Genetic differences in hemoglobin function between highland and lowland deer mice

Local adaptation, plasticity, and evolved resistance to hypoxic cold stress in high-altitude deer mice

A fundamental question in evolutionary biology concerns the relative contributions of phenotypic plasticity vs. local adaptation (genotypic specialization) in enabling wide-ranging species to inhabit diverse environmental conditions. Here we conduct a long-term hypoxia acclimation experiment to assess the relative roles of local adaptation and plasticity in enabling highland and lowland deer mice (Peromyscus maniculatus) to sustain aerobic thermogenesis at progressively increasing elevations. We assessed the relative physiological performance capacities of highland and lowland natives as they were exposed to progressive, stepwise increases in hypoxia, simulating the gradual ascent from sea level to an elevation of 6000 m. The final elevation of 6000 m far exceeds the highest attainable elevations within the species' range, and therefore tests the animals' ability to tolerate levels of hypoxia that surpass the prevailing conditions within their current distributional limits. Our results demonstrate that highland natives exhibit superior thermogenic capacities at the most severe levels of hypoxia, suggesting that the species' broad fundamental niche and its ability to inhabit such a broad range of elevational zones is attributable to a combination of genetically based local adaptation and plasticity. Transcriptomic and physiological measurements identify evolved changes in the acclimation response to hypoxia that contribute to the enhanced thermogenic capacity of highland natives.

Clinical Analysis of Myocardial Injury in Highlanders with Pulmonary Hypertension

Background: Pulmonary hypertension (PH) is a prevalent adverse cardiovascular event at high-altitude environments. Prolonged exposure to high altitudes may result in myocardial injury, which is associated with poor clinical outcomes. This study aims to investigate the clinical characteristics of myocardial injury in patients with PH at high altitude. Methods: Consecutive patients admitted to a general tertiary hospital at the altitude of 3,650 m were selected into this retrospective study. Clinical and biochemical data were collected, as well as based on cardiac troponin I (cTnI) and echocardiography, patients were divided into myocardial injury group and non-myocardial injury group. Results: A total of 231 patients were enrolled, among whom 29 (12.6%) had myocardial injury. We found that body mass index, left ventricular end-diastolic dimension, and serum level of creatine kinase-MB (CK-MB) in myocardial injury group were significantly higher than non-myocardial injury group. Spearman correlation analysis revealed that cTnI has a significant positive correlation with CK-MB and lactic dehydrogenase instead of aspartate aminotransferase. A receiver operating characteristic curve was drawn to demonstrate that CK-MB could significantly predict the occurrence of myocardial injury with an area under the curve of 0.749, and a level of 3.035 (sensitivity = 59.3%, specificity = 90.5%) was optimal cutoff value. Conclusion: The incidence of myocardial injury in highlanders with PH is significant. CK-MB, as a convenient and efficient marker, has been found to be closely associated with cTnI and plays a predictive role in the occurrence of myocardial injury with PH in individuals exposed to high altitude.

Convergent High O2 Affinity but Distinct ATP-Mediated Allosteric Regulation of Hemoglobins in Oviparous and Viviparous Eremias Lizards from the Qinghai-Tibet Plateau

The functional adaptation and underlying molecular mechanisms of hemoglobins (Hbs) have primarily concentrated on mammals and birds, with few reports on reptiles. This study aimed to investigate the convergent and species-specific high-altitude adaptation mechanisms of Hbs in two Eremias lizards from the Qinghai-Tibet Plateau. The Hbs of high-altitude E. argus and E. multiocellata were characterized by significantly high overall and intrinsic Hb-O2 affinity compared to their low-altitude populations. Despite the similarly low Cl- sensitivities, the Hbs of high-altitude E. argus exhibited higher ATP sensitivity and ATP-dependent Bohr effects than that of E. multiocellata, which could facilitate O2 unloading in respiring tissues. Eremias lizards Hbs exhibited similarly low temperature sensitivities and relatively high Bohr effects at lower temperatures, which could help to stably deliver and release O2 to cold extremities at low temperatures. The oxygenation properties of Hbs in high-altitude populations might be attributed to varying ratios of β2/β1 globin and substitutions on the β2-type globin. Notably, the Asn12Ala in lowland E. argus could cause localized destabilization of the E-helix in the tetrameric Hb by elimination of hydrogen bonds, thereby resulting in its lowest O2 affinity. This study provides a valuable reference for the high-altitude adaptation mechanisms of hemoglobins in reptiles.

Plasticity and environment-specific relationships between gene expression and fitness in Saccharomyces cerevisiae

Phenotypic evolution is shaped by interactions between organisms and their environments. The environment influences how an organism's genotype determines its phenotype and how this phenotype affects its fitness. To better understand this dual role of the environment in the production and selection of phenotypic variation, we empirically determined and compared the genotype-phenotype-fitness relationship for mutant strains of the budding yeast Saccharomyces cerevisiae in four environments. Specifically, we measured how mutations in the promoter of the metabolic gene TDH3 modified its expression level and affected its growth on media with four different carbon sources. In each environment, we observed a clear relationship between TDH3 expression level and fitness, but this relationship differed among environments. Genetic variants with similar effects on TDH3 expression in different environments often had different effects on fitness and vice versa. Such environment-specific relationships between phenotype and fitness can shape the evolution of phenotypic plasticity. The set of mutants we examined also allowed us to compare the effects of mutations disrupting binding sites for key transcriptional regulators and the TATA box, which is part of the core promoter sequence. Mutations disrupting the binding sites for the transcription factors had more variable effects on expression among environments than mutations disrupting the TATA box, yet mutations with the most environmentally variable effects on fitness were located in the TATA box. This observation suggests that mutations affecting different molecular mechanisms are likely to contribute unequally to regulatory sequence evolution in changing environments.

Function of left ventricle mitochondria in highland deer mice and lowland mice

To gain insight into the mitochondrial mechanisms of hypoxia tolerance in high-altitude natives, we examined left ventricle mitochondrial function of highland deer mice compared with lowland native deer mice and white-footed mice. Highland and lowland native deer mice (Peromyscus maniculatus) and lowland white-footed mice (P. leucopus) were first-generation born and raised in common lab conditions. Adult mice were acclimated to either normoxia or hypoxia (60 kPa) equivalent to ~ 4300 m for at least 6 weeks. Left ventricle mitochondrial physiology was assessed by determining respiration in permeabilized muscle fibers with carbohydrates, lipids, and lactate as substrates. We also measured the activities of several left ventricle metabolic enzymes. Permeabilized left ventricle muscle fibers of highland deer mice showed greater rates of respiration with lactate than either lowland deer mice or white-footed mice. This was associated with higher activities of lactate dehydrogenase in tissue and isolated mitochondria in highlanders. Normoxia-acclimated highlanders also showed higher respiratory rates with palmitoyl-carnitine than lowland mice. Maximal respiratory capacity through complexes I and II was also greater in highland deer mice but only compared with lowland deer mice. Acclimation to hypoxia had little effect on respiration rates with these substrates. In contrast, left ventricle activities of hexokinase increased in both lowland and highland deer mice after hypoxia acclimation. These data suggest that highland deer mice support an elevated cardiac function in hypoxia, in part, with high ventricle cardiomyocyte respiratory capacities supported by carbohydrates, fatty acids, and lactate.

Evolved reductions in body temperature and the metabolic costs of thermoregulation in deer mice native to high altitude

The evolution of endothermy was instrumental to the diversification of birds and mammals, but the energetic demands of maintaining high body temperature could offset the advantages of endothermy in some environments. We hypothesized that reductions in body temperature help high-altitude natives overcome the metabolic challenges of cold and hypoxia in their native environment. Deer mice (Peromyscus maniculatus) from high-altitude and low-altitude populations were bred in captivity to the second generation and were acclimated as adults to warm normoxia or cold hypoxia. Subcutaneous temperature (Tsub, used as a proxy for body temperature) and cardiovascular function were then measured throughout the diel cycle using biotelemetry. Cold hypoxia increased metabolic demands, as reflected by increased food consumption and heart rate (associated with reduced vagal tone). These increased metabolic demands were offset by plastic reductions in Tsub (approx. 2°C) in response to cold hypoxia, and highlanders had lower Tsub (approx. 1°C) than lowlanders in both environmental treatments. Empirical and theoretical evidence suggested that these reductions could together reduce metabolic demands by approximately 10-30%. Therefore, plastic and evolved reductions in body temperature can help mammals overcome the metabolic challenges at high altitude and may be a valuable energy-saving strategy in some non-hibernating endotherms in extreme environments.

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.

Genetic variation in HIF-2α attenuates ventilatory sensitivity and carotid body growth in chronic hypoxia in high-altitude deer mice

KEY POINTS

High-altitude natives of many species have experienced natural selection on the gene encoding HIF-2α, Epas1, including high-altitude populations of deer mice. HIF-2α regulates ventilation and carotid body growth in hypoxia, so the genetic variants in Epas1 in high-altitude natives may underlie evolved changes in control of breathing. Deer mice from controlled crosses between high- and low-altitude populations were used to examine the effects of Epas1 genotype on an admixed genomic background. The high-altitude variant was associated with reduced ventilatory chemosensitivity and carotid body growth in chronic hypoxia, but had no effects on haematology. The results help us better understand the genetic basis for the unique physiological phenotype of high-altitude natives.

ABSTRACT

The gene encoding HIF-2α, Epas1, has experienced a history of natural selection in many high-altitude taxa, but the functional role of mutations in this gene are still poorly understood. We investigated the influence of the high-altitude variant of Epas1 in North American deer mice (Peromyscus maniculatus) on control of breathing and carotid body growth during chronic hypoxia. We created hybrids between high- and low-altitude populations of deer mice to disrupt linkages between genetic loci so physiological effects of Epas1 alleles (Epas1^H and Epas1^L , respectively) could be examined on an admixed genomic background. In general, chronic hypoxia (4 weeks at 12 kPa O₂ ) enhanced ventilatory chemosensitivity (assessed as the acute ventilatory response to hypoxia), increased total ventilation and arterial O₂ saturation during progressive poikilocapnic hypoxia, and increased haematocrit and blood haemoglobin content across genotypes. However, effects of chronic hypoxia on ventilatory chemosensitivity were attenuated in mice that were homozygous for the high-altitude Epas1 allele (Epas1^H/H ). Carotid body growth and glomus cell hyperplasia, which was strongly induced in Epas1^L/L mice in chronic hypoxia, was not observed in Epas1^H/H mice. Epas1 genotype also modulated the effects of chronic hypoxia on metabolism and body temperature depression in hypoxia, but had no effects on haematological traits. These findings confirm the important role of HIF-2α in modulating ventilatory sensitivity and carotid body growth in chronic hypoxia, and show that genetic variation in Epas1 is responsible for evolved changes in the control of breathing and metabolism in high-altitude deer mice. Abstract figure legend ventilation and carotid body growth in hypoxia, so we investigated the role genetic variants in Epas1 in highaltitude deer mice on the control of breathing. In the lab, hybrids between high- and lowaltitude populations of deer mice were created to disrupt linkages between genetic loci so physiological effects of Epas1 alleles (Epas1H and Epas1L, respectively) could be examined on an admixed genomic background. The high-altitude variant was associated with reduced ventilatory chemosensitivity and carotid body growth after 4 weeks of chronic hypoxia, compared to mice homozygous for the low-altitude allele (Epas1LL). These results help us better understand the genetic basis for the unique physiological phenotype of high-altitude natives. This article is protected by copyright. All rights reserved.

Altitude acclimatization, hemoglobin-oxygen affinity, and circulatory oxygen transport in hypoxia

In mammals and other air-breathing vertebrates that live at high altitude, adjustments in convective O₂ transport via changes in blood hemoglobin (Hb) content and/or Hb-O₂ affinity can potentially mitigate the effects of arterial hypoxemia. However, there are conflicting views about the optimal values of such traits in hypoxia, partly due to the intriguing observation that hypoxia-induced acclimatization responses in humans and other predominantly lowland mammals are frequently not aligned in the same direction as evolved phenotypic changes in high-altitude natives. Here we review relevant theoretical and empirical results and we highlight experimental studies of rodents and humans that provide insights into the combination of hematological changes that help attenuate the decline in aerobic performance in hypoxia. For a given severity of hypoxia, experimental results suggest that optimal values for hematological traits are conditional on the states of other interrelated phenotypes that govern different steps in the O₂-transport pathway.

Genetic variation in haemoglobin is associated with evolved changes in breathing in high-altitude deer mice

Physiological systems often have emergent properties but the effects of genetic variation on physiology are often unknown, which presents a major challenge to understanding the mechanisms of phenotypic evolution. We investigated whether genetic variants in haemoglobin (Hb) that contribute to high-altitude adaptation in deer mice (Peromyscus maniculatus) are associated with evolved changes in the control of breathing. We created F2 inter-population hybrids of highland and lowland deer mice to test for phenotypic associations of α- and β-globin variants on a mixed genetic background. Hb genotype had expected effects on Hb-O2 affinity that were associated with differences in arterial O2 saturation in hypoxia. However, high-altitude genotypes were also associated with breathing phenotypes that should contribute to enhancing O2 uptake in hypoxia. Mice with highland α-globin exhibited a more effective breathing pattern, with highland homozygotes breathing deeper but less frequently across a range of inspired O2, and this difference was comparable to the evolved changes in breathing pattern in deer mouse populations native to high altitude. The ventilatory response to hypoxia was augmented in mice that were homozygous for highland β-globin. The association of globin variants with variation in breathing phenotypes could not be recapitulated by acute manipulation of Hb-O2 affinity, because treatment with efaproxiral (a synthetic drug that acutely reduces Hb-O2 affinity) had no effect on breathing in normoxia or hypoxia. Therefore, adaptive variation in Hb may have unexpected effects on physiology in addition to the canonical function of this protein in circulatory O2 transport.

Adrenergic control of the cardiovascular system in deer mice native to high altitude

Studies of animals native to high altitude can provide valuable insight into physiological mechanisms and evolution of performance in challenging environments. We investigated how mechanisms controlling cardiovascular function may have evolved in deer mice (Peromyscus maniculatus) native to high altitude. High-altitude deer mice and low-altitude white-footed mice (P. leucopus) were bred in captivity at sea level, and first-generation lab progeny were raised to adulthood and acclimated to normoxia or hypoxia. We then used pharmacological agents to examine the capacity for adrenergic receptor stimulation to modulate heart rate (f_H) and mean arterial pressure (P_mean) in anaesthetized mice, and used cardiac pressure-volume catheters to evaluate the contractility of the left ventricle. We found that highlanders had a consistently greater capacity to increase f_H via pharmacological stimulation of β₁-adrenergic receptors than lowlanders. Also, whereas hypoxia acclimation reduced the capacity for increasing P_mean in response to α-adrenergic stimulation in lowlanders, highlanders exhibited no plasticity in this capacity. These differences in highlanders may help augment cardiac output during locomotion or cold stress, and may preserve their capacity for α-mediated vasoconstriction to more effectively redistribute blood flow to active tissues. Highlanders did not exhibit any differences in some measures of cardiac contractility (maximum pressure derivative, dP/dt_max, or end-systolic elastance, E_es), but ejection fraction was highest in highlanders after hypoxia acclimation. Overall, our results suggest that evolved changes in sensitivity to adrenergic stimulation of cardiovascular function may help deer mice cope with the cold and hypoxic conditions at high altitude.

•

High-altitude deer mice have evolved increased aerobic capacity in hypoxia.

•

Cardiovascular regulation was examined in normoxia and chronic hypoxia.

•

Highland mice had increased capacity for β₁-adrenergic stimulation of heart rate.

•

Hypoxia reduced vascular α-adrenergic sensitivity in lowland but not highland mice.

•

Cardiac ejection fraction was elevated in highland mice in chronic hypoxia.

Comparison of hematological traits and oxygenation properties of hemoglobins from highland and lowland Asiatic toad (Bufo gargarizans)

The Asiatic toad (Bufo gargarizans) belonging to the family of Bufonidae (Anura: Amphibia) is successfully residing on the Qinghai-Tibetan Plateau (QTP). To investigate whether the oxygen delivery undergoes adaptive adjustments to high-altitude environments in Asian toads inhabiting the QTP (Zoige County, 3446 m), choosing low-altitude populations (Chengdu City, 500 m) as control, we measured hematological traits, O₂ affinities of whole blood, Hb-O₂ affinities of purified Hbs, their sensitivities to temperature, and allosteric effectors (H⁺, Cl^- and ATP). Our results showed that high-altitude Asiatic toads possessed significantly increased hemoglobin concentration, hematocrit, and red blood cell count, but significantly decreased erythrocyte volume compared with low-altitude toads. The whole blood and purified Hbs of high-altitude Asiatic toads both exhibited significantly higher O₂ affinities compared with low-altitude toads. Substantially increased intrinsic Hb-O₂ affinities of high-altitude Asiatic toads Hbs are likely to be the main reason for its elevated Hb-O₂ affinities given the anionic cofactor sensitivities of high- and low-altitude toads were similar. The Hbs of high-altitude toads were also characterized by distinctly strong Bohr effects at the low temperature and low-temperature sensitivities. The adaptive adjustments of hematological traits could enhance the blood-O₂ carrying capacity of high-altitude Asiatic toads. The increased Hb-O₂ affinities could safeguard the pulmonary O₂ uploading under hypoxia. The strong Bohr effects at the low temperature could help the release of O₂ in metabolic tissues and cold limbs, while low-temperature sensitivity could minimize the effect of temperature fluctuation on the Hb-O₂ affinity.

Broad Concordance in the Spatial Distribution of Adaptive and Neutral Genetic Variation across an Elevational Gradient in Deer Mice

When species are continuously distributed across environmental gradients, the relative strength of selection and gene flow shape spatial patterns of genetic variation, potentially leading to variable levels of differentiation across loci. Determining whether adaptive genetic variation tends to be structured differently than neutral variation along environmental gradients is an open and important question in evolutionary genetics. We performed exome-wide population genomic analysis on deer mice sampled along an elevational gradient of nearly 4,000 m of vertical relief. Using a combination of selection scans, genotype-environment associations, and geographic cline analyses, we found that a large proportion of the exome has experienced a history of altitude-related selection. Elevational clines for nearly 30% of these putatively adaptive loci were shifted significantly up- or downslope of clines for loci that did not bear similar signatures of selection. Many of these selection targets can be plausibly linked to known phenotypic differences between highland and lowland deer mice, although the vast majority of these candidates have not been reported in other studies of highland taxa. Together, these results suggest new hypotheses about the genetic basis of physiological adaptation to high altitude, and the spatial distribution of adaptive genetic variation along environmental gradients.

Distinct Mechanisms Underlie Developmental Plasticity and Adult Acclimation of Thermogenic Capacity in High-Altitude Deer Mice

Developmental plasticity can elicit phenotypic adjustments that help organisms cope with environmental change, but the relationship between developmental plasticity and plasticity in adult life (e.g., acclimation) remains unresolved. We sought to examine developmental plasticity and adult acclimation in response to hypoxia of aerobic capacity (V̇O_2max) for thermogenesis in deer mice (Peromyscus maniculatus) native to high altitude. Deer mice were bred in captivity and exposed to normoxia or one of four hypoxia treatments (12 kPa O₂) across life stages: adult hypoxia (6–8 weeks), post-natal hypoxia (birth to adulthood), life-long hypoxia (before conception to adulthood), and parental hypoxia (mice conceived and raised in normoxia, but parents previously exposed to hypoxia). Hypoxia during perinatal development increased V̇O_2max by a much greater magnitude than adult hypoxia. The amplified effect of developmental hypoxia resulted from physiological plasticity that did not occur with adult hypoxia – namely, increases in lung ventilation and volume. Evolved characteristics of deer mice enabled developmental plasticity, because white-footed mice (P. leucopus; a congener restricted to low altitudes) could not raise pups in hypoxia. Parental hypoxia had no persistent effects on V̇O_2max. Therefore, developmental plasticity can have much stronger phenotypic effects and can manifest from distinct physiological mechanisms from adult acclimation.

Physiological insight into the evolution of complex phenotypes: aerobic performance and the O2 transport pathway of vertebrates

Evolutionary physiology strives to understand how the function and integration of physiological systems influence the way in which organisms evolve. Studies of the O2 transport pathway - the integrated physiological system that transports O2 from the environment to mitochondria - are well suited to this endeavour. We consider the mechanistic underpinnings across the O2 pathway for the evolution of aerobic capacity, focusing on studies of artificial selection and naturally selected divergence among wild populations of mammals and fish. We show that evolved changes in aerobic capacity do not require concerted changes across the O2 pathway and can arise quickly from changes in one or a subset of pathway steps. Population divergence in aerobic capacity can be associated with the evolution of plasticity in response to environmental variation or activity. In some cases, initial evolutionary divergence of aerobic capacity arose exclusively from increased capacities for O2 diffusion and/or utilization in active O2-consuming tissues (muscle), which may often constitute first steps in adaptation. However, continued selection leading to greater divergence in aerobic capacity is often associated with increased capacities for circulatory and pulmonary O2 transport. Increases in tissue O2 diffusing capacity may augment the adaptive benefit of increasing circulatory O2 transport owing to their interactive influence on tissue O2 extraction. Theoretical modelling of the O2 pathway suggests that O2 pathway steps with a disproportionately large influence over aerobic capacity have been more likely to evolve, but more work is needed to appreciate the extent to which such physiological principles can predict evolutionary outcomes.

Introgressive Hybridization and Hypoxia Adaptation in High-Altitude Vertebrates

In natural populations of animals, a growing body of evidence suggests that introgressive hybridization may often serve as an important source of adaptive genetic variation. Population genomic studies of high-altitude vertebrates have provided strong evidence of positive selection on introgressed allelic variants, typically involving a long-term highland species as the donor and a more recently arrived colonizing species as the recipient. In high-altitude humans and canids from the Tibetan Plateau, case studies of adaptive introgression involving the HIF transcription factor, EPAS1, have provided insights into complex histories of ancient introgression, including examples of admixture from now-extinct source populations. In Tibetan canids and Andean waterfowl, directed mutagenesis experiments involving introgressed hemoglobin variants successfully identified causative amino acid mutations and characterized their phenotypic effects, thereby providing insights into the functional properties of selectively introgressed alleles. We review case studies of adaptive introgression in high-altitude vertebrates and we highlight findings that may be of general significance for understanding mechanisms of environmental adaptation involving different sources of genetic variation.

The adaptive benefit of evolved increases in hemoglobin-O2 affinity is contingent on tissue O2 diffusing capacity in high-altitude deer mice

BACKGROUND

Complex organismal traits are often the result of multiple interacting genes and sub-organismal phenotypes, but how these interactions shape the evolutionary trajectories of adaptive traits is poorly understood. We examined how functional interactions between cardiorespiratory traits contribute to adaptive increases in the capacity for aerobic thermogenesis (maximal O₂ consumption, V̇O₂max, during acute cold exposure) in high-altitude deer mice (Peromyscus maniculatus). We crossed highland and lowland deer mice to produce F₂ inter-population hybrids, which expressed genetically based variation in hemoglobin (Hb) O₂ affinity on a mixed genetic background. We then combined physiological experiments and mathematical modeling of the O₂ transport pathway to examine the links between cardiorespiratory traits and V̇O₂max.

RESULTS

Physiological experiments revealed that increases in Hb-O₂ affinity of red blood cells improved blood oxygenation in hypoxia but were not associated with an enhancement in V̇O₂max. Sensitivity analyses performed using mathematical modeling showed that the influence of Hb-O₂ affinity on V̇O₂max in hypoxia was contingent on the capacity for O₂ diffusion in active tissues.

CONCLUSIONS

These results suggest that increases in Hb-O₂ affinity would only have adaptive value in hypoxic conditions if concurrent with or preceded by increases in tissue O₂ diffusing capacity. In high-altitude deer mice, the adaptive benefit of increasing Hb-O₂ affinity is contingent on the capacity to extract O₂ from the blood, which helps resolve controversies about the general role of hemoglobin function in hypoxia tolerance.

Commentary: Hierarchical reductionism approach to understanding adaptive variation in animal performance

Aerobic capacity is a complex performance trait with important consequences for fitness, and is determined by the integrated function of the O₂ transport pathway. The components of the O₂ pathway interact and function as an integrated physiological system, which could strongly influence the contribution of each component to variation in aerobic capacity. In this commentary, we highlight the value of hierarchical reductionism - combining studies of how component parts work in isolation with studies of how components interact within integrated systems - for understanding the evolution of aerobic capacity. This is achieved by focussing on the role of haemoglobin in adaptive increases in aerobic capacity in high-altitude deer mice (Peromyscus maniculatus). High-altitude deer mice have evolved increased aerobic capacity in hypoxia, in association with evolved changes in several subordinate traits across the O₂ pathway. This includes an evolved increase in Hb-O₂ affinity - which helps safeguard arterial O₂ saturation in hypoxia - and reductionist approaches have been successful at identifying the genetic, structural, and biochemical underpinnings of variation in this trait. However, theoretical modelling and empirical measurements suggest that increased Hb-O₂ affinity may not augment aerobic capacity on its own. The adaptive benefit of increased Hb-O₂ affinity in high-altitude deer mice appears to have been contingent upon antecedent changes in other traits in the O₂ pathway, particularly an increased capacity for O₂ diffusion and utilization in active tissues. These findings highlight the importance of understanding the interactions between the components of integrated systems for fully appreciating the evolution of complex performance phenotypes.

Limited Evidence for Parallel Evolution Among Desert-Adapted Peromyscus Deer Mice

Warming climate and increasing desertification urge the identification of genes involved in heat and dehydration tolerance to better inform and target biodiversity conservation efforts. Comparisons among extant desert-adapted species can highlight parallel or convergent patterns of genome evolution through the identification of shared signatures of selection. We generate a chromosome-level genome assembly for the canyon mouse (Peromyscus crinitus) and test for a signature of parallel evolution by comparing signatures of selective sweeps across population-level genomic resequencing data from another congeneric desert specialist (Peromyscus eremicus) and a widely distributed habitat generalist (Peromyscus maniculatus), that may be locally adapted to arid conditions. We identify few shared candidate loci involved in desert adaptation and do not find support for a shared pattern of parallel evolution. Instead, we hypothesize divergent molecular mechanisms of desert adaptation among deer mice, potentially tied to species-specific historical demography, which may limit or enhance adaptation. We identify a number of candidate loci experiencing selective sweeps in the P. crinitus genome that are implicated in osmoregulation (Trypsin, Prostasin) and metabolic tuning (Kallikrein, eIF2-alpha kinase GCN2, APPL1/2), which may be important for accommodating hot and dry environmental conditions.

High-Altitude Adaptation: Mechanistic Insights from Integrated Genomics and Physiology

Population genomic analyses of high-altitude humans and other vertebrates have identified numerous candidate genes for hypoxia adaptation, and the physiological pathways implicated by such analyses suggest testable hypotheses about underlying mechanisms. Studies of highland natives that integrate genomic data with experimental measures of physiological performance capacities and subordinate traits are revealing associations between genotypes (e.g., hypoxia-inducible factor gene variants) and hypoxia-responsive phenotypes. The subsequent search for causal mechanisms is complicated by the fact that observed genotypic associations with hypoxia-induced phenotypes may reflect second-order consequences of selection-mediated changes in other (unmeasured) traits that are coupled with the focal trait via feedback regulation. Manipulative experiments to decipher circuits of feedback control and patterns of phenotypic integration can help identify causal relationships that underlie observed genotype–phenotype associations. Such experiments are critical for correct inferences about phenotypic targets of selection and mechanisms of adaptation.

Effect of NH2-terminal acetylation on the oxygenation properties of vertebrate haemoglobin

In vertebrate haemoglobin (Hb), the NH2-terminal residues of the α- and β-chain subunits are thought to play an important role in the allosteric binding of protons (Bohr effect), CO2 (as carbamino derivatives), chloride ions, and organic phosphates. Accordingly, acetylation of the α- and/or β-chain NH2-termini may have significant effects on the oxygenation properties of Hb. Here we investigate the effect of NH2-terminal acetylation by using a newly developed expression plasmid system that enables us to compare recombinantly expressed Hbs that are structurally identical except for the presence or absence of NH2-terminal acetyl groups. Experiments with native and recombinant Hbs of representative vertebrates reveal that NH2-terminal acetylation does not impair the Bohr effect, nor does it significantly diminish responsiveness to allosteric cofactors, such as chloride ions or organic phosphates. These results suggest that observed variation in the oxygenation properties of vertebrate Hbs is principally explained by amino acid divergence in the constituent globin chains rather than post-translational modifications of the globin chain NH2-termini.

Physiological Genomics of Adaptation to High-Altitude Hypoxia

Population genomic studies of humans and other animals at high altitude have generated many hypotheses about the genes and pathways that may have contributed to hypoxia adaptation. Future advances require experimental tests of such hypotheses to identify causal mechanisms. Studies to date illustrate the challenge of moving from lists of candidate genes to the identification of phenotypic targets of selection, as it can be difficult to determine whether observed genotype-phenotype associations reflect causal effects or secondary consequences of changes in other traits that are linked via homeostatic regulation. Recent work on high-altitude models such as deer mice has revealed both plastic and evolved changes in respiratory, cardiovascular, and metabolic traits that contribute to aerobic performance capacity in hypoxia, and analyses of tissue-specific transcriptomes have identified changes in regulatory networks that mediate adaptive changes in physiological phenotype. Here we synthesize recent results and discuss lessons learned from studies of high-altitude adaptation that lie at the intersection of genomics and physiology.

Control of Oxygen Affinity in Mammalian Hemoglobins: Implications for a System Biology Description of the Respiratory Properties of the Red Blood Cell

Hemoglobin and myoglobin have been considered for a long time the paradigmatic model systems for protein function, to the point of being defined the "hydrogen atom[s] of biology". Given this privileged position and the huge amount of quantitative information available on these proteins, the red blood cell might appear as the model system and"hydrogen atom" of system biology. Indeed, since the red cell's main function is O2 transport by hemoglobin, the gap between the protein and the cell may appear quite small. Yet, a surprisingly large amount of detailed biochemical information is required for the modelization of the respiratory properties of the erythrocyte. This problem is compounded if modelization aims at uncovering or explaining evolutionarily selected functional properties of hemoglobin. The foremost difficulty lies in the fact that hemoglobins having different intrinsic properties and relatively ancient evolutionary divergence may behave similarly in the complex milieu of blood, whereas very similar hemoglobins sharing a substantial sequence similarity may present important functional differences because of the mutation of a few key residues. Thus, the functional properties of hemoglobin and blood may reflect more closely the recent environmental challenges than the remote evolutionary history of the animal. We summarize in this review the case of hemoglobins from mammals, in an attempt to provide a reasoned summary of their complexity that, we hope, may be of help to scientists interested in the quantitative exploration of the evolutionary physiology of respiration. Indeed the basis of a meaningful modelization of the red cell requires a large amount of information collected in painstaking and often forgotten studies of the biochemical properties of hemoglobin carried out over more than a century.

Life-long exposure to hypoxia affects metabolism and respiratory physiology across life stages in high-altitude deer mice (Peromyscus maniculatus)

Hypoxia exposure can have distinct physiological effects between early developmental and adult life stages, but it is unclear how the effects of hypoxia may progress during continuous exposure throughout life. We examined this issue in deer mice (Peromyscus maniculatus) from a population native to high altitude. Mice were bred in captivity in one of three treatment groups: normoxia (controls), life-long hypoxia (∼12 kPa O₂ from conception to adulthood) and parental hypoxia (normoxia from conception to adulthood, but parents previously exposed to hypoxia). Metabolic, thermoregulatory and ventilatory responses to progressive stepwise hypoxia and haematology were then measured at post-natal day (P) 14 and 30 and/or in adulthood. Life-long hypoxia had consistent effects across ages on metabolism, attenuating the declines in O₂ consumption rate (V̇ _O2 ) and body temperature during progressive hypoxia compared with control mice. However, life-long hypoxia had age-specific effects on breathing, blunting the hypoxia-induced increases in air convection requirement (quotient of total ventilation and V̇ _O2 ) at P14 and P30 only, but then shifting breathing pattern towards deeper and/or less frequent breaths at P30 and adulthood. Hypoxia exposure also increased blood-O₂ affinity at P14 and P30, in association with an increase in arterial O₂ saturation in hypoxia at P30. In contrast, parental hypoxia had no effects on metabolism or breathing, but it increased blood-O₂ affinity and decreased red cell haemoglobin content at P14 (but not P30). Therefore, hypoxia exposure has some consistent effects across early life and adulthood, and some other effects that are unique to specific life stages.

Developmental and reproductive physiology of small mammals at high altitude: challenges and evolutionary innovations

High-altitude environments, characterized by low oxygen levels and low ambient temperatures, have been repeatedly colonized by small altricial mammals. These species inhabit mountainous regions year-round, enduring chronic cold and hypoxia. The adaptations that allow small mammals to thrive at altitude have been well studied in non-reproducing adults; however, our knowledge of adaptations specific to earlier life stages and reproductive females is extremely limited. In lowland natives, chronic hypoxia during gestation affects maternal physiology and placental function, ultimately limiting fetal growth. During post-natal development, hypoxia and cold further limit growth both directly by acting on neonatal physiology and indirectly via impacts on maternal milk production and care. Although lowland natives can survive brief sojourns to even extreme high altitude as adults, reproductive success in these environments is very low, and lowland young rarely survive to sexual maturity in chronic cold and hypoxia. Here, we review the limits to maternal and offspring physiology - both pre-natal and post-natal - that highland-adapted species have overcome, with a focus on recent studies on high-altitude populations of the North American deer mouse (Peromyscus maniculatus). We conclude that a combination of maternal and developmental adaptations were likely to have been critical steps in the evolutionary history of high-altitude native mammals.

Adaptive evolution of β-globin gene in subterranean in South America octodontid rodents

The convergent evolution of subterranean rodents is an excellent model to study how natural selection operates and the genetic bases of these adaptations, but the study on the different taxa has been very uneven and still insufficient. In the octodontoid caviomorph rodent superfamily there are two independent lineages where they have recently evolved into totally underground lifestyles: the genera Ctenomys (tuco-tucos) and Spalacopus (coruro). The underground habitat is characterized by an hypoxic and hypercapnic atmosphere, thus gas exchange is one of the most important challenges for these animals. The invasion of the underground niche could have modified the selective regimes of proteins involved in the respiration and transport of O₂ of these rodents, positively selecting mutations of higher affinity for O₂. Here we examine the sequence variation in the beta globin gene in these two lineages, within a robust phylogenetic context. Using different approaches (classical and Bayesian maximum likelihood (PAML/Datamonkey) and alternatives methods (TreeSAAP)) we found at least three sites with evidence of positive selection in underground lineages, especially the basal branch that leads to the Octodontidae family and the branch that leads to the coruro, suggesting some adaptive changes to the underground life. We also found a convergence with another underground rodent, which cannot be identified by the above methods.

Biochemical pedomorphosis and genetic assimilation in the hypoxia adaptation of Tibetan antelope

Developmental shifts in stage-specific gene expression can provide a ready mechanism of phenotypic change by altering the rate or timing of ontogenetic events. We found that the high-altitude Tibetan antelope (Panthelops hodgsonii) has evolved an adaptive increase in blood-O2 affinity by truncating the ancestral ontogeny of globin gene expression such that a high-affinity juvenile hemoglobin isoform (isoHb) completely supplants the lower-affinity isoHb that is expressed in the adult red blood cells of other bovids. This juvenilization of blood properties represents a canalization of an acclimatization response to hypoxia that has been well documented in adult goats and sheep. We also found the genomic mechanism underlying this regulatory isoHb switch, revealing how a reversible acclimatization response became genetically assimilated as an irreversible adaptation to chronic hypoxia.

Coordinated changes across the O2 transport pathway underlie adaptive increases in thermogenic capacity in high-altitude deer mice

Animals native to the hypoxic and cold environment at high altitude provide an excellent opportunity to elucidate the integrative mechanisms underlying the adaptive evolution and plasticity of complex traits. The capacity for aerobic thermogenesis can be a critical determinant of survival for small mammals at high altitude, but the physiological mechanisms underlying the evolution of this performance trait remain unresolved. We examined this issue by comparing high-altitude deer mice (Peromyscus maniculatus) with low-altitude deer mice and white-footed mice (P. leucopus). Mice were bred in captivity and adults were acclimated to each of four treatments: warm (25°C) normoxia, warm hypoxia (12 kPa O2), cold (5°C) normoxia or cold hypoxia. Acclimation to hypoxia and/or cold increased thermogenic capacity in deer mice, but hypoxia acclimation led to much greater increases in thermogenic capacity in highlanders than in lowlanders. The high thermogenic capacity of highlanders was associated with increases in pulmonary O2 extraction, arterial O2 saturation, cardiac output and arterial-venous O2 difference. Mechanisms underlying the evolution of enhanced thermogenic capacity in highlanders were partially distinct from those underlying the ancestral acclimation responses of lowlanders. Environmental adaptation has thus enhanced phenotypic plasticity and expanded the physiological toolkit for coping with the challenges at high altitude.

Evolution of Hemoglobin Genes in a Subterranean Rodent Species (Lasiopodomys mandarinus)

The Mandarin vole (Lasiopodomys mandarinus), a typical subterranean rodent, has undergone hematological adaptations to tolerate the hypoxic/hypercapnic underground environment. Hemoglobin (Hb) genes encode respiratory proteins functioning principally in oxygen binding and transport to various tissues and organs. To investigate the evolution of α- and β-hemoglobin (Hb) in subterranean rodent species, we sequenced Hb genes of the Mandarin vole and the related aboveground Brandt's vole (L. brandtii). Sequencing showed that in both voles, α-globin was encoded by a cluster of five functional genes in the following linkage order: HBZ, HBA-T1, HBQ-T1, HBA-T2, and HBQ-T2; among these, HBQ-T2 is a pseudogene in both voles. The β-globin gene cluster in both voles also included five functional genes in the following linkage order: HBE, HBE/HBG, HBG, HBB-T1, and HBB-T2. Phylogenetic analysis revealed that the Mandarin vole underwent convergent evolution with its related aboveground species (Brandt's vole) but not with other subterranean rodent species. Selection pressure analyses revealed that α- and β-globin genes are under strong purifying selection (ω < 1), and branch-site analyses identified positive selection sites on HBAT-T1 and HBB-T1 in different subterranean rodent species. This suggests that the adaptive evolution of these genes enhanced the ability of Hb to store and transport oxygen in subterranean rodent species. Our findings highlight the critical roles of Hb genes in the evolution of hypoxia tolerance in subterranean rodent species.

Ontogenesis of evolved changes in respiratory physiology in deer mice native to high altitude

High-altitude environments are cold and hypoxic, and many high-altitude natives have evolved changes in respiratory physiology that improve O2 uptake in hypoxia as adults. Altricial mammals undergo a dramatic metabolic transition from ectothermy to endothermy in early post-natal life, which may influence the ontogenetic development of respiratory traits at high altitude. We examined the developmental changes in respiratory and haematological traits in deer mice (Peromyscus maniculatus) native to high altitude, comparing the respiratory responses to progressive hypoxia between highland and lowland deer mice. Among adults, highlanders exhibited higher total ventilation and a more effective breathing pattern (relatively deeper tidal volumes), for mice that were caught and tested at their native altitudes and those lab-raised in normoxia. Lab-raised progeny of each population were also tested at post-natal day (P)7, 14, 21 and 30. Highlanders developed an enhanced hypoxic ventilatory response by P21, concurrent with the full maturation of the carotid bodies, and their more effective breathing pattern arose by P14; these ages correspond to critical benchmarks in the full development of homeothermy in highlanders. However, highlanders exhibited developmental delays in ventilatory sensitivity to hypoxia, hyperplasia of type I cells in the carotid body and increases in blood haemoglobin content compared with lowland mice. Nevertheless, highlanders maintained consistently higher arterial O2 saturation in hypoxia across development, in association with increases in blood-O2 affinity that were apparent from birth. We conclude that evolved changes in respiratory physiology in high-altitude deer mice become expressed in association with the post-natal development of endothermy.

Oxygenation properties of hemoglobin and the evolutionary origins of isoform multiplicity in an amphibious air-breathing fish, the blue-spotted mudskipper (Boleophthalmus pectinirostris)

Among the numerous lineages of teleost fish that have independently transitioned from obligate water breathing to facultative air breathing, evolved properties of hemoglobin (Hb)-O₂ transport may have been shaped by the prevalence and severity of aquatic hypoxia (which influences the extent to which fish are compelled to switch to aerial respiration) as well as the anatomical design of air-breathing structures and the cardiovascular system. Here, we examined the structure and function of Hbs in an amphibious, facultative air-breathing fish, the blue-spotted mudskipper (Boleophthalmus pectinirostris). We also characterized the genomic organization of the globin gene clusters of the species and we integrated phylogenetic and comparative genomic analyses to unravel the duplicative history of the genes that encode the subunits of structurally distinct mudskipper Hb isoforms (isoHbs). The B. pectinirostris isoHbs exhibit high intrinsic O₂ affinities, similar to those of hypoxia-tolerant, water-breathing teleosts, and remarkably large Bohr effects. Genomic analysis of conserved synteny revealed that the genes that encode the α-type subunits of the two main adult isoHbs are members of paralogous gene clusters that represent products of the teleost-specific whole-genome duplication. Experiments revealed no appreciable difference in the oxygenation properties of co-expressed isoHbs in spite of extensive amino acid divergence between the alternative α-chain subunit isoforms. It therefore appears that the ability to switch between aquatic and aerial respiration does not necessarily require a division of labor between functionally distinct isoHbs with specialized oxygenation properties.

Adaptive Changes in Hemoglobin Function in High-Altitude Tibetan Canids Were Derived via Gene Conversion and Introgression

A key question in evolutionary biology concerns the relative importance of different sources of adaptive genetic variation, such as de novo mutations, standing variation, and introgressive hybridization. A corollary question concerns how allelic variants derived from these different sources may influence the molecular basis of phenotypic adaptation. Here, we use a protein-engineering approach to examine the phenotypic effect of putatively adaptive hemoglobin (Hb) mutations in the high-altitude Tibetan wolf that were selectively introgressed into the Tibetan mastiff, a high-altitude dog breed that is renowned for its hypoxia tolerance. Experiments revealed that the introgressed coding variants confer an increased Hb–O₂ affinity in conjunction with an enhanced Bohr effect. We also document that affinity-enhancing mutations in the β-globin gene of Tibetan wolf were originally derived via interparalog gene conversion from a tandemly linked β-globin pseudogene. Thus, affinity-enhancing mutations were introduced into the β-globin gene of Tibetan wolf via one form of intragenomic lateral transfer (ectopic gene conversion) and were subsequently introduced into the Tibetan mastiff genome via a second form of lateral transfer (introgression). Site-directed mutagenesis experiments revealed that the increased Hb–O₂ affinity requires a specific two-site combination of amino acid replacements, suggesting that the molecular underpinnings of Hb adaptation in Tibetan mastiff (involving mutations that arose in a nonexpressed gene and which originally fixed in Tibetan wolf) may be qualitatively distinct from functionally similar changes in protein function that could have evolved via sequential fixation of de novo mutations during the breed’s relatively short duration of residency at high altitude.

Physiological and genomic evidence that selection on the transcription factor Epas1 has altered cardiovascular function in high-altitude deer mice

Evolutionary adaptation to extreme environments often requires coordinated changes in multiple intersecting physiological pathways, but how such multi-trait adaptation occurs remains unresolved. Transcription factors, which regulate the expression of many genes and can simultaneously alter multiple phenotypes, may be common targets of selection if the benefits of induced changes outweigh the costs of negative pleiotropic effects. We combined complimentary population genetic analyses and physiological experiments in North American deer mice (Peromyscus maniculatus) to examine links between genetic variation in transcription factors that coordinate physiological responses to hypoxia (hypoxia-inducible factors, HIFs) and multiple physiological traits that potentially contribute to high-altitude adaptation. First, we sequenced the exomes of 100 mice sampled from different elevations and discovered that several SNPs in the gene Epas1, which encodes the oxygen sensitive subunit of HIF-2α, exhibited extreme allele frequency differences between highland and lowland populations. Broader geographic sampling confirmed that Epas1 genotype varied predictably with altitude throughout the western US. We then discovered that Epas1 genotype influences heart rate in hypoxia, and the transcriptomic responses to hypoxia (including HIF targets and genes involved in catecholamine signaling) in the heart and adrenal gland. Finally, we used a demographically-informed selection scan to show that Epas1 variants have experienced a history of spatially varying selection, suggesting that differences in cardiovascular function and gene regulation contribute to high-altitude adaptation. Our results suggest a mechanism by which Epas1 may aid long-term survival of high-altitude deer mice and provide general insights into the role that highly pleiotropic transcription factors may play in the process of environmental adaptation.

Oxygenation properties and underlying molecular mechanisms of hemoglobins in plateau zokor (Eospalax baileyi)

The plateau zokor (Eospalax baileyi) is a species of subterranean rodent endemic to the Tibetan Plateau. It is well adapted to the cold and hypoxic and hypercapnic burrow. To study the oxygenation properties of plateau zokor hemoglobins (Hbs), we measured intrinsic Hb-O₂ affinities and their sensitivities to pH (Bohr effect); CO₂; Cl^-, 2,3-diphosphoglycerate (DPG); and temperature using purified Hbs from zokor and mouse. The optimal deoxyHb model of plateau zokor was constructed and used to study its structural characteristics by molecular dynamics simulations. O₂ binding results revealed that plateau zokor Hbs exhibit remarkably high intrinsic Hb-O₂ affinity, low CO₂ effects compared with human and the relatively low anion allosteric effector sensitivities (DPG and Cl^-) at normal temperature, which would safeguard the pulmonary Hb-O₂ loading under hypoxic and hypercapnic conditions. Furthermore, the high anion allosteric effector sensitivities at low temperature and low temperature sensitivities of plateau zokor Hbs would facilitate the releasing of O₂ in cold extremities and metabolic tissues. However, the high Hb-O₂ affinity of plateau zokor is not compensated by high pH sensitivity as the Bohr factors of plateau zokor Hbs were as low as those of mouse. The results of molecular dynamics simulations revealed the reduced hydrogen bonding between the α1β1- and α2β2-dimer interface of deoxyHb in zokor compared with mouse. It may be the primary mechanism of the high intrinsic Hb-O₂ affinities in zokor. Specifically, substitution of the 131Ser→Asn in the α2-chain weakened the connection between α1- and β2-subunit.

Life Ascending: Mechanism and Process in Physiological Adaptation to High-Altitude Hypoxia

To cope with the reduced availability of O₂ at high altitude, air-breathing vertebrates have evolved myriad adjustments in the cardiorespiratory system to match tissue O₂ delivery with metabolic O₂ demand. We explain how changes at interacting steps of the O₂ transport pathway contribute to plastic and evolved changes in whole-animal aerobic performance under hypoxia. In vertebrates native to high altitude, enhancements of aerobic performance under hypoxia are attributable to a combination of environmentally induced and evolved changes in multiple steps of the pathway. Additionally, evidence suggests that many high-altitude natives have evolved mechanisms for attenuating maladaptive acclimatization responses to hypoxia, resulting in counter-gradient patterns of altitudinal variation for key physiological phenotypes. For traits that exhibit counteracting environmental and genetic effects, evolved changes in phenotype may be cryptic under field conditions and can only be revealed by rearing representatives of high-and low-altitude populations under standardized environmental conditions to control for plasticity.

The Genome Landscape of Tibetan Sheep Reveals Adaptive Introgression from Argali and the History of Early Human Settlements on the Qinghai-Tibetan Plateau

Tibetan sheep are the most common and widespread domesticated animals on the Qinghai-Tibetan Plateau (QTP) and have played an essential role in the permanent human occupation of this high-altitude region. However, the precise timing, route, and process of sheep pastoralism in the QTP region remain poorly established, and little is known about the underlying genomic changes that occurred during the process. Here, we investigate the genomic variation in Tibetan sheep using whole-genome sequences, single nucleotide polymorphism arrays, mitochondrial DNA, and Y-chromosomal variants in 986 samples throughout their distribution range. We detect strong signatures of selection in genes involved in the hypoxia and ultraviolet signaling pathways (e.g., HIF-1 pathway and HBB and MITF genes) and in genes associated with morphological traits such as horn size and shape (e.g., RXFP2). We identify clear signals of argali (Ovis ammon) introgression into sympatric Tibetan sheep, covering 5.23-5.79% of their genomes. The introgressed genomic regions are enriched in genes related to oxygen transportation system, sensory perception, and morphological phenotypes, in particular the genes HBB and RXFP2 with strong signs of adaptive introgression. The spatial distribution of genomic diversity and demographic reconstruction of the history of Tibetan sheep show a stepwise pattern of colonization with their initial spread onto the QTP from its northeastern part ∼3,100 years ago, followed by further southwest expansion to the central QTP ∼1,300 years ago. Together with archeological evidence, the date and route reveal the history of human expansions on the QTP by the Tang-Bo Ancient Road during the late Holocene. Our findings contribute to a depth understanding of early pastoralism and the local adaptation of Tibetan sheep as well as the late-Holocene human occupation of the QTP.

Evolution of physiological performance capacities and environmental adaptation: insights from high-elevation deer mice (Peromyscus maniculatus)

Analysis of variation in whole-animal performance can shed light on causal connections between specific traits, integrated physiological capacities, and Darwinian fitness. Here, we review and synthesize information on naturally occurring variation in physiological performance capacities and how it relates to environmental adaptation in deer mice (Peromyscus maniculatus). We discuss how evolved changes in aerobic exercise capacity and thermogenic capacity have contributed to adaptation to high elevations. Comparative work on deer mice at high and low elevations has revealed evolved differences in aerobic performance capacities in hypoxia. Highland deer mice have consistently higher aerobic performance capacities under hypoxia relative to lowland natives, consistent with the idea that it is beneficial to have a higher maximal metabolic rate (as measured by the maximal rate of O₂ consumption, VO_2max) in an environment characterized by lower air temperatures and lower O₂ availability. Observed differences in aerobic performance capacities between highland and lowland deer mice stem from changes in numerous subordinate traits that alter the flux capacity of the O₂-transport system, the oxidative capacity of tissue mitochondria, and the relationship between O₂ consumption and ATP synthesis. Many such changes in physiological phenotype are associated with hypoxia-induced changes in gene expression. Research on natural variation in whole-animal performance forms a nexus between physiological ecology and evolutionary biology that requires insight into the natural history of the study species.

Remodeling Ancestral Phenotypic Plasticity in Local Adaptation: A New Framework to Explore the Role of Genetic Compensation in the Evolution of Homeostasis

Phenotypic plasticity is not universally adaptive. In certain cases, plasticity can result in phenotypic shifts that reduce fitness relative to the un-induced state. A common cause of such maladaptive plasticity is the co-option of ancestral developmental and physiological response systems to meet novel challenges. Because these systems evolved to meet specific challenges in an ancestral environment (e.g., localized and transient hypoxia), their co-option to meet a similar, but novel, stressor (e.g., reductions in ambient pO2 at high elevation) can lead to misdirected responses that reduce fitness. In such cases, natural selection should act to remodel phenotypic plasticity to suppress the expression of these maladaptive responses. Because these maladaptive responses reduce the fitness of colonizers in new environments, this remodeling of ancestral plasticity may be among the earliest steps in adaptive walks toward new local optima. Genetic compensation has been proposed as a general form of adaptive evolution that leads to the suppression of maladaptive plasticity to restore the ancestral trait value in the face of novel stimuli. Given their central role in the regulation of basic physiological functions, we argue that genetic compensation may often be achieved by modifications of homeostatic regulatory systems. We further suggest that genetic compensation to modify homeostatic systems can be achieved by two alternative strategies that differ in their mechanistic underpinnings; to our knowledge, these strategies have not been formally recognized by previous workers. We then consider how the mechanistic details of these alternative strategies may constrain their evolution. These considerations lead us to argue that genetic compensation is most likely to evolve by compensatory physiological changes that safeguard internal homeostatic conditions to prevent the expression of maladaptive portions of conserved reaction norms, rather than direct evolution of plasticity itself. Finally, we outline a simple experimental framework to test this hypothesis. Our goal is to stimulate research aimed at providing a deeper mechanistic understanding of whether and how phenotypic plasticity can be remodeled following environmental shifts that render ancestral responses maladaptive, an issue with increasing importance in our current era of rapid environmental change.

Genome-Wide Microarray Analysis Suggests Transcriptomic Response May Not Play a Major Role in High- to Low-Altitude Acclimation in Harvest Mouse (Micromys minutus)

Simple Summary

Micromys minutus is a small rodent species that has a wide range of vertical distribution in Taiwan. By comparing the gene expression profile of the skeletal muscle tissues taken from individuals native to the high-altitude environment and those transferred to the low-altitude captive site, the Tnfrsf12a gene was demonstrated to have a differential expression pattern. Although this finding may be correlated with the altitude acclimation, the observation of only one gene transcript with significant alteration leads us to suggest that genetic response may not play a major role in altitude acclimation in M. minutus. Future comparative functional genomics studies involving other organ systems (in addition to skeletal muscles) and alarger sample size are warranted for better insight into the altitude acclimation of this small rodent species.

Abstract

The harvest mouse (Micromys minutus) is a small rodent species with a wide range of vertical distribution in Taiwan, extending from the sea level to 3100 m altitude. This species has recently suffered from habitat loss in high-altitude areas due to orchard cultivation, which may have resulted in mouse migration from high to low altitude. To investigate whether there is any physiological mechanism involved in altitude acclimation, rat cDNA microarray was used to compare transcriptomic patterns of the skeletal muscle tissues taken from individuals native to the high-altitude environment and those transferred to the low-altitude captive site. Of the 23,188 genes being analyzed, 47 (33 up-regulated and 14 down-regulated) were found to have differential expression (fold change > 4 or < −4, ANOVA p < 0.05). However, after multiple testing correction with a false discovery rate (FDR), only the result for Tnfrsf12a was found to be statistically significant (fold change = 13, FDR p < 0.05). The result was confirmed by quantitative polymerase chain reaction (q-PCR). The expression of Tnfrsf12a possibly relates to the skeletal muscle biology and thus can be correlated with altitude acclimation. However, finding only one gene transcript with significant alteration suggests that transcriptomic response may not play a major role in high- to low-altitude acclimation in harvest mouse.

Acclimatization of low altitude-bred deer mice ( Peromyscus maniculatus) to high altitude

A colony of deer mice subspecies ( Peromyscus maniculatus sonoriensis) native to high altitude (HA) has been maintained at sea level for 18-20 generations and remains genetically unchanged. To determine if these animals retain responsiveness to hypoxia, one group (9-11 wk old) was acclimated to HA (3,800 m) for 8 wk. Age-matched control animals were acclimated to a lower altitude (LA; 252 m). Maximal O₂ uptake (V̇o_2max) was measured at the respective altitudes. On a separate day, lung volume, diffusing capacity for carbon monoxide (DL_CO), and pulmonary blood flow were measured under anesthesia using a rebreathing technique at two inspired O₂ tensions. The HA-acclimated deer mice maintained a normal V̇o_2max relative to LA baseline. Compared with LA control mice, antemortem lung volume was larger in HA mice in a manner dependent on alveolar O₂ tension. Systemic hematocrit, pulmonary blood flow, and standardized DL_CO did not differ significantly between groups. HA mice showed a higher postmortem alveolar-capillary hematocrit, larger alveolar ducts, and smaller distal conducting structures. In HA mice, absolute volumes of alveolar type I epithelia and endothelia were higher whereas that of interstitia was lower than in LA mice. These structural changes occurred without a net increase in whole-lung septal tissue-capillary volumes or surface areas. Thus, deer mice bred and raised to adulthood at LA retain phenotypic plasticity and adapt to HA without a decrement in V̇o_2max via structural (enlarged airspaces, alveolar septal remodeling) and nonstructural (lung expansion under hypoxia) mechanisms and without an increase in systemic hematocrit or compensatory lung growth. NEW & NOTEWORTHY Deer mice ( Peromyscus maniculatus) are robust and very active mammals that are found across the North American continent. They are also highly adaptable to extreme environments. When introduced to high altitude they retain remarkable adaptive ability to the low-oxygen environment via lung expansion and remodeling of existing lung structure, thereby maintaining normal aerobic capacity without generating more red blood cells or additional lung tissue.

Divergent and parallel routes of biochemical adaptation in high-altitude passerine birds from the Qinghai-Tibet Plateau

When different species experience similar selection pressures, the probability of evolving similar adaptive solutions may be influenced by legacies of evolutionary history, such as lineage-specific changes in genetic background. Here we test for adaptive convergence in hemoglobin (Hb) function among high-altitude passerine birds that are native to the Qinghai-Tibet Plateau, and we examine whether convergent increases in Hb-O₂ affinity have a similar molecular basis in different species. We documented that high-altitude parid and aegithalid species from the Qinghai-Tibet Plateau have evolved derived increases in Hb-O₂ affinity in comparison with their closest lowland relatives in East Asia. However, convergent increases in Hb-O₂ affinity and convergence in underlying functional mechanisms were seldom attributable to the same amino acid substitutions in different species. Using ancestral protein resurrection and site-directed mutagenesis, we experimentally confirmed two cases in which parallel substitutions contributed to convergent increases in Hb-O₂ affinity in codistributed high-altitude species. In one case involving the ground tit (Parus humilis) and gray-crested tit (Lophophanes dichrous), parallel amino acid replacements with affinity-enhancing effects were attributable to nonsynonymous substitutions at a CpG dinucleotide, suggesting a possible role for mutation bias in promoting recurrent changes at the same site. Overall, most altitude-related changes in Hb function were caused by divergent amino acid substitutions, and a select few were caused by parallel substitutions that produced similar phenotypic effects on the divergent genetic backgrounds of different species.

Life-history characteristics influence physiological strategies to cope with hypoxia in Himalayan birds

Hypobaric hypoxia at high elevation represents an important physiological stressor for montane organisms, but optimal physiological strategies to cope with hypoxia may vary among species with different life histories. Montane birds exhibit a range of migration patterns; elevational migrants breed at high elevations but winter at low elevations or migrate further south, while high-elevation residents inhabit the same elevation throughout the year. Optimal physiological strategies to cope with hypoxia might therefore differ between species that exhibit these two migratory patterns, because they differ in the amount time spent at high elevation. We examined physiological parameters associated with blood-oxygen transport (haemoglobin concentration and haematocrit, i.e. the proportion of red blood cells in blood) in nine species of elevational migrants and six species of high-elevation residents that were sampled along a 2200 m (1000-3200 m) elevational gradient. Haemoglobin concentration increased with elevation within species regardless of migratory strategy, but it was only significantly correlated with haematocrit in elevational migrants. Surprisingly, haemoglobin concentration was not correlated with haematocrit in high-elevation residents, and these species exhibited higher mean cellular haemoglobin concentration than elevational migrants. Thus, alternative physiological strategies to regulate haemoglobin concentration and blood O₂ carrying capacity appear to differ among birds with different annual elevational movement patterns.

Control of breathing and ventilatory acclimatization to hypoxia in deer mice native to high altitudes

AIM

We compared the control of breathing and heart rate by hypoxia between high- and low-altitude populations of Peromyscus mice, to help elucidate the physiological specializations that help high-altitude natives cope with O₂ limitation.

METHODS

Deer mice (Peromyscus maniculatus) native to high altitude and congeneric mice native to low altitude (Peromyscus leucopus) were bred in captivity at sea level. The F1 progeny of each population were raised to adulthood and then acclimated to normoxia or hypobaric hypoxia (12 kPa, simulating hypoxia at ~4300 m) for 5 months. Responses to acute hypoxia were then measured during stepwise reductions in inspired O₂ fraction.

RESULTS

Lowlanders exhibited ventilatory acclimatization to hypoxia (VAH), in which hypoxia acclimation enhanced the hypoxic ventilatory response, made breathing pattern more effective (higher tidal volumes and lower breathing frequencies at a given total ventilation), increased arterial O₂ saturation and heart rate during acute hypoxia, augmented respiratory water loss and led to significant growth of the carotid body. In contrast, highlanders did not exhibit VAH - exhibiting a fixed increase in breathing that was similar to hypoxia-acclimated lowlanders - and they maintained even higher arterial O₂ saturations in hypoxia. However, the carotid bodies of highlanders were not enlarged by hypoxia acclimation and were similar in size to those of normoxic lowlanders. Highlanders also maintained consistently higher heart rates than lowlanders during acute hypoxia.

CONCLUSIONS

Our results suggest that highland deer mice have evolved high rates of alveolar ventilation and respiratory O₂ uptake without the significant enlargement of the carotid bodies that is typical of VAH in lowlanders, possibly to adjust the hypoxic chemoreflex for life in high-altitude hypoxia.

Signatures of positive selection and local adaptation to urbanization in white-footed mice (Peromyscus leucopus)

Urbanization significantly alters natural ecosystems and has accelerated globally. Urban wildlife populations are often highly fragmented by human infrastructure, and isolated populations may adapt in response to local urban pressures. However, relatively few studies have identified genomic signatures of adaptation in urban animals. We used a landscape genomic approach to examine signatures of selection in urban populations of white-footed mice (Peromyscus leucopus) in New York City. We analysed 154,770 SNPs identified from transcriptome data from 48 P. leucopus individuals from three urban and three rural populations and used outlier tests to identify evidence of urban adaptation. We accounted for demography by simulating a neutral SNP data set under an inferred demographic history as a null model for outlier analysis. We also tested whether candidate genes were associated with environmental variables related to urbanization. In total, we detected 381 outlier loci and after stringent filtering, identified and annotated 19 candidate loci. Many of the candidate genes were involved in metabolic processes and have well-established roles in metabolizing lipids and carbohydrates. Our results indicate that white-footed mice in New York City are adapting at the biomolecular level to local selective pressures in urban habitats. Annotation of outlier loci suggests selection is acting on metabolic pathways in urban populations, likely related to novel diets in cities that differ from diets in less disturbed areas.

O2 binding and CO2 sensitivity in haemoglobins of subterranean African mole rats

Inhabiting deep and sealed subterranean burrows, mole rats exhibit a remarkable suite of specializations, including eusociality (living in colonies with single breeding queens), extraordinary longevity, cancer immunity and poikilothermy, and extreme tolerance of hypoxia and hypercapnia. With little information available on adjustments in haemoglobin (Hb) function that may mitigate the impact of exogenous and endogenous constraints on the uptake and internal transport of O₂, we measured haematological characteristics, as well as Hb-O₂ binding affinity and sensitivity to pH (Bohr effect), CO₂, temperature and 2,3-diphosphoglycerate (DPG, the major allosteric modulator of Hb-O₂ affinity in red blood cells) in four social and two solitary species of African mole rats (family Bathyergidae) originating from different biomes and soil types across Central and Southern Africa. We found no consistent patterns in haematocrit (Hct) and blood and red cell DPG and Hb concentrations or in intrinsic Hb-O₂ affinity and its sensitivity to pH and DPG that correlate with burrowing, sociality and soil type. However, the results reveal low specific (pH independent) effects of CO₂ on Hb-O₂ affinity compared with humans that predictably safeguard pulmonary loading under hypoxic and hypercapnic burrow conditions. The O₂ binding characteristics are discussed in relation to available information on the primary structure of Hbs from adult and developmental stages of mammals subjected to hypoxia and hypercapnia and the molecular mechanisms underlying functional variation in rodent Hbs.

Circulatory mechanisms underlying adaptive increases in thermogenic capacity in high-altitude deer mice

We examined the circulatory mechanisms underlying adaptive increases in thermogenic capacity in deer mice (Peromyscus maniculatus) native to the cold hypoxic environment at high altitudes. Deer mice from high- and low-altitude populations were born and raised in captivity to adulthood, and then acclimated to normoxia or hypobaric hypoxia (simulating hypoxia at ∼4300 m). Thermogenic capacity [maximal O₂ consumption (V̇_O2,max), during cold exposure] was measured in hypoxia, along with arterial O₂ saturation (Sa_O2 ) and heart rate (f_H). Hypoxia acclimation increased V̇_O2,max by a greater magnitude in highlanders than in lowlanders. Highlanders also had higher Sa_O2  and extracted more O₂ from the blood per heartbeat (O₂ pulse=V̇_O2,max/f_H). Hypoxia acclimation increased f_H, O₂ pulse and capillary density in the left ventricle of the heart. Our results suggest that adaptive increases in thermogenic capacity involve integrated functional changes across the O₂ cascade that augment O₂ circulation and extraction from the blood.

Characterizing the reproductive transcriptomic correlates of acute dehydration in males in the desert-adapted rodent, Peromyscus eremicus

BACKGROUND

The understanding of genomic and physiological mechanisms related to how organisms living in extreme environments survive and reproduce is an outstanding question facing evolutionary and organismal biologists. One interesting example of adaptation is related to the survival of mammals in deserts, where extreme water limitation is common. Research on desert rodent adaptations has focused predominantly on adaptations related to surviving dehydration, while potential reproductive physiology adaptations for acute and chronic dehydration have been relatively neglected. This study aims to explore the reproductive consequences of acute dehydration by utilizing RNAseq data in the desert-specialized cactus mouse (Peromyscus eremicus).

RESULTS

We exposed 22 male cactus mice to either acute dehydration or control (fully hydrated) treatment conditions, quasimapped testes-derived reads to a cactus mouse testes transcriptome, and then evaluated patterns of differential transcript and gene expression. Following statistical evaluation with multiple analytical pipelines, nine genes were consistently differentially expressed between the hydrated and dehydrated mice. We hypothesized that male cactus mice would exhibit minimal reproductive responses to dehydration; therefore, this low number of differentially expressed genes between treatments aligns with current perceptions of this species' extreme desert specialization. However, these differentially expressed genes include Insulin-like 3 (Insl3), a regulator of male fertility and testes descent, as well as the solute carriers Slc45a3 and Slc38a5, which are membrane transport proteins that may facilitate osmoregulation.

CONCLUSIONS

These results suggest that in male cactus mice, acute dehydration may be linked to reproductive modulation via Insl3, but not through gene expression differences in the subset of other a priori tested reproductive hormones. Although water availability is a reproductive cue in desert-rodents exposed to chronic drought, potential reproductive modification via Insl3 in response to acute water-limitation is a result which is unexpected in an animal capable of surviving and successfully reproducing year-round without available external water sources. Indeed, this work highlights the critical need for integrative research that examines every facet of organismal adaptation, particularly in light of global climate change, which is predicted, amongst other things, to increase climate variability, thereby exposing desert animals more frequently to the acute drought conditions explored here.

Stability-Mediated Epistasis Restricts Accessible Mutational Pathways in the Functional Evolution of Avian Hemoglobin

If the fitness effects of amino acid mutations are conditional on genetic background, then mutations can have different effects depending on the sequential order in which they occur during evolutionary transitions in protein function. A key question concerns the fraction of possible mutational pathways connecting alternative functional states that involve transient reductions in fitness. Here we examine the functional effects of multiple amino acid substitutions that contributed to an evolutionary transition in the oxygenation properties of avian hemoglobin (Hb). The set of causative changes included mutations at intradimer interfaces of the Hb tetramer. Replacements at such sites may be especially likely to have epistatic effects on Hb function since residues at intersubunit interfaces are enmeshed in networks of salt bridges and hydrogen bonds between like and unlike subunits; mutational reconfigurations of these atomic contacts can affect allosteric transitions in quaternary structure and the propensity for tetramer-dimer dissociation. We used ancestral protein resurrection in conjunction with a combinatorial protein engineering approach to synthesize genotypes representing the complete set of mutational intermediates in all possible forward pathways that connect functionally distinct ancestral and descendent genotypes. The experiments revealed that 1/2 of all possible forward pathways included mutational intermediates with aberrant functional properties because particular combinations of mutations promoted tetramer-dimer dissociation. The subset of mutational pathways with unstable intermediates may be selectively inaccessible, representing evolutionary roads not taken. The experimental results also demonstrate how epistasis for particular functional properties of proteins may be mediated indirectly by mutational effects on quaternary structural stability.