Evolution of the human pygmy phenotype

Exploring Adaptive Phenotypes for the Human Calcium-Sensing Receptor Polymorphism R990G

Rainforest hunter-gatherers from Southeast Asia are characterized by specific morphological features including a particularly dark skin color (D), short stature (S), woolly hair (W), and the presence of steatopygia (S)-fat accumulation localized in the hips (DSWS phenotype). Based on previous evidence in the Andamanese population, we first characterized signatures of adaptive natural selection around the calcium-sensing receptor gene in Southeast Asian rainforest groups presenting the DSWS phenotype and identified the R990G substitution (rs1042636) as a putative adaptive variant for experimental follow-up. Although the calcium-sensing receptor has a critical role in calcium homeostasis by directly regulating the parathyroid hormone secretion, it is expressed in different tissues and has been described to be involved in many biological functions. Previous works have also characterized the R990G substitution as an activating polymorphism of the calcium-sensing receptor associated with hypocalcemia. Therefore, we generated a knock-in mouse for this substitution and investigated organismal phenotypes that could have become adaptive in rainforest hunter-gatherers from Southeast Asia. Interestingly, we found that mouse homozygous for the derived allele show not only lower serum calcium concentration but also greater body weight and fat accumulation, probably because of enhanced preadipocyte differentiation and lipolysis impairment resulting from the calcium-sensing receptor activation mediated by R990G. We speculate that such differential features in humans could have facilitated the survival of hunter-gatherer groups during periods of nutritional stress in the challenging conditions of the Southeast Asian tropical rainforests.

Human subsistence and signatures of selection on chemosensory genes

Chemosensation (olfaction, taste) is essential for detecting and assessing foods, such that dietary shifts elicit evolutionary changes in vertebrate chemosensory genes. The transition from hunting and gathering to agriculture dramatically altered how humans acquire food. Recent genetic and linguistic studies suggest agriculture may have precipitated olfactory degeneration. Here, we explore the effects of subsistence behaviors on olfactory (OR) and taste (TASR) receptor genes among rainforest foragers and neighboring agriculturalists in Africa and Southeast Asia. We analyze 378 functional OR and 26 functional TASR genes in 133 individuals across populations in Uganda (Twa, Sua, BaKiga) and the Philippines (Agta, Mamanwa, Manobo) with differing subsistence histories. We find no evidence of relaxed selection on chemosensory genes in agricultural populations. However, we identify subsistence-related signatures of local adaptation on chemosensory genes within each geographic region. Our results highlight the importance of culture, subsistence economy, and drift in human chemosensory perception.

Variability and the form-function framework in evolutionary biomechanics and human locomotion

The form-function conceptual framework, which assumes a strong relationship between the structure of a particular trait and its function, has been crucial for understanding morphological variation and locomotion among extant and fossil species across many disciplines. In biological anthropology, it is the lens through which many important questions and hypotheses have been tackled with respect to relationships between morphology and locomotor kinematics, energetics and performance. However, it is becoming increasingly evident that the morphologies of fossil hominins, apes and humans can confer considerable locomotor diversity and flexibility, and can do so with a range of kinematics depending on soft tissue plasticity and environmental and cultural factors. This complexity is not built into traditional biomechanical or mathematical models of relationships between structure and kinematics or energetics, limiting our interpretation of what bone structure is telling us about behaviour in the past. The nine papers presented in this Special Collection together address some of the challenges that variation in the relationship between form and function pose in evolutionary biomechanics, to better characterise the complexity linking structure and function and to provide tools through which we may begin to incorporate some of this complexity into our functional interpretations.

Sex differences in adipose development in a hunter-gatherer population

OBJECTIVE

Humans are unusually sexually dimorphic in body composition, with adult females having on average nearly twice the fat mass as males. The development of adipose sex differences has been well characterized for children growing up in food-abundant environments, with less known about cross-cultural variation, particularly in populations without exposure to market foods, mechanized technologies, schooling, vaccination, or other medical interventions.

METHODS

To add to the existing cross-cultural data, we fit multiple growth curves to body composition and anthropometric data to describe adipose development for the Savanna Pumé, South American hunter-gatherers.

RESULTS

(1) Little evidence is found for an adiposity 'rebound' at the end of early childhood among either Savanna Pumé girls or boys. (2) Rather, fat deposition fluctuates during childhood, from age ~4 to ~9 years, with no appreciable accumulation until the onset of puberty, a pattern also observed among Congo Baka hunter-gatherers. (3) Body fat fluctuations are more pronounced for girls than boys. (4) The age of peak skeletal, weight, and adipose gains are staggered to a much greater extent among the Savanna Pumé compared to the National Health and Nutrition Examination Survey (NHANES III) reference, suggesting this is an important developmental strategy in lean populations.

CONCLUSION

Documenting growth patterns under diverse preindustrial energetic conditions provides an important baseline for understanding sex differences in body fat emerging today under food abundance.

Morphological variation of the deciduous second molars in the Baka Pygmies

The Baka Pygmies are known for their short stature resulting from a reduced growth rate during infancy. They are peculiar also for their teeth erupt earlier than in any other African population, and their posterior dentition is larger than in non-Pygmy populations. However, the Baka's dental morphology, like several other aspects of their biology, is still understudied. Here, we explore the variation of the Baka's deciduous upper and lower second molars (dm2s) in comparison to a geographically heterogeneous human sample by means of 3D geometric morphometrics and analysis of dental traits. Our results show that the different populations largely overlap based on the shape of their dm2s, especially the lower ones. Their distal region and the height of the dentinal crown differ the most, with the Baka showing the most extreme range of variation. Upper and lower dm2s covary to a great extent (RV = 0.82). The Baka's and South Americans' dm2s were confirmed among the largest in our sample. Despite the Baka's unique growth pattern, long-lasting isolation, and extreme dental variation, it is not possible to distinguish them from other populations based on their dm2s' morphology only.

Human biological variation and the "normal"

Anatomically modern human being is a relatively young species (~300 000 years old) with small amounts of genetic variation contained within them. The vast majority of its existence was spent in Eastern Africa, migration out of the region began around 100 000 YBP. Sub-Saharan African populations have the greatest amount of human genetic variation. However, migration allowed populations to accumulate genomic variation associated with living in the arctic, higher altitudes, disease resistance, living on high fat or starchy foods, surviving toxic arsenic-rich environments, lactase persistence, changing skin pigmentation, gaining thicker hair, and changing height and body mass index. Understanding these aspects of human evolution forces us to reconsider our notion of the "normal." Thus, normal for our species includes having dark melanic skin, brown eyes, and brown tightly curled hair. Derived features include lighter skin (~10 000 YBP), blue eyes (~6000 YBP), and blond straight hair (~6000 YBP). Yet in reality, "normal" has no meaning for a species that inhabits such a broad geographic range. Natural selection and genetic drift have genetically differentiated human populations in ways that impact our morphological and physiological traits. The genomic differentiation is small and does not allow any unambiguous classification of human populations into biological races. Despite these now well-established facts of human variation, significant confusion associated with Eurocentric notions of the normal still persist in both the lay public and various professions such as biomedical research and clinical practice.

Anthropometric, biochemical and hormonal profiles of the partially admixed pygmoid group in Rampasasa (Flores, Indonesia)

OBJECTIVES

We performed a cross-sectional study on anthropometric and laboratory characteristics of inhabitants of Rampasasa (Flores, Indonesia). Adults were categorised according to ancestry into three groups: pygmoid (P/P, offspring of pygmoid parents, n=8), mixed pygmoid (P/N, offspring of pygmoid and non-pygmoid parents, n=12) and non-pygmoid (N/N, n=10). Children (n=28) were P/N.

METHODS

Measurements included height, weight, sitting height, arm span, head circumference, haematological analysis and serum albumin, calcium, vitamin D, insulin-like growth factor-I (IGF-I) and IGF binding protein 3 (IGFBP-3). Pubertal stage and bone age was assessed in children. Anthropometric data were expressed as standard deviation score (SDS) for age. IGF-I, IGFBP-3 and IGF-I/IGFBP-3 ratio were expressed as SDS for age, bone age and pubertal stage.

RESULTS

Mean height SDS showed a gradient from P/P (-4.0) via P/N (-3.2) to N/N (-2.3) (-3.4, -3.1 and -2.2 adjusted for age-associated shrinking). Sitting height and head circumference showed similar gradients. Serum IGF-I SDS was similar among groups (approximately -1 SDS). IGFBP-3 SDS tended toward a gradient from P/P (-1.9) via P/N (-1.5) to N/N (-1.1), but IGF-I/IGFBP-3 ratio was normal in all groups. In P/P and P/N, mean head circumference SDS was >2 SD greater than mean height SDS. Children showed a progressive growth failure and bone age delay, delayed female pubertal onset and an initial low serum IGF-I, normal IGFBP-3 and low IGF-I/IGFBP-3 ratio.

CONCLUSIONS

P/P showed proportionate short stature with relative macrocephaly and relatively low IGFBP-3; P/N presented an intermediate pattern. P/N children were progressively short, showed delayed skeletal maturation, delayed puberty in girls and low IGF-I and IGF-I/IGFBP-3.

The distinct morphological phenotypes of Southeast Asian aborigines are shaped by novel mechanisms for adaptation to tropical rainforests

Southeast Asian aborigines, the hunter-gatherer populations living in tropical rainforests, exhibit distinct morphological phenotypes, including short stature, dark skin, curly hair and a wide and snub nose. The underlying genetic architecture and evolutionary mechanism of these phenotypes remain a long-term mystery. We conducted whole genome deep sequencing of 81 Cambodian aborigines from eight ethnic groups. Through a genome-wide scan of selective sweeps, we discovered key genes harboring Cambodian-enriched mutations that may contribute to their phenotypes, including two hair morphogenesis genes (TCHH and TCHHL1), one nasal morphology gene (PAX3) and a set of genes (such as ENTPD1-AS1) associated with short stature. The identified new genes and novel mutations suggest an independent origin of the distinct phenotypes in Cambodian aborigines through parallel evolution, refuting the long-standing argument on the common ancestry of these phenotypes among the worldwide rainforest hunter-gatherers. Notably, our discovery reveals that various types of molecular mechanisms, including antisense transcription and epigenetic regulation, contribute to human morphogenesis, providing novel insights into the genetics of human environmental adaptation.

Phenotypic diversity and history of the Congo Basin populations: Equatorial Guinea, Bantu Speaking Central Africans and African Pygmies

BACKGROUND

African Pygmy Populations (APP) are believed to be one of the first groups of the Congo Basin rainforest peoples to separate from the rest of modern humanity. The arrival of Bantu speaking agriculturalists from 5,000 BP led to the formation of a large number of ethnic complexes in Central Africa and the Atlantic coastal area, mainly due to a one-way flow of pygmy women. There are now only a few small contingents of African Pygmy population groups who are mixed or who have almost disappeared as a result of migratory flows from Cameroon.

AIMS

We analysed the adult phenotypic diversity of 9 populations (17 groups of both sexes) of the Congo basin and Bioko Island, which were anthropometrically characterised in 1948. The phenotypic clusters that we detected, which we interpret as likely mixing of local Pygmy populations and Bantus, may be useful as references for future studies, particularly genetics.

SUBJECTS AND METHODS

The matrix of inter-distances between populations was generated, using the 21 variables, with the Euclidean distance between the mean vectors relating to the standardised variables. When the UPGMA (Unweighted Pair Group Method with Arithmetic Mean) was used separately in men and women, the phylogenetic trees showed a clear separation between populations.

RESULTS

The body measurements that most effectively distinguished the groups are linear dimensions and the width of the hips and mean thoracic circumference. In this study, the cephalo-facial dimensions were of little value in identifying the groups.

CONCLUSIONS

The samples of Equatorial Guinea show a major inter-group overlap, and considerable intra-group variations. There are also notable differences amongst African Pygmy populations in terms of height, but not in body proportions.

The same growth pattern from puberty suggests that modern human diversity results from changes during pre-pubertal development

Patterns of human growth established for one population have rarely been tested in other populations. In a previous study, three growth curves from puberty were modelled for each sex in a longitudinal study of a Caucasian population based on stature, age at peak of growth and biological maturation. Each curve represents the canalisation of growth associated with the type of puberty. The high precision (± 3 cm) of individual adult stature predictions shows that growth kinetics are already set up at puberty and are canalised depending on biological maturity. Our aim is to assess whether this model can be extrapolated to other populations to test whether growth canalisation is a population-dependent phenomenon or if the model reflects a canalisation pattern specific to our species. The modelled curves predicted adult stature with the same high degree of precision in basketball players and the Baka pygmies. Therefore, (1) the relationship between growth kinetics and age at maturity is similar in all populations and (2) growth according to pubertal stages follows the same canalisation patterns in the populations despite the wide differences in their average adult statures. It suggests that morphological diversity in modern humans results from processes taking place in early development.

Identification of novel genetic variants associated with short stature in a Baka Pygmies population

Human growth is a complex trait determined by genetic factors in combination with external stimuli, including environment, nutrition and hormonal status. In the past, several genome-wide association studies (GWAS) have collectively identified hundreds of genetic variants having a putative effect on determining adult height in different worldwide populations. Theoretically, a valuable approach to better understand the mechanisms of complex traits as adult height is to study a population exhibiting extreme stature phenotypes, such as African Baka Pygmies. After phenotypic characterization, we sequenced the whole exomes of a cohort of Baka Pygmies and their non-Pygmies Bantu neighbors to highlight genetic variants associated with the reduced stature. Whole exome data analysis revealed 29 single nucleotide polymorphisms (SNPs) significantly associated with the reduced height in the Baka group. Among these variants, we focused on SNP rs7629425, located in the 5′-UTR of the Hyaluronidase-2 (HYAL2) gene. The frequency of the alternative allele was significantly increased compared to African and non-African populations. In vitro luciferase assay showed significant differences in transcription modulation by rs7629425 C/T alleles. In conclusion, our results suggested that the HYAL2 gene variants may play a role in the etiology of short stature in Baka Pygmies population.

Self-reported Health is Related to Body Height and Waist Circumference in Rural Indigenous and Urbanised Latin-American Populations

Body height is a life-history component. It involves important costs for its expression and maintenance, which may originate trade-offs on other costly components such as reproduction or immunity. Although previous evidence has supported the idea that human height could be a sexually selected trait, the explanatory mechanisms that underlie this selection are poorly understood. Despite extensive studies on the association between height and attractiveness, the role of immunity in linking this relation is scarcely studied, particularly in non-Western populations. Here, we tested whether human height is related to health measured by self-perception, and relevant nutritional and health anthropometric indicators in three Latin-American populations that widely differ in socioeconomic and ecological conditions: two urbanised populations from Bogota (Colombia) and Mexico City (Mexico), and one isolated indigenous population (Me'Phaa, Mexico). Results showed that self-reported health is best predicted by an interaction between height and waist circumference: the presumed benefits of being taller are waist-dependent, and affect taller people more than shorter individuals. If health and genetic quality cues play an important role in human mate-choice, and height and waist interact to signal health, its evolutionary consequences, including cognitive and behavioural effects, should be addressed in future research.

Evolutionary Strategies for Body Size

Humans show marked variation in body size around the world, both within and among populations. At present, the tallest people in the world are from the Netherlands and the Balkan countries, while the shortest populations are central African Pygmies. There are genetic, genetic plasticity, developmental, and environmental bases for size variation in Homo sapiens from the recent past and the present. Early populations of Homo species also have shown considerable size variation. Populations from the present and the past are also marked by sexual dimorphism, which, itself, shows group variation. There is abundant evidence for the effects of limited food and disease on human growth and resultant adult body size. This environmental influence has been reflected in "secular trends" (over a span of years) in growth and adult size from socioeconomic prosperity or poverty (availability of resources). Selective and evolutionary advantages of small or large body size also have been documented. Heritability for human height is relatively great with current genome-wide association studies (GWAS) identifying hundreds of genes leading to causes of growth and adult size variation. There are also endocrinological pathways limiting growth. An example is the reduced tissue sensitivity to human growth hormone (HGH) and insulin-like growth factor (IGF-1) in Philippine and African hunter-gatherer populations. In several short-statured hunter-gatherer populations (Asian, African, and South American), it has been hypothesized that short life expectancy has selected for early maturity and truncated growth to enhance fertility. Some island populations of humans and other mammals are thought to have been selected for small size because of limited resources, especially protein. The high-protein content of milk as a staple food may contribute to tall stature in East African pastoral peoples. These and other evolutionary questions linked to life history, male competition, reproduction, and mobility are explored in this paper.

Genetic Pathways of Aging and Their Relevance in the Dog as a Natural Model of Human Aging

Aging research has experienced a burst of scientific efforts in the last decades as the growing ratio of elderly people has begun to pose an increased burden on the healthcare and pension systems of developed countries. Although many breakthroughs have been reported in understanding the cellular mechanisms of aging, the intrinsic and extrinsic factors that contribute to senescence on higher biological levels are still barely understood. The dog, Canis familiaris, has already served as a valuable model of human physiology and disease. The possible role the dog could play in aging research is still an open question, although utilization of dogs may hold great promises as they naturally develop age-related cognitive decline, with behavioral and histological characteristics very similar to those of humans. In this regard, family dogs may possess unmatched potentials as models for investigations on the complex interactions between environmental, behavioral, and genetic factors that determine the course of aging. In this review, we summarize the known genetic pathways in aging and their relevance in dogs, putting emphasis on the yet barely described nature of certain aging pathways in canines. Reasons for highlighting the dog as a future aging and gerontology model are also discussed, ranging from its unique evolutionary path shared with humans, its social skills, and the fact that family dogs live together with their owners, and are being exposed to the same environmental effects.

Complex Phenotypes: Mechanisms Underlying Variation in Human Stature

PURPOSE OF REVIEW

The goal of the review is to provide a comprehensive overview of the current understanding of the mechanisms underlying variation in human stature.

RECENT FINDINGS

Human height is an anthropometric trait that varies considerably within human populations as well as across the globe. Historically, much research focus was placed on understanding the biology of growth plate chondrocytes and how modifications to core chondrocyte proliferation and differentiation pathways potentially shaped height attainment in normal as well as pathological contexts. Recently, much progress has been made to improve our understanding regarding the mechanisms underlying the normal and pathological range of height variation within as well as between human populations, and today, it is understood to reflect complex interactions among a myriad of genetic, environmental, and evolutionary factors. Indeed, recent improvements in genetics (e.g., GWAS) and breakthroughs in functional genomics (e.g., whole exome sequencing, DNA methylation analysis, ATAC-sequencing, and CRISPR) have shed light on previously unknown pathways/mechanisms governing pathological and common height variation. Additionally, the use of an evolutionary perspective has also revealed important mechanisms that have shaped height variation across the planet. This review provides an overview of the current knowledge of the biological mechanisms underlying height variation by highlighting new research findings on skeletal growth control with an emphasis on previously unknown pathways/mechanisms influencing pathological and common height variation. In this context, this review also discusses how evolutionary forces likely shaped the genomic architecture of height across the globe.

Tooth dimensions and body size in a Pygmy population

Background: The relationship between tooth size and stature has been analysed extensively at the interspecies level but has received less attention at the intraspecies level. The relationship between these two parameters does not seem to be the same among modern human populations.Aim: The aim of this study is to analyse the relationship between tooth dimensions and body measurements in the Baka Pygmies.Subjects and methods: Height, weight, and tooth dimensions were obtained for 45 adult Baka females and 17 males from Le Bosquet (Cameroon). Correlations were obtained between the variables and compared to results for other human populations.Results: The Baka population is distinctive in the small number of significant correlations. Only two buccolingual diameters among Baka females show any significant correlation with height. The lack of significant correlations between tooth dimensions and body dimensions among the Baka means that changes in body size are accompanied by random variations in tooth dimensions.Conclusion: The absence of correlations may be accounted for by the impact of environmental effects on the somatic growth of the Baka producing a Pygmy phenotype adapted to live in the forest. It is worth noting that many correlations become significant when sexes are pooled.

Population genomics perspectives on convergent adaptation

Convergent adaptation is the independent evolution of similar traits conferring a fitness advantage in two or more lineages. Cases of convergent adaptation inform our ideas about the ecological and molecular basis of adaptation. In judging the degree to which putative cases of convergent adaptation provide an independent replication of the process of adaptation, it is necessary to establish the degree to which the evolutionary change is unexpected under null models and to show that selection has repeatedly, independently driven these changes. Here, we discuss the issues that arise from these questions particularly for closely related populations, where gene flow and standing variation add additional layers of complexity. We outline a conceptual framework to guide intuition as to the extent to which evolutionary change represents the independent gain of information owing to selection and show that this is a measure of how surprised we should be by convergence. Additionally, we summarize the ways population and quantitative genetics and genomics may help us address questions related to convergent adaptation, as well as open new questions and avenues of research. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.

Nicotinamide as Independent Variable for Intelligence, Fertility, and Health: Origin of Human Creative Explosions?

Meat and nicotinamide acquisition was a defining force during the 2-million-year evolution of the big brains necessary for, anatomically modern, Homo sapiens to survive. Our next move was down the food chain during the Mesolithic 'broad spectrum', then horticultural, followed by the Neolithic agricultural revolutions and progressively lower average 'doses' of nicotinamide. We speculate that a fertility crisis and population bottleneck around 40 000 years ago, at the time of the Last Glacial Maximum, was overcome by Homo (but not the Neanderthals) by concerted dietary change plus profertility genes and intense sexual selection culminating in behaviourally modern Homo sapiens. Increased reliance on the 'de novo' synthesis of nicotinamide from tryptophan conditioned the immune system to welcome symbionts, such as TB (that excrete nicotinamide), and to increase tolerance of the foetus and thereby fertility. The trade-offs during the warmer Holocene were physical and mental stunting and more infectious diseases and population booms and busts. Higher nicotinamide exposure could be responsible for recent demographic and epidemiological transitions to lower fertility and higher longevity, but with more degenerative and auto-immune disease.

Trait variation and trait stability in common marmosets (Callithrix jacchus) inhabiting ecologically distinct habitats in northeastern Brazil

Understanding the set of factors that promote and constrain a species' ability to exploit ecologically distinct habitats is central for addressing questions of intraspecific variability in behavior and morphology. In this study, we compared newly collected data with published data on body measurements, group size and composition, daily path length, home range, and reproductive output in wild common marmosets naturally inhabiting two contrasting environments in northeastern Brazil: the Atlantic Forest (AF), which is characterized by high biodiversity and reduced seasonality in food availability and the Caatinga (CAT), which is characterized by a severe hot and dry season lasting from 5 to 11 months, drought-resistant plant species, and reduced primary productivity. Despite marked differences in ecological conditions, CAT marmosets and AF marmosets differed minimally in daily path length, home range, reproductive output, and infant survivorship. CAT marmosets were found to live in smaller groups containing fewer adult females than AF marmosets, and also were characterized by a greater surface area to body mass ratio, a trait that may represent an adaptation to the hot and dry conditions of the Caatinga. We propose that in conjunction with body mass reduction, minor adjustments in behavior, the exploitation of cacti as a source of water and nutrients, and access to exudates as a dependable year-round food resource, common marmosets successfully used the same adaptive pattern to maintain high reproductive output and infant survivorship in exploiting these two ecologically distinct environments.

Polygenic adaptation and convergent evolution on growth and cardiac genetic pathways in African and Asian rainforest hunter-gatherers

Different human populations facing similar environmental challenges have sometimes evolved convergent biological adaptations, for example, hypoxia resistance at high altitudes and depigmented skin in northern latitudes on separate continents. The "pygmy" phenotype (small adult body size), characteristic of hunter-gatherer populations inhabiting both African and Asian tropical rainforests, is often highlighted as another case of convergent adaptation in humans. However, the degree to which phenotypic convergence in this polygenic trait is due to convergent versus population-specific genetic changes is unknown. To address this question, we analyzed high-coverage sequence data from the protein-coding portion of the genomes of two pairs of populations: Batwa rainforest hunter-gatherers and neighboring Bakiga agriculturalists from Uganda and Andamanese rainforest hunter-gatherers and Brahmin agriculturalists from India. We observed signatures of convergent positive selection between the rainforest hunter-gatherers across the set of genes with "growth factor binding" functions ([Formula: see text]). Unexpectedly, for the rainforest groups, we also observed convergent and population-specific signatures of positive selection in pathways related to cardiac development (e.g., "cardiac muscle tissue development"; [Formula: see text]). We hypothesize that the growth hormone subresponsiveness likely underlying the adult small body-size phenotype may have led to compensatory changes in cardiac pathways, in which this hormone also plays an essential role. Importantly, in the agriculturalist populations, we did not observe similar patterns of positive selection on sets of genes associated with growth or cardiac development, indicating our results most likely reflect a history of convergent adaptation to the similar ecology of rainforests rather than a more general evolutionary pattern.

Locomotor constraints favour the evolution of the human pygmy phenotype in tropical rainforests

The convergent evolution of the human pygmy phenotype in tropical rainforests is widely assumed to reflect adaptation in response to the distinct ecological challenges of this habitat (e.g. high levels of heat and humidity, high pathogen load, low food availability, and dense forest structure), yet few precise adaptive benefits of this phenotype have been proposed. Here, we describe and test a biomechanical model of how the rainforest environment can alter gait kinematics such that short stature is advantageous in dense habitats. We hypothesized that environmental constraints on step length in rainforests alter walking mechanics such that taller individuals are expected to walk more slowly due to their inability to achieve preferred step lengths in the rainforest. We tested predictions from this model with experimental field data from two short-statured populations that regularly forage in the rainforest: the Batek of Peninsular Malaysia and the Tsimane of the Bolivian Amazon. In accordance with model expectations, we found stature-dependent constraints on step length in the rainforest and concomitant reductions in walking speed that are expected to compromise foraging efficiency. These results provide the first evidence that the human pygmy phenotype is beneficial in terms of locomotor performance and highlight the value of applying laboratory-derived biomechanical models to field settings for testing evolutionary hypotheses.

The demographic and adaptive history of central African hunter-gatherers and farmers

Central Africa, a forested region that supports an exceptionally high biodiversity, hosts the world's largest group of hunter-gatherers, who live in close proximity with groups that have adopted agriculture over the past 5000 years. Our understanding of the prehistory of these populations has been dramatically hampered by the almost total absence of fossil remains in this region, a limitation that has recently been circumvented by population genomics approaches. Different studies have estimated that ancestors of rainforest hunter-gatherers and Bantu-speaking farmers separated more than 60 000 years ago, supporting the occurrence of ancient population structure in Africa since the Late Pleistocene. Conversely, the Holocene in central Africa was characterized by large-scale population migrations associated with the emergence of agriculture, and increased genetic interactions between autochthonous rainforest hunter-gatherers and expanding Bantu-speaking farmers. Genomic scans have detected numerous candidate loci for positive selection in these populations, including convergent adaptation for short stature in groups of rainforest hunter-gatherers and local adaptation to endemic malaria in western and central Africans. Furthermore, there is recent increasing evidence that adaptive variation has been acquired by various African populations through admixture, suggesting a previously unappreciated role of intraspecies gene flow in local adaptation. Ancient and modern DNA studies will greatly broaden, and probably challenge, our view on the past history of central Africa, where introgression from yet uncharacterized archaic hominins and long-term adaptation to distinct ecological niches are suspected.

A genome scan for genes underlying adult body size differences between Central African hunter-gatherers and farmers

The evolutionary and biological bases of the Central African "pygmy" phenotype, a characteristic of rainforest hunter-gatherers defined by reduced body size compared with neighboring farmers, remain largely unknown. Here, we perform a joint investigation in Central African hunter-gatherers and farmers of adult standing height, sitting height, leg length, and body mass index (BMI), considering 358 hunter-gatherers and 169 farmers with genotypes for 153,798 SNPs. In addition to reduced standing heights, hunter-gatherers have shorter sitting heights and leg lengths and higher sitting/standing height ratios than farmers and lower BMI for males. Standing height, sitting height, and leg length are strongly correlated with inferred levels of farmer genetic ancestry, whereas BMI is only weakly correlated, perhaps reflecting greater contributions of non-genetic factors to body weight than to height. Single- and multi-marker association tests identify one region and eight genes associated with hunter-gatherer/farmer status, and 24 genes associated with the height-related traits. Many of these genes have putative functions consistent with roles in determining their associated traits and the pygmy phenotype, and they include three associated with standing height in non-Africans (PRKG1, DSCAM, MAGI2). We find evidence that European height-associated SNPs or variants in linkage disequilibrium with them contribute to standing- and sitting-height determination in Central Africans, but not to the differential status of hunter-gatherers and farmers. These findings provide new insights into the biological basis of the pygmy phenotype, and they highlight the potential of cross-population studies for exploring the genetic basis of phenotypes that vary naturally across populations.

Effect of maternal height on caesarean section and neonatal mortality rates in sub-Saharan Africa: An analysis of 34 national datasets

Rationale

The lifecycle perspective reminds us that the roots of adult ill-health may start in-utero or in early childhood. Nutritional and infectious disease insults in early life, the critical first 1000 days, are associated with stunting in childhood, and subsequent short adult stature. There is limited or no opportunity for stunted children above 2 years of age to experience catch-up growth. Some previous research has shown short maternal height to lead to adverse birth outcomes. In this paper, we document the association between maternal height and caesarean section, and between maternal height and neonatal mortality in 34 sub-Saharan African countries. We also explore the appropriate height cut-offs to use. Our paper contributes arguments to support a focus on preventing non-communicable risk factors, namely early childhood under-nutrition, as part of the fight to reduce caesarean section rates and other adverse maternal and newborn health outcomes, particularly neonatal mortality. We focus on the Sub-Saharan Africa region because it carries the highest burden of maternal and neonatal ill-health.

Methods

We used the most recent Demographic and Health Survey for 34 sub-Saharan African countries. The distribution of heights of women who had given birth in the 5 years before the survey was explored. We adopted the following cut-offs: Very Short (<145.0cm), Short (145.0–149.9cm), Short-average (150.0–154.9cm), Average (155.0–159.9cm), Average-tall (160.0–169.9cm) and Tall (≥170.0cm). Multivariate logistic regression was used to assess the contribution of maternal stature to the odds ratio of caesarean section delivery, adjusting for other exposures, such as age at index birth, residence, maternal BMI, maternal education, wealth index quintile, previous caesarean section, multiple birth, birth order and country of survey. We also look at its contribution to neonatal mortality adjusting for age at index birth, residence, maternal BMI, maternal education, wealth index quintile, multiple birth, birth order and country of survey.

Results

There was a gradual increase in the rate of caesarean section with decreasing maternal height. Compared to women of Average height (155.0–159.9cm), taller women were protected. The adjusted odds ratio (aOR) for Tall women was 0.67 (95% CI:0.52–0.87) and for Average-tall women was 0.78 (95% CI:0.69–0.89). Compared to women of Average height, shorter women were at increased risk. The aOR for Short-average women was 1.19 (95% CI:1.03–1.37), for Short women was 2.06 (95% CI:1.71–2.48), and for Very Short women was 2.50 (95% CI:1.85–3.38). There was evidence that compared to Average height women, Very Short and Short women had increased odds of experiencing a neonatal death aOR = 1.95 (95% CI 1.17–3.25) and aOR = 1.66 (95% CI 1.20–2.28) respectively. When we focused on the period of highest risk, the day of delivery and first postnatal day, these aORs increased to 2.36 (95% CI 1.57–3.55) and 2.34 (95% CI 1.19–4.60) respectively. The aORs for the first week of life (early neonatal mortality) were 1.90 (95% CI 1.07–3.36) and 1.83 (95% CI 1.30–2.59) respectively.

Conclusions

Short stature is associated with an increased prevalence of caesarean section and neonatal mortality, particularly on the newborn’s first days. These results are even more striking because we know that caesarean section rates tend to be higher among wealthier and more educated women, who are often taller and that the same patterns may hold for neonatal survival; in such cases, adjusting for wealth, education and urban residence would attenuate these associations. Caesarean sections can be lifesaving operations; however, they cost the health system and families more, and are associated with worse health outcomes. We suggest that our findings be used to argue for policies targeting stunting in infant girls and potential catch-up growth in adolescence and early adulthood, aiming to increase their adult height and thus decrease their subsequent risk of experiencing caesarean section and adverse birth outcomes.

Loci associated with skin pigmentation identified in African populations

Despite the wide range of skin pigmentation in humans, little is known about its genetic basis in global populations. Examining ethnically diverse African genomes, we identify variants in or near SLC24A5, MFSD12, DDB1, TMEM138, OCA2, and HERC2 that are significantly associated with skin pigmentation. Genetic evidence indicates that the light pigmentation variant at SLC24A5 was introduced into East Africa by gene flow from non-Africans. At all other loci, variants associated with dark pigmentation in Africans are identical by descent in South Asian and Australo-Melanesian populations. Functional analyses indicate that MFSD12 encodes a lysosomal protein that affects melanogenesis in zebrafish and mice, and that mutations in melanocyte-specific regulatory regions near DDB1/TMEM138 correlate with expression of ultraviolet response genes under selection in Eurasians.

Long-term patterns of body mass and stature evolution within the hominin lineage

Body size is a central determinant of a species' biology and adaptive strategy, but the number of reliable estimates of hominin body mass and stature have been insufficient to determine long-term patterns and subtle interactions in these size components within our lineage. Here, we analyse 254 body mass and 204 stature estimates from a total of 311 hominin specimens dating from 4.4 Ma to the Holocene using multi-level chronological and taxonomic analytical categories. The results demonstrate complex temporal patterns of body size variation with phases of relative stasis intermitted by periods of rapid increases. The observed trajectories could result from punctuated increases at speciation events, but also differential proliferation of large-bodied taxa or the extinction of small-bodied populations. Combined taxonomic and temporal analyses show that in relation to australopithecines, early Homo is characterized by significantly larger average body mass and stature but retains considerable diversity, including small body sizes. Within later Homo, stature and body mass evolution follow different trajectories: average modern stature is maintained from ca 1.6 Ma, while consistently higher body masses are not established until the Middle Pleistocene at ca 0.5-0.4 Ma, likely caused by directional selection related to colonizing higher latitudes. Selection against small-bodied individuals (less than 40 kg; less than 140 cm) after 1.4 Ma is associated with a decrease in relative size variability in later Homo species compared with earlier Homo and australopithecines. The isolated small-bodied individuals of Homo naledi (ca 0.3 Ma) and Homo floresiensis (ca 100-60 ka) constitute important exceptions to these general patterns, adding further layers of complexity to the evolution of body size within the genus Homo. At the end of the Late Pleistocene and Holocene, body size in Homo sapiens declines on average, but also extends to lower limits not seen in comparable frequency since early Homo.

The evolution of body size and shape in the human career

Body size is a fundamental biological property of organisms, and documenting body size variation in hominin evolution is an important goal of palaeoanthropology. Estimating body mass appears deceptively simple but is laden with theoretical and pragmatic assumptions about best predictors and the most appropriate reference samples. Modern human training samples with known masses are arguably the 'best' for estimating size in early bipedal hominins such as the australopiths and all members of the genus Homo, but it is not clear if they are the most appropriate priors for reconstructing the size of the earliest putative hominins such as Orrorin and Ardipithecus The trajectory of body size evolution in the early part of the human career is reviewed here and found to be complex and nonlinear. Australopith body size varies enormously across both space and time. The pre-erectus early Homo fossil record from Africa is poor and dominated by relatively small-bodied individuals, implying that the emergence of the genus Homo is probably not linked to an increase in body size or unprecedented increases in size variation. Body size differences alone cannot explain the observed variation in hominin body shape, especially when examined in the context of small fossil hominins and pygmy modern humans.This article is part of the themed issue 'Major transitions in human evolution'.

Going global by adapting local: A review of recent human adaptation

The spread of modern humans across the globe has led to genetic adaptations to diverse local environments. Recent developments in genomic technologies, statistical analyses, and expanded sampled populations have led to improved identification and fine-mapping of genetic variants associated with adaptations to regional living conditions and dietary practices. Ongoing efforts in sequencing genomes of indigenous populations, accompanied by the growing availability of "-omics" and ancient DNA data, promises a new era in our understanding of recent human evolution and the origins of variable traits and disease risks.

Tropical forests and the genus Homo

Tropical forests constitute some of the most diverse and complex terrestrial ecosystems on the planet. From the Miocene onward, they have acted as a backdrop to the ongoing evolution of our closest living relatives, the great apes, and provided the cradle for the emergence of early hominins, who retained arboreal physiological adaptations at least into the Late Pliocene. There also now exists growing evidence, from the Late Pleistocene onward, for tool-assisted intensification of tropical forest occupation and resource extraction by our own species, Homo sapiens. However, between the Late Pliocene and Late Pleistocene there is an apparent gap in clear and convincing evidence for the use of tropical forests by hominins, including early members of our own genus. In discussions of Late Pliocene and Early Pleistocene hominin evolution, including the emergence and later expansion of Homo species across the globe, tropical forest adaptations tend to be eclipsed by open, savanna environments. Thus far, it is not clear whether this Early-Middle Pleistocene lacuna in Homo-rainforest interaction is real and representative of an adaptive shift with the emergence of our species or if it is simply reflective of preservation bias.

Intraspecific variation in an Ediacaran skeletal metazoan: Namacalathus from the Nama Group, Namibia

Namacalathus hermanastes is one of the oldest known skeletal metazoans, found in carbonate settings of the terminal Ediacaran (~550-541 million years ago [Ma]). The palaeoecology of this widespread, goblet-shaped, benthic organism is poorly constrained yet critical for understanding the dynamics of the earliest metazoan communities. Analysis of in situ assemblages from the Nama Group, Namibia (~548-541 Ma), shows that Namacalathus exhibited size variation in response to differing water depths, hydrodynamic conditions and substrate types. In low-energy, inner ramp environments, Namacalathus attains the largest average sizes but grew in transient, loosely aggregating, monospecific aggregations attached to microbial mats. In high-energy mid-ramp reefs, Namacalathus spatially segregated into different palaeoecological habitats with distinct size distributions. In outer ramp environments, individuals were small and formed patchy, dense, monospecific aggregations attached to thin microbial mats. Asexual budding is common in all settings. We infer that variations in size distribution in Namacalathus reflect differences in habitat heterogeneity and stability, including the longevity of mechanically stable substrates and oxic conditions. In the Nama Group, long-lived skeletal metazoan communities developed within topographically heterogeneous mid-ramp reefs, which provided diverse mechanically stable microbial substrates in persistently oxic waters, while inner and outer ramp communities were often ephemeral, developing during fleeting episodes of either oxia and/or substrate stability. We conclude that Namacalathus, which forms a component of these communities in the Nama Group, was a generalist that adapted to various palaeoecological habitats within a heterogeneous ecosystem landscape where favourable conditions persisted, and was also able to opportunistically colonise transiently hospitable environments. These early skeletal metazoans colonised previously unoccupied substrates in thrombolitic reefs and other microbial carbonate settings, and while they experienced relatively low levels of interspecific competition, they were nonetheless adapted to the diverse environments and highly dynamic redox conditions present in the terminal Ediacaran.

Hunter-gatherer genomics: evolutionary insights and ethical considerations

Hunting and gathering societies currently comprise only a small proportion of all human populations. However, the geographic and environmental diversity of modern hunter-gatherer groups, their inherent dependence on ecological resources, and their connection to patterns of behavior and subsistence that represent the vast majority of human history provide opportunities for scientific research to deliver major insights into the evolutionary history of our species. We review recent evolutionary genomic studies of hunter-gatherers, focusing especially on those that identify and functionally characterize phenotypic adaptations to local environments. We also call attention to specific ethical issues that scientists conducting hunter-gatherer genomics research ought to consider, including potential social and economic tensions between traditionally mobile hunter-gatherers and the land ownership-based nation-states by which they are governed, and the implications of genomic-based evidence of long-term evolutionary associations with particular habitats.

Diversity in tooth eruption and life history in humans: illustration from a Pygmy population

Life history variables (LHV) in primates are closely correlated with the ages of tooth eruption, which are a useful proxy to predict growth and development in extant and extinct species. However, it is not known how tooth eruption ages interact with LHV in polymorphic species such as modern humans. African pygmies are at the one extreme in the range of human size variation. LHV in the Baka pygmies are similar to those in standard populations. We would therefore expect tooth eruption ages to be similar also. This mixed (longitudinal and cross-sectional) study of tooth eruption in Baka individuals of known age reveals that eruption in all tooth classes occurs earlier than in any other human population. Earlier tooth eruption can be related to the particular somatic growth in the Baka but cannot be correlated with LHV. The link between LHV and tooth eruption seems disrupted in H. sapiens, allowing adaptive variations in tooth eruption in response to different environmental constraints while maintaining the unique human life cycle.

Factors influencing the effect size distribution of adaptive substitutions

The distribution of effect sizes of adaptive substitutions has been central to evolutionary biology since the modern synthesis. Early theory proposed that because large-effect mutations have negative pleiotropic consequences, only small-effect mutations contribute to adaptation. More recent theory suggested instead that large-effect mutations could be favoured when populations are far from their adaptive peak. Here we suggest that the distributions of effect sizes are expected to differ among study systems, reflecting the wide variation in evolutionary forces and ecological conditions experienced in nature. These include selection, mutation, genetic drift, gene flow, and other factors such as the degree of pleiotropy, the distance to the phenotypic optimum, whether the optimum is stable or moving, and whether new mutation or standing genetic variation provides the source of adaptive alleles. Our goal is to review how these factors might affect the distribution of effect sizes and to identify new research directions. Until more theory and empirical work is available, we feel that it is premature to make broad generalizations about the effect size distribution of adaptive substitutions important in nature.

The impact of agricultural emergence on the genetic history of African rainforest hunter-gatherers and agriculturalists

The emergence of agriculture in West-Central Africa approximately 5,000 years ago, profoundly modified the cultural landscape and mode of subsistence of most sub-Saharan populations. How this major innovation has had an impact on the genetic history of rainforest hunter-gatherers-historically referred to as 'pygmies'-and agriculturalists, however, remains poorly understood. Here we report genome-wide SNP data from these populations located west-to-east of the equatorial rainforest. We find that hunter-gathering populations present up to 50% of farmer genomic ancestry, and that substantial admixture began only within the last 1,000 years. Furthermore, we show that the historical population sizes characterizing these communities already differed before the introduction of agriculture. Our results suggest that the first socio-economic interactions between rainforest hunter-gatherers and farmers introduced by the spread of farming were not accompanied by immediate, extensive genetic exchanges and occurred on a backdrop of two groups already differentiated by their specialization in two ecotopes with differing carrying capacities.

Adult height, nutrition, and population health

In this review, the potential causes and consequences of adult height, a measure of cumulative net nutrition, in modern populations are summarized. The mechanisms linking adult height and health are examined, with a focus on the role of potential confounders. Evidence across studies indicates that short adult height (reflecting growth retardation) in low- and middle-income countries is driven by environmental conditions, especially net nutrition during early years. Some of the associations of height with health and social outcomes potentially reflect the association between these environmental factors and such outcomes. These conditions are manifested in the substantial differences in adult height that exist between and within countries and over time. This review suggests that adult height is a useful marker of variation in cumulative net nutrition, biological deprivation, and standard of living between and within populations and should be routinely measured. Linkages between adult height and health, within and across generations, suggest that adult height may be a potential tool for monitoring health conditions and that programs focused on offspring outcomes may consider maternal height as a potentially important influence.

Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection

African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due to their unique lifestyle in the Central African rainforest. To identify genomic targets of adaptation, we sequenced the genomes of four Biaka Pygmies from the Central African Republic and jointly analyzed these data with the genome sequences of three Baka Pygmies from Cameroon and nine Yoruba famers. To account for the complex demographic history of these populations that includes both isolation and gene flow, we fit models using the joint allele frequency spectrum and validated them using independent approaches. Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 yr ago. We also find that bidirectional asymmetric gene flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. We then applied complementary statistics to scan the genome for evidence of selective sweeps and polygenic selection. We found that conventional statistical outlier approaches were biased toward identifying candidates in regions of high mutation or low recombination rate. To avoid this bias, we assigned P-values for candidates using whole-genome simulations incorporating demography and variation in both recombination and mutation rates. We found that genes and gene sets involved in muscle development, bone synthesis, immunity, reproduction, cell signaling and development, and energy metabolism are likely to be targets of positive natural selection in Western African Pygmies or their recent ancestors.

Architecture and functional ecology of the human gastrocnemius muscle-tendon unit

The gastrocnemius muscle-tendon unit (MTU) is central to human locomotion. Structural variation in the human gastrocnemius MTU is predicted to affect the efficiency of locomotion, a concept most often explored in the context of performance activities. For example, stiffness of the Achilles tendon varies among individuals with different histories of competitive running. Such a finding highlights the functional variation of individuals and raises the possibility of similar variation between populations, perhaps in response to specific ecological or environmental demands. Researchers often assume minimal variation in human populations, or that industrialized populations represent the human species as well as any other. Yet rainforest hunter-gatherers, which often express the human pygmy phenotype, contradict such assumptions. Indeed, the human pygmy phenotype is a potential model system for exploring the range of ecomorphological variation in the architecture of human hindlimb muscles, a concept we review here.

The epigenomic landscape of African rainforest hunter-gatherers and farmers

The genetic history of African populations is increasingly well documented, yet their patterns of epigenomic variation remain uncharacterized. Moreover, the relative impacts of DNA sequence variation and temporal changes in lifestyle and habitat on the human epigenome remain unknown. Here we generate genome-wide genotype and DNA methylation profiles for 362 rainforest hunter-gatherers and sedentary farmers. We find that the current habitat and historical lifestyle of a population have similarly critical impacts on the methylome, but the biological functions affected strongly differ. Specifically, methylation variation associated with recent changes in habitat mostly concerns immune and cellular functions, whereas that associated with historical lifestyle affects developmental processes. Furthermore, methylation variation—particularly that correlated with historical lifestyle—shows strong associations with nearby genetic variants that, moreover, are enriched in signals of natural selection. Our work provides new insight into the genetic and environmental factors affecting the epigenomic landscape of human populations over time.

Genetic and environmental factors affect genome-wide patterns of epigenetic variation. Here, the authors show that while current habitat and historical lifestyle impact the methylome of rainforest hunter-gatherers and sedentary farmers, the biological functions affected and the degree of genetic control differ.

Growth pattern from birth to adulthood in African pygmies of known age

The African pygmy phenotype stems from genetic foundations and is considered to be the product of a disturbance in the growth hormone–insulin-like growth factor (GH–IGF) axis. However, when and how the pygmy phenotype is acquired during growth remains unknown. Here we describe growth patterns in Baka pygmies based on two longitudinal studies of individuals of known age, from the time of birth to the age of 25 years. Body size at birth among the Baka is within standard limits, but their growth rate slows significantly during the first two years of life. It then more or less follows the standard pattern, with a growth spurt at adolescence. Their life history variables do not allow the Baka to be distinguished from other populations. Therefore, the pygmy phenotype in the Baka is the result of a change in growth that occurs during infancy, which differentiates them from East African pygmies revealing convergent evolution.

The African pygmies are known for their short stature, yet it is unclear when and how this phenotype is acquired during growth. Here the authors show that the pygmies' small stature results primarily from slow growth during infancy.

"Small size" in the Philippine human fossil record: is it meaningful for a better understanding of the evolutionary history of the negritos?

"Pygmy populations" are recognized in several places over the world, especially in Western Africa and in Southeast Asia (Philippine "negritos," for instance). Broadly defined as "small-bodied Homo sapiens" (compared with neighboring populations), their origins and the nature of the processes involved in the maintenance of their phenotype over time are highly debated. Major results have been recently obtained from population genetics on present-day negrito populations, but their evolutionary history remains largely unresolved. We present and discuss the Upper Pleistocene human remains recovered from Tabon Cave and Callao Cave in the Philippines, which are potentially highly relevant to these research questions. Human fossils have been recovered in large numbers from Tabon Cave (Palawan Island) but mainly from reworked and mixed sediments from several archaeological layers. We review and synthesize the long and meticulous collaborative work done on the archives left from the 1960s excavations and on the field. The results demonstrate the long history of human occupations in the cave, since at least ~30,000 BP. The examination of the Tabon human remains shows a large variability: large and robust for one part of the sample, and small and gracile for the other part. The latter would fit quite comfortably within the range of variation of Philippine negritos. Farther north, on Luzon Island, the human third metatarsal recently recovered from Callao Cave and dated to ~66,000 BP is now the oldest direct evidence of human presence in the Philippines. Previous data show that, compared with H. sapiens (including Philippine negritos), this bone presents a very small size and several unusual morphological characteristics. We present a new analytical approach using three-dimensional geometric morphometrics for comparing the Callao fossil to a wide array of extant Asian mammals, including nonhuman primates and H. sapiens. The results demonstrate that the shape of the Callao metatarsal is definitely closer to humans than to any other groups. The fossil clearly belongs to the genus Homo; however, it remains at the margin of the variation range of H. sapiens. Because of its great antiquity and the presence of another diminutive species of the genus Homo in the Wallace area during this time period (H. floresiensis), we discuss here in detail the affinities and potential relatedness of the Callao fossil with negritos that are found today on Luzon Island.

Detection of convergent genome-wide signals of adaptation to tropical forests in humans

Tropical forests are believed to be very harsh environments for human life. It is unclear whether human beings would have ever subsisted in those environments without external resources. It is therefore possible that humans have developed recent biological adaptations in response to specific selective pressures to cope with this challenge. To understand such biological adaptations we analyzed genome-wide SNP data under a Bayesian statistics framework, looking for outlier markers with an overly large extent of differentiation between populations living in a tropical forest, as compared to genetically related populations living outside the forest in Africa and the Americas. The most significant positive selection signals were found in genes related to lipid metabolism, the immune system, body development, and RNA Polymerase III transcription initiation. The results are discussed in the light of putative tropical forest selective pressures, namely food scarcity, high prevalence of pathogens, difficulty to move, and inefficient thermoregulation. Agreement between our results and previous studies on the pygmy phenotype, a putative prototype of forest adaptation, were found, suggesting that a few genetic regions previously described as associated with short stature may be evolving under similar positive selection in Africa and the Americas. In general, convergent evolution was less pervasive than local adaptation in one single continent, suggesting that Africans and Amerindians may have followed different routes to adapt to similar environmental selective pressures.

Cultural variation in the use of overimitation by the Aka and Ngandu of the Congo Basin

Studies in Western cultures have observed that both children and adults tend to overimitate, copying causally irrelevant actions in the presence of clear causal information. Investigation of this feature in non-Western groups has found little difference cross-culturally in the frequency or manner with which individuals overimitate. However, each of the non-Western populations studied thus far has a history of close interaction with Western cultures, such that they are now far removed from life in a hunter-gatherer or other small-scale culture. To investigate overimitation in a context of limited Western cultural influences, we conducted a study with the Aka hunter-gatherers and neighboring Ngandu horticulturalists of the Congo Basin rainforest in the southern Central African Republic. Aka children, Ngandu children, and Aka adults were presented with a reward retrieval task similar to those performed in previous studies, involving a demonstrated sequence of causally relevant and irrelevant actions. Aka children were found not to overimitate as expected, instead displaying one of the lowest rates of overimitation seen under similar conditions. Aka children copied fewer irrelevant actions than Aka adults, used a lower proportion of irrelevant actions than Ngandu children and Aka adults, and had less copying fidelity than Aka adults. Measures from Ngandu children were intermediate between the two Aka groups. Of the participants that succeeded in retrieving the reward, 60% of Aka children used emulation rather than imitation, compared to 15% of Ngandu children, 11% of Aka adults, and 0% of Western children of similar age. From these results, we conclude that cross-cultural variation exists in the use of overimitation during childhood. Further study is needed under a more diverse representation of cultural and socioeconomic groups in order to investigate the cognitive underpinnings of overimitation and its possible influences on social learning and the biological and cultural evolution of our species.