Physiological and Genetic Adaptations to Diving in Sea Nomads

Scanning the human genome for "signatures" of positive selection: Transformative opportunities and ethical obligations

The relationship history of evolutionary anthropology and genetics is complex. At best, genetics is a beautifully integrative part of the discipline. Yet this integration has also been fraught, with punctuated, disruptive challenges to dogma, periodic reluctance by some members of the field to embrace results from analyses of genetic data, and occasional over-assertions of genetic definitiveness by geneticists. At worst, evolutionary genetics has been a tool for reinforcing racism and colonialism. While a number of genetics/genomics papers have disproportionately impacted evolutionary anthropology, here we highlight the 2002 presentation of an elegantly powerful approach for identifying "signatures" of past positive selection from haplotype-based patterns of genetic variation. Together with technological advances in genotyping methods, this article transformed our field by facilitating genome-wide "scans" for signatures of past positive selection in human populations. This approach helped researchers test longstanding evolutionary anthropology hypotheses while simultaneously providing opportunities to develop entirely new ones. Genome-wide scans for signatures of positive selection have since been conducted in diverse worldwide populations, with striking findings of local adaptation and convergent evolution. Yet there are ethical considerations with respect to the ubiquity of these studies and the cross-application of the genome-wide scan approach to existing datasets, which we also discuss.

Hypoxic Respiratory Chemoreflex Control in Young Trained Swimmers

During an apnea, changes in PaO₂ activate peripheral chemoreceptors to increase respiratory drive. Athletes with continuous apnea, such as breath-hold divers, have shown a decrease in hypoxic ventilatory response (HVR), which could explain the long apnea times; however, this has not been studied in swimmers. We hypothesize that the long periods of voluntary apnea in swimmers is related to a decreased HVR. Therefore, we sought to determine the HVR and cardiovascular adjustments during a maximum voluntary apnea in young-trained swimmers. In fifteen trained swimmers and twenty-seven controls we studied minute ventilation (V_E), arterial saturation (SpO₂), heart rate (HR), and autonomic response [through heart rate variability (HRV) analysis], during acute chemoreflex activation (five inhalations of pure N₂) and maximum voluntary apnea test. In apnea tests, the maximum voluntary apnea time and the end-apnea HR were higher in swimmers than in controls (p < 0.05), as well as a higher low frequency component of HRV (p < 0.05), than controls. Swimmers showed lower HVR than controls (p < 0.01) without differences in cardiac hypoxic response (CHR). We conclude that swimmers had a reduced HVR response and greater maximal voluntary apnea duration, probably due to decreased HVR.

Six weeks of dynamic apnoeic training stimulates erythropoiesis but does not increase splenic volume

Purpose

This study examined the influence of dynamic apnoea training on splenic volume and haematological responses in non-breath-hold divers (BHD).

Methods

Eight non-BHD performed ten maximal dynamic apnoeas, four times a week for  six weeks. Splenic volumes were assessed ultrasonically, and blood samples were drawn for full blood count analysis, erythropoietin, iron, ferritin, albumin, protein and osmolality at baseline, 24 h post the completion of each week’s training sessions and seven days post the completion of the training programme. Additionally, blood samples were drawn for haematology at 30, 90, and 180 min post session one, twelve and twenty-four.

Results

Erythropoietin was only higher than baseline (6.62 ± 3.03 mlU/mL) post session one, at 90 (9.20 ± 1.88 mlU/mL, p = 0.048) and 180 min (9.04 ± 2.35 mlU/mL, p = 0.046). Iron increased from baseline (18 ± 3 µmol/L) post week five (23 ± 2 µmol/L, p = 0.033) and six (21 ± 6 µmol/L; p = 0.041), whereas ferritin was observed to be lower than baseline (111 ± 82 µg/L) post week five (95 ± 75 µg/L; p = 0.016), six (84 ± 74 µg/L; p = 0.012) and one week post-training (81 ± 63 µg/L; p = 0.008). Reticulocytes increased from baseline (57 ± 12 × 10⁹/L) post week one (72 ± 17 × 10⁹/L, p = 0.037) and six (71 ± 17 × 10⁹/L, p = 0.021) while no changes were recorded in erythrocytes (p = 0.336), haemoglobin (p = 0.124) and splenic volumes (p = 0.357).

Conclusions

Six weeks of dynamic apnoeic training increase reticulocytes without altering mature erythrocyte concentration and splenic volume.

Shared Signature of Recent Positive Selection on the TSBP1-BTNL2-HLA-DRA Genes in Five Native Populations from North Borneo

North Borneo (NB) is home to more than 40 native populations. These natives are believed to have undergone local adaptation in response to environmental challenges such as the mosquito-abundant tropical rainforest. We attempted to trace the footprints of natural selection from the genomic data of NB native populations using a panel of ∼2.2 million genome-wide single nucleotide polymorphisms. As a result, an ∼13-kb haplotype in the Major Histocompatibility Complex Class II region encompassing candidate genes TSBP1–BTNL2–HLA-DRA was identified to be undergoing natural selection. This putative signature of positive selection is shared among the five NB populations and is estimated to have arisen ∼5.5 thousand years (∼220 generations) ago, which coincides with the period of Austronesian expansion. Owing to the long history of endemic malaria in NB, the putative signature of positive selection is postulated to be driven by Plasmodium parasite infection. The findings of this study imply that despite high levels of genetic differentiation, the NB populations might have experienced similar local genetic adaptation resulting from stresses of the shared environment.

Physiological resiliency in diving mammals: Insights on hypoxia protection using the Krogh principle to understand COVID-19 symptoms

Sequential diving by wild marine mammals results in a lifetime of rapid physiological transitions between lung collapse-reinflation, bradycardia-tachycardia, vasoconstriction-vasodilation, and oxygen store depletion-restoration. The result is a cycle of normoxia and hypoxia in which blood oxygen partial pressures can decline to <20–30 mmHg during a dive, a level considered injurious to oxygen-dependent human tissues (i.e., brain, heart). Safeguards in the form of enhanced on-board oxygen stores, selective oxygen transport, and unique tissue buffering capacities enable marine-adapted mammals to maintain physiological homeostasis and energy metabolism even when breathing and pulmonary gas exchange cease. This stands in stark contrast to the vulnerability of oxygen-sensitive tissues in humans that may undergo irreversible damage within minutes of ischemia and tissue hypoxia. Recently, these differences in protection against hypoxic injury have become evident in the systemic, multi-organ physiological failure during COVID-19 infection in humans. Prolonged recoveries in some patients have led to delays in the return to normal exercise levels and cognitive function even months later. Rather than a single solution to this problem, we find that marine mammals rely on a unique, integrative assemblage of protections to avoid the deleterious impacts of hypoxia on tissues. Built across evolutionary time, these solutions provide a natural template for identifying the potential for tissue damage when oxygen is lacking, and for guiding management decisions to support oxygen-deprived tissues in other mammalian species, including humans, challenged by hypoxia.

Chromatin accessibility landscape and regulatory network of high-altitude hypoxia adaptation

High-altitude adaptation of Tibetans represents a remarkable case of natural selection during recent human evolution. Previous genome-wide scans found many non-coding variants under selection, suggesting a pressing need to understand the functional role of non-coding regulatory elements (REs). Here, we generate time courses of paired ATAC-seq and RNA-seq data on cultured HUVECs under hypoxic and normoxic conditions. We further develop a variant interpretation methodology (vPECA) to identify active selected REs (ASREs) and associated regulatory network. We discover three causal SNPs of EPAS1, the key adaptive gene for Tibetans. These SNPs decrease the accessibility of ASREs with weakened binding strength of relevant TFs, and cooperatively down-regulate EPAS1 expression. We further construct the downstream network of EPAS1, elucidating its roles in hypoxic response and angiogenesis. Collectively, we provide a systematic approach to interpret phenotype-associated noncoding variants in proper cell types and relevant dynamic conditions, to model their impact on gene regulation.

Spleen contraction elevates hemoglobin concentration at high altitude during rest and exercise

PURPOSE

Hypoxia and exercise are known to separately trigger spleen contraction, leading to release of stored erythrocytes. We studied spleen volume and hemoglobin concentration (Hb) during rest and exercise at three altitudes.

METHODS

Eleven healthy lowlanders did a 5-min modified Harvard step test at 1370, 3700 and 4200 m altitude. Spleen volume was measured via ultrasonic imaging and capillary Hb with Hemocue during rest and after the step test, and arterial oxygen saturation (SaO₂), heart rate (HR), expiratory CO₂ (ETCO₂) and respiratory rate (RR) across the test.

RESULTS

Resting spleen volume was reduced with increasing altitude and further reduced with exercise at all altitudes. Mean (SE) baseline spleen volume at 1370 m was 252 (20) mL and after exercise, it was 199 (15) mL (P < 0.01). At 3700 m, baseline spleen volume was 231 (22) mL and after exercise 166 (12) mL (P < 0.05). At 4200 m baseline volume was 210 (23) mL and after exercise 172 (20) mL (P < 0.05). After 10 min, spleen volume increased to baseline at all altitudes (NS). Baseline Hb increased with altitude from 138.9 (6.1) g/L at 1370 m, to 141.2 (4.1) at 3700 m and 152.4 (4.0) at 4200 m (P < 0.01). At all altitudes Hb increased from baseline during exercise to 146.8 (5.7) g/L at 1370 m, 150.4 (3.8) g/L at 3700 m and 157.3 (3.8) g/L at 4200 m (all P < 0.05 from baseline). Hb had returned to baseline after 10 min rest at all altitudes (NS). The spleen-derived Hb elevation during exercise was smaller at 4200 m compared to 3700 m (P < 0.05). Cardiorespiratory variables were also affected by altitude during both rest and exercise.

CONCLUSIONS

The spleen contracts and mobilizes stored red blood cells during rest at high altitude and contracts further during exercise, to increase oxygen delivery to tissues during acute hypoxia. The attenuated Hb response to exercise at the highest altitude is likely due to the greater recruitment of the spleen reserve during rest, and that maximal spleen contraction is reached with exercise.

Identifying adaptive alleles in the human genome: from selection mapping to functional validation

The suite of phenotypic diversity across geographically distributed human populations is the outcome of genetic drift, gene flow, and natural selection throughout human evolution. Human genetic variation underlying local biological adaptations to selective pressures is incompletely characterized. With the emergence of population genetics modeling of large-scale genomic data derived from diverse populations, scientists are able to map signatures of natural selection in the genome in a process known as selection mapping. Inferred selection signals further can be used to identify candidate functional alleles that underlie putative adaptive phenotypes. Phenotypic association, fine mapping, and functional experiments facilitate the identification of candidate adaptive alleles. Functional investigation of candidate adaptive variation using novel techniques in molecular biology is slowly beginning to unravel how selection signals translate to changes in biology that underlie the phenotypic spectrum of our species. In addition to informing evolutionary hypotheses of adaptation, the discovery and functional annotation of adaptive alleles also may be of clinical significance. While selection mapping efforts in non-European populations are growing, there remains a stark under-representation of diverse human populations in current public genomic databases, of both clinical and non-clinical cohorts. This lack of inclusion limits the study of human biological variation. Identifying and functionally validating candidate adaptive alleles in more global populations is necessary for understanding basic human biology and human disease.

Spleen Size and Function in Sherpa Living High, Sherpa Living Low and Nepalese Lowlanders

High-altitude (HA) natives have evolved some beneficial responses leading to superior work capacity at HA compared to native lowlanders. Our aim was to study two responses potentially protective against hypoxia: the spleen contraction elevating hemoglobin concentration (Hb) and the cardiovascular diving response in Sherpa highlanders, compared to lowlanders. Male participants were recruited from three groups: (1) 21 Sherpa living at HA (SH); (2) seven Sherpa living at low altitude (SL); and (3) ten native Nepalese lowlanders (NL). They performed three apneas spaced by a two-min rest at low altitude (1370 m). Their peripheral oxygen saturation (SpO₂), heart rate (HR), and spleen volume were measured across the apnea protocol. Spleen volume at rest was 198 ± 56 mL in SH and 159 ± 35 mL in SL (p = 0.047). The spleen was larger in Sherpa groups compared to the 129 ± 22 mL in NL (p < 0.001 compared to SH; p = 0.046 compared to SL). Spleen contraction occurred in all groups during apnea, but it was greater in Sherpa groups compared to NL (p < 0.001). HR was lower in Sherpa groups compared to NL both during rest (SL: p < 0.001; SH: p = 0.003) and during maximal apneas (SL: p < 0.001; SH: p = 0.06). The apnea-induced HR reduction was 8 ± 8% in SH, 10 ± 4% in SL (NS), and 18 ± 6% in NL (SH: p = 0.005; SL: p = 0.021 compared to NL). Resting SpO₂ was similar in all groups. The progressively decreasing baseline spleen size across SH, SL, and NL suggests a role of the spleen at HA and further that both genetic predisposition and environmental exposure determine human spleen size. The similar HR responses of SH and SL suggest that a genetic component is involved in determining the cardiovascular diving response.

Arctic-adapted dogs emerged at the Pleistocene-Holocene transition

Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups. We applied a genomic approach to investigate their spatiotemporal emergence by sequencing the genomes of 10 modern Greenland sled dogs, an ~9500-year-old Siberian dog associated with archaeological evidence for sled technology, and an ~33,000-year-old Siberian wolf. We found noteworthy genetic similarity between the ancient dog and modern sled dogs. We detected gene flow from Pleistocene Siberian wolves, but not modern American wolves, to present-day sled dogs. The results indicate that the major ancestry of modern sled dogs traces back to Siberia, where sled dog-specific haplotypes of genes that potentially relate to Arctic adaptation were established by 9500 years ago.

Splenic responses to a series of repeated maximal static and dynamic apnoeas with whole-body immersion in water

NEW FINDINGS

What is the central question of this study? Splenic contractions occur in response to apnoea-induced hypoxia with and without face immersion in water. However, the splenic responses to a series of static or dynamic apnoeas with whole-body water immersion in non-divers and elite breath-hold divers are unknown. What is the main finding and its importance? Static and dynamic apnoeas were equally effective in stimulating splenic contractions across non-divers and elite breath-hold divers. These findings demonstrate that the magnitude of the splenic response is largely dictated by the degree of the hypoxemic stress encountered during voluntary apnoeic epochs.

ABSTRACT

Splenic contractions occur in response to apnoea-induced hypoxia with and without facial water immersion. However, the splenic responses to a series of static (STA) or dynamic (DYN) apnoeas with whole-body water immersion in non-divers (NDs) and elite breath-hold divers (EBHDs) are unknown. EBHD (n = 8), ND (n = 10) and control participants (n = 8) were recruited. EBHD and ND performed a series of five maximal DYN or STA on separate occasions. Control performed a static eupnoeic (STE) protocol to control against any effects of water immersion and diurnal variation on splenic volume and haematology. Heart rate (HR) and peripheral oxygen saturation (SpO₂ ) were monitored for 30 s after each apnoea. Pre- and post-apnoeic splenic volumes were quantified ultrasonically, and blood samples were drawn for haematology. For EBHD and ND end-apnoeic HR was higher (P < 0.001) and SpO₂ was lower in DYN (P = 0.024) versus STA. EBHD attained lower end-apnoeic SpO₂ during DYN and STA than NDs (P < 0.001). Splenic contractions occurred following DYN (EBHD, -47 ± 6%; ND, -37 ± 4%; P < 0.001) and STA (EBHD, -26 ± 4%; ND, -26 ± 8%; P < 0.01). DYN-associated splenic contractions were greater than STA in EBHD only (P = 0.042). Haemoglobin concentrations were higher following DYN only (EBHD, +5 ± 8g/L  , +4 ± 2%; ND, +8 ± 3 g/L , +4.9 ± 3%; P = 0.019). Haematocrit remained unchanged after each protocol. There were no between group differences in post-apnoeic splenic volume or haematology. In both groups, splenic contractions occurred in response to STA and DYN when combined with whole-body immersion. DYN apnoeas, were effective at increasing haemoglobin concentrations but not STA apnoeas. Thus, the magnitude of the splenic response relates to the hypoxemic stress encountered during apnoeic epochs.

The Mammalian Diving Response: Inroads to Its Neural Control

The mammalian diving response (DR) is a remarkable behavior that was first formally studied by Laurence Irving and Per Scholander in the late 1930s. The DR is called such because it is most prominent in marine mammals such as seals, whales, and dolphins, but nevertheless is found in all mammals studied. It consists generally of breathing cessation (apnea), a dramatic slowing of heart rate (bradycardia), and an increase in peripheral vasoconstriction. The DR is thought to conserve vital oxygen stores and thus maintain life by directing perfusion to the two organs most essential for life-the heart and the brain. The DR is important, not only for its dramatic power over autonomic function, but also because it alters normal homeostatic reflexes such as the baroreceptor reflex and respiratory chemoreceptor reflex. The neurons driving the reflex circuits for the DR are contained within the medulla and spinal cord since the response remains after the brainstem transection at the pontomedullary junction. Neuroanatomical and physiological data suggesting brainstem areas important for the apnea, bradycardia, and peripheral vasoconstriction induced by underwater submersion are reviewed. Defining the brainstem circuit for the DR may open broad avenues for understanding the mechanisms of suprabulbar control of autonomic function in general, as well as implicate its role in some clinical states. Knowledge of the proposed diving circuit should facilitate studies on elite human divers performing breath-holding dives as well as investigations on sudden infant death syndrome (SIDS), stroke, migraine headache, and arrhythmias. We have speculated that the DR is the most powerful autonomic reflex known.

Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits

Understanding the genetic changes underlying phenotypic variation in sheep (Ovis aries) may facilitate our efforts towards further improvement. Here, we report the deep resequencing of 248 sheep including the wild ancestor (O. orientalis), landraces, and improved breeds. We explored the sheep variome and selection signatures. We detected genomic regions harboring genes associated with distinct morphological and agronomic traits, which may be past and potential future targets of domestication, breeding, and selection. Furthermore, we found non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds. We identified PDGFD as a likely causal gene for fat deposition in the tails of sheep through transcriptome, RT-PCR, qPCR, and Western blot analyses. Our results provide insights into the demographic history of sheep and a valuable genomic resource for future genetic studies and improved genome-assisted breeding of sheep and other domestic animals.

Diving deep: understanding the genetic components of hypoxia tolerance in marine mammals

Marine mammals have highly specialized physiology, exhibited in many species by extreme breath-holding capabilities that allow deep dives and extended submergence. Cardiovascular control and cell-level hypoxia tolerance are key features of this phenotype. Identifying genomic signatures tied to physiology will be valuable in understanding these natural model species, which may generate translational opportunities to human diseases arising from hypoxic stress or tissue injury. Genomic analyses have now been conducted in dolphins, river dolphins, minke whales, bowhead whales, and polar bears, with multispecies studies exploring evolutionary signals across marine mammal lineages, encompassing extinct and extant divers. Single-species genome studies for sirenians do not yet exist. Extant marine mammals arose in three lineages from separate aquatic recolonizations. Their physiological specializations, along with these independent origins create an interesting case to examine convergent evolution. Although molecular mechanisms of hypoxia tolerance are not universally apparent across marine mammal genomic studies, altered evolutionary rates have been identified for genes linked to oxygen binding and transport (e.g., MB, HBA, and HBB), blood pressure control (e.g., endothelin pathway genes), and cell protection in multiple species. Despite convergent phenotypes across clades, instances of identical molecular convergence have been uncommon. Given the inherent logistical and regulatory difficulties associated with functional genetic experiments in marine mammals, several avenues of further investigation are suggested to enable validation of candidate genes for hypoxia tolerance: leveraging phylogeny to better understand convergent phenotypes; ontogenic studies to identify regulation of key genes underlying the elite, adult, hypoxia-tolerant physiology; and cell culture manipulations to understand gene function.

How Natural Genetic Variation Shapes Behavior

Nervous systems allow animals to acutely respond and behaviorally adapt to changes and recurring patterns in their environment at multiple timescales-from milliseconds to years. Behavior is further shaped at intergenerational timescales by genetic variation, drift, and selection. This sophistication and flexibility of behavior makes it challenging to measure behavior consistently in individual subjects and to compare it across individuals. In spite of these challenges, careful behavioral observations in nature and controlled measurements in the laboratory, combined with modern technologies and powerful genetic approaches, have led to important discoveries about the way genetic variation shapes behavior. A critical mass of genes whose variation is known to modulate behavior in nature is finally accumulating, allowing us to recognize emerging patterns. In this review, we first discuss genetic mapping approaches useful for studying behavior. We then survey how variation acts at different levels-in environmental sensation, in internal neuronal circuits, and outside the nervous system altogether-and then discuss the sources and types of molecular variation linked to behavior and the mechanisms that shape such variation. We end by discussing remaining questions in the field.

Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes

Copy number variants (CNVs) are subject to stronger selective pressure than single-nucleotide variants, but their roles in archaic introgression and adaptation have not been systematically investigated. We show that stratified CNVs are significantly associated with signatures of positive selection in Melanesians and provide evidence for adaptive introgression of large CNVs at chromosomes 16p11.2 and 8p21.3 from Denisovans and Neanderthals, respectively. Using long-read sequence data, we reconstruct the structure and complex evolutionary history of these polymorphisms and show that both encode positively selected genes absent from most human populations. Our results collectively suggest that large CNVs originating in archaic hominins and introgressed into modern humans have played an important role in local population adaptation and represent an insufficiently studied source of large-scale genetic variation.

Dimensionality reduction reveals fine-scale structure in the Japanese population with consequences for polygenic risk prediction

The diversity in our genome is crucial to understanding the demographic history of worldwide populations. However, we have yet to know whether subtle genetic differences within a population can be disentangled, or whether they have an impact on complex traits. Here we apply dimensionality reduction methods (PCA, t-SNE, PCA-t-SNE, UMAP, and PCA-UMAP) to biobank-derived genomic data of a Japanese population (n = 169,719). Dimensionality reduction reveals fine-scale population structure, conspicuously differentiating adjacent insular subpopulations. We further enluciate the demographic landscape of these Japanese subpopulations using population genetics analyses. Finally, we perform phenome-wide polygenic risk score (PRS) analyses on 67 complex traits. Differences in PRS between the deconvoluted subpopulations are not always concordant with those in the observed phenotypes, suggesting that the PRS differences might reflect biases from the uncorrected structure, in a trait-dependent manner. This study suggests that such an uncorrected structure can be a potential pitfall in the clinical application of PRS.

Adaptation to Extreme Environments in an Admixed Human Population from the Atacama Desert

Inorganic arsenic (As) is a toxic xenobiotic and carcinogen associated with severe health conditions. The urban population from the Atacama Desert in northern Chile was exposed to extremely high As levels (up to 600 µg/l) in drinking water between 1958 and 1971, leading to increased incidence of urinary bladder cancer (BC), skin cancer, kidney cancer, and coronary thrombosis decades later. Besides, the Andean Native-American ancestors of the Atacama population were previously exposed for millennia to elevated As levels in water (∼120 µg/l) for at least 5,000 years, suggesting adaptation to this selective pressure. Here, we performed two genome-wide selection tests—PBS_n1 and an ancestry-enrichment test—in an admixed population from Atacama, to identify adaptation signatures to As exposure acquired before and after admixture with Europeans, respectively. The top second variant selected by PBS_n1 was associated with LCE4A-C1orf68, a gene that may be involved in the immune barrier of the epithelium during BC. We performed association tests between the top PBS_n1 hits and BC occurrence in our population. The strongest association (P = 0.012) was achieved by the LCE4A-C1orf68 variant. The ancestry-enrichment test detected highly significant signals (P = 1.3 × 10⁻⁹) mapping MAK16, a gene with important roles in ribosome biogenesis during the G1 phase of the cell cycle. Our results contribute to a better understanding of the genetic factors involved in adaptation to the pathophysiological consequences of As exposure.

Spleen size improvement in advanced heart failure patients using a left ventricular assist device

The spleen has been recognized as an important organ that holds a reserve of 20% to 30% of the total blood volume. Spleen contraction and splenic volume reduction occur in patients with hypovolemic shock. However, the change in the spleen volume and the association between spleen size and hemodynamic parameters remain unclear in patients with advanced heart failure (HF) who need left ventricular assist device (LVAD) support. This study was performed to investigate the change in spleen size and the relationship between spleen size and hemodynamic parameters before and after LVAD implantation in patients with advanced HF. We enrolled 20 patients with advanced HF on LVAD support. All patients underwent right heart catheterization and computed tomography before and after LVAD implantation. The spleen size was measured by computed tomography volumetry. We excluded patients with a mean right atrial pressure (RAP) of <5 mm Hg because of the possibility of hypovolemia and those with a cardiac index of >2.2 L/min/m² before LVAD implantation. The splenic volume significantly increased from 160.6 ± 46.9 mL before LVAD implantation to 224.6 ± 73.5 mL after LVAD implantation (P < .001). Before LVAD implantation, there was a significant negative correlation between spleen volume and systemic vascular resistance (SVR). After LVAD implantation, however, there were significant correlations between spleen volume and the cardiac index, RAP, and pulmonary capillary wedge pressure despite the absence of a significant correlation between spleen volume and SVR. Furthermore, one patient developed reworsening HF because of LVAD failure due to pump thrombosis. In this case, the splenic volume was 212 mL before LVAD implantation and increased to 418 mL after LVAD implantation, although it decreased to 227 mL after LVAD failure. The spleen size may change depending on hemodynamics in patients with advanced HF with LVAD support, reflecting sympathetic nerve activity and the systemic volume status.

Rewriting Human History and Empowering Indigenous Communities with Genome Editing Tools

Appropriate empirical-based evidence and detailed theoretical considerations should be used for evolutionary explanations of phenotypic variation observed in the field of human population genetics (especially Indigenous populations). Investigators within the population genetics community frequently overlook the importance of these criteria when associating observed phenotypic variation with evolutionary explanations. A functional investigation of population-specific variation using cutting-edge genome editing tools has the potential to empower the population genetics community by holding "just-so" evolutionary explanations accountable. Here, we detail currently available precision genome editing tools and methods, with a particular emphasis on base editing, that can be applied to functionally investigate population-specific point mutations. We use the recent identification of thrifty mutations in the CREBRF gene as an example of the current dire need for an alliance between the fields of population genetics and genome editing.

Skeletal muscle, haematological and splenic volume characteristics of elite breath-hold divers

Purpose

The aim of the study was to provide an evaluation of the oxygen transport, exchange and storage capacity of elite breath-hold divers (EBHD) compared with non-divers (ND).

Methods

Twenty-one healthy males’ (11 EBHD; 10 ND) resting splenic volumes were assessed by ultrasound and venous blood drawn for full blood count analysis. Percutaneous skeletal muscle biopsies were obtained from the m. vastus lateralis to measure capillarisation, and fibre type-specific localisation and distribution of myoglobin and mitochondrial content using quantitative immunofluorescence microscopy.

Results

Splenic volume was not different between groups. Reticulocytes, red blood cells and haemoglobin concentrations were higher (+ 24%, p < 0.05; + 9%, p < 0.05; + 3%, p < 0.05; respectively) and mean cell volume was lower (− 6.5%, p < 0.05) in the EBHD compared with ND. Haematocrit was not different between groups. Capillary density was greater (+ 19%; p < 0.05) in the EBHD. The diffusion distance (R₉₅) was lower in type I versus type II fibres for both groups (EBHD, p < 0.01; ND, p < 0.001), with a lower R₉₅ for type I fibres in the EBHD versus ND (− 13%, p < 0.05). Myoglobin content was higher in type I than type II fibres in EBHD (+ 27%; p < 0.01) and higher in the type I fibres of EBHD than ND (+ 27%; p < 0.05). No fibre type differences in myoglobin content were observed in ND. Mitochondrial content was higher in type I than type II fibres in EBHD (+ 35%; p < 0.05), with no fibre type differences in ND or between groups.

Conclusions

In conclusion, EBDH demonstrate enhanced oxygen storage in both blood and skeletal muscle and a more efficient oxygen exchange capacity between blood and skeletal muscle versus ND.

Natural Tolerance to Ischemia and Hypoxemia in Diving Mammals: A Review

Reperfusion injury follows ischemia/reperfusion events occurring during myocardial infarction, stroke, embolism, and other peripheral vascular diseases. Decreased blood flow and reduced oxygen tension during ischemic episodes activate cellular pathways that upregulate pro-inflammatory signaling and promote oxidant generation. Reperfusion after ischemia recruits inflammatory cells to the vascular wall, further exacerbating oxidant production and ultimately resulting in cell death, tissue injury, and organ dysfunction. Diving mammals tolerate repetitive episodes of peripheral ischemia/reperfusion as part of the cardiovascular adjustments supporting long duration dives. These adjustments allow marine mammals to optimize the use of their body oxygen stores while diving but can result in selectively reduced perfusion to peripheral tissues. Remarkably, diving mammals show no apparent detrimental effects associated with these ischemia/reperfusion events. Here, we review the current knowledge regarding the strategies marine mammals use to suppress inflammation and cope with oxidant generation potentially derived from diving-induced ischemia/reperfusion.

Post-splenectomy sepsis: preventative strategies, challenges, and solutions

Removal of the spleen had already been established as a routine technique to treat splenic trauma and other diseases affecting the spleen before the anatomy, physiology, and function of the spleen were known in the mid-twentieth century. It is now widely accepted that the splenectomized individual is at increased risk for infection, in particular, overwhelming post-splenectomy infection (OPSI). OPSI is a syndrome of fulminant sepsis occurring in splenectomized (asplenic) or hyposplenic individuals that is associated with high mortality and morbidity. Poorly opsonized bacteria such as encapsulated bacteria, in particular, Streptococcus pneumoniae, are often implicated in sepsis. The spleen is a reticuloendothelial organ that facilitates opsonization and phagocytosis of pathogens, in addition to cellular maintenance. Splenectomy is associated with an impairment in immunoglobulin production, antibody-mediated clearance, and phagocytosis, leading to an increased risk of infection and sepsis. Early identification of the at-risk patient, early blood cultures prior to antibiotic administration, urgent blood smears and fast pathogen-detection tests, and sepsis bundles should be utilized in these patients. Prompt management and aggressive treatment can alter the course of disease in the at-risk splenectomized patient. Overwhelming post-splenectomy infection can be prevented through vaccination, chemoprophylaxis, and patient education. This article evaluates post-splenectomy sepsis by summarizing the anatomy and function of the spleen, physiological changes after splenectomy that predispose the splenectomized patient to infection, and current management and prevention strategies.

An approximate full-likelihood method for inferring selection and allele frequency trajectories from DNA sequence data

Most current methods for detecting natural selection from DNA sequence data are limited in that they are either based on summary statistics or a composite likelihood, and as a consequence, do not make full use of the information available in DNA sequence data. We here present a new importance sampling approach for approximating the full likelihood function for the selection coefficient. Our method CLUES treats the ancestral recombination graph (ARG) as a latent variable that is integrated out using previously published Markov Chain Monte Carlo (MCMC) methods. The method can be used for detecting selection, estimating selection coefficients, testing models of changes in the strength of selection, estimating the time of the start of a selective sweep, and for inferring the allele frequency trajectory of a selected or neutral allele. We perform extensive simulations to evaluate the method and show that it uniformly improves power to detect selection compared to current popular methods such as nSL and SDS, and can provide reliable inferences of allele frequency trajectories under many conditions. We also explore the potential of our method to detect extremely recent changes in the strength of selection. We use the method to infer the past allele frequency trajectory for a lactase persistence SNP (MCM6) in Europeans. We also infer the trajectory of a SNP (EDAR) in Han Chinese, finding evidence that this allele's age is much older than previously claimed. We also study a set of 11 pigmentation-associated variants. Several genes show evidence of strong selection particularly within the last 5,000 years, including ASIP, KITLG, and TYR. However, selection on OCA2/HERC2 seems to be much older and, in contrast to previous claims, we find no evidence of selection on TYRP1.

The Magnitude of Diving Bradycardia During Apnea at Low-Altitude Reveals Tolerance to High Altitude Hypoxia

Acute mountain sickness (AMS) is a potentially life-threatening illness that may develop during exposure to hypoxia at high altitude (HA). Susceptibility to AMS is highly individual, and the ability to predict it is limited. Apneic diving also induces hypoxia, and we aimed to investigate whether protective physiological responses, i.e., the cardiovascular diving response and spleen contraction, induced during apnea at low-altitude could predict individual susceptibility to AMS. Eighteen participants (eight females) performed three static apneas in air, the first at a fixed limit of 60 s (A1) and two of maximal duration (A2-A3), spaced by 2 min, while SaO₂, heart rate (HR) and spleen volume were measured continuously. Tests were conducted in Kathmandu (1470 m) before a 14 day trek to mount Everest Base Camp (5360 m). During the trek, participants reported AMS symptoms daily using the Lake Louise Questionnaire (LLQ). The apnea-induced HR-reduction (diving bradycardia) was negatively correlated with the accumulated LLQ score in A1 (r _s = -0.628, p = 0.005) and A3 (r _s = -0.488, p = 0.040) and positively correlated with SaO₂ at 4410 m (A1: r = 0.655, p = 0.003; A2: r = 0.471, p = 0.049; A3: r = 0.635, p = 0.005). Baseline spleen volume correlated negatively with LLQ score (r _s = -0.479, p = 0.044), but no correlation was found between apnea-induced spleen volume reduction with LLQ score (r _s = 0.350, p = 0.155). The association between the diving bradycardia and spleen size with AMS symptoms suggests links between physiological responses to HA and apnea. Measuring individual responses to apnea at sea-level could provide means to predict AMS susceptibility prior to ascent.

Successful publishing of research: An editor's view

Authors often are frustrated by responses they receive from editors when their manuscripts are rejected and do not understand from an editor's view what is needed to successfully publish their work. Editors receive sometimes several manuscripts a day and have to develop methods to screen out the ones that are likely not to pass the review process. They also want papers to be able to be written in such a way that it is clear why the studies of which they report are important and novel and worth publishing. Thus, advice is given in the following article that begins with how to choose an appropriate journal, to the surprising importance of a title and ends with how one should conclude the manuscript.

Reexamination of the chromium-51-labeled posttransfusion red blood cell recovery method

BACKGROUND

The chromium-51-labeled posttransfusion recovery (PTR) study has been the gold-standard test for assessing red blood cell (RBC) quality. Despite guiding RBC storage development for decades, it has several potential sources for error.

METHODS

Four healthy adult volunteers each donated an autologous, leukoreduced RBC unit, aliquots were radiolabeled with technetium-99m after 1 and 6 weeks of storage, and then infused. Subjects were imaged by single-photon-emission computed tomography immediately and 4 hours after infusion. Additionally, from subjects described in a previously published study, adenosine triphosphate levels in transfusates infused into 52 healthy volunteers randomized to a single autologous, leukoreduced, RBC transfusion after 1, 2, 3, 4, 5, or 6 weeks of storage were correlated with PTR and laboratory parameters of hemolysis.

RESULTS

Evidence from one subject imaged after infusion of technetium-99m-labeled RBCs suggests that, in some individuals, RBCs may be temporarily sequestered in the liver and spleen immediately following transfusion and then subsequently released back into circulation; this could be one source of error leading to PTR results that may not accurately predict the true quantity of RBCs cleared by intra- and/or extravascular hemolysis. Indeed, adenosine triphosphate levels in the transfusates correlated more robustly with measures of extravascular hemolysis in vivo (e.g., serum iron, indirect bilirubin, non-transferrin-bound iron) than with PTR results or measures of intravascular hemolysis (e.g., plasma free hemoglobin).

CONCLUSIONS

Sources of measurement error are inherent in the chromium-51 PTR method. Transfusion of an entire unlabeled RBC unit, followed by quantifying extravascular hemolysis markers, may more accurately measure true posttransfusion RBC recovery.

The spleen morphophysiology of fruit bats

Spleen is one of the important lymphoid organs with wide variations of morphological and physiological functions according to species. Morphology and function of the spleen in bats, which are hosts to several viral strains without exhibiting clinical symptoms, remain to be fully elucidated. This study aims to examine the spleen morphology of fruit bats associated with their physiological functions. Spleen histological observations were performed in three fruit bats species: Cynopterus titthaecheilus (n = 9), Rousettus leschenaultii (n = 3) and Pteropus vampyrus (n = 3). The spleens of these fruit bats were surrounded by a thin capsule. Red pulp consisted of splenic cord and wide vascular space filled with blood. Ellipsoids in all three studied species were found numerously and adjacent to one another forming macrophages aggregates. White pulp consisted of periarteriolar lymphoid sheaths (PALS), lymphoid follicles and marginal zone. The lymphoid follicle contained a germinal centre and a tingible body macrophage that might reflect an active immune system. The marginal zone was prominent and well developed. This study reports some differences in spleen structure of fruit bats compared to other bat species previously reported and discusses possible physiological implications of the spleen based on its morphology.

Non-communicable diseases among low income adults in rural coastal communities in Eastern Sabah, Malaysia

Background

Rural coastal communities in Sabah are still overly represented in the hardcore poor economic status. The aim of this study was to determine the prevalence of hypertension, diabetes mellitus and hypercholesterolemia among adults, in relation to economic status.

Methods

A cross-sectional study using stratified random sampling was conducted in seven coastal villages in Semporna, Sabah: Kabogan Laut, Salimbangun, Pekalangan, Pokas, Tampi-Tampi Timbayan, Sum Sum and Selinggit. Socio-demographic data were obtained via interviewer administered questionnaires in Sabah Malay creole. Anthropometric measurements, blood pressure, fasting blood glucose and blood lipids were obtained.

Results

A total of 330 adults (133 males, 197 females) completed the study. Mean age was 43.7 ± 15.8 years. Most participants (87%) were living below the Poverty Line Income. Median per capita household income was RM83.33/month (≈ USD20/month). The number of newly diagnosed cases of hypercholesterolemia was 40.6%, diabetes mellitus was 5.8%, and hypertension was 24.5%. Adults from the hardcore poor economic status (household income ≤RM760/month (≈USD183/month) were the most represented in those who did not have a blood pressure, blood sugar and blood lipids check in the 12 months preceding the study (Χ², p < 0.01). Adults from hardcore poor economic status were also the most represented in undiagnosed hypertension and uncontrolled blood pressure among those diagnosed (Χ², p = 0.013). Among diabetics from the hardcore poor group, the undiagnosed fasting blood glucose was 11.2 ± 4.5 compared to 5.1 ± 0.6 mmol/L for diagnosed diabetics (p < 0.001). Among hypercholesterolemics from the hardcore poor group, total cholesterol and LDL cholesterol values were significantly higher in the undiagnosed group compared to the diagnosed group (p < 0.001).

Conclusion

Many people in this rural coastal community were unaware that they had high cholesterol level (40.6%) and elevated blood pressure (24.5%). Routine health check is not common among low income adults in rural coastal communities in Semporna. The findings suggest public health initiatives should emphasize access to and the necessity of routine health checks for those aged 40 years.

Eight weeks of static apnea training increases spleen volume but not acute spleen contraction

Splenic contraction is an important response to acute apnea causing the release of red blood cells into blood circulation. Current literature shows higher spleen volumes and greater spleen contractions in trained apnea divers compared to untrained individuals, but the influence of training is presently unknown. Thirteen subjects daily performed five static apneas for 8 weeks. Before, halfway through and after the apnea training period, subjects performed five maximal breath-holds at the laboratory. Baseline values for and changes in splenic volume and hemoglobin ([Hb]) were assessed. Although baseline spleen volume had increased (from 241 ± 55 mL PRE to 299 ± 51 mL POST training, p = 0.007), the absolute spleen contraction (142 ± 52 mL PRE and 139 ± 34 mL POST training, p = 0.868) and the acute increase in [Hb] remained unchanged. The present study shows that apnea training can increase the size of the spleen but that eight weeks of training is not sufficient to elicit significant training adaptations on the acute response.

Linking a mutation to survival in wild mice

Adaptive evolution in new or changing environments can be difficult to predict because the functional connections between genotype, phenotype, and fitness are complex. Here, we make these explicit connections by combining field and laboratory experiments in wild mice. We first directly estimate natural selection on pigmentation traits and an underlying pigment locus, Agouti, by using experimental enclosures of mice on different soil colors. Next, we show how a mutation in Agouti associated with survival causes lighter coat color through changes in its protein binding properties. Together, our findings demonstrate how a sequence variant alters phenotype and then reveal the ensuing ecological consequences that drive changes in population allele frequency, thereby illuminating the process of evolution by natural selection.

Novel insight into the genetic basis of high-altitude pulmonary hypertension in Kyrgyz highlanders

The Central Asian Kyrgyz highland population provides a unique opportunity to address genetic diversity and understand the genetic mechanisms underlying high-altitude pulmonary hypertension (HAPH). Although a significant fraction of the population is unaffected, there are susceptible individuals who display HAPH in the absence of any lung, cardiac or hematologic disease. We report herein the analysis of the whole-genome sequencing of healthy individuals compared with HAPH patients and other controls (total n = 33). Genome scans reveal selection signals in various regions, encompassing multiple genes from the first whole-genome sequences focusing on HAPH. We show here evidence of three candidate genes MTMR4, TMOD3 and VCAM1 that are functionally associated with well-known molecular and pathophysiological processes and which likely lead to HAPH in this population. These processes are (a) dysfunctional BMP signaling, (b) disrupted tissue repair processes and (c) abnormal endothelial cell function. Whole-genome sequence of well-characterized patients and controls and using multiple statistical tools uncovered novel candidate genes that belong to pathways central to the pathogenesis of HAPH. These studies on high-altitude human populations are pertinent to the understanding of sea level diseases involving hypoxia as a main element of their pathophysiology.

Exaptation at the molecular genetic level

The realization that body parts of animals and plants can be recruited or coopted for novel functions dates back to, or even predates the observations of Darwin. S.J. Gould and E.S. Vrba recognized a mode of evolution of characters that differs from adaptation. The umbrella term aptation was supplemented with the concept of exaptation. Unlike adaptations, which are restricted to features built by selection for their current role, exaptations are features that currently enhance fitness, even though their present role was not a result of natural selection. Exaptations can also arise from nonaptations; these are characters which had previously been evolving neutrally. All nonaptations are potential exaptations. The concept of exaptation was expanded to the molecular genetic level which aided greatly in understanding the enormous potential of neutrally evolving repetitive DNA-including transposed elements, formerly considered junk DNA-for the evolution of genes and genomes. The distinction between adaptations and exaptations is outlined in this review and examples are given. Also elaborated on is the fact that such distinctions are sometimes more difficult to determine; this is a widespread phenomenon in biology, where continua abound and clear borders between states and definitions are rare.

Differential responses of Lasiopodomys mandarinus and Lasiopodomys brandtii to chronic hypoxia: a cross-species brain transcriptome analysis

BACKGROUND

Subterranean rodents have evolved many features to adapt to their hypoxic environment. The brain is an organ that is particularly vulnerable to damage caused by exposure to hypoxic conditions. To investigate the mechanisms of adaption to a hypoxic underground environment, we carried out a cross-species brain transcriptome analysis by RNA sequencing and identified genes that are differentially expressed between the subterranean vole Lasiopodomys mandarinus and the closely related above-ground species Lasiopodomys brandtii under chronic hypoxia [10.0% oxygen (O2)] and normoxia (20.9% O2).

RESULTS

A total of 355 million clean reads were obtained, including 69,611 unigenes in L. mandarinus and 69,360 in L. brandtii. A total of 235 and 92 differentially expressed genes (DEGs) were identified by comparing the hypoxic and control groups of L. mandarinus and L. brandtii, respectively. A Gene Ontology (GO) analysis showed that upregulated DEGs in both species had similar functions in response to hypoxia, whereas downregulated DEGs in L. mandarinus were enriched GO terms related to enzymes involved in aerobic reactions. In the Kyoto Encyclopedia of Genes and Genomes pathway analysis, upregulated DEGs in L. mandarinus were associated with angiogenesis and the increased O2 transport capacity of red blood cells, whereas downregulated DEGs were associated with immune responses. On the other hand, upregulated DEGs in L. brandtii were associated with cell survival, vascular endothelial cell proliferation, and neuroprotection, while downregulated genes were related to the synaptic transmission by neurons.

CONCLUSIONS

L. mandarinus actively adapts its physiological functions to hypoxic conditions, for instance by increasing O2 transport capacity and modulating O2 consumption. In contrast, L. brandtii reacts passively to hypoxia by decreasing overall activity in order to reduce O2 consumption. These results provide insight into hypoxia adaptation mechanisms in subterranean rodents that may be applicable to humans living at high altitudes or operating in other O2-poor environments.

Quantifying how constraints limit the diversity of viable routes to adaptation

Convergent adaptation occurs at the genome scale when independently evolving lineages use the same genes to respond to similar selection pressures. These patterns of genetic repeatability provide insights into the factors that facilitate or constrain the diversity of genetic responses that contribute to adaptive evolution. A first step in studying such factors is to quantify the observed amount of repeatability relative to expectations under a null hypothesis. Here, we formulate a novel index to quantify the constraints driving the observed amount of repeated adaptation in pairwise contrasts based on the hypergeometric distribution, and then generalize this for simultaneous analysis of multiple lineages. This index is explicitly based on the probability of observing a given amount of repeatability by chance under a given null hypothesis and is readily compared among different species and types of trait. We also formulate an index to quantify the effective proportion of genes in the genome that have the potential to contribute to adaptation. As an example of how these indices can be used to draw inferences, we assess the amount of repeatability observed in existing datasets on adaptation to stress in yeast and climate in conifers. This approach provides a method to test a wide range of hypotheses about how different kinds of factors can facilitate or constrain the diversity of genetic responses observed during adaptive evolution.

How many ways can evolution solve the same adaptive problem? While convergent adaptation is evident in many organisms at the phenotypic level, we are only beginning to understand how commonly this convergence extends to the genome scale. Quantifying the repeatability of adaptation at the genome scale is therefore critical for assessing how constraints affect the diversity of viable genetic responses. Here, we develop probability-based indices to quantify the deviation between observed repeatability and expectations under a range of null hypotheses, and an estimator of the proportion of loci in the genome that can contribute to adaptation. We demonstrate the usage of these indices with individual-based simulations and example datasets from yeast and conifers and discuss how they differ from previously developed approaches to studying repeatability. Because these indices are unitless, they provide a general approach to quantifying and comparing how constraints drive convergence at the genome scale across a wide range of traits and taxa.

Human adaptation to extreme environmental conditions

Modern humans inhabit most of earth's harshest environments and display a wide array of lifestyles. Biological adaptations, in addition to technological innovations, have enabled these geographical and cultural explorations. The study of these adaptations helps not only to fundamentally understand our evolution as a species, but also may have increasing relevance as genomics transforms fields such as personalized medicine. Here we review three cultural and environmental shifts that have brought about adaptations in modern humans; the arctic, high altitudes, and a subsistence dependent on breath-hold diving.