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Yaws affects children in tropical regions, while syphilis primarily affects sexually active adults worldwide. Despite various campaigns towards the eradication of yaws and elimination of syphilis, these two diseases are still present in Ghana. The aetiological agents of both diseases, two Treponema pallidum subspecies, are genetically similar. This study aimed to assess the prevalence of these treponematoses and the occurrence of pathogens causing similar skin lesions in the Ashanti region of Ghana. A point-of-care test was used to determine the seroprevalence of the treponematoses. Both yaws and syphilis were identified in the Ashanti region of Ghana. Multiplex PCR was used to identify treponemes and other pathogens that cause similar skin lesions. The results indicated that the seroprevalences of T. pallidum in individuals with yaws-like and syphilis-like lesions were 17.2% and 10.8%, respectively. Multiplex PCR results showed that 9.1%, 1.8% and 0.9% of yaws-like lesions were positive for Haemophilus ducreyi, herpes simplex virus-1 (HSV-1) and T. pallidum respectively. Among syphilis-like lesions, 28.3% were positive for herpes simplex virus -2 (HSV-2) by PCR. To our knowledge, this is the first time HSV-I and HSV-2 have been reported from yaws-like and syphilis-like lesions, respectively, in Ghana. The presence of other organisms apart from T. pallidum in yaws-like and syphilis-like lesions could impede the total healing of these lesions and the full recovery of patients. This may complicate efforts to achieve yaws eradication by 2030 and the elimination of syphilis and warrants updated empirical treatment guidelines for skin ulcer diseases.

The Naxos dome, in the middle of the Aegean domain, exposes the former root of the Alpine orogenic belt and represents a key natural example to investigate the development of gravitational instabilities during orogenic evolution and their impact on crustal differentiation. The Naxos dome is cored by migmatites with structures depicting second order domes with a diameter of 1–2 km nested in the first order deca-kilometer scale dome that formed at the onset of orogenic collapse. Zircon grains from the migmatites record a succession of crystallization-dissolution cycles with a period of 1–2 Myr. These features have been attributed to the development of convective and diapiric gravitational instabilities, related to thermally induced and compositional buoyancy. In this paper, we test the pertinence of this model with a thermal-mechanical numerical experiment performed with a volume of fluid method (VOF) known to preserve material phase interfaces during large deformation of viscous layers. Partial melting of the crust is modeled by strain-rate and temperature dependent viscosity and temperature dependent density. Moreover, horizontal layers with density, viscosity and heat production variations mimic more felsic or more mafic lithologies in a crust of intermediate composition. With basal heating, gravitational instabilities initiate with local segregation of the buoyant versus heavier layers, followed by diapiric upwelling of buoyant pockets of aggregated less dense material. Convection starts after 5 Myr, approximately when half of the crust has a viscosity lower than 1019 Pa s. The size of the convection cells increases as the temperature rises in the crust and reaches ∼25 km in diameter after ca. 20 Myr, which defines the size of first order domes. Some of the heterogeneous material is entrained in the convection cells with a revolution period of 1 to 3 Myr. However, most of the denser material accumulates in the lower crust, while the buoyant material segregates at the top of the convection cells and forms diapirs that correspond to second order domes, of several kilometers in diameter and nested within the first order domes. This model, which reproduces the first order characteristic dimensions of the Naxos nested domes and the periodicity of their zircon geochronological record, demonstrates the efficiency of gravitational instabilities in the formation of migmatite domes and, more generally, in the multi-scale dynamics of crustal differentiation leading to a felsic upper crust, an intermediate middle crust and a mafic lower crust.

Here we investigate the effects of extensive sociality and mobility on the oral microbiome of 138 Agta hunter–gatherers from the Philippines. Our comparisons of microbiome composition showed that the Agta are more similar to Central African BaYaka hunter–gatherers than to neighbouring farmers. We also defined the Agta social microbiome as a set of 137 oral bacteria (only 7% of 1980 amplicon sequence variants) significantly influenced by social contact (quantified through wireless sensors of short-range interactions). We show that large interaction networks including strong links between close kin, spouses and even unrelated friends can significantly predict bacterial transmission networks across Agta camps. Finally, we show that more central individuals to social networks are also bacterial supersharers. We conclude that hunter–gatherer social microbiomes are predominantly pathogenic and were shaped by evolutionary tradeoffs between extensive sociality and disease spread.

Recent studies have reported evidence suggesting that portions of contemporary human genomes introgressed from archaic hominin populations went to high frequencies due to positive selection. However, no study to date has specifically addressed the postintrogression population dynamics of these putative cases of adaptive introgression. Here, for the first time, we specifically define cases of immediate adaptive introgression (iAI) in which archaic haplotypes rose to high frequencies in humans as a result of a selective sweep that occurred shortly after the introgression event. We define these cases as distinct from instances of selection on standing introgressed variation (SI), in which an introgressed haplotype initially segregated neutrally and subsequently underwent positive selection. Using a geographically diverse data set, we report novel cases of selection on introgressed variation in living humans and shortlist among these cases those whose selective sweeps are more consistent with having been the product of iAI rather than SI. Many of these novel inferred iAI haplotypes have potential biological relevance, including three that contain immune-related genes in West Siberians, South Asians, and West Eurasians. Overall, our results suggest that iAI may not represent the full picture of positive selection on archaically introgressed haplotypes in humans and that more work needs to be done to analyze the role of SI in the archaic introgression landscape of living humans.

High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.

The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama-Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25-40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10-32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama-Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51-72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.

The domestication of plants and animals marks one of the most significant transitions in human, and indeed global, history. Traditionally, study of the domestication process was the exclusive domain of archaeologists and agricultural scientists; today it is an increasingly multidisciplinary enterprise that has come to involve the skills of evolutionary biologists and geneticists. Although the application of new information sources and methodologies has dramatically transformed our ability to study and understand domestication, it has also generated increasingly large and complex datasets, the interpretation of which is not straightforward. In particular, challenges of equifinality, evolutionary variance, and emergence of unexpected or counter-intuitive patterns all face researchers attempting to infer past processes directly from patterns in data. We argue that explicit modeling approaches, drawing upon emerging methodologies in statistics and population genetics, provide a powerful means of addressing these limitations. Modeling also offers an approach to analyzing datasets that avoids conclusions steered by implicit biases, and makes possible the formal integration of different data types. Here we outline some of the modeling approaches most relevant to current problems in domestication research, and demonstrate the ways in which simulation modeling is beginning to reshape our understanding of the domestication process.

Migmatites and granitic-gneisses exhumed in Archean to Phanerozoic segments are former partially molten crustal roots, display typical domes structures ranging in size from kilometres to decakilometres, and are often interpreted as resulting from the development of diapiric or convective gravitational instabilities. In previous work (part I), we determined various regimes of gravity-driven segregation, by considering a thick continental crust heated from below and containing melt related heterogeneities. These heterogeneities, represented by inclusions of distinct densities and viscosities with respect to the ambient partially molten material, can be entrained into convection cells (in the 'suspension' and 'layering' regimes) and/or accumulate as clusters (in the 'layering' and 'diapirism' regimes). Here we further investigate the specific conditions that allow for the formation and preservation of domes resulting from diapirism at the top of convective cells. We show that both the cessation of basal heating and the freezing of the buoyant inclusions density favour their stacking and preservation at ca. 15 km depth, within about 10 Myr. The buoyant inclusions form domes, 5–20 km in size, that also record several convective cycles at velocities ranging from 0.5–4 cm yr−1. 3-D models demonstrate their radial geometrical nature. The influence of the size and concentration of the inclusions is also assessed, complementing the characteristics of crustal heterogeneity in driving its differentiation and the formation of migmatite domes. [ABSTRACT FROM AUTHOR]

Literacy is more diverse than ever before, and information and communication technologies are playing a central role in the diversification and dissemination of literacy practices. Digital literacy occupies an important place among the skills and competences of 21st century citizens. This is the focus of the first part of this article. In the second part, I provide an overview of the concept of digital literacy based on the most recent literature, before moving to a synthesis of the concept structured in three dimensions, namely: communication skills, understanding of the impact of technology and media in the world around us, and understanding of how technology can be used in formal or informal learning. Then I move on to examine a number of open or sensitive questions dealing with the relationships between digital and traditional literacy — both in terms of acquisition and of practice; with the articulation of digital literacy with traditional learning and communication, as well as with extracurricular literacy. Finally, I focus on its presence in practices as an extension of communicative repertoires and on the effects of ’complexification’ and ’facilitation’ of the development of literacies.