Time Domains of Hypoxia Responses and -Omics Insights.

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

Varied Reproductive Histories of Ethnically Tibetan Women.

BACKGROUND: The U.N. health and well-being goals for 2030 focus on maternal and child health outcomes, among others. Challenges to meeting those goals vary widely throughout Nepal owing to the range of sociocultural factors, infrastructural limitations, physical geography and altitudes. This article explores sociocultural and biological influences on fertility and child survival among ethnically Tibetan women in Nepal. METHODS: This is a cross sectional study of 430 women, age 46-86 years old, citizens of Nepal and native residents above 3500m in Mustang District, who provided interview and physiological data. Univariate Poisson regression analyses selected significant variables to include in multivariate Poisson regressions investigating the number of pregnancies, livebirths, child survival and death outcomes. RESULTS: Earlier age at first pregnancy, later age at last pregnancy, and miscarriages associated with more pregnancies. Miscarriages and stillbirths associated with fewer livebirths. Higher maternal BMI and FEV6 associated with fewer children dying before age 15. Marital characteristics (status, type, continuity), contraceptive use, relative wealth, and education influenced these covariates. CONCLUSIONS: Low maternal pulmonary function and nutritional status predict poorer child survival in Upper Mustang. Addressing poor lung function and nutrition may improve reproductive outcomes among ethnically Tibetan women living at high altitude.

Repeatability of adaptive traits among ethnic Tibetan highlanders.

OBJECTIVES: Connecting traits to biological pathways and genes relies on stable observations. Researchers typically determine traits once, expecting careful study protocols to yield measurements free of noise. This report examines that expectation with test-retest repeatability analyses for traits used regularly in research on adaptation to high-altitude hypoxia, often in settings without climate control. METHODS: Two hundred ninety-one ethnic Tibetan women residing from 3500 to 4200 m in Upper Mustang District, Nepal, provided three observations of hemoglobin concentration, percent of oxygen saturation of hemoglobin, and pulse by noninvasive pulse oximetry under conditions designed to minimize environmental noise. RESULTS: High-intraclass correlation coefficients and low within-subject coefficients of variation reflected consistent measurements. Percent of oxygen saturation had the highest intraclass correlation coefficient and the smallest within-subject coefficient of variability; measurement noise occurred mainly in the lower values. Hemoglobin concentration and pulse presented slightly higher within-subject coefficients of variation; measurement noise occurred across the range of values. The women had performed the same measurements 7 years earlier using the same devices and protocol. The sample means and SD observed across 7 years differed little. Hemoglobin concentration increased substantially after menopause. CONCLUSIONS: Analyzing repeatability features of traits may improve our interpretation of statistical analyses and detection of variation from measurement or biology. The high levels of measurement repeatability and biological stability support the continued use of these robust traits for investigating human adaptation in this altitude range.

The genetic prehistory of the Andean highlands 7000 years BP though European contact.

The peopling of the Andean highlands above 2500 m in elevation was a complex process that included cultural, biological, and genetic adaptations. Here, we present a time series of ancient whole genomes from the Andes of Peru, dating back to 7000 calendar years before the present (BP), and compare them to 42 new genome-wide genetic variation datasets from both highland and lowland populations. We infer three significant features: a split between low- and high-elevation populations that occurred between 9200 and 8200 BP; a population collapse after European contact that is significantly more severe in South American lowlanders than in highland populations; and evidence for positive selection at genetic loci related to starch digestion and plausibly pathogen resistance after European contact. We do not find selective sweep signals related to known components of the human hypoxia response, which may suggest more complex modes of genetic adaptation to high altitude.

Detecting past and ongoing natural selection among ethnically Tibetan women at high altitude in Nepal.

Adaptive evolution in humans has rarely been characterized for its whole set of components, i.e. selective pressure, adaptive phenotype, beneficial alleles and realized fitness differential. We combined approaches for detecting polygenic adaptations and for mapping the genetic bases of physiological and fertility phenotypes in approximately 1000 indigenous ethnically Tibetan women from Nepal, adapted to high altitude. The results of genome-wide association analyses and tests for polygenic adaptations showed evidence of positive selection for alleles associated with more pregnancies and live births and evidence of negative selection for those associated with higher offspring mortality. Lower hemoglobin level did not show clear evidence for polygenic adaptation, despite its strong association with an EPAS1 haplotype carrying selective sweep signals.

Correction: A longitudinal cline characterizes the genetic structure of human populations in the Tibetan plateau.

[This corrects the article DOI: 10.1371/journal.pone.0175885.].

Antioxidant defense and oxidative damage vary widely among high-altitude residents.

OBJECTIVES: People living at high altitude experience unavoidable low oxygen levels (hypoxia). While acute hypoxia causes an increase in oxidative stress and damage despite higher antioxidant activity, the consequences of chronic hypoxia are poorly understood. The aim of the present study is to assess antioxidant activity and oxidative damage in high-altitude natives and upward migrants. METHODS: Individuals from two indigenous high-altitude populations (Amhara, n = 39), (Sherpa, n = 34), one multigenerational high-altitude population (Oromo, n = 42), one upward migrant population (Nepali, n = 12), and two low-altitude reference populations (Amhara, n = 29; Oromo, n = 18) provided plasma for measurement of superoxide dismutase (SOD) activity as a marker of antioxidant capacity, and urine for measurement of 8-hydroxy-2'-deoxyguanosine (8-OHdG) as a marker of DNA oxidative damage. RESULTS: High-altitude Amhara and Sherpa had the highest SOD activity, while highland Oromo and Nepalis had the lowest among high-altitude populations. High-altitude Amhara had the lowest DNA damage, Sherpa intermediate levels, and high-altitude Oromo had the highest. CONCLUSIONS: High-altitude residence alone does not associate with high antioxidant defenses; residence length appears to be influential. The single-generation upward migrant sample had the lowest defense and nearly the highest DNA damage. The two high-altitude resident samples with millennia of residence had higher defenses than the two with multiple or single generations of residence.

Ethnically Tibetan women in Nepal with low hemoglobin concentration have better reproductive outcomes.

Background and objectives: Tibetans have distinctively low hemoglobin concentrations at high altitudes compared with visitors and Andean highlanders. This study hypothesized that natural selection favors an unelevated hemoglobin concentration among Tibetans. It considered nonheritable sociocultural factors affecting reproductive success and tested the hypotheses that a higher percent of oxygen saturation of hemoglobin (indicating less stress) or lower hemoglobin concentration (indicating dampened response) associated with higher lifetime reproductive success. Methodology: We sampled 1006 post-reproductive ethnically Tibetan women residing at 3000-4100 m in Nepal. We collected reproductive histories by interviews in native dialects and noninvasive physiological measurements. Regression analyses selected influential covariates of measures of reproductive success: the numbers of pregnancies, live births and children surviving to age 15. Results: Taking factors such as marriage status, age of first birth and access to health care into account, we found a higher percent of oxygen saturation associated weakly and an unelevated hemoglobin concentration associated strongly with better reproductive success. Women who lost all their pregnancies or all their live births had hemoglobin concentrations significantly higher than the sample mean. Elevated hemoglobin concentration associated with a lower probability a pregnancy progressed to a live birth. Conclusions and implications: These findings are consistent with the hypothesis that unelevated hemoglobin concentration is an adaptation shaped by natural selection resulting in the relatively low hemoglobin concentration of Tibetans compared with visitors and Andean highlanders.

A longitudinal cline characterizes the genetic structure of human populations in the Tibetan plateau.

Indigenous populations of the Tibetan plateau have attracted much attention for their good performance at extreme high altitude. Most genetic studies of Tibetan adaptations have used genetic variation data at the genome scale, while genetic inferences about their demography and population structure are largely based on uniparental markers. To provide genome-wide information on population structure, we analyzed new and published data of 338 individuals from indigenous populations across the plateau in conjunction with worldwide genetic variation data. We found a clear signal of genetic stratification across the east-west axis within Tibetan samples. Samples from more eastern locations tend to have higher genetic affinity with lowland East Asians, which can be explained by more gene flow from lowland East Asia onto the plateau. Our findings corroborate a previous report of admixture signals in Tibetans, which were based on a subset of the samples analyzed here, but add evidence for isolation by distance in a broader geospatial context.

Alternative hematological and vascular adaptive responses to high-altitude hypoxia in East African highlanders.

Elevation of hemoglobin concentration, a common adaptive response to high-altitude hypoxia, occurs among Oromo but is dampened among Amhara highlanders of East Africa. We hypothesized that Amhara highlanders offset their smaller hemoglobin response with a vascular response. We tested this by comparing Amhara and Oromo highlanders at 3,700 and 4,000 m to their lowland counterparts at 1,200 and 1,700 m. To evaluate vascular responses, we assessed urinary levels of nitrate (NO3-) as a readout of production of the vasodilator nitric oxide and its downstream signal transducer cyclic guanosine monophosphate (cGMP), along with diastolic blood pressure as an indicator of vasomotor tone. To evaluate hematological responses, we measured hemoglobin and percent oxygen saturation of hemoglobin. Amhara highlanders, but not Oromo, had higher NO3- and cGMP compared with their lowland counterparts. NO3- directly correlated with cGMP (Amhara R2 = 0.25, P < 0.0001; Oromo R2 = 0.30, P < 0.0001). Consistent with higher levels of NO3- and cGMP, diastolic blood pressure was lower in Amhara highlanders. Both highland samples had apparent left shift in oxyhemoglobin saturation characteristics and maintained total oxyhemoglobin content similar to their lowland counterparts. However, deoxyhemoglobin levels were significantly higher, much more so among Oromo than Amhara. In conclusion, the Amhara balance minimally elevated hemoglobin with vasodilatory response to environmental hypoxia, whereas Oromo rely mainly on elevated hemoglobin response. These results point to different combinations of adaptive responses in genetically similar East African highlanders.

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.

Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.

Closing the Womb Door: Contraception Use and Fertility Transition Among Culturally Tibetan Women in Highland Nepal.

Objectives Whether in metropoles or remote mountain communities, the availability and adoption of contraceptive technologies prompt serious and wide-ranging biological, social, and political-economic questions. The potential shifts in women's capacities to create spaces between pregnancies or to prevent future pregnancies have profound and often positive biological, demographic, and socioeconomic implications. Less acknowledged, however, are the ambivalences that women experience around contraception use-vacillations between moral frameworks, generational difference, and gendered forms of labor that have implications well beyond the boundaries of an individual's reproductive biology. This paper hones in on contraceptive use of culturally Tibetan women in two regions of highland Nepal whose reproductive lives occurred from 1943 to 2012. Methods We describe the experiences of the 296 women (out of a study of more than 1000 women's reproductive histories) who used contraception, and under what circumstances, examining socioeconomic, geographic, and age differences as well as points of access and patterns of use. We also provide a longitudinal perspective on fertility. Results Our results relate contraception usage to fertility decline, as well as to differences in access between the two communities of women. Conclusions We argue that despite seemingly similar social ecologies of these two study sites-including stated reasons for the adoption of contraception and expressed ambivalence around its use, some of which are linked to moral and cosmological understandings that emerge from Buddhism-the dynamics of contraception uptake in these two regions are distinct, as are, therefore, patterns of fertility transition.

Global diversity, population stratification, and selection of human copy-number variation.

In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single-nucleotide-variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load.

Collecting women's reproductive histories.

The importance of women's reproductive histories for scientific questions mandates rigor in collecting data. Unfortunately, few studies say much about how histories were constructed and validated. The aim of this report, therefore, is to illustrate the elements of a rigorous system of data collection. It focuses particularly on potential sources of inaccuracy in collecting reproductive histories and on options for avoiding them and evaluating the results. A few studies are exemplary in their description of methods of data collection and evaluation of data quality because they clearly address the main issues of ascertaining whether or not an event occurred and, if so, its timing. Fundamental variables such as chronological age, live birth, or marriage may have different meanings in different cultures or communities. Techniques start with asking the appropriate people meaningful questions that they can and will answer, in suitable settings, about themselves and others. Good community relations and well-trained, aware interviewers who check and cross-check, are fundamental. A range of techniques estimate age, date events, and optimize the value of imperfect data. Robust data collection procedures rely on skillful and knowledgeable interviewing. Reliability can be improved, evaluated and explained. Researchers can plan to implement robust data collection procedures and should assess their data for the scientific community to raise confidence in reproductive history data.

Admixture facilitates genetic adaptations to high altitude in Tibet.

Admixture is recognized as a widespread feature of human populations, renewing interest in the possibility that genetic exchange can facilitate adaptations to new environments. Studies of Tibetans revealed candidates for high-altitude adaptations in the EGLN1 and EPAS1 genes, associated with lower haemoglobin concentration. However, the history of these variants or that of Tibetans remains poorly understood. Here we analyse genotype data for the Nepalese Sherpa, and find that Tibetans are a mixture of ancestral populations related to the Sherpa and Han Chinese. EGLN1 and EPAS1 genes show a striking enrichment of high-altitude ancestry in the Tibetan genome, indicating that migrants from low altitude acquired adaptive alleles from the highlanders. Accordingly, the Sherpa and Tibetans share adaptive haemoglobin traits. This admixture-mediated adaptation shares important features with adaptive introgression. Therefore, we identify a novel mechanism, beyond selection on new mutations or on standing variation, through which populations can adapt to local environments.