Oculocutaneous albinism type 1 (OCA1) caused by pathogenic variants of the TYR gene is an autosomal recessive disorder of pigmentation characterized by reduced biosynthesis of melanin pigment in skin, hair, and eyes. We had the opportunity to examine five East Cameroon Baka rainforest hunter-gatherers (historically called "Pygmies") with albinism and belonging to three different families. Screening of known albinism genes revealed a homozygous missense variant in the TYR gene, NM_000372.5: c.1109T>C; p.Met370Thr. In addition, one patient was also hemizygous for a variant in GPR143, the gene involved in ocular albinism (OA1). Another patient was also heterozygous for the common African and Afro-American 2.7-kb deletion in the OCA2 gene indicating admixture of one parent with neighboring Nzimé Bantu-speaking farmers. This is the first report of the occurrence of OCA1 in African rainforest hunter-gatherers.

Aging is associated with genome-wide changes in DNA methylation in humans, facilitating the development of epigenetic age prediction models. However, these models have been trained primarily on European-ancestry individuals and none account for the impact of methylation quantitative trait loci (meQTL). To address these gaps, we analyze the relationships between age, genotype, and CpG methylation in 3 understudied populations: central African Baka (n = 35), southern African ‡Khomani San (n = 52), and southern African Himba (n = 51). We show that published prediction methods yield higher mean errors in these cohorts compared to European-ancestry individuals and find that unaccounted-for DNA sequence variation may be a significant factor underlying this loss of accuracy. We leverage information about the associations between DNA genotype and CpG methylation to develop an age predictor that is minimally influenced by meQTL and show that this model remains accurate across a broad range of genetic backgrounds. Intriguingly, we also find that the older individuals and those with lower epigenetic age acceleration carry more genetic variants linked to reduced epigenetic age. These findings support the hypothesis that multiple heritable factors collectively influence healthspan and longevity in human populations.

The deep history of humans in Africa and the complex divergences and migrations among ancient human genetic lineages remain poorly understood and are the subject of ongoing debate. We produced 73 high-quality whole genome sequences from 14 Central and Southern African populations with diverse, well-documented, languages, subsistence strategies, and socio-cultural practices, and jointly analyze this novel data with 104 African and non-African previously-released whole genomes. We find vast genome-wide diversity and individual pairwise differentiation within and among African populations at continental, regional, and even local geographical scales, often uncorrelated with linguistic affiliations and cultural practices. We combine populations in 54 different ways and, for each population combination separately, we conduct extensive machine-learning Approximate Bayesian Computation inferences relying on genome-wide simulations of 48 competing evolutionary scenarios. We thus reconstruct jointly the tree-topologies and migration processes among ancient and recent lineages best explaining the diversity of extant genomic patterns. Our results show the necessity to explicitly consider the genomic diversity of African populations at a local scale, without merging population samples indiscriminately into larger a priori categories based on geography, subsistence-strategy, and/or linguistics criteria, in order to reconstruct the diverse evolutionary histories of our species. We find that, for all different combinations of Central and Southern African populations, a tree-like evolution with long periods of drift between short periods of unidirectional gene-flow among pairs of ancient or recent lineages best explain observed genomic patterns compared to recurring gene-flow processes among lineages. Moreover, we find that, for 25 combinations of populations, the lineage ancestral to extant Southern African Khoe-San populations diverged around 300,000 years ago from a lineage ancestral to Rainforest Hunter-Gatherers and neighboring agriculturalist populations. We also find that short periods of ancient or recent asymmetrical gene-flow among lineages often coincided with epochs of major cultural and ecological changes previously identified by paleo-climatologists and archaeologists in Sub-Saharan Africa. ### Competing Interest Statement The authors have declared no competing interest.

De la fin du 18ème siècle au milieu du 19ème, la cranioscopie, ou phrénologie, prétend diagnostiquer les comportements déviants par l’examen des reliefs crâniens. Cette piste n’aboutira pas mais permettra la collecte d’un matériel important qui servira à l’édification de la craniométrie comme science descriptive de la diversité humaine. Les développements récents de l’imagerie cérébrale montrent cependant que si la phrénologie avait pressenti les aires fonctionnelles du cerveau, elle n’a plus qu’un intérêt historique, et n’apporte rien à la bioarchéologie. On peut alors penser que les efforts futurs pour tenter de construire une paléopathologie mentale, voire sociale, pour le moment inexistante, se détourneront de l’anatomie pour, grâce à la paléogénomique, s’aventurer vers la psycho-génétique, un domaine qui reste toutefois très controversé.

Industrialization has impacted the human gut ecosystem, resulting in altered microbiome composition and diversity. Whether bacterial genomes may also adapt to the industrialization of their host populations remains largely unexplored. Here, we investigate the extent to which the rates and targets of horizontal gene transfer (HGT) vary across thousands of bacterial strains from 15 human populations spanning a range of industrialization. We show that HGTs have accumulated in the microbiome over recent host generations and that HGT occurs at high frequency within individuals. Comparison across human populations reveals that industrialized lifestyles are associated with higher HGT rates and that the functions of HGTs are related to the level of host industrialization. Our results suggest that gut bacteria continuously acquire new functionality based on host lifestyle and that high rates of HGT may be a recent development in human history linked to industrialization.

Notre collègue Georgius Johannes Adrianus Koppert (fig.1), né à Zoetermeer (Pays-Bas) le 16 avril 1950, vient de disparaître des suites d’une leucémie foudroyante à l’âge de 69 ans. Membre de la Société d’anthropologie de Paris qui lui doit un tribut tout particulier car il s’est longtemps occupé de l’édition de nos Bulletins, il était un des plus brillants spécialistes de l’anthropologie de l’alimentation, au sein de l’équipe fondée par le regretté Igor de Garine. Titulaire d’un doctorat en anthropologie de l’université d’Aix-en-Provence (1988) et d’un doctorat en nutrition humaine et statistiques appliquées de l’université agronomique de Wageningen (Pays Bas, 1980), ainsi que d’une licence en mathématiques appliquées aux sciences sociales de l’université de Pau (1980), il avait développé une expertise toute particulière dans les enquêtes quantitatives de consommation alimentaire, pour lesquelles il avait tout à la fois réalisé un travail de terrain considérable et proposé des méthodes informatiques innovantes. Chercheur contractuel mobile, il avait occupé divers postes en accueil au Centre national de la recherche scientifique, à l’Office de la recherche scientifique et technique outre-mer (actuel Institut de recherche pour le développement), au Cameroun, où il était resté 8 ans, puis au Muséum national d’Histoire naturelle à Brunoy, où il s’était établi. Se lançant dans la consultance internationale à la suite de ses études d’impact de l’oléoduc Tchad-Cameroun, il avait fait de nombreuses missions de par le monde, dans le domaine socioéconomique et agricole, et dans la sphère du développement participatif. Polyglotte et enthousiaste, il laisse le souvenir d’un chercheur créatif, exigeant et atypique, à l’intelligence vive. Ses enquêtes sont probablement les meilleures et les plus précises jamais pratiquées au niveau international. A son épouse Naomi et à ses cinq enfants, nous présentons nos condoléances attristées.

Introduction: Recent paleopathological cases have shown the usefulness of interdisciplinary odontological studies in the investigation of historical figures. Observation: A macroscopic examination of the mandible of Saint-Louis (13th c. AD), conserved in the cathedral of Notre-Dame (Paris, France) was carried out, and compared with biographical data about the life and death of the King, and contemporaneous cases of infectious/inflammatory diseases. We found post-mortem tooth loss associated with moderate signs of infectious and inflammatory diseases, which precise diagnoses are discussed facing historical chronicles and sources: main diagnosis is scurvy, potentially associated with bacterial infection. Discussion: Our results support the identification of the relics, and improve the knowledge about the saint's circumstances of death related to metabolic deficiencies and infections. (C) 2019 Elsevier Masson SAS. All rights reserved.

Urban populations from highly industrialized countries are characterized by a lower gut bacterial diversity as well as by changes in composition compared to rural populations from less industrialized countries. To unveil the mechanisms and factors leading to this diversity loss, it is necessary to identify the factors associated with urbanization-induced shifts at a smaller geographical scale, especially in less industrialized countries. To do so, we investigated potential associations between a variety of dietary, medical, parasitological and socio-cultural factors and the gut and saliva microbiomes of 147 individuals from three populations along an urbanization gradient in Cameroon. We found that the presence of Entamoeba sp., a commensal gut protozoan, followed by stool consistency, were major determinants of the gut microbiome diversity and composition. Interestingly, urban individuals have retained most of their gut eukaryotic and bacterial diversity despite significant changes in diet compared to the rural areas, suggesting that the loss of bacterial microbiome diversity observed in industrialized areas is likely associated with medication. Finally, we observed a weak positive correlation between the gut and the saliva microbiome diversity and composition, even though the saliva microbiome is mainly shaped by habitat-related factors.

Following publication of the original article [1], a typographical error in the formula for calculating d i in the “Scans for local adaptation” subsection in the Method section, was identified. The correct formula should be

African rainforests support exceptionally high biodiversity and host the world's largest number of active hunter-gatherers [1-3]. The genetic history of African rainforest hunter-gatherers and neighboring farmers is characterized by an ancient divergence more than 100,000 years ago, together with recent population collapses and expansions, respectively [4-12]. While the demographic past of rainforest hunter-gatherers has been deeply characterized, important aspects of their history of genetic adaptation remain unclear. Here, we investigated how these groups have adapted-through classic selective sweeps, polygenic adaptation, and selection since admixture-to the challenging rainforest environments. To do so, we analyzed a combined dataset of 566 high-coverage exomes, including 266 newly generated exomes, from 14 populations of rainforest hunter-gatherers and farmers, together with 40 newly generated, low-coverage genomes. We find evidence for a strong, shared selective sweep among all hunter-gatherer groups in the regulatory region of TRPS1-primarily involved in morphological traits. We detect strong signals of polygenic adaptation for height and life history traits such as reproductive age; however, the latter appear to result from pervasive pleiotropy of height-associated genes. Furthermore, polygenic adaptation signals for functions related to responses of mast cells to allergens and microbes, the IL-2 signaling pathway, and host interactions with viruses support a history of pathogen-driven selection in the rainforest. Finally, we find that genes involved in heart and bone development and immune responses are enriched in both selection signals and local hunter-gatherer ancestry in admixed populations, suggesting that selection has maintained adaptive variation in the face of recent gene flow from farmers.

La pratique du soin et la preservation de la sante ont toujours represente une preoccupation majeure pour l’ensemble des societes humaines, depuis les premieres organisations sociales jusqu’a nos jours, et ce, sur tous les continents. L’approche archeologique et anthropologique adoptee dans cet ouvrage permet de retracer, sur plusieurs dizaines de milliers d’annees, la maniere dont les groupes humains ont apprehende la maladie, le handicap et le soin. De la prehistoire a l’epoque contemporaine, les contributeurs et contributrices nous racontent aussi la diversite des pratiques, car a chaque mal correspond un remede determine par des normes sociales et des choix contextuels. Cet ouvrage est le fruit d’une collaboration pluridisciplinaire entre archeologues, anthropologues, biologistes et historiens qui, dans une double approche sociale et biologique, se posent la question du soin et de la sante a l’echelle des individus comme des populations.

OBJECTIVES:The Sahel/Savannah belt is a region where two sympatric human subsistence strategies-nomadic pastoralism and sedentary farming-have been coexisting for millennia. While earlier studies focused on estimating population differentiation and genetic structure of this ecologically remarkable region's inhabitants, less effort has been expended on understanding the morphological variation among local populations.MATERIALS AND METHODS:To fill this gap, we used geometric morphometrics to analyze the facial features of three groups of pastoralists and three groups of sedentary farmers belonging to three language families (Niger-Congo, Nilo-Saharan, and Afro-Asiatic) whose mitochondrial DNA sequences have been published previously.RESULTS:Our results show that pastoralists differ from farmers with several facial features. We also found that individuals who bear maternally inherited haplotypes of Eurasian ancestry do not significantly morphologically differ from individuals whose maternal ancestry is sub-Saharan.CONCLUSIONS:Our study follows up and builds upon population genetic and phylogeographic studies of Eurasian haplogroups in the Fulani pastoralists and sub-Saharan haplogroups in the Arab pastoralists, as well as studies on the spread of lactase persistence mutations and other genetic markers. Our results suggest that recent gene flows across the Sahel/Savannah belt were not strong enough to erase a genetic structure established by Paleolithic foragers and further shaped by the adoption of agropastoral food-producing strategies.

Anatomically modern humans arose in Africa ∼300,000 years ago, but the demographic and adaptive histories of African populations are not well-characterized. Here, we have generated a genome-wide dataset from 840 Africans, residing in western, eastern, southern, and northern Africa, belonging to 50 ethnicities, and speaking languages belonging to four language families. In addition to agriculturalists and pastoralists, our study includes 16 populations that practice, or until recently have practiced, a hunting-gathering (HG) lifestyle. We observe that genetic structure in Africa is broadly correlated not only with geography, but to a lesser extent, with linguistic affiliation and subsistence strategy. Four East African HG (EHG) populations that are geographically distant from each other show evidence of common ancestry: the Hadza and Sandawe in Tanzania, who speak languages with clicks classified as Khoisan; the Dahalo in Kenya, whose language has remnant clicks; and the Sabue in Ethiopia, who speak an unclassified language. Additionally, we observed common ancestry between central African rainforest HGs and southern African San, the latter of whom speak languages with clicks classified as Khoisan. With the exception of the EHG, central African rainforest HGs, and San, other HG groups in Africa appear genetically similar to neighboring agriculturalist or pastoralist populations. We additionally demonstrate that infectious disease, immune response, and diet have played important roles in the adaptive landscape of African history. However, while the broad biological processes involved in recent human adaptation in Africa are often consistent across populations, the specific loci affected by selective pressures more often vary across populations.