Alain Froment

Institute of Research for Development | IRD · 208 - Local Heritage (PaLoc)

Aging is associated with genome-wide changes in DNA methylation in humans, facilitating the development of epigenetic age prediction models. However, most of 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 analyzed th...

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...

L'accumulation exponentielle des innovations technologiques, notamment dans le domaine médical, et des perturbations environnementales propulse l'humanité dans un avenir incertain, dont la direction sur le long terme est impossible à définir, et même à imaginer, faisant de la futurologie une science-fiction hautement spéculative et hasardeuse. L'év...

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 thousa...

Recent paleopathological cases have shown the usefulness of interdisciplinary odontological studies in the investigation of historical figures. 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...

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-i...

Horizontal Gene Transfer, the process by which bacteria acquire new genes and functions from non-parental sources, is common in the human microbiome. If the timescale of HGT is rapid compared to the timescale of human colonization, then it could have the effect of "personalizing" bacterial genomes by providing incoming strains with the genes necess...

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

Colloque Archéologie de la Santé, Anthropologie du Soin, Paris, FRA, 30-/11/2016 - 01/12/2016

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, respecti...

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...

Background Africa is the origin of modern humans within the past 300 thousand years. To infer the complex demographic history of African populations and adaptation to diverse environments, we sequenced the genomes of 92 individuals from 44 indigenous African populations. Results Genetic structure analyses indicate that among Africans, genetic ance...

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 fo...

Protozoa have long been considered undesirable residents of the human gut, but recent findings suggest that some of them may positively affect the gut ecosystem. To better understand the role and ecological dynamics of these commensal and potentially beneficial protozoan symbionts, we need efficient methods to detect them, as well as accurate estim...

Information about the samples used in the study including per-sample results after filtering of the multi-mapped reads. (XLSX)

Logistic regression models: effect of country and subsistence mode on Entamoeba prevalence in non-industrialized countries. (XLSX)

Distribution of Blastocystis sp. subtypes within individuals. (PDF)

List of protozoan genomes and SSU sequences used for mapping of metagenomic data. (XLSX)

Prevalence of detected protozoan species in different populations. (XLSX)

Distribution of mapped reads along genome scaffolds/contigs. (PDF)

Logistic regression models: effect of country and subsistence mode on Blastocystis prevalence in non-industrialized countries. (XLSX)

Logistic regression models: effect of country and subsistence mode on Enteromonas prevalence in non-industrialized countries. (XLSX)

Prevalence of Enteromonas hominis across populations. (PDF)

Coinfection patterns including all protozoan species. (PDF)

Distribution of Entamoeba species within individuals. (PDF)

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 l...

The earliest cranial surgery (trepanation) has been attested since the Mesolithic period. The meaning of such a practice remains elusive but it is evident that, even in prehistoric times, humans from this period and from the Neolithic period had already achieved a high degree of mastery of surgical techniques practiced on bones. How such mastery wa...

Understanding how deleterious genetic variation is distributed across human populations is of key importance in evolutionary biology and medical genetics. However, the impact of population size changes and gene flow on the corresponding mutational load remains a controversial topic. Here, we report high-coverage exomes from 300 rainforest hunter-ga...

Besides their small body size, the various Pygmy groups found across different African regions have generally been described as presenting particular body proportions. This could result from a reduction of scale (allometry) during growth, relatively to non-Pygmy groups. However, morphological differences may also exist between the Pygmy groups. In...

Background Central African hunter-gatherer Pygmy populations have reduced body size compared with their often much larger agricultural non-Pygmy neighbors, potentially reflecting adaptation to the anatomical and physiological constraints of their lifestyle in tropical rainforests. Earlier studies investigating the genetics of the pygmy phenotype ha...

Aging is associated with widespread changes in genome-wide patterns of DNA methylation. Thousands of CpG sites whose tissue-specific methylation levels are strongly correlated with chronological age have been previously identified. However, the majority of these studies have focused primarily on cosmopolitan populations living in the developed worl...

Bantu languages are spoken by about 310 million Africans, yet the genetic history of Bantu-speaking populations remains largely unexplored. We generated genomic data for 1318 individuals from 35 populations in western central Africa, where Bantu languages originated. We found that early Bantu speakers first moved southward, through the equatorial r...

The distribution of deleterious genetic variation across human populations is a key issue in evolutionary biology and medical genetics. However, the impact of different modes of subsistence on recent changes in population size, patterns of gene flow, and deleterious mutational load remains unclear. Here, we report high-coverage exome sequencing dat...

The skull of René Descartes is held in the National Museum of Natural History since the 19th c. Up to date, only anthropological examinations were carried out, focusing on the cranial capacity and phrenological interpretation of the skull morphology. Using CT-scan based 3D technology, a reconstruction of the endocast was performed, allowing for its...

En 1863 et 1864, sous l’impulsion de Jacques Boucher de Perthes (1788-1868), une série de restes humains fut mise au jour dans la carrière de Moulin Quignon, près d’Abbeville dans la Somme, site connu quelques temps auparavant pour avoir livré des industries lithiques de type acheuléen permettant la reconnaissance « officielle » de la grande antiqu...

En mars 1863, Jacques Boucher de Perthes découvre dans les alluvions de Moulin Quignon (Abbeville, France) une mandibule humaine associée à des artéfacts lithiques et à des ossements de grands mammifères fossiles. Rapidement contestée, cette découverte va apparaître comme une supercherie dont le préhistorien aurait été la victime. Depuis cette époq...

La collection de Moulin Quignon est une collection cohérente, malgré la diversité de ses pièces, dans la certitude de sa provenance et dans son rattachement aux recherches menées sur le site en 1863–1864. Considérée comme historique et patrimoniale, son étude a permis néanmoins de livrer des informations scientifiques importantes et valables pour l...

Aging is associated with widespread changes in genome-wide patterns of DNA methylation. Thousands of CpG sites whose tissue-specific methylation levels are strongly correlated with chronological age have been previously identified. However, the majority of these studies have focused primarily on cosmopolitan populations living in the developed worl...

A medical tomodensitometric study (TDM) was performed on a dry skull from the necropolis of Ancón in Peru. The skull, housed at the Muséum national d’histoire naturelle in Paris, displays an anteroposterior, brachycephalic, oblique, asymmetric, and bilobar deformation. TDM permitted 3-D reconstructions of the skull, endocranium, and vault thickness...

Immunosuppression resulting from HIV infection increases the risk of progression to active tuberculosis (TB) both in individuals newly exposed to Mycobacterium tuberculosis (MTB) and in those with latent infections. We hypothesized that HIV-positive individuals who do not develop TB, despite living in areas where it is hyperendemic, provide a model...

During years 1863 and 1864, Jacques Boucher de Perthes (1788-1868) drove the discovery of a series of human remains from the Moulin Quignon stone pit, near Abbeville (Somme, France), site known for a while for its Acheulean lithic industry regarded as an official evidence for the great antiquity of Man. These anthropological remains, instead of sup...

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 profile...

The human gut microbiota is impacted by host nutrition and health status and therefore represents a potentially adaptive phenotype influenced by metabolic and immune constraints. Previous studies contrasting rural populations in developing countries to urban industrialized ones have shown that industrialization is strongly correlated with patterns...

Significance of covariates describing composition of gut microbiota. Summary of p-values from a PERMANOVA analysis of microbiome composition (OTUs): (i) merged (OTUs collapsed based on shared taxonomic identifier) and filtered (> = 0.1% in > = 4 individuals), (ii) merged and unfiltered, (iii) partially merged (OTUs collapsed only when family, genus...

Metadata for study. Summary of metadata for all 64 individuals included in this study. For 5 individuals, we collected two fecal samples (7 days apart for 4 samples and 1 day apart for 1 sample). For parasites detection, we identified Ascaris (ASC), Ancylostoma (ANC), Trichuris (TRI) and Entamoeba (ENT). When none of these were detected, the indivi...

Summary of significant taxa across covariates. Summary of the number of significant taxa (q < 0.05; ANOVA) for covariates that were identified as being significant for at least one taxon. Analysis is based on abundances of OTUs that were merged based on taxa names such that abundances for all OTUs with identical identifiers were combined. Merged OT...

RFC predictions for subsistence. Summary of random forest classifier (RFC) model predictions for four subsistence groups (Fis = fishing population, Far(S) = farmers from the South, Far(N) = farmers from the North, and HG = hunter-gatherers) based on individual gut microbiome composition. A RFC with 2000 decision trees was trained on the data with 5...

Alpha diversity across Entamoeba status. Comparison of alpha diversity for Entamoeba negative (Ent-) and positive (Ent+) individuals using the Shannon Index (a) and Simpson’s Index (b). P-values are based on a Welch’s t-test. (TIFF)

Phyla significantly correlated with alpha diversity across Entamoeba status. Phyla (occurring at > = 0.1% in at least 4 individuals) for which abundance is significantly correlated with alpha diversity (phylogenetic distance whole tree metric) in Entamoeba negative (Ent-, blue) and positive (Ent+, red) individuals. q < 0.05; ANOVA. (TIFF)

Summary of relative abundance of taxa across subsistence. Summary of the relative abundance of taxa (occurring > = 0.1% in at least 4 individuals) for individuals across locations. The Ndtoua village is not considered here as it only includes two individuals. Taxa are colored by phylum (Actinobacteria (Act.) = red, Bacteroidetes (Bact.) = green, Cy...

Significantly different taxa across subsistence groups. Summary of means and q-values (ANOVA) for all taxa (> = 0.1% in at least 4 individuals) that differ significantly between subsistence groups based on merged (OTUs collapsed based on taxa name) and partially merged (OTUs collapsed based on taxa name restricted to below the family level) OTU tab...

Age of Entamoeba positive and negative individuals. Mean age of Entamoeba negative (Ent-) and positive (Ent+) individuals. P-value are based on a Welch’s t-test. (TIFF)

Beta diversity estimates within individuals, subsistence group, and location. (a) Beta diversity estimates between all pairs of individuals, for pairs within subsistence groups, within locations, and within individuals based on weighted (left panel) and unweighted (right panel) UniFrac distances. P-values are from a Wilcox Rank Sum test. (b) Multid...

Multidimensional Scaling plots for weighted UniFrac distances for Entamoeba status and subsistence. Multidimensional Scaling plots for (a) weighted UniFrac distances colored by Entamoeba status (b) weighted UniFrac distances colored by subsistence (Fis = fishing population, Far(S) = farmers from the South, Far(N) = farmers from the North, and HG =...

Beta diversity across Entamoeba status. Comparison of beta diversity for Entamoeba negative (Ent-), positive (Ent+), and between Ent- and Ent+ individuals based on weighted UniFrac distances. P-values are based on a Welch’s t-test. (TIFF)

Summary of predicted metagenomic composition across Entamoeba status. Summary of predicted metagenomic composition for Entamoeba negative (Ent-) and positive (Ent+) individuals based on phylotypic investigation of communities by reconstruction of unobserved states (PICRUSt). Relative abundance of (a) the most abundant (> = 0.4% in at least one grou...

Summary of relative abundance of taxa across Entamoeba status. Summary of the relative abundance of taxa (> = 0.1% in at least 4 individuals) for the number of infecting parasites in the absence of Entamoeba infection (0–3). Taxa are colored by phylum (Acinobacteria (Act.) = red, Bacteroidetes (Bact.) = green, Cyanobacteria (Cyan.) = black, Elusimi...

Random forest classifier predictions for subsistence. Summary of the ten most discriminating taxa identified by a random forest classifier (RFC) model to be predictive of subsistence group. A RFC with 2000 decision trees was trained on the data (relative abundances of all taxa occurring at > = 0.1% in at least 4 individuals) with 5-fold cross-valid...

Significantly different taxa across Entamoeba status. Summary of means and q-values (ANOVA) for all taxa (occurring at > = 0.1% in at least 4 individuals) that differ significantly between Entamoeba negative (Ent-) and positive (Ent+) individuals based on merged (OTUs collapsed based on taxa name) and partially merged (OTUs collapsed only when fami...

Significantly different KEGG pathways across subsistence and Entamoeba status. Summary of means and q-values (ANOVA) for all abundant level 3 KEGG pathways (> = 0.4% in at least 4 individuals) across Entamoeba infection status and subsistence group (Fis: Fishing population; Far(S): Farmers from the South; Far(N): Farmers from the North; HG: Hunter-...

Parasite prevalence across subsistence groups. Prevalence of individual infection by four parasites (Trichuris, Ascaris, Ancylostoma, and Entamoeba) across the four subsistence groups. Fis = fishing population, Far(S) = farmers from the South, Far(N) = farmers from the North, and HG = hunter-gatherers. The total number of samples in each population...

Alpha rarefaction curves for across subsistence groups. Alpha rarefaction curves for the four subsistence groups using the Phylogenetic Distance Whole Tree metric for alpha diversity (means across 10 iterations). Fis = fishing population, Far(S) = farmers from the South, Far(N) = farmers from the North, and HG = hunter-gatherers. Variance is among...

Summary of RFC top ten taxa for Entamoeba status. Summary of the ten most discriminating taxa identified by a random forest classifier (RFC) model to be predictive of Entamoeba infection status. A RFC with 2000 decision trees was trained on the data (relative abundances of all taxa occurring at > = 0.1% in at least 4 individuals) with 5-fold cross-...

Alpha diversity across infecting parasite richness. Alpha diversity across individuals grouped by the number of infecting parasite species in the absence of Entamoeba infection (0–3) using the phylogenetic distance whole tree metric. P-values are based on a Welch’s t-test. (TIFF)

Shannon and Simpson’s diversity across subsistence. Comparison of individual gut microbial diversity across subsistence modes based on (a) the Shannon Index and (b) the Simpson’s Index metrics for alpha diversity. P-values are based on Welch’s t-tests. Fis = Fishing population; Far(S) = Farmers from the South; Far(N) = Farmers from the North; HG =...

Weighted UniFrac distance across subsistence and location. Beta diversity between individuals based on weighted UniFrac distances across (a) subsistence modes and (b) location. (c) Beta diversity between pairs of subsistence groups. All p-values are based on Welch’s t-tests. Subsistence: Fis = Fishing population (blue); Far(S) = Farmers from the So...