Structurally divergent and recurrently mutated regions of primate genomes.

We sequenced and assembled using multiple long-read sequencing technologies the genomes of chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, owl monkey, and marmoset. We identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. We estimate that 819.47 Mbp or ∼27% of the genome has been affected by SVs across primate evolution. We identify 1,607 structurally divergent regions wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (e.g., CARD, C4, and OLAH gene families) and additional lineage-specific genes are generated (e.g., CKAP2, VPS36, ACBD7, and NEK5 paralogs), becoming targets of rapid chromosomal diversification and positive selection (e.g., RGPD gene family). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species.

Brain volume, energy balance, and cardiovascular health in two nonindustrial South American populations.

Little is known about brain aging or dementia in nonindustrialized environments that are similar to how humans lived throughout evolutionary history. This paper examines brain volume (BV) in middle and old age among two indigenous South American populations, the Tsimane and Moseten, whose lifestyles and environments diverge from those in high-income nations. With a sample of 1,165 individuals aged 40 to 94, we analyze population differences in cross-sectional rates of decline in BV with age. We also assess the relationships of BV with energy biomarkers and arterial disease and compare them against findings in industrialized contexts. The analyses test three hypotheses derived from an evolutionary model of brain health, which we call the embarrassment of riches (EOR). The model hypothesizes that food energy was positively associated with late life BV in the physically active, food-limited past, but excess body mass and adiposity are now associated with reduced BV in industrialized societies in middle and older ages. We find that the relationship of BV with both non-HDL cholesterol and body mass index is curvilinear, positive from the lowest values to 1.4 to 1.6 SDs above the mean, and negative from that value to the highest values. The more acculturated Moseten exhibit a steeper decrease in BV with age than Tsimane, but still shallower than US and European populations. Lastly, aortic arteriosclerosis is associated with lower BV. Complemented by findings from the United States and Europe, our results are consistent with the EOR model, with implications for interventions to improve brain health.

The Role of Selection and Migration in the Evolution of (Auto)Immunity Genes.

The genetic architecture of multiple sclerosis is complicated. Additionally, the disease incidence varies per population or per geographical region. A recent study gives convincing explanations about the north-south incidence gradient of multiple sclerosis in Europe, by analyzing ancient and modern human genomes. Interestingly, the evidence shows that multiple sclerosis associated immunogenetic variants underwent positive selection in Asian and European populations. Lifestyle and pathogen infections probably shaped the overall multiple sclerosis risk. These results complete the findings of previous studies that showed that a high percentage of the autoimmunity associated genetic variants are under selection pressure.

Evolution of the human birth canal.

It seems puzzling why humans have evolved such a small and rigid birth canal that entails a relatively complex process of labor compared with the birth canal of our closest relatives, the great apes. This study reviewed insights into the evolution of the human birth canal from recent theoretical and empirical studies and discussed connections to obstetrics, gynecology, and orthopedics. Originating from the evolution of bipedality and the large human brain million years ago, the evolution of the human birth canal has been characterized by complex trade-off dynamics among multiple biological, environmental, and sociocultural factors. The long-held notion that a wider pelvis has not evolved because it would be disadvantageous for bipedal locomotion has not yet been empirically verified. However, recent clinical and biomechanical studies suggest that a larger birth canal would compromise pelvic floor stability and increase the risk of incontinence and pelvic organ prolapse. Several mammals have neonates that are equally large or even larger than human neonates compared to the size of the maternal birth canal. In these species, the pubic symphysis opens widely to allow successful delivery. Biomechanical and developmental constraints imposed by bipedality have hindered this evolutionary solution in humans and led to the comparatively rigid pelvic girdle in pregnant women. Mathematical models have shown why the evolutionary compromise to these antagonistic selective factors inevitably involves a certain rate of fetopelvic disproportion. In addition, these models predict that cesarean deliveries have disrupted the evolutionary equilibrium and led to new and ongoing evolutionary changes. Different forms of assisted birth have existed since the stone age and have become an integral part of human reproduction. Paradoxically, by buffering selection, they may also have hindered the evolution of a larger birth canal. Many of the biological, environmental, and sociocultural factors that have influenced the evolution of the human birth canal vary globally and are subject to ongoing transitions. These differences may have contributed to the global variation in the form of the birth canal and the difficulty of labor, and they likely continue to change human reproductive anatomy.

Evolutionary medicine approaches to chronic disease: The case of irritable bowel syndrome.

Irritable bowel syndrome (IBS), a gastrointestinal disease, is a global phenomenon correlated with industrialization. We propose that an evolutionary medicine approach is useful to understand this disease from an ultimate perspective and conducted a scoping literature review to synthesize the IBS literature within this framework. Our review suggests five potential evolutionary hypotheses for the cause of IBS, including (a) a dietary mismatch accompanying a nutritional transition, (b) an early hygienic life environment leading to the immune system and microbiotic changes, (c) an outcome of decreased physical activity, (d) a response to changes in environmental light-dark cycles, and (e) an artifact of an evolved fight or flight response. We find key limitations in the available data needed to understand early life, nutritional, and socioeconomic experiences that would allow us to understand evolutionarily relevant risk factors and identify a need for further empirical research to distinguish potential causes and test evolutionary hypotheses.

Human behaviors driving disease emergence.

Interactions between humans, animals, and the environment facilitate zoonotic spillover-the transmission of pathogens from animals to humans. Narratives that cast modern humans as exogenous and disruptive forces that encroach upon "natural" disease systems limit our understanding of human drivers of disease. This review leverages theory from evolutionary anthropology that situates humans as functional components of disease ecologies, to argue that human adaptive strategies to resource acquisition shape predictable patterns of high-risk human-animal interactions, (2) humans construct ecological processes that facilitate spillover, and (3) contemporary patterns of epidemiological risk are emergent properties of interactions between human foraging ecology and niche construction. In turn, disease ecology serves as an important vehicle to link what some cast as opposing bodies of theory in human ecology. Disease control measures should consider human drivers of disease as rational, adaptive, and dynamic and capitalize on our capacity to influence ecological processes to mitigate risk.

Evolutionary physiology at 30+: Has the promise been fulfilled?: Advances in Evolutionary Physiology: Advances in Evolutionary Physiology.

Three decades ago, interactions between evolutionary biology and physiology gave rise to evolutionary physiology. This caused comparative physiologists to improve their research methods by incorporating evolutionary thinking. Simultaneously, evolutionary biologists began focusing more on physiological mechanisms that may help to explain constraints on and trade-offs during microevolutionary processes, as well as macroevolutionary patterns in physiological diversity. Here we argue that evolutionary physiology has yet to reach its full potential, and propose new avenues that may lead to unexpected advances. Viewing physiological adaptations in wild animals as potential solutions to human diseases offers enormous possibilities for biomedicine. New evidence of epigenetic modifications as mechanisms of phenotypic plasticity that regulate physiological traits may also arise in coming years, which may also represent an overlooked enhancer of adaptation via natural selection to explain physiological evolution. Synergistic interactions at these intersections and other areas will lead to a novel understanding of organismal biology.

Combat stress in a small-scale society suggests divergent evolutionary roots for posttraumatic stress disorder symptoms.

Military personnel in industrialized societies often develop posttraumatic stress disorder (PTSD) during combat. It is unclear whether combat-related PTSD is a universal evolutionary response to danger or a culture-specific syndrome of industrialized societies. We interviewed 218 Turkana pastoralist warriors in Kenya, who engage in lethal cattle raids, about their combat experiences and PTSD symptoms. Turkana in our sample had a high prevalence of PTSD symptoms, but Turkana with high symptom severity had lower prevalence of depression-like symptoms than American service members with high symptom severity. Symptoms that facilitate responding to danger were better predicted by combat exposure, whereas depressive symptoms were better predicted by exposure to combat-related moral violations. The findings suggest that some PTSD symptoms stem from an evolved response to danger, while depressive PTSD symptoms may be caused by culturally specific moral norm violations.

Learning from disability studies to introduce the role of the individual to naturalistic accounts of disease.

Disability studies have been successfully focusing on individuals' lived experiences, the personalization of goals, and the constitution of the individual in defining disease and restructuring public understandings of disability. Although they had a strong influence in the policy making and medical modeling of disease, their framework has not been translated to traditional naturalistic accounts of disease. I will argue that, using new developments in evolutionary biology (Extended Evolutionary Synthesis [EES] about questions of proper function) and behavioral ecology (Niche conformance and construction about the questions of reference classes in biostatistics accounts), the main elements of the framework of disability studies can be used to represent life histories at the conceptual level of the two main "non-normative" accounts of disease. I chose these accounts since they are related to medicine in a more descriptive way. The success of the practical aspects of disability studies this way will be communicated without causing injustice to the individual since they will represent the individuality of the patient in two main naturalistic accounts of disease: the biostatistical account and the evolutionary functional account. Although most accounts criticizing the concept of disease as value-laden do not supply a positive element, disability studies can supply a good point for descriptive extension of the concept through inclusion of epistemic agency.

Evolution of the DAN gene family in vertebrates.

The DAN gene family (DAN, Differential screening-selected gene Aberrant in Neuroblastoma) is a group of genes that is expressed during development and plays fundamental roles in limb bud formation and digitation, kidney formation and morphogenesis and left-right axis specification. During adulthood the expression of these genes are associated with diseases, including cancer. Although most of the attention to this group of genes has been dedicated to understanding its role in physiology and development, its evolutionary history remains poorly understood. Thus, the goal of this study is to investigate the evolutionary history of the DAN gene family in vertebrates, with the objective of complementing the already abundant physiological information with an evolutionary context. Our results recovered the monophyly of all DAN gene family members and divide them into five main groups. In addition to the well-known DAN genes, our phylogenetic results revealed the presence of two new DAN gene lineages; one is only retained in cephalochordates, whereas the other one (GREM3) was only identified in cartilaginous fish, holostean fish, and coelacanth. According to the phyletic distribution of the genes, the ancestor of gnathostomes possessed a repertoire of eight DAN genes, and during the radiation of the group GREM1, GREM2, SOST, SOSTDC1, and NBL1 were retained in all major groups, whereas, GREM3, CER1, and DAND5 were differentially lost.

Labour's pain: strenuous subsistence work, mechanical wear-and-tear and musculoskeletal pain in a non-industrialized population.

Musculoskeletal pain is the most debilitating human health condition. Neurophysiological pain mechanisms are highly conserved and promote somatic maintenance and learning to avoid future harm. However, some chronic pain might be more common owing to mismatches between modern lifestyles and traits that originally evolved under distinct premodern conditions. To inform assumptions about factors affecting chronic pain vulnerability prior to industrialization, we assess pain prevalence, perceived causes, and predictors among Tsimane forager-horticulturalists. Habitual subsistence work is the primary reported cause of pain throughout life for both sexes, and pain is more common with age, especially in the back, and for those with more musculoskeletal problems. Sex differences in pain are relatively weak, and we find no association between women's reproductive history and pain, contrary to the hypothesis that reproduction causes women's greater pain susceptibility. Age-standardized current pain prevalence is 1.7-8.2 times higher for Tsimane than other select populations, and Tsimane chronic pain prevalence is within the range of variation observed elsewhere. Chronic low back pain is not a 'mismatch disease' limited to post-industrialized populations. Hominin musculoskeletal changes supporting bipedalism probably imposed health costs, which, after millions of years of evolution, remain an epidemiological burden that may be exacerbated by modern conditions.

Hunter-gatherer diets and activity as a model for health promotion: Challenges, responses, and confirmations.

Beginning in 1985, we and others presented estimates of hunter-gatherer (and ultimately ancestral) diet and physical activity, hoping to provide a model for health promotion. The Hunter-Gatherer Model was designed to offset the apparent mismatch between our genes and the current Western-type lifestyle, a mismatch that arguably affects prevalence of many chronic degenerative diseases. The effort has always been controversial and subject to both scientific and popular critiques. The present article (1) addresses eight such challenges, presenting for each how the model has been modified in response, or how the criticism can be rebutted; (2) reviews new epidemiological and experimental evidence (including especially randomized controlled clinical trials); and (3) shows how official recommendations put forth by governments and health authorities have converged toward the model. Such convergence suggests that evolutionary anthropology can make significant contributions to human health.

The pandemic exposes human nature: 10 evolutionary insights.

Humans and viruses have been coevolving for millennia. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, the virus that causes COVID-19) has been particularly successful in evading our evolved defenses. The outcome has been tragic-across the globe, millions have been sickened and hundreds of thousands have died. Moreover, the quarantine has radically changed the structure of our lives, with devastating social and economic consequences that are likely to unfold for years. An evolutionary perspective can help us understand the progression and consequences of the pandemic. Here, a diverse group of scientists, with expertise from evolutionary medicine to cultural evolution, provide insights about the pandemic and its aftermath. At the most granular level, we consider how viruses might affect social behavior, and how quarantine, ironically, could make us susceptible to other maladies, due to a lack of microbial exposure. At the psychological level, we describe the ways in which the pandemic can affect mating behavior, cooperation (or the lack thereof), and gender norms, and how we can use disgust to better activate native "behavioral immunity" to combat disease spread. At the cultural level, we describe shifting cultural norms and how we might harness them to better combat disease and the negative social consequences of the pandemic. These insights can be used to craft solutions to problems produced by the pandemic and to lay the groundwork for a scientific agenda to capture and understand what has become, in effect, a worldwide social experiment.

Evolution of insulin at the edge of foldability and its medical implications.

Proteins have evolved to be foldable, and yet determinants of foldability may be inapparent once the native state is reached. Insight has emerged from studies of diseases of protein misfolding, exemplified by monogenic diabetes mellitus due to mutations in proinsulin leading to endoplasmic reticulum stress and ß-cell death. Cellular foldability of human proinsulin requires an invariant Phe within a conserved crevice at the receptor-binding surface (position B24). Any substitution, even related aromatic residue TyrB24, impairs insulin biosynthesis and secretion. As a seeming paradox, a monomeric TyrB24 insulin analog exhibits a native-like structure in solution with only a modest decrement in stability. Packing of TyrB24 is similar to that of PheB24, adjoining core cystine B19-A20 to seal the core; the analog also exhibits native self-assembly. Although affinity for the insulin receptor is decreased ∼20-fold, biological activities in cells and rats were within the range of natural variation. Together, our findings suggest that the invariance of PheB24 among vertebrate insulins and insulin-like growth factors reflects an essential role in enabling efficient protein folding, trafficking, and secretion, a function that is inapparent in native structures. In particular, we envision that the para-hydroxyl group of TyrB24 hinders pairing of cystine B19-A20 in an obligatory on-pathway folding intermediate. The absence of genetic variation at B24 and other conserved sites near this disulfide bridge-excluded due to ß-cell dysfunction-suggests that insulin has evolved to the edge of foldability. Nonrobustness of a protein's fitness landscape underlies both a rare monogenic syndrome and "diabesity" as a pandemic disease of civilization.

The pathological anatomical collection of the Natural History Museum Vienna.

The pathological anatomical collection Vienna (Pathologisch-Anatomische Sammlung Wien; PASW) is a living and still growing research collection. It was established as early as 1796 as part of the Medical University of Vienna, acquired the status of an independent federal museum in 1971, and was assigned to the Natural History Museum Vienna in 2012. It houses a wide range of human wet and dry specimens and further objects, such as moulages, medical devices, microbiological and histological specimens, and a photo archive (approximately 50,000 objects), which, as a meaningful source, may contribute to disclosing not only aspects of the medical history and the development of corresponding museums in Vienna, but is also considered a collection of cultural and current scientific relevance, quite comparable to today's biobanks. Most of the tissue amassment represents wet organic specimens and human skeletons or skeletal elements representing, e.g., congenital and metabolic disorders, infectious diseases, injuries, neoplasms, or musculoskeletal diseases, basically collected as descriptive anatomical teaching aids. This article reviews the current medical issues on which research has been and is being conducted by including PASW specimens (hereby using the ICD-10 code), and the extent to and ethical conditions under which this important heritage could be used as a reference collection for clinical and bioanthropological (paleopathological and palaeoepidemiological) studies; finally, this article reflects on the value and future research prospects, taking into account different positions and the ongoing discussions in pathological anatomical human tissue collections.

Evolution of Renal-Disease Factor APOL1 Results in Cis and Trans Orientations at the Endoplasmic Reticulum That Both Show Cytotoxic Effects.

The recent and exclusively in humans and a few other higher primates expressed APOL1 (apolipoprotein L1) gene is linked to African human trypanosomiasis (also known as African sleeping sickness) as well as to different forms of kidney diseases. Whereas APOL1's role as a trypanolytic factor is well established, pathobiological mechanisms explaining its cytotoxicity in renal cells remain unclear. In this study, we compared the APOL family members using a combination of evolutionary studies and cell biological experiments to detect unique features causal for APOL1 nephrotoxic effects. We investigated available primate and mouse genome and transcriptome data to apply comparative phylogenetic and maximum likelihood selection analyses. We suggest that the APOL gene family evolved early in vertebrates and initial splitting occurred in ancestral mammals. Diversification and differentiation of functional domains continued in primates, including developing the two members APOL1 and APOL2. Their close relationship could be diagnosed by sequence similarity and a shared ancestral insertion of an AluY transposable element. Live-cell imaging analyses showed that both expressed proteins show a strong preference to localize at the endoplasmic reticulum (ER). However, glycosylation and secretion assays revealed that-unlike APOL2-APOL1 membrane insertion or association occurs in different orientations at the ER, with the disease-associated mutants facing either the luminal (cis) or cytoplasmic (trans) side of the ER. The various pools of APOL1 at the ER offer a novel perspective in explaining the broad spectrum of its observed toxic effects.

Cellular Biogenetic Law and Its Distortion by Protein Interactions: A Possible Unified Framework for Cancer Biology and Regenerative Medicine.

The biogenetic law (recapitulation law) states that ontogenesis recapitulates phylogenesis. However, this law can be distorted by the modification of development. We showed the recapitulation of phylogenesis during the differentiation of various cell types, using a meta-analysis of human single-cell transcriptomes, with the control for cell cycle activity and the improved phylostratigraphy (gene dating). The multipotent progenitors, differentiated from pluripotent embryonic stem cells (ESC), showed the downregulation of unicellular (UC) genes and the upregulation of multicellular (MC) genes, but only in the case of those originating up to the Euteleostomi (bony vertebrates). This picture strikingly resembles the evolutionary profile of regulatory gene expansion due to gene duplication in the human genome. The recapitulation of phylogenesis in the induced pluripotent stem cells (iPSC) during their differentiation resembles the ESC pattern. The unipotent erythroblasts differentiating into erythrocytes showed the downregulation of UC genes and the upregulation of MC genes originating after the Euteleostomi. The MC interactome neighborhood of a protein encoded by a UC gene reverses the gene expression pattern. The functional analysis showed that the evolved environment of the UC proteins is typical for protein modifiers and signaling-related proteins. Besides a fundamental aspect, this approach can provide a unified framework for cancer biology and regenerative/rejuvenation medicine because oncogenesis can be defined as an atavistic reversal to a UC state, while regeneration and rejuvenation require an ontogenetic reversal.

Helicobacter pylori: an evolutionary perspective.

Since the description of Helicobacter pylori (HP) as the most common cause of gastritis and its neoplastic complications, numerous articles have been written about the epidemiology, clinical features, diagnostic methods, histopathology, pathogenesis, molecular biology and treatment of this infection. This review focuses on those aspects of the infection that challenge the universality of the medical implications through the lens of evolutionary science applied to medicine. The divergent epidemiological and clinical outcomes observed in different populations and the possible beneficial aspects of the infection are discussed. Also reviewed are Correa's seminal contributions to our understanding of gastric cancer in particular and postinflammatory tumours in general, and the renewed interest in intestinal metaplasia and its clinical implications.

Inflammaging: Blame the sons. Relationships between the number of sons and the level of inflammatory mediators among post-reproductive women.

OBJECTIVES: Reproduction is costly, but sons and daughters differently influence maternal physiology, also in older age. In particular, having sons may negatively influence maternal health and may be associated with a shorter life span of mothers. Sons may also contribute to increased inflammaging, a chronic sub-clinical systemic inflammatory state characterized by elevated levels of serum inflammatory mediators. The aim of this study was to examine the impact of the total number of children, and the number of daughters and sons separately on concentrations of C-reactive protein (CRP), and proinflammatory cytokines such as interleukin 6 (IL-6) and tumor necrosis factor-α (TNF-α). MATERIALS AND METHODS: The participants were 378 women aged 45-92 who had 3.9 (SD 2.12, median = 4, range = 0-13) children, including 2.1 (SD 1.46, median = 2, range = 0-8) sons and 1.8 (SD 1.44, median = 2, range = 0-7) daughters on average. RESULTS: We found a positive relationship between the overall number of children and IL-6 levels. CRP and IL-6 concentrations were positively associated with the number of sons but not with the number of daughters. Each son increased maternal CRP level by 11%, and IL-6 level by 6%. Neither the total number of children nor the number of daughters or sons were related to the TNF-α concentration. DISCUSSION: Aging-associated inflammation in post-reproductive mothers with a higher number of sons supports the hypothesis of trade-offs between reproduction and health. Furthermore, these results provide new evidence contributing to the idea that having sons may have more detrimental effects on the maternal organism than having daughters.

Genomic history of the Italian population recapitulates key evolutionary dynamics of both Continental and Southern Europeans.

BACKGROUND: The cline of human genetic diversity observable across Europe is recapitulated at a micro-geographic scale by variation within the Italian population. Besides resulting from extensive gene flow, this might be ascribable also to local adaptations to diverse ecological contexts evolved by people who anciently spread along the Italian Peninsula. Dissecting the evolutionary history of the ancestors of present-day Italians may thus improve the understanding of demographic and biological processes that contributed to shape the gene pool of European populations. However, previous SNP array-based studies failed to investigate the full spectrum of Italian variation, generally neglecting low-frequency genetic variants and examining a limited set of small effect size alleles, which may represent important determinants of population structure and complex adaptive traits. To overcome these issues, we analyzed 38 high-coverage whole-genome sequences representative of population clusters at the opposite ends of the cline of Italian variation, along with a large panel of modern and ancient Euro-Mediterranean genomes. RESULTS: We provided evidence for the early divergence of Italian groups dating back to the Late Glacial and for Neolithic and distinct Bronze Age migrations having further differentiated their gene pools. We inferred adaptive evolution at insulin-related loci in people from Italian regions with a temperate climate, while possible adaptations to pathogens and ultraviolet radiation were observed in Mediterranean Italians. Some of these adaptive events may also have secondarily modulated population disease or longevity predisposition. CONCLUSIONS: We disentangled the contribution of multiple migratory and adaptive events in shaping the heterogeneous Italian genomic background, which exemplify population dynamics and gene-environment interactions that played significant roles also in the formation of the Continental and Southern European genomic landscapes.