence in a hypoxic environment. Tibetans are protected against many of the harmful responses exhibited by non-adapted populations upon exposure to severe hypoxia, including elevated hemoglobin concentration (i.e., polycythemia). Recent studies have highlighted several genes subject to natural selection in native high-altitude Tibetans. Three of these genes, EPAS1, EGLN1 and PPARA, regulate or are regulated by hypoxia inducible factor, a principal controller of erythropoiesis and other organismal functions. Uncovering the molecular basis of hypoxic adaptation should have implications for understanding hematological and other adaptations involved in hypoxia tolerance. Because the hypoxia response involves a variety of cardiovascular, pulmonary and metabolic functions, this knowledge would improve our understanding of disease mechanisms and could ultimately be translated into targeted therapies for oxygen deprivation, cardiopulmonary and cerebral pathologies, and metabolic disorders such as diabetes and obesity.     

Evolutionary adaptations of cochlear function in Jamaican mormoopid bats

Mormoopid bat species have their echolocation system adapted to different hunting strategies. To study the corresponding mechanical properties of their inner ear, we measured distortion-product otoacoustic emissions to assess cochlear sensitivity and tuning. Mormoops blainvillii, Pteronotus macleayii and P. quadridens use frequency-modulated echolocation signals, sometimes preceded by a short narrowband signal component. Their distortion-product otoacoustic emission-threshold curves are most sensitive between 30 and 50 kHz and show no adaptation to the narrowband echolocation components. In contrast, the constant-frequency bat P. parnellii always uses long constant-frequency call components. Its inner ear is maximally sensitive at 62 kHz, the echo-frequency of the dominant constant-frequency component, and pronounced insensitivities at 61 and 93 kHz (CF2 and CF3 call frequency) are the major evolutionary change in comparison to its relatives. Furthermore, in P. parnellii, the optimum cochlear frequency separation is minimal at 62 and 93 kHz, associated with enhanced cochlear tuning, while for the other mormoopids there is no indication of enhanced tuning. The phylogeny of mormoopids, assessed by mitochondrial DNA analysis, shows a close relationship between the Pteronotus species. This suggests that major cochlear redesign, associated with the acquisition of echolocation-call specific cochlear processing in P. parnellii, has occurred within a relatively short evolutionary time scale. Accepted: 30 April 1999     

Genomic basis of high-altitude adaptation in Tibetan Prunus fruit trees

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Tibetan and Andean patterns of adaptation to high-altitude hypoxia

Understanding the workings of the evolutionary process in contemporary humans requires linking the evolutionary history of traits with their current genetics and biology. Unusual environments provide natural experimental settings to investigate evolution and adaptation. The example of high-altitude hypoxia illustrates some of the progress and many of the remaining challenges for studies of evolution in contemporary populations. Current studies exemplify the frequently encountered problem of determining whether large, consistent population differences in mean values of a trait reflect genetic differences. In this review I describe 4 quantitative traits that provide evidence that indigenous populations of the Tibetan and Andean plateaus differ in their phenotypic adaptive responses to high-altitude hypoxia. These 4 traits are resting ventilation, hypoxic ventilatory response, oxygen saturation, and hemoglobin concentration. The Tibetan means of the first 2 traits were more than 0.5 standard deviation higher than the Aymara means, whereas the Tibetan means were more than 1 standard deviation lower than the Aymara means for the last 2 traits. Quantitative genetic analyses of within-population variance revealed significant genetic variance in all 4 traits in the Tibetan population but only in hypoxic ventilatory response and hemoglobin concentration in the Aymara population. A major gene for oxygen saturation was detected among the Tibetans. These findings are interpreted as indirect evidence of population genetic differences. It appears that the biological characteristics of sea-level humans did not constrain high-altitude colonists of the 2 plateaus to a single adaptive response. Instead, microevolutionary processes may have operated differently in the geographically separated Tibetan and Andean populations exposed to the same environmental stress. Knowledge of the genetic bases of these traits will be necessary to evaluate these inferences. Future research will likely be directed toward determining whether the population means reflect differences identified at the chromosomal level. Future research will also likely consider the biological pathways and environmental influences linking genotypes to phenotypes, the costs and benefits of the Tibetan and Andean patterns of adaptation, and the question of whether the observed phenotypes are indeed adaptations that enhance Darwinian fitness.     

藏鸡心脏高海拔低氧适应相关酶的研究

目的：研究藏鸡心脏对高海拔低氧适应性的生理特征。方法：本研究将藏鸡、矮小隐性白和寿光鸡分别饲养在低海拔和高海拔环境,测定10周龄时心脏重量、心肌乳酸（LA）和乳酸脱氢酶（LDH）、琥珀酸脱氢酶（SDH）活性。结果：结果显示藏鸡在高海拔环境中,心脏相对重量未明显增加,心肌LA低于对照鸡,LDH与对照鸡差异不显著,而SDH活性明显高于对照鸡。结论：结果说明了藏鸡对高海拔低氧环境的适应,不是通过增加心脏器官的重量,也不是通过提高无氧代谢的水平,较高的SDH活力对藏鸡心肌低氧适应有一定的意义。SDH是藏鸡适应低氧的一种标志酶。     

Muscle tissue adaptations of high-altitude natives to training in chronic hypoxia or acute normoxia

Desplanches, D., H. Hoppeler, L. Tüscher, M. H. Mayet,H. Spielvogel, G. Ferretti, B. Kayser, M. Leuenberger, A. Grünenfelder, and R. Favier. Muscle tissue adaptations ofhigh-altitude natives to training in chronic hypoxia or acute normoxia.J. Appl. Physiol. 81(5):1946-1951, 1996.Twenty healthy high-altitude natives, residentsof La Paz, Bolivia (3,600 m), participated in 6 wk of enduranceexercise training on bicycle ergometers, 5 times/wk, 30 min/session, aspreviously described in normoxia-trained sea-level natives (H. Hoppeler, H. Howald, K. E. Conley, S. L. Lindstedt, H. Claassen, P. Vock, and E. R. Weibel. J. Appl.Physiol. 59: 320-327, 1985). A first group of 10 subjects was trained in chronic hypoxia (HT; barometricpressure = 500 mmHg; inspired O₂fraction = 0.209); a second group of 10 subjects was trained in acutenormoxia (NT; barometric pressure = 500 mmHg; inspired O₂ fraction = 0.314). Theworkloads were adjusted to ~70% of peak O₂ consumption(O_{2 peak}) measuredeither in hypoxia for the HT group or in normoxia for the NT group.O_{2 peak} determination and biopsies of the vastus lateralis muscle were taken before and afterthe training program.O_{2 peak} in the HTgroup was increased (14%) in a way similar to that in NT sea-levelnatives with the same protocol. Moreover,O_{2 peak} in the NTgroup was not further increased by additionalO₂ delivery during the training session. HT or NT induced similar increases in musclecapillary-to-fiber ratio (26%) and capillary density (19%) as well asin the volume density of total mitochondria and citrate synthaseactivity (45%). It is concluded that high-altitude natives have areduced capillarity and muscle tissue oxidative capacity; however,their training response is similar to that of sea-level residents,independent of whether training is carried out in hypobaric hypoxia orhypobaric normoxia.

     

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.     

Evolutionary variants of the mos gene

The occurence of members of mos oncogene family in the vertebrates genome has been studied with the help of highly labeled single-stranded DNA probes. These included subgenic v-mos clones as well as the unique sequence--specific recombinants from mos-related human locus gp5 and the K51 locus from rat genome. The probe from gp5 (mos pseudogene) interacts only with DNA of primates and of rodents. On the other hand, mos gene and the gene from K51 locus are present in all vertberates tested. Recent duplication of the main mos gene in Artiodactyla and Perissodactyla orders of mammals was identified. The persistence of K51 and mos genes during evolution indicates their importance. The segregation of three mos-related genes in human-hamster hybrids points to their location on different human chromosomes.     

Population history and genomic signatures for high-altitude adaptation in Tibetan pigs

Background

The Tibetan pig is one of domestic animals indigenous to the Qinghai-Tibet Plateau. Several geographically isolated pig populations are distributed throughout the Plateau. It remained an open question if these populations have experienced different demographic histories and have evolved independent adaptive loci for the harsh environment of the Plateau. To address these questions, we herein investigated ~ 40,000 genetic variants across the pig genome in a broad panel of 678 individuals from 5 Tibetan geographic populations and 34 lowland breeds.

Results

Using a series of population genetic analyses, we show that Tibetan pig populations have marked genetic differentiations. Tibetan pigs appear to be 3 independent populations corresponding to the Tibetan, Gansu and Sichuan & Yunnan locations. Each population is more genetically similar to its geographic neighbors than to any of the other Tibetan populations. By applying a locus-specific branch length test, we identified both population-specific and -shared candidate genes under selection in Tibetan pigs. These genes, such as PLA2G12A, RGCC, C9ORF3, GRIN2B, GRID1 and EPAS1, are involved in high-altitude physiology including angiogenesis, pulmonary hypertension, oxygen intake, defense response and erythropoiesis. A majority of these genes have not been implicated in previous studies of highlanders and high-altitude animals.

Conclusion

Tibetan pig populations have experienced substantial genetic differentiation. Historically, Tibetan pigs likely had admixture with neighboring lowland breeds. During the long history of colonization in the Plateau, Tibetan pigs have developed a complex biological adaptation mechanism that could be different from that of Tibetans and other animals. Different Tibetan pig populations appear to have both distinct and convergent adaptive loci for the harsh environment of the Plateau.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-834) contains supplementary material, which is available to authorized users.     

Andean, Tibetan, and Ethiopian patterns of adaptation to high-altitude hypoxia

Research on humans at high-altitudes contributes to understandingthe processes of human adaptation to the environment and evolution.The unique stress at high altitude is hypobaric hypoxia causedby the fall in barometric pressure with increasing altitudeand the consequently fewer oxygen molecules in a breath of air,as compared with sea level. The natural experiment of humancolonization of high-altitude plateaus on three continents hasresulted in two—perhaps three—quantitatively differentarterial-oxygen-content phenotypes among indigenous Andean,Tibetan and Ethiopian high-altitude populations. This paperillustrates these contrasting phenotypes by presenting evidencefor higher hemoglobin concentration and percent of oxygen saturationof hemoglobin among Andean highlanders as compared with Tibetansat the same altitude and evidence that Ethiopian highlandersdo not differ from sea-level in these two traits. Evolutionaryprocesses may have acted differently on the colonizing populationsto cause the different patterns of adaptation. Hemoglobin concentrationhas significant heritability in Andean and Tibetan samples.Oxygen saturation has no heritability in the Andean sample,but does among Tibetans where an autosomal dominant major genefor higher oxygen saturation has been detected. Women estimatedwith high probability to have high oxygen saturation genotypeshave more surviving children than women estimated with highprobability to have the low oxygen saturation genotype. Thesefindings suggest the hypothesis that ongoing natural selectionis increasing the frequency of the high saturation allele atthis major gene locus.     

Evolutionary significance of morphogenetic mechanisms

Different approaches to interpretation of ontogenesis are compared. The importance is emphasized of Ber’s theory of developmental patterns and the law of embryonic similarity. The significance of evolutionary rationalization of morphogenetic mechanisms is discussed (V.N. Beklemishev, V.A. Dogel’ and O.M. Ivanova-Kazas). There are two main pathways of rationalization of morphogenetic mechanisms: by means of epithelial morphogenesis and at the expense of oligocellular primordia (V.N. Beklemishev). When the developmental plans of the taxonomical types are determined, it is important to take into consideration the diversity of morphogenetic mechanisms within a given group in order to reveal morphological spectrums of morphogenetic mechanisms. A comparison of morphogenetic spectrums in different groups provides a wide evolutionary picture and helps us to reconstruct the phylogeny. Influence of morphogenetic mechanisms on the structure of definitive forms is demonstrated: construction technologies determine types of organs, anatomical and histological systems, and even symmetrical features of organisms and their complex parts.     

Evolutionary adaptations in four hippoboscid fly species belonging to three different subfamilies

Lipoptena cervi (Linnaeus, 1758), Lipoptena fortisetosa Maa, 1965, Hippobosca equina Linnaeus, 1758, and Pseudolynchia canariensis (Macquart, 1840) (Diptera: Hippoboscidae) are haematophagous ectoparasites that infest different mammal and bird species and occasionally attack humans. They are known for the health implications they have as vectors of pathogens to humans and animals, and for the injuries they inflict on their host's skin. This study focused on the morphological structures evolved by parasites in terms of their biology and the different environment types that they inhabit. To this aim, we examined four hippoboscid species, as well as their hosts' fur (ungulate and horse), and feather (pigeon) through light and Scanning Electron Microscopy (SEM) observations in order to highlight the main morphological features that evolved differently in these flies and to explain the effect of hosts' fur/feather microhabitats on the morphological specializations observed in the investigated ectoparasites. The studied species showed main convergent characters in mouthparts while remarkable differences have been detected on the antennal sensillar pattern as well as on the leg acropod that displayed divergent characters evolved in relation to the host.     

Evolutionary significance of stress-induced mutagenesis in bacteria

Mutagenesis is often increased in bacterial populations as a consequence of stress-induced genetic pathways. Analysis of the molecular mechanisms involved suggests that mutagenesis might be increased as a by-product of the stress response of the organism. By contrast, computer simulations and analyses of stress-inducible phenotypes among natural isolates of Escherichia coli suggest that stress-induced mutagenesis (SIM) could be the result of selection because of the beneficial mutations that such a process can potentially generate. Regardless of the nature of the selective pressure acting on SIM, it is possible that the resulting increased genetic variability plays an important role in bacterial evolution.     

Evolutionary dynamics of wAu-like Wolbachia variants in neotropical Drosophila spp

Wolbachia bacteria are common intracellular symbionts of arthropods and have been extensively studied in Drosophila. Most research focuses on two Old Word hosts, Drosophila melanogaster and Drosophila simulans, and does not take into account that some of the Wolbachia associations in these species may have evolved only after their fast global expansion and after the exposure to Wolbachia of previously isolated habitats. Here we looked at Wolbachia of Neotropical Drosophila species. Seventy-one lines of 16 Neotropical Drosophila species sampled in different regions and at different time points were analyzed. Wolbachia is absent in lines of Drosophila willistoni collected before the 1970s, but more recent samples are infected with a strain designated wWil. Wolbachia is absent in all other species of the willistoni group. Polymorphic wWil-related strains were detected in some saltans group species, with D. septentriosaltans being coinfected with at least four variants. Based on wsp and ftsZ sequence data, wWil of D. willistoni is identical to wAu, a strain isolated from D. simulans, but can be discriminated when using a polymorphic minisatellite marker. In contrast to wAu, which infects both germ line and somatic tissues of D. simulans, wWil is found exclusively in the primordial germ line cells of D. willistoni embryos. We report on a pool of closely related Wolbachia strains in Neotropical Drosophila species as a potential source for the wAu strain in D. simulans. Possible evolutionary scenarios reconstructing the infection history of wAu-like Wolbachia in Neotropical Drosophila species and the Old World species D. simulans are discussed.     

Association between MT-CO3 haplotypes and high-altitude adaptation in Tibetan chicken

Genetic mutation in cytochrome c oxidase subunit III gene (MT-CO3) could influence the kinetics of cytochrome c oxidase (COX), which catalyzes oxygen transport capacity in oxidative phosphorylation. However, the potential relationship between MT-CO3 variants and high-altitude adaptation remains poorly understood in Tibetan chicken. Here, we sequenced MT-CO3 gene of 125 Tibetan chickens and 144 Chinese domestic chickens in areas at a low elevation (below 1000 m). Eight single nucleotide polymorphisms (SNPs) were detected; and five of them (m.10081A>G, m.10115G>A, m.10270G>A, m.10336A>G and m.10447C>T) shared by Tibetan chicken and lowland chicken with the significant difference in their respective allele frequencies. Nine haplotypes (H1–H9) were finally defined. Among them, haplotype H4 was positively associated with high-altitude adaptation whereas haplotypes H6, H7 and H8 had negative association with high-altitude adaptation. The Median-joining profile suggested that haplotype H5 had the ancestral position to the other haplotypes but had no significant relationship with high-altitude adaptation. However, there was only m.10081A>G mutation differed from haplotype H4 and H5. Results also suggested that chickens with A allele at m.10081A>G, had over 2.6 times than those with G allele in the probability of the ability to adapt hypoxia. It suggests that the synonymous mutation m.10081A>G may be a prerequisite for shaping high-altitude adaptation-specific haplotypes.     

Evolutionary significance of isopreneemission from mosses

Isoprene emission has been documented and characterized from species in all major groups of vascular plants. We report in our survey that isoprene emission is much more common in mosses and ferns than later divergent land plants but is absent in liverworts and hornworts. The light and temperature responses of isoprene emission from Sphagnum capillifolium (Ehrh.) Hedw. are similar to those of other land plants. Isoprene increases thermotolerance of S. capillifolium to the same extent seen in higher plants as measured by chlorophyll fluorescence. Sphagnum species in a northern Wisconsin bog experienced large temperature fluctuations similar to those reported in tree canopies. Since isoprene has been shown to help plants cope with large, rapid temperature fluctuations, we hypothesize the thermal and correlated dessication stress experienced by early land plants provided the selective pressure for the evolution of light-dependent isoprene emission in the ancestors of modern mosses. As plants radiated into different habitats, this capacity was lost multiple times in favor of other thermal protective mechanisms.     

Evolutionary adaptations of ruminants and their potential relevance for modern production systems

Comparative physiology applies methods established in domestic animal science to a wider variety of species. This can lead to improved insight into evolutionary adaptations of domestic animals, by putting domestic species into a broader context. Examples include the variety of responses to seasonally fluctuating environments, different adaptations to heat and drought, and in particular adaptations to herbivory and various herbivore niches. Herbivores generally face the challenge that a high food intake compromises digestive efficiency (by reducing ingesta retention time and time available for selective feeding and for food comminution), and a variety of digestive strategies have evolved in response. Ruminants are very successful herbivores. They benefit from potential advantages of a forestomach without being constrained in their food intake as much as other foregut fermenters, because of their peculiar reticuloruminal sorting mechanism that retains food requiring further digestion but clears the forestomach of already digested material; the same mechanism also optimises food comminution. Wild ruminants vary widely in the degree to which their rumen contents 'stratify', with little stratification in 'moose-type' ruminants (which are mostly restricted to a browse niche) and a high degree of stratification into gas, particle and fluid layers in 'cattle-type' ruminants (which are more flexible as intermediate feeders and grazers). Yet all ruminants uniformly achieve efficient selective particle retention, suggesting that functions other than particle retention played an important role in the evolution of stratification-enhancing adaptations. One interesting emerging hypothesis is that the high fluid turnover observed in 'cattle-type' ruminants - which is a prerequisite for stratification - is an adaptation that not only leads to a shift of the sorting mechanism from the reticulum to the whole reticulo-rumen, but also optimises the harvest of microbial protein from the forestomach. Although potential benefits of this adaptation have not been quantified, the evidence for convergent evolution toward stratification suggests that they must be substantial. In modern production systems, the main way in which humans influence the efficiency of energy uptake is by manipulating diet quality. Selective breeding for conversion efficiency has resulted in notable differences between wild and domestic animals. With increased knowledge on the relevance of individual factors, that is fluid throughput through the reticulo-rumen, more specific selection parameters for breeding could be defined to increase productivity of domestic ruminants by continuing certain evolutionary trajectories.     

Evolutionary significance of gene expression divergence

Recent large-scale studies of evolutionary changes in gene expression among mammalian species have led to the proposal that gene expression divergence may be neutral with respect to organismic fitness. Here, we employ a comparative analysis of mammalian gene sequence divergence and gene expression divergence to test the hypothesis that the evolution of gene expression is predominantly neutral. Two models of neutral gene expression evolution are considered: 1-purely neutral evolution (i.e., no selective constraint) of gene expression levels and patterns and 2-neutral evolution accompanied by selective constraint. With respect to purely neutral evolution, levels of change in gene expression between human-mouse orthologs are correlated with levels of gene sequence divergence that are determined largely by purifying selection. In contrast, evolutionary changes of tissue-specific gene expression profiles do not show such a correlation with sequence divergence. However, divergence of both gene expression levels and profiles are significantly lower for orthologous human-mouse gene pairs than for pairs of randomly chosen human and mouse genes. These data clearly point to the action of selective constraint on gene expression divergence and are inconsistent with the purely neutral model; however, there is likely to be a neutral component in evolution of gene expression, particularly, in tissues where the expression of a given gene is low and functionally irrelevant. The model of neutral evolution with selective constraint predicts a regular, clock-like accumulation of gene expression divergence. However, relative rate tests of the divergence among human-mouse-rat orthologous gene sets reveal clock-like evolution for gene sequence divergence, and to a lesser extent for gene expression level divergence, but not for the divergence of tissue-specific gene expression profiles. Taken together, these results indicate that gene expression divergence is subject to the effects of purifying selective constraint and suggest that it might also be substantially influenced by positive Darwinian selection.