Looking for signatures of sex-specific demography and local adaptation on the X chromosome

A genome-wide study of X chromosome genetic diversity in human populations shows the impact of social organization and local adaptation

Genetic diversity and the emergence of ethnic groups in Central Asia

This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Elevated rates of horizontal gene transfer in the industrialized human microbiome

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.Peer reviewe

Lactase Persistence in Central Asia: Phenotype, Genotype, and Evolution

The aim of the present study is to document the evolution of the lactase persistence trait in Central Asia, a geographical area that is thought to have been a region of long-term pastoralism. Several ethnic groups co-exist in this area: Indo-Iranian speakers who are traditionally agriculturist (Tajik) and Turkic speakers who used to be nomadic herders (Kazakh, Karakalpak, Kyrgyz, Turkmen). It was recently demonstrated that horse milking practice existed in the Botai culture of Kazakhstan as early as 5,500 BP (Outram et al. 2009). However, the frequency of the lactase persistence trait and its genetic basis in Central Asian populations remain largely unknown. We propose here the first genotype-phenotype study of lactase persistence in Central Asia based on 183 individuals, as well as the estimation of the time of expansion of the lactasepersistence associated polymorphism. Our results show a remarkable geneticphenotypic correlation, with the causal polymorphism being the same than in Europe (-13.910C T, rs4988235). The lactase persistence trait is at low frequency in these populations: between 25% and 32% in the Kazakh population (traditionally herders), according to phenotype used, and between 11% and 30% in the Tajiko-Uzbek population (agriculturalists). The difference in lactase persistence between populations, even if small, is significant when using individuals concordant for both excretion of breath hydrogen and the lactose tolerance blood glucose test phenotypes (P 0.018, 25% for Kazakh vs. 11% for Tajiko-Uzbeks), and the difference in frequency of the 13.910*T allele is almost significant (P 0.06, 30% for Kazakhs vs. 19% for Tajiko-Uzbeks). Using the surrounding haplotype, we estimate a date of expansion of the T allele around 6,000–12,000 yrs ago, which is consistent with archaeological records for the emergence of agropastoralism and pastoralism in Central Asia

Human Genetic Data Reveal Contrasting Demographic Patterns between Sedentary and Nomadic Populations That Predate the Emergence of Farming

International audienceDemographic changes are known to leave footprints on genetic polymorphism. Together with the increased availability of large polymorphism data sets, coalescent-based methods allow inferring the past demography of populations from their present-day patterns of genetic diversity. Here, we analyzed both nuclear (20 noncoding regions) and mitochondrial (HVS-I) resequencing data to infer the demographic history of 66 African and Eurasian human populations presenting contrasting lifestyles (nomadic hunter-gatherers, nomadic herders, and sedentary farmers). This allowed us to investigate the relationship between lifestyle and demography and to address the long-standing debate about the chronology of demographic expansions and the Neolithic transition. In Africa, we inferred expansion events for farmers, but constant population sizes or contraction events for hunter-gatherers. In Eurasia, we inferred higher expansion rates for farmers than herders with HVS-I data, except in Central Asia and Korea. Although isolation and admixture processes could have impacted our demographic inferences, these processes alone seem unlikely to explain the contrasted demographic histories inferred in populations with different lifestyles. The small expansion rates or constant population sizes inferred for herders and hunter-gatherers may thus result from constraints linked to nomadism. However, autosomal data revealed contraction events for two sedentary populations in Eurasia, which may be caused by founder effects. Finally, the inferred expansions likely predated the emergence of agriculture and herding. This suggests that human populations could have started to expand in Paleolithic times, and that strong Paleolithic expansions in some populations may have ultimately favored their shift toward agriculture during the Neolithic

25 années d’archéologie royale (1990-2015)

Le colloque « 25 années d’archéologie royale, 1990-2015 » a été organisé pour faire le bilan des recherches menées dans les domaines de Versailles, Trianon et Marly au cours de ce quart de siècle, mais aussi des travaux récents réalisés dans les autres domaines royaux. Il a été l’occasion de mesurer l’extension chronologique de l’archéologie : désormais la période moderne fait résolument partie de son champ de compétence. L’archéologie des jardins, son corollaire, devenue une discipline scientifique à part entière, a été amplement évoquée. Enfin l’apport des sciences originellement étrangères à l’archéologie a été souligné : géologie, malacologie, parasitologie... La première intervention archéologique dans le domaine de Versailles a eu lieu en 1990, à l’occasion du lancement de la replantation du parc, après le passage de la tempête du 3 février. Cette replantation devant s’accompagner de la restitution des aménagements – souvent disparus – qu’avait conçus André Le Nôtre, l’investigation archéologique s’est imposée. Depuis 1990, ce sont près d’une douzaine d’opérations qui ont été conduites dans le domaine de Versailles, la plupart dans le parc. Quelques chantiers ont néanmoins été menés hors de cet espace, notamment dans les cours du château et du Grand Commun, et dans le domaine de Trianon Le rattachement, en 2009, du domaine de Marly à celui de Versailles a réuni sous une même administration les trois châteaux fondés par Louis XIV. Rasé peu de temps après la Révolution, il ne reste de Marly qu’un écrin vide, mais ce site magnifique renferme des richesses en sous-sol. Cependant, Versailles et ses satellites ne sont pas les seuls châteaux royaux à s’ouvrir à l’archéologie : les Tuileries, Vincennes, Saint-Germain, Fontainebleau et Chambord ont fait aussi l’objet de recherches, en archéologie médiévale d’abord (à Vincennes), puis, rapidement, cette recherche s’est étendue aux époques postérieures. Le parti a été pris de se limiter pour ce colloque à l’Époque moderne. Colloque organisé par le Centre de recherche du château de Versailles. Voir le programme complet. Responsable scientifique : Annick Heitzmann Partenaires : Établissement public du château, du musée et du domaine national de Versailles, DRAC Île-de-France et Service régional de l’archéologie, INRAP, Association Volutes, Musée-promenade de Marly-le-Roi Louveciennes. En partenariat avec le réseau Archéologia.be. Dix-sept communications au colloque sur vingt sont publiées ici, sous la direction d’Annick Heitzmann. Les autres sont consultables sous forme audio. The conference “25 Years of Royal Archaeology, 1990–2015” was organized to review not only the research undertaken in the domains of Versailles, Trianon and Marly over the last quarter century, but also recent work in other royal domains. It was the opportunity to measure the chronological extension of the archaeology: the modern period is now resolutely within its field of competence. The archaeology of the gardens, their corollaries, which has become a scientific discipline in its own right, was widely alluded to. Finally, the contribution of sciences originally foreign to archaeology has been emphasized: geology, malacology, parasitology, for example. The first archaeological intervention in the ​​Versailles domain took place in 1990, at the same time as the replanting of the park, after the storm of 3 February. As this replantation was to be accompanied by the restitution of the layouts – that had often disappeared – which André Le Nôtre had designed, archaeological investigation was essential. Since 1990 almost a dozen operations have been conducted in the ​​Versailles domain, most of them in the park. Some projects were undertaken at other sites, particularly in the courtyards of the château and the Grand Commun, and in the Trianon domain. The incorporation, in 2009, of the Marly domain with that of Versailles brought the three castles founded by Louis XIV together under one administration. Razed shortly after the Revolution, there is only one empty enclosure at Marly, but this magnificent site contains wealth below the ground. However Versailles and its satellites are not the only royal castles that have opened to archaeology: the Tuileries, Vincennes, Saint-Germain, Fontainebleau and Chambord have also been the subject of research, first in medieval archaeology (Vincennes) then the research rapidly extended to later periods. It was decided that this conference would confine itself to the modern era. Conference organized by the Centre de Recherche du château de Versailles. See the full programme. Research Director: Annick Heitzmann Partners: Public Establishment of the Palace, the Museum and the National Estate of Versailles, DRAC Île-de-France and Regional Services for Archaeology, INRAP, Association Volutes, Musée-Promenade de Marly-le-Roi Louveciennes. With the partnerhship of the Archéologia.be network. Seventeen of the twenty conference papers are published here, edited by Annick Heitzmann. The others are available in audio format

Codiversification of gut microbiota with humans

International audienceThe gut microbiomes of human populations worldwide have many core microbial species in common. However, within a species, some strains can show remarkable population specificity. The question is whether such specificity arises from a shared evolutionary history (codiversification) between humans and their microbes. To test for codiversification of host and microbiota, we analyzed paired gut metagenomes and human genomes for 1225 individuals in Europe, Asia, and Africa, including mothers and their children. Between and within countries, a parallel evolutionary history was evident for humans and their gut microbes. Moreover, species displaying the strongest codiversification independently evolved traits characteristic of host dependency, including reduced genomes and oxygen and temperature sensitivity. These findings all point to the importance of understanding the potential role of population-specific microbial strains in microbiome-mediated disease phenotypes

The human gut microbiome and health inequities

Individuals who are minoritized as a result of race, sexual identity, gender, or socioeconomic status experience a higher prevalence of many diseases. Understanding the biological processes that cause and maintain these socially driven health inequities is essential for addressing them. The gut microbiome is strongly shaped by host environments and affects host metabolic, immune, and neuroendocrine functions, making it an important pathway by which differences in experiences caused by social, political, and economic forces could contribute to health inequities. Nevertheless, few studies have directly integrated the gut microbiome into investigations of health inequities. Here, we argue that accounting for host-gut microbe interactions will improve understanding and management of health inequities, and that health policy must begin to consider the microbiome as an important pathway linking environments to population health