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An amendment to this paper has been published and can be accessed via a link at the top of the paper. [ABSTRACT FROM AUTHOR]

Thermophilization is the directional change in species community composition towards greater relative abundances of species associated with warmer environments. This process is well-documented in temperate and Neotropical plant communities, but it is uncertain whether this phenomenon occurs elsewhere in the tropics. Here we extend the search for thermophilization to equatorial Africa, where lower tree diversity compared to other tropical forest regions and different biogeographic history could affect community responses to climate change. Using re-census data from 17 forest plots in three mountain regions of Africa, we find a consistent pattern of thermophilization in tree communities. Mean rates of thermophilization were +0.0086 °C·y−1 in the Kigezi Highlands (Uganda), +0.0032 °C·y−1 in the Virunga Mountains (Rwanda-Uganda-Democratic Republic of the Congo) and +0.0023 °C·y−1 in the Udzungwa Mountains (Tanzania). Distinct from other forests, both recruitment and mortality were important drivers of thermophilzation in the African plots. The forests studied currently act as a carbon sink, but the consequences of further thermophilization are unclear. Thermophilization is a change in species community composition towards greater abundances of species associated with warmer environments. This study provides evidence of thermophilization in understudied Afromontane forests, but with drivers that are distinct from other forest types. [ABSTRACT FROM AUTHOR]

Many bacterial pathogens, including the human exclusive pathogen Salmonella Typhi, express capsular polysaccharides as a crucial virulence factor. Here, through S. Typhi whole genome sequence analyses and functional studies, we found a list of single point mutations that make S. Typhi hypervirulent. We discovered a single point mutation in the Vi biosynthesis enzymes that control Vi polymerization or acetylation is enough to result in different capsule variants of S. Typhi. All variant strains are pathogenic, but the hyper Vi capsule variants are particularly hypervirulent, as demonstrated by the high morbidity and mortality rates observed in infected mice. The hypo Vi capsule variants have primarily been identified in Africa, whereas the hyper Vi capsule variants are distributed worldwide. Collectively, these studies increase awareness about the existence of different capsule variants of S. Typhi, establish a solid foundation for numerous future studies on S. Typhi capsule variants, and offer valuable insights into strategies to combat capsulated bacteria. Here, Lee and Song describe missense mutations in the viaB locus in clinical isolates of Salmonella Typhi that result in hypo- and hyper-virulent phenotypes due to changes in the capsule. [ABSTRACT FROM AUTHOR]

Off-grid photovoltaic systems have been proposed as a panacea for economies with poor electricity access, offering a lower-cost "leapfrog" over grid infrastructure used in higher-income economies. Previous research examining pathways to electricity access may understate the role of off-grid photovoltaics as it has not considered reliability and carbon pricing impacts. We perform high-resolution geospatial analysis on universal household electricity access in Sub-Saharan Africa that includes these aspects via least-cost pathways at different electricity demand levels. Under our "Tier 3" demand reference scenario, 24% of our study's 470 million people obtaining electricity access by 2030 do so via off-grid photovoltaics. Including a unit cost for unmet demand of 0.50 US dollars ($)/kWh, to penalise poor system reliability increases this share to 41%. Applying a carbon price (around $80/tonne CO2-eq) increases it to 38%. Our results indicate considerable diversity in the level of policy intervention needed between countries and suggest several regions where lower levels of policy intervention may be effective. This study investigates the role of off-grid solar in achieving SDG7 in Africa, focusing on understanding the impact of carbon pricing and supply reliability. It uses high-resolution spatial analysis and demand modelling to explore policy interventions for universal electricity access. [ABSTRACT FROM AUTHOR]

The global population is aging at the same time as heat exposures are increasing due to climate change. Age structure, and its biological and socio-economic drivers, determine populations' vulnerability to high temperatures. Here we combine age-stratified demographic projections with downscaled temperature projections to mid-century and find that chronic exposure to heat doubles across all warming scenarios. Moreover, >23% of the global population aged 69+ will inhabit climates whose 95th percentile of daily maximum temperature exceeds the critical threshold of 37.5 °C, compared with 14% today, exposing an additional 177–246 million older adults to dangerous acute heat. Effects are most severe in Asia and Africa, which also have the lowest adaptive capacity. Our results facilitate regional heat risk assessments and inform public health decision-making. By 2050 > 23% of the global population aged 69 + will live in climates with acute heat exposure– the 95th percentile of the distribution of maximum daily temperatures–greater than the critical threshold of 37.5C, compared with 14% in 2020, an increase of 177–246 million older adults exposed to dangerous acute heat. [ABSTRACT FROM AUTHOR]

Africa produces around 60% of the rice the continent consumes, relying heavily on rice imports to fulfill the rest of the domestic demand. Over the past 10 years, the rice-agricultural area increased nearly 40%, while average yield remained stagnant. Here we used a process-based crop simulation modelling approach combined with local weather, soil, and management datasets to evaluate the potential to increase rice production on existing cropland area in Africa and assess cropland expansion and rice imports by year 2050 for different scenarios of yield intensification. We find that Africa can avoid further increases in rice imports, and even reduce them, through a combination of cropland expansion following the historical trend together with closure of the current exploitable yield gap by half or more. Without substantial increase in rice yields, meeting future rice demand will require larger rice imports and/or land conversion than now. Here the authors demonstrate that cropland expansion following the historical trend together with closing the current exploitable yield gap by half or more across Africa reduces the continent's reliance on land conversions and imports by 2050. [ABSTRACT FROM AUTHOR]

Vaccines and clean water shortages continue to give rise to cholera outbreaks in Africa. Coordinated efforts to increase vaccine distribution and improve physical infrastructure are needed while considering future outbreaks and water demands due to conflicts and climate events. [ABSTRACT FROM AUTHOR]

Most hypertension-related genome-wide association studies (GWASs) focus on non-African populations, despite hypertension (a major risk factor for cardiovascular disease) being highly prevalent in Africa. The AWI-Gen study GWAS meta-analysis for blood pressure (BP)-related traits (systolic and diastolic BP, pulse pressure, mean-arterial pressure and hypertension) from three sub-Saharan African geographic regions (N = 10,775), identifies two novel genome-wide significant signals (p < 5E-08): systolic BP near P2RY1 (rs77846204; intergenic variant, p = 4.95E-08) and pulse pressure near LINC01256 (rs80141533; intergenic variant, p = 1.76E-08). No genome-wide signals are detected for the AWI-Gen GWAS meta-analysis with previous African-ancestry GWASs (UK Biobank (African), Uganda Genome Resource). Suggestive signals (p < 5E-06) are observed for all traits, with 29 SNPs associating with more than one trait and several replicating known associations. Polygenic risk scores (PRSs) developed from studies on different ancestries have limited transferability, with multi-ancestry PRS providing better prediction. This study provides insights into the genetics of BP variation in African populations. Hypertension is a major risk factor for cardiovascular disease prevalent in Africa. Here the authors report a genome-wide study providing insights into the genetics and physiology of blood pressure variation in African populations. [ABSTRACT FROM AUTHOR]

Drawing on perspectives from West and Southern Africa, this Comment critically examines the current state of neuroscience progress in Africa, describing the unique landscape and ongoing challenges as embedded within wider socio-political realities. Distinct research opportunities in the African context are explored to include genetic and bio-diversity, multilingual and multicultural populations, life-course development, clinical neuroscience and neuropsychology, with applications to machine learning models, in light of complex post-colonial legacies that often impede research progress. Key determinants needed to accelerate African neuroscience are then discussed, as well as cautionary underpinnings that together create an equitable neuroscience framework. [ABSTRACT FROM AUTHOR]

Long-acting injectable medications, such as atovaquone, offer the prospect of a "chemical vaccine" for malaria, combining drug efficacy with vaccine durability. However, selection and transmission of drug-resistant parasites is of concern. Laboratory studies have indicated that atovaquone resistance disadvantages parasites in mosquitoes, but lack of data on clinically relevant Plasmodium falciparum has hampered integration of these variable findings into drug development decisions. Here we generate atovaquone-resistant parasites that differ from wild type parent by only a Y268S mutation in cytochrome b, a modification associated with atovaquone treatment failure in humans. Relative to wild type, Y268S parasites evidence multiple defects, most marked in their development in mosquitoes, whether from Southeast Asia (Anopheles stephensi) or Africa (An. gambiae). Growth of asexual Y268S P. falciparum in human red cells is impaired, but parasite loss in the mosquito is progressive, from reduced gametocyte exflagellation, to smaller number and size of oocysts, and finally to absence of sporozoites. The Y268S mutant fails to transmit from mosquitoes to mice engrafted with human liver cells and erythrocytes. The severe-to-lethal fitness cost of clinically relevant atovaquone resistance to P. falciparum in the mosquito substantially lessens the likelihood of its transmission in the field. Malaria parasites from patients who fail atovaquone therapies are highly drug-resistant, with mutations at Y268 in cytochrome b. Here the authors show that this mutation results in multiple defects in the parasite's development and prevents transmission from mosquitoes to mice. [ABSTRACT FROM AUTHOR]

Streamlined data-driven drug discovery remains challenging, especially in resource-limited settings. We present ZairaChem, an artificial intelligence (AI)- and machine learning (ML)-based tool for quantitative structure-activity/property relationship (QSAR/QSPR) modelling. ZairaChem is fully automated, requires low computational resources and works across a broad spectrum of datasets. We describe an end-to-end implementation at the H3D Centre, the leading integrated drug discovery unit in Africa, at which no prior AI/ML capabilities were available. By leveraging in-house data collected over a decade, we have developed a virtual screening cascade for malaria and tuberculosis drug discovery comprising 15 models for key decision-making assays ranging from whole-cell phenotypic screening and cytotoxicity to aqueous solubility, permeability, microsomal metabolic stability, cytochrome inhibition, and cardiotoxicity. We show how computational profiling of compounds, prior to synthesis and testing, can inform progression of frontrunner compounds at H3D. This project is a first-of-its-kind deployment at scale of AI/ML tools in a research centre operating in a low-resource setting. Streamlined data-driven drug discovery remains challenging, especially in resource-limited settings. Here, the authors present ZairaChem, an AI/ML tool that streamlines QSAR/QSPR modelling, implemented for the first time at the H3D Centre in South Africa. [ABSTRACT FROM AUTHOR]

Previous research suggests that dog mass vaccination campaigns can eliminate rabies locally, resulting in large human and animal life gains. Despite these demonstrated benefits, dog vaccination programs remain scarce on the African continent. We conducted a benefit-cost analysis to demonstrate that engaging into vaccination campaigns is the dominant strategy for most countries even in the absence of coordinated action between them. And quantify how coordinated policy measures across countries in Africa could impact rabies incidence and associated costs. We show that coordinated dog mass vaccination between countries and PEP would lead to the elimination of dog rabies in Africa with total welfare gains of USD 9.5 billion (95% CI: 8.1 – 11.4 billion) between 2024 and 2054 (30 years). Coordinated disease control between African countries can lead to more socially and ecologically equitable outcomes by reducing the number of lost human lives to almost zero and possibly eliminating rabies. Control of rabies in Africa through mass vaccination of dogs may be compromised by cross-border transmission. Here, the authors use mathematical modelling and a benefit-cost analysis to demonstrate that coordinating rabies control measures across borders could lead to the elimination of dog rabies in Africa. [ABSTRACT FROM AUTHOR]

Rift Valley fever virus (RVFV) is an emerging mosquito-transmitted virus that circulates in livestock and humans in Africa and the Middle East. Outbreaks lead to high rates of miscarriages in domesticated livestock. Women are also at risk of vertical virus transmission and late-term miscarriages. MAb RVFV-268 is a highly potent recombinant neutralizing human monoclonal antibody that targets RVFV. Here we show that mAb RVFV-268 reduces viral replication in rat placenta explant cultures and prevents vertical transmission in a rat model of congenital RVF. Passive transfer of mAb RVFV-268 from mother to fetus occurs as early as 6 h after administration and persists through 24 h. Administering mAb RVFV-268 2 h prior to RVFV challenge or 24 h post-challenge protects the dams and offspring from RVFV infection. These findings support mAb RVFV-268 as a pre- and post-infection treatment to subvert RVFV infection and vertical transmission, thus protecting the mother and offspring. Rift valley fever virus (RVFV) infection during pregnancy has been associated with late-term fetal loss. Here, the authors show that a neutralizing monoclonal antibody can prevent vertical transmission of RVFV when administered either pre- or post-infection in a rodent model. [ABSTRACT FROM AUTHOR]

The consistent monitoring of trees both inside and outside of forests is key to sustainable land management. Current monitoring systems either ignore trees outside forests or are too expensive to be applied consistently across countries on a repeated basis. Here we use the PlanetScope nanosatellite constellation, which delivers global very high-resolution daily imagery, to map both forest and non-forest tree cover for continental Africa using images from a single year. Our prototype map of 2019 (RMSE = 9.57%, bias = −6.9%). demonstrates that a precise assessment of all tree-based ecosystems is possible at continental scale, and reveals that 29% of tree cover is found outside areas previously classified as tree cover in state-of-the-art maps, such as in croplands and grassland. Such accurate mapping of tree cover down to the level of individual trees and consistent among countries has the potential to redefine land use impacts in non-forest landscapes, move beyond the need for forest definitions, and build the basis for natural climate solutions and tree-related studies. Recent analyses have suggested that tree cover in non-forest ecosystems may be much higher than expected. Here, the authors map tree cover down to the individual tree level for the entire continent of Africa and find that almost 30% is found outside areas classified as forests. [ABSTRACT FROM AUTHOR]

Under-utilised orphan crops hold the key to diversified and climate-resilient food systems. Here, we report on orphan crop genomics using the case of Lablab purpureus (L.) Sweet (lablab) - a legume native to Africa and cultivated throughout the tropics for food and forage. Our Africa-led plant genome collaboration produces a high-quality chromosome-scale assembly of the lablab genome. Our assembly highlights the genome organisation of the trypsin inhibitor genes - an important anti-nutritional factor in lablab. We also re-sequence cultivated and wild lablab accessions from Africa confirming two domestication events. Finally, we examine the genetic and phenotypic diversity in a comprehensive lablab germplasm collection and identify genomic loci underlying variation of important agronomic traits in lablab. The genomic data generated here provide a valuable resource for lablab improvement. Our inclusive collaborative approach also presents an example that can be explored by other researchers sequencing indigenous crops, particularly from low and middle-income countries (LMIC). Lablab is a legume native to Africa and cultivated throughout the tropics for food and forage; however, as an orphan crop, limited genomic resources hampers its genetic improvement. Here, an African-led South-North plant genome collaboration produces an improved genome assembly and population genomic resource to accelerate its breeding. [ABSTRACT FROM AUTHOR]

The malaria parasite Plasmodium falciparum causes substantial human mortality, primarily in equatorial Africa. Enriched in affected African populations, the B*53 variant of HLA-B, a cell surface protein that presents peptide antigens to cytotoxic lymphocytes, confers protection against severe malaria. Gorilla, chimpanzee, and bonobo are humans' closest living relatives. These African apes have HLA-B orthologs and are infected by parasites in the same subgenus (Laverania) as P. falciparum, but the consequences of these infections are unclear. Laverania parasites infect bonobos (Pan paniscus) at only one (TL2) of many sites sampled across their range. TL2 spans the Lomami River and has genetically divergent subpopulations of bonobos on each side. Papa-B, the bonobo ortholog of HLA-B, includes variants having a B*53-like (B07) peptide-binding supertype profile. Here we show that B07 Papa-B occur at high frequency in TL2 bonobos and that malaria appears to have independently selected for different B07 alleles in the two subpopulations. A variant of MHC class I is protective against severe malaria disease and enriched in affected African populations. Here, Wroblewski et al., characterise the consequences of malaria infection in wild bonobo populations showing that the presence of malaria drives a similar evolution in immune genes. [ABSTRACT FROM AUTHOR]

Biomass burning (BB) is a major source of aerosols that remain the most uncertain components of the global radiative forcing. Current global models have great difficulty matching observed aerosol optical depth (AOD) over BB regions. A common solution to address modelled AOD biases is scaling BB emissions. Using the relationship from an ensemble of aerosol models and satellite observations, we show that the bias in aerosol modelling results primarily from incorrect lifetimes and underestimated mass extinction coefficients. In turn, these biases seem to be related to incorrect precipitation and underestimated particle sizes. We further show that boosting BB emissions to correct AOD biases over the source region causes an overestimation of AOD in the outflow from Africa by 48%, leading to a double warming effect compared with when biases are simultaneously addressed for both aforementioned factors. Such deviations are particularly concerning in a warming future with increasing emissions from fires. Error attribution based on modelled relationships and satellite observations suggests that errors in global models are more important and require more concerns than emission errors in creating the overall uncertainties for biomass burning aerosols. [ABSTRACT FROM AUTHOR]

Evaluating the impact and implications of eolian repositories that mark large-scale climatic transitions requires knowledge about the timing of their emplacement and the mechanisms responsible for their production, which remain highly uncertain. Here we apply numerical modeling of cosmogenic nuclide data, measured in the largest continuous terrestrial body of sand on Earth, to determine settings under which the sand was generated, by constraining the timing of sand introduction into the interior of southern Africa. Our findings reveal that major events of sand formation and accumulation in the Kalahari Basin occurred between ~2.2 and 1 Myr ago. The establishment of the Kalahari sand field corresponds to regional, continental, and global scale morphotectonic and climatic changes that contributed to the mass production and widespread dispersion of sand. These changes substantially altered existing habitats, thus constituting a crucial milestone for flora, fauna, and hominins in southern Africa during the Pleistocene. Modeling cosmogenic nuclides concentrations from Kalahari Desert Sand reveals the time of sand introduction into the landscape. This coincides with morphotectonic and climatic changes that could have triggered sand production and its impact on the environment. [ABSTRACT FROM AUTHOR]

Diversified cropping systems, especially those including legumes, have been proposed to enhance food production with reduced inputs and environmental impacts. However, the impact of legume pre-crops on main crop yield and its drivers has never been systematically investigated in a global context. Here, we synthesize 11,768 yield observations from 462 field experiments comparing legume-based and non-legume cropping systems and show that legumes enhanced main crop yield by 20%. These yield advantages decline with increasing N fertilizer rates and crop diversity of the main cropping system. The yield benefits are consistent among main crops (e.g., rice, wheat, maize) and evident across pedo-climatic regions. Moreover, greater yield advantages (32% vs. 7%) are observed in low- vs. high-yielding environments, suggesting legumes increase crop production with low inputs (e.g., in Africa or organic agriculture). In conclusion, our study suggests that legume-based rotations offer a critical pathway for enhancing global crop production, especially when integrated into low-input and low-diversity agricultural systems. Crop rotations including legumes have been proposed as a strategy to enhance food production. Here, the authors conduct a global meta-analysis on legume-based crop rotations, showing that legume pre-crops increase 20% of yield in average across various crops and climatic regions. [ABSTRACT FROM AUTHOR]

Precipitation-based assessments show a lengthening of tropical dry seasons under climate change, without considering simultaneous changes in ecosystem water demand. Here, we compare changes in tropical dry season length and timing when dry season is defined as the period when precipitation is less than: its climatological average, potential evapotranspiration, or actual evapotranspiration. While all definitions show more widespread tropical drying than wetting for 1983-2016, we find the largest fraction (48.7%) of tropical land probably experiencing longer dry seasons when dry season is defined as the period when precipitation cannot meet the need of actual evapotranspiration. Southern Amazonia (due to delayed end) and central Africa (due to earlier onset and delayed end) are hotspots of dry season lengthening, with greater certainty when accounting for water demand changes. Therefore, it is necessary to account for changing water demand when characterizing changes in tropical dry periods and ecosystem water deficits. Changing precipitation pattern has been suggested to expand tropical dry seasons. Here, the authors show that this lengthening can be even more severe when accounting for the simultaneous rise of ecosystem water demand in a warmer climate. [ABSTRACT FROM AUTHOR]

Droughts that exceed the magnitudes of historical variation ranges could occur increasingly frequently under future climate conditions. However, the time of the emergence of unprecedented drought conditions under climate change has rarely been examined. Here, using multimodel hydrological simulations, we investigate the changes in the frequency of hydrological drought (defined as abnormally low river discharge) under high and low greenhouse gas concentration scenarios and existing water resource management measures and estimate the time of the first emergence of unprecedented regional drought conditions centered on the low-flow season. The times are detected for several subcontinental-scale regions, and three regions, namely, Southwestern South America, Mediterranean Europe, and Northern Africa, exhibit particularly robust results under the high-emission scenario. These three regions are expected to confront unprecedented conditions within the next 30 years with a high likelihood regardless of the emission scenarios. In addition, the results obtained herein demonstrate the benefits of the lower-emission pathway in reducing the likelihood of emergence. The Paris Agreement goals are shown to be effective in reducing the likelihood to the unlikely level in most regions. However, appropriate and prior adaptation measures are considered indispensable when facing unprecedented drought conditions. The results of this study underscore the importance of improving drought preparedness within the considered time horizons. Significant regional disparities exist in the time left to prepare for unprecedented drought and how much we can buy time depending on climate scenarios. Specific regions pass this timing by the middle of 21st century even with stringent mitigation. [ABSTRACT FROM AUTHOR]

To identify areas at highest risk of infectious disease transmission in Africa, we develop a physical distancing index (PDI) based on the share of households without access to private toilets, water, space, transportation, and communication technology and weight it with population density. Our results highlight that in addition to improving health systems, countries across Africa, especially in the western part of Africa, need to address the lack of essential domestic infrastructure. Missing infrastructure prevents societies from limiting the spread of communicable diseases by undermining the effectiveness of governmental regulations on physical distancing. We also provide high-resolution risk maps that show which regions are most limited in protecting themselves. We find considerable spatial heterogeneity of the PDI within countries and show that it is highly correlated with detected COVID-19 cases. Governments could pay specific attention to these areas to target limited resources more precisely to prevent disease transmission. Lack of private infrastructure remains a major challenge potentially hampering a societies' ability to contain the transmission of communicable diseases. Areas at high risk in Africa are identified based on access to essential basic infrastructure. [ABSTRACT FROM AUTHOR]

Controlled human malaria infection (CHMI) has supported Plasmodium falciparum (Pf) malaria vaccine development by providing preliminary estimates of vaccine efficacy (VE). Because CHMIs generally use Pf strains similar to vaccine strains, VE against antigenically heterogeneous Pf in the field has been required to establish VE. We increased the stringency of CHMI by selecting a Brazilian isolate, Pf7G8, which is genetically distant from the West African parasite (PfNF54) in our PfSPZ vaccines. Using two regimens to identically immunize US and Malian adults, VE over 24 weeks in the field was as good as or better than VE against CHMI at 24 weeks in the US. To explain this finding, here we quantify differences in the genome, proteome, and predicted CD8 T cell epitopes of PfNF54 relative to 704 Pf isolates from Africa and Pf7G8. We show that Pf7G8 is more distant from PfNF54 than any African isolates tested. We propose VE against Pf7G8 CHMI for providing pivotal data for malaria vaccine licensure for travelers to Africa, and potentially for endemic populations, because the genetic distance of Pf7G8 from the Pf vaccine strain makes it a stringent surrogate for Pf parasites in Africa. Here the authors show that controlled human malaria infection with a Brazilian parasite highly divergent from vaccine and West African field strains can provide estimates of vaccine efficacy in Mali, and could replace field testing, streamlining vaccine development. [ABSTRACT FROM AUTHOR]

The human parasite Plasmodium malariae has relatives infecting African apes (Plasmodium rodhaini) and New World monkeys (Plasmodium brasilianum), but its origins remain unknown. Using a novel approach to characterise P. malariae-related sequences in wild and captive African apes, we found that this group comprises three distinct lineages, one of which represents a previously unknown, highly divergent species infecting chimpanzees, bonobos and gorillas across central Africa. A second ape-derived lineage is much more closely related to the third, human-infective lineage P. malariae, but exhibits little evidence of genetic exchange with it, and so likely represents a separate species. Moreover, the levels and nature of genetic polymorphisms in P. malariae indicate that it resulted from the zoonotic transmission of an African ape parasite, reminiscent of the origin of P. falciparum. In contrast, P. brasilianum falls within the radiation of human P. malariae, and thus reflects a recent anthroponosis. Plasmodium malariae is a cause of malaria in humans and related species have been identified in non-human primates. Here, the authors use genomic analyses to establish that human P. malariae arose from a host switch of an ape parasite whilst a species infecting New World monkeys can be traced to a reverse zoonosis. [ABSTRACT FROM AUTHOR]

Daily temporal organisation offers a fitness advantage and is determined by an interplay between environmental rhythms and circadian clocks. While light:dark cycles robustly synchronise circadian clocks, it is not clear how animals experiencing only weak environmental cues deal with this problem. Like humans, Drosophila originate in sub-Saharan Africa and spread North up to the polar circle, experiencing long summer days or even constant light (LL). LL disrupts clock function, due to constant activation of CRYPTOCHROME, which induces degradation of the clock protein TIMELESS (TIM), but temperature cycles are able to overcome these deleterious effects of LL. We show here that for this to occur a recently evolved natural timeless allele (ls-tim) is required, encoding the less light-sensitive L-TIM in addition to S-TIM, the only form encoded by the ancient s-tim allele. We show that only ls-tim flies can synchronise their behaviour to semi-natural conditions typical for Northern European summers, suggesting that this functional gain is driving the Northward ls-tim spread. The genus Drosophila originate in subSaharan Africa and spread North up to the polar circle where they experience long days in the summer or even constant light. Here, the authors show that a form of the TIMELESS protein enables flies to synchronise their behavioural activity to long summer days [ABSTRACT FROM AUTHOR]

Large variations in the growth of atmospheric methane, a prominent greenhouse gas, are driven by a diverse range of anthropogenic and natural emissions and by loss from oxidation by the hydroxyl radical. We used a decade-long dataset (2010–2019) of satellite observations of methane to show that tropical terrestrial emissions explain more than 80% of the observed changes in the global atmospheric methane growth rate over this period. Using correlative meteorological analyses, we show strong seasonal correlations (r = 0.6–0.8) between large-scale changes in sea surface temperature over the tropical oceans and regional variations in methane emissions (via changes in rainfall and temperature) over tropical South America and tropical Africa. Existing predictive skill for sea surface temperature variations could therefore be used to help forecast variations in global atmospheric methane. Methane is a powerful greenhouse gas with emissions that are challenging to constrain. Here the authors use 10 years of satellite observations and show tropical terrestrial emissions account for 80% of observed global methane increases. [ABSTRACT FROM AUTHOR]

The terrestrial carbon sink slows the accumulation of carbon dioxide (CO2) in the atmosphere by absorbing roughly 30% of anthropogenic CO2 emissions, but varies greatly from year to year. The resulting variations in the atmospheric CO2 growth rate (CGR) have been related to tropical temperature and water availability. The apparent sensitivity of CGR to tropical temperature ( γ CGR T ) has changed markedly over the past six decades, however, the drivers of the observation to date remains unidentified. Here, we use atmospheric observations, multiple global vegetation models and machine learning products to analyze the cause of the sensitivity change. We found that a threefold increase in γ CGR T emerged due to the long-term changes in the magnitude of CGR variability (i.e., indicated by one standard deviation of CGR; STDCGR), which increased 34.7% from 1960-1979 to 1985-2004 and subsequently decreased 14.4% in 1997-2016. We found a close relationship (r2 = 0.75, p < 0.01) between STDCGR and the tropical vegetated area (23°S – 23°N) affected by extreme droughts, which influenced 6-9% of the tropical vegetated surface. A 1% increase in the tropical area affected by extreme droughts led to about 0.14 Pg C yr−1 increase in STDCGR. The historical changes in STDCGR were dominated by extreme drought-affected areas in tropical Africa and Asia, and semi-arid ecosystems. The outsized influence of extreme droughts over a small fraction of vegetated surface amplified the interannual variability in CGR and explained the observed long-term dynamics of γ CGR T . The apparent temperature sensitivity of atmospheric CO2 growth rate has increased markedly over the past six decades, however, the increase remains unexplained. Here we show that tropical extreme droughts amplified the interannual variability in atmospheric CO2 growth rate and drove the sensitivity change. [ABSTRACT FROM AUTHOR]

In spring 2021, an increasing number of infections was observed caused by the hitherto rarely described SARS-CoV-2 variant A.27 in south-west Germany. From December 2020 to June 2021 this lineage has been detected in 31 countries. Phylogeographic analyses of A.27 sequences obtained from national and international databases reveal a global spread of this lineage through multiple introductions from its inferred origin in Western Africa. Variant A.27 is characterized by a mutational pattern in the spike gene that includes the L18F, L452R and N501Y spike amino acid substitutions found in various variants of concern but lacks the globally dominant D614G. Neutralization assays demonstrate an escape of A.27 from convalescent and vaccine-elicited antibody-mediated immunity. Moreover, the therapeutic monoclonal antibody Bamlanivimab and partially the REGN-COV2 cocktail fail to block infection by A.27. Our data emphasize the need for continued global monitoring of novel lineages because of the independent evolution of new escape mutations. The A.27 SARS-CoV-2 lineage spread globally in 2021 but did not become dominant. Here, the authors show that A.27 shares some mutations in the spike gene that are present in variants of concern, but lacks the D614G mutation, indicating independent evolution of immune escape properties. [ABSTRACT FROM AUTHOR]

Despite only 8% of cattle being found in Europe, European breeds dominate current genetic resources. This adversely impacts cattle research in other important global cattle breeds, especially those from Africa for which genomic resources are particularly limited, despite their disproportionate importance to the continent's economies. To mitigate this issue, we have generated assemblies of African breeds, which have been integrated with genomic data for 294 diverse cattle into a graph genome that incorporates global cattle diversity. We illustrate how this more representative reference assembly contains an extra 116.1 Mb (4.2%) of sequence absent from the current Hereford sequence and consequently inaccessible to current studies. We further demonstrate how using this graph genome increases read mapping rates, reduces allelic biases and improves the agreement of structural variant calling with independent optical mapping data. Consequently, we present an improved, more representative, reference assembly that will improve global cattle research. Cattle reference genomes are valuable resources but are currently heavily biased towards European breeds. Here the authors integrate assemblies for African breeds into a more representative cattle graph genome capturing global breed diversity. [ABSTRACT FROM AUTHOR]

Agroforestry systems have the potential to sequester carbon and offer numerous benefits to rural communities, but their capacity to offer valuable cooling services has not been quantified on continental scales. Here, we find that trees in pasturelands ("silvopasture") across Latin America and Africa can offer substantial cooling benefits. These cooling benefits increase linearly by −0.32 °C to −2.4 °C per 10 metric tons of woody carbon per hectare, and importantly do not depend on the spatial extent of the silvopasture systems. Thus, even smallholders can reap important cooling services from intensifying their silvopasture practices. We then map where realistic (but ambitious) silvopasture expansion could counteract a substantial fraction of the local projected warming in 2050 due to climate change. Our findings indicate where and to what extent silvopasture systems can counteract local temperature increases from global climate change and help vulnerable communities adapt to a warming world. A new study shows that tropical silvopasture systems can provide significant cooling services for local communities, and identifies where these silvopasture systems can most effectively counteract global climate change to help communities adapt to warming. [ABSTRACT FROM AUTHOR]

In 2016 the World Health Organization set the goal of eliminating hepatitis B globally by 2030. Horizontal transmission has been greatly reduced in most countries by scaling up coverage of the infant HBV vaccine series, and vertical transmission is therefore becoming increasingly dominant. Here we show that scaling up timely hepatitis B birth dose vaccination to 90% of new-borns in 110 low- and middle-income countries by 2030 could prevent 710,000 (580,000 to 890,000) deaths in the 2020 to 2030 birth cohorts compared to status quo, with the greatest benefits in Africa. Maintaining this could lead to elimination by 2030 in the Americas, but not before 2059 in Africa. Drops in coverage due to disruptions in 2020 may lead to 15,000 additional deaths, mostly in South-East Asia and the Western Pacific. Delays in planned scale-up could lead to an additional 580,000 deaths globally in the 2020 to 2030 birth cohorts. The timely hepatitis B birth dose vaccination is recommended for all new-borns by the WHO, but coverage is inconsistent. Here, the authors model the impact of scaling-up coverage in 110 low and middle income countries and assess how it may be affected by delays for example caused by the COVID-19 pandemic. [ABSTRACT FROM AUTHOR]

Mantles of rocky planets are dominantly composed of olivine and its high-pressure polymorphs, according to seismic data of Earth's interior, the mineralogy of natural samples, and modelling results. The missing mantle problem represents the paucity of olivine-rich material among meteorite samples and remote observation of asteroids, given how common differentiated planetesimals were in the early Solar System. Here we report the discovery of new olivine-rich meteorites that have asteroidal origins and are related to V-type asteroids or vestoids. Northwest Africa 12217, 12319, and 12562 are dunites and lherzolite cumulates that have siderophile element abundances consistent with origins on highly differentiated asteroidal bodies that experienced core formation, and with trace element and oxygen and chromium isotopic compositions associated with the howardite-eucrite-diogenite meteorites. These meteorites represent a step towards the end of the shortage of olivine-rich material, allowing for full examination of differentiation processes acting on planetesimals in the earliest epoch of the Solar System. Ultramafic olivine-rich achondrites provide insight into the missing mantle problem in the asteroid belt. The petrology and geochemistry of these samples suggests they are related to Vesta or the Vestoids. [ABSTRACT FROM AUTHOR]

By structuring farmers' informal networks of seed exchange, kinship systems play a key role in the dynamics of crop genetic diversity in smallholder farming systems. However, because many crop diseases are propagated through infected germplasm, local seed systems can also facilitate the dissemination of seedborne pathogens. Here, we investigate how the interplay of kinship systems and local networks of germplasm exchange influences the metapopulation dynamics of viruses responsible for the cassava mosaic disease (CMD), a major threat to food security in Africa. Combining anthropological, genetic and plant epidemiological data, we analyzed the genetic structure of local populations of the African cassava mosaic virus (ACMV), one of the main causal agents of CMD. Results reveal contrasted patterns of viral diversity in patrilineal and matrilineal communities, consistent with local modes of seed exchange. Our results demonstrate that plant virus ecosystems have also a cultural component and that social factors that shape regional seed exchange networks influence the genetic structure of plant virus populations. This study combines ethnobotanical and epidemiological data to understand how social networks of seed exchange influence the genetic structure of the African cassava mosaic virus in Gabon. Results reveal contrasted patterns of viral diversity in patrilineal and matrilineal communities, consistent with cultural differences in modes of seed exchange. [ABSTRACT FROM AUTHOR]

Finance is vital for the green energy transition, but access to low cost finance is uneven as the cost of capital differs substantially between regions. This study shows how modelled decarbonisation pathways for developing economies are disproportionately impacted by different weighted average cost of capital (WACC) assumptions. For example, representing regionally-specific WACC values indicates 35% lower green electricity production in Africa for a cost-optimal 2 °C pathway than when regional considerations are ignored. Moreover, policy interventions lowering WACC values for low-carbon and high-carbon technologies by 2050 would allow Africa to reach net-zero emissions approximately 10 years earlier than when the cost of capital reduction is not considered. A climate investment trap arises for developing economies when climate-related investments remain chronically insufficient. Current finance frameworks present barriers to these finance flows and radical changes are needed so that capital is more equitably distributed. Access to low cost finance is vital for developing economies' transition to green energy. Here the authors show how modelled decarbonization pathways for developing economies are disproportionately impacted by different weighted average cost of capital (WACC) assumptions. [ABSTRACT FROM AUTHOR]

Studies about the impact of future climate change on diseases have mostly focused on standard Representative Concentration Pathway climate change scenarios. These scenarios do not account for the non-linear dynamics of the climate system. A rapid ice-sheet melting could occur, impacting climate and consequently societies. Here, we investigate the additional impact of a rapid ice-sheet melting of Greenland on climate and malaria transmission in Africa using several malaria models driven by Institute Pierre Simon Laplace climate simulations. Results reveal that our melting scenario could moderate the simulated increase in malaria risk over East Africa, due to cooling and drying effects, cause a largest decrease in malaria transmission risk over West Africa and drive malaria emergence in southern Africa associated with a significant southward shift of the African rain-belt. We argue that the effect of such ice-sheet melting should be investigated further in future public health and agriculture climate change risk assessments. Release of freshwater into the oceans as a result of ice sheet melting could impact the distribution of climate-sensitive diseases. Here, the authors show that a rapid ice sheet melting in Greenland could cause an emergence of malaria in Southern Africa whilst transmission risks in West Africa may decline. [ABSTRACT FROM AUTHOR]

Insecticide-treated nets (ITNs) are one of the most widespread and impactful malaria interventions in Africa, yet a spatially-resolved time series of ITN coverage has never been published. Using data from multiple sources, we generate high-resolution maps of ITN access, use, and nets-per-capita annually from 2000 to 2020 across the 40 highest-burden African countries. Our findings support several existing hypotheses: that use is high among those with access, that nets are discarded more quickly than official policy presumes, and that effectively distributing nets grows more difficult as coverage increases. The primary driving factors behind these findings are most likely strong cultural and social messaging around the importance of net use, low physical net durability, and a mixture of inherent commodity distribution challenges and less-than-optimal net allocation policies, respectively. These results can inform both policy decisions and downstream malaria analyses. Insecticide treated nets (ITNs) are an important part of malaria control in Africa and WHO targets aim for 80% coverage. This study estimates the spatio-temporal access and use of ITNs in Africa from 2000-2020, and shows that both metrics have improved over time but access remains below WHO targets. [ABSTRACT FROM AUTHOR]

The re-emergence of stem rust on wheat in Europe and Africa is reinforcing the ongoing need for durable resistance gene deployment. Here, we isolate from wheat, Sr26 and Sr61, with both genes independently introduced as alien chromosome introgressions from tall wheat grass (Thinopyrum ponticum). Mutational genomics and targeted exome capture identify Sr26 and Sr61 as separate single genes that encode unrelated (34.8%) nucleotide binding site leucine rich repeat proteins. Sr26 and Sr61 are each validated by transgenic complementation using endogenous and/or heterologous promoter sequences. Sr61 orthologs are absent from current Thinopyrum elongatum and wheat pan genome sequences, contrasting with Sr26 where homologues are present. Using gene-specific markers, we validate the presence of both genes on a single recombinant alien segment developed in wheat. The co-location of these genes on a small non-recombinogenic segment simplifies their deployment as a gene stack and potentially enhances their resistance durability. The tall wheat grass-derived stem rust resistance genes Sr26 and Sr61 are among a few ones that are effective to all current dominant races of stem rust, including Ug99. Here, the authors show that the two genes are present in a small non-recombinogenic segment but encode two unrelated NLR proteins. [ABSTRACT FROM AUTHOR]

Chemical events involving deep carbon- and water-rich fluids impact the continental lithosphere over its history. Diamonds are a by-product of such episodic fluid infiltrations, and entrapment of these fluids as microinclusions in lithospheric diamonds provide unique opportunities to investigate their nature. However, until now, direct constraints on the timing of such events have not been available. Here we report three alteration events in the southwest Kaapvaal lithosphere using U-Th-He geochronology of fluid-bearing diamonds, and constrain the upper limit of He diffusivity (to D ≈ 1.8 × 10−19 cm2 s−1), thus providing a means to directly place both upper and lower age limits on these alteration episodes. The youngest, during the Cretaceous, involved highly saline fluids, indicating a relationship with late-Mesozoic kimberlite eruptions. Remnants of two preceding events, by a Paleozoic silicic fluid and a Proterozoic carbonatitic fluid, are also encapsulated in Kaapvaal diamonds and are likely coeval with major surface tectonic events (e.g. the Damara and Namaqua–Natal orogenies). Diamonds encapsulate the deep Earth fluids that form them, providing windows to deep mantle processes. This study constrains their ages, based on uranium-thorium-to-helium radioactive decay in the fluids and helium diffusivity in diamond, and relates diamond formation to geological events in Southern Africa. [ABSTRACT FROM AUTHOR]

The genetic modules that contribute to human evolution are poorly understood. Here we investigate positive selection in the Epidermal Differentiation Complex locus for skin barrier adaptation in diverse HapMap human populations (CEU, JPT/CHB, and YRI). Using Composite of Multiple Signals and iSAFE, we identify selective sweeps for LCE1A-SMCP and involucrin (IVL) haplotypes associated with human migration out-of-Africa, reaching near fixation in European populations. CEU-IVL is associated with increased IVL expression and a known epidermis-specific enhancer. CRISPR/Cas9 deletion of the orthologous mouse enhancer in vivo reveals a functional requirement for the enhancer to regulate Ivl expression in cis. Reporter assays confirm increased regulatory and additive enhancer effects of CEU-specific polymorphisms identified at predicted IRF1 and NFIC binding sites in the IVL enhancer (rs4845327) and its promoter (rs1854779). Together, our results identify a selective sweep for a cis regulatory module for CEU-IVL, highlighting human skin barrier evolution for increased IVL expression out-of-Africa. Selection on alleles contributing to human evolution is not well understood. Here, the authors investigate positive selection on skin barrier adaptation, identifying a selective sweep on involucrin alleles associated with migration out of Africa, and confirming enhancer regulatory effects with functional assays. [ABSTRACT FROM AUTHOR]

In marine and freshwater oxygen-deficient zones, the remineralization of sinking organic matter from the photic zone is central to driving nitrogen loss. Deep blooms of photosynthetic bacteria, which form the suboxic/anoxic chlorophyll maximum (ACM), widespread in aquatic ecosystems, may also contribute to the local input of organic matter. Yet, the influence of the ACM on nitrogen and carbon cycling remains poorly understood. Using a suite of stable isotope tracer experiments, we examined the transformation of nitrogen and carbon under an ACM (comprising of Chlorobiaceae and Synechococcales) and a non-ACM scenario in the anoxic zone of Lake Tanganyika. We find that the ACM hosts a tight coupling of photo/litho-autotrophic and heterotrophic processes. In particular, the ACM was a hotspot of organic matter remineralization that controlled an important supply of ammonium driving a nitrification-anammox coupling, and thereby played a key role in regulating nitrogen loss in the oxygen-deficient zone. Enigmatic blooms of phytoplankton in aquatic oxygen-deficient zones could exacerbate depletion of nitrogen. Here the authors perform stable isotope experiments on the oxygen-deficient waters of Lake Tanganyika in Africa, finding that blooms drive down fixed nitrogen and could expand as a result of climate change. [ABSTRACT FROM AUTHOR]

Consuming the milk of other species is a unique adaptation of Homo sapiens, with implications for health, birth spacing and evolution. Key questions nonetheless remain regarding the origins of dairying and its relationship to the genetically-determined ability to drink milk into adulthood through lactase persistence (LP). As a major centre of LP diversity, Africa is of significant interest to the evolution of dairying. Here we report proteomic evidence for milk consumption in ancient Africa. Using liquid chromatography tandem mass spectrometry (LC-MS/MS) we identify dairy proteins in human dental calculus from northeastern Africa, directly demonstrating milk consumption at least six millennia ago. Our findings indicate that pastoralist groups were drinking milk as soon as herding spread into eastern Africa, at a time when the genetic adaptation for milk digestion was absent or rare. Our study links LP status in specific ancient individuals with direct evidence for their consumption of dairy products. Consuming the milk of other species is a unique adaptation of Homo sapiens. Here, the authors carry out proteomic analysis of dental calculus of 41 ancient individuals from Sudan and Kenya, indicating milk consumption occurred as soon as herding spread into eastern Africa. [ABSTRACT FROM AUTHOR]

Zika virus (ZIKV) emerged from obscurity in 2013 to spread from Asia to the South Pacific and the Americas, where millions of people were infected, accompanied by severe disease including microcephaly following congenital infections. Phylogenetic studies have shown that ZIKV evolved in Africa and later spread to Asia, and that the Asian lineage is responsible for the recent epidemics in the South Pacific and Americas. However, the reasons for the sudden emergence of ZIKV remain enigmatic. Here we report evolutionary analyses that revealed four mutations, which occurred just before ZIKV introduction to the Americas, represent direct reversions of previous mutations that accompanied earlier spread from Africa to Asia and early circulation there. Our experimental infections of Aedes aegypti mosquitoes, human cells, and mice using ZIKV strains with and without these mutations demonstrate that the original mutations reduced fitness for urban, human-amplifed transmission, while the reversions restored fitness, increasing epidemic risk. These findings include characterization of three transmission-adaptive ZIKV mutations, and demonstration that these and one identified previously restored fitness for epidemic transmission soon before introduction into the Americas. The initial mutations may have followed founder effects and/or drift when the virus was introduced decades ago into Asia. The trajectory of the emergence of Zika virus (ZIKV) into the Americas remains unclear. Here, the authors find that four mutations originated before ZIKV introduction to the Americas are direct reversions of previous mutations that accompanied spread many decades ago from ZIKV's native Africa to Asia, and show in experimental infections of mosquitoes, human cells, and mice that the original mutations reduced fitness for urban transmission, while the reversions restored fitness, likely increasing epidemic risk. [ABSTRACT FROM AUTHOR]

Current knowledge about the evolutionary history of donkeys is still incomplete due to the lack of archeological and whole-genome diversity data. To fill this gap, we have de novo assembled a chromosome-level reference genome of one male Dezhou donkey and analyzed the genomes of 126 domestic donkeys and seven wild asses. Population genomics analyses indicate that donkeys were domesticated in Africa and conclusively show reduced levels of Y chromosome variability and discordant paternal and maternal histories, possibly reflecting the consequences of reproductive management. We also investigate the genetic basis of coat color. While wild asses show diluted gray pigmentation (Dun phenotype), domestic donkeys display non-diluted black or chestnut coat colors (non-Dun) that were probably established during domestication. Here, we show that the non-Dun phenotype is caused by a 1 bp deletion downstream of the TBX3 gene, which decreases the expression of this gene and its inhibitory effect on pigment deposition. A new donkey reference genome and comparisons with wild asses yields insights into the evolutionary history of donkey domestication and identifies a genetic variant that results in the non-Dun coat colours of domestic donkeys. [ABSTRACT FROM AUTHOR]

Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr Virus (EBV) establish life-long infections and are associated with malignancies. Striking geographic variation in incidence and the fact that virus alone is insufficient to cause disease, suggests other co-factors are involved. Here we present epidemiological analysis and genome-wide association study (GWAS) in 4365 individuals from an African population cohort, to assess the influence of host genetic and non-genetic factors on virus antibody responses. EBV/KSHV co-infection (OR = 5.71(1.58–7.12)), HIV positivity (OR = 2.22(1.32–3.73)) and living in a more rural area (OR = 1.38(1.01–1.89)) are strongly associated with immunogenicity. GWAS reveals associations with KSHV antibody response in the HLA-B/C region (p = 6.64 × 10−09). For EBV, associations are identified for VCA (rs71542439, p = 1.15 × 10−12). Human leucocyte antigen (HLA) and trans-ancestry fine-mapping substantiate that distinct variants in HLA-DQA1 (p = 5.24 × 10−44) are driving associations for EBNA-1 in Africa. This study highlights complex interactions between KSHV and EBV, in addition to distinct genetic architectures resulting in important differences in pathogenesis and transmission. Disease prognosis after infection with Kaposi's sarcoma-associated herpesvirus and Epstein-Barr Virus is highly variable. Here the authors carry out epidemiological and genetic analysis of a Ugandan cohort and suggest complex interactions may influence pathogenesis and transmission. [ABSTRACT FROM AUTHOR]

Plasmodium falciparum in pregnancy is a major cause of adverse pregnancy outcomes. We combine performance estimates of standard rapid diagnostic tests (RDT) from trials of intermittent screening and treatment in pregnancy (ISTp) with modelling to assess whether screening at antenatal visits improves upon current intermittent preventative therapy with sulphadoxine-pyrimethamine (IPTp-SP). We estimate that RDTs in primigravidae at first antenatal visit are substantially more sensitive than in non-pregnant adults (OR = 17.2, 95% Cr.I. 13.8-21.6), and that sensitivity declines in subsequent visits and with gravidity, likely driven by declining susceptibility to placental infection. Monthly ISTp with standard RDTs, even with highly effective drugs, is not superior to monthly IPTp-SP. However, a hybrid strategy, recently adopted in Tanzania, combining testing and treatment at first visit with IPTp-SP may offer benefit, especially in areas with high-grade SP resistance. Screening and treatment in the first trimester, when IPTp-SP is contraindicated, could substantially improve pregnancy outcomes. Plasmodium falciparum infection in pregnancy is a major cause of adverse pregnancy outcomes. Here, the authors combine performance estimates of standard rapid diagnostic tests with modelling to assess whether screening at antenatal visits improves upon current intermittent preventative therapy. [ABSTRACT FROM AUTHOR]

The human- and animal-adapted lineages of the Mycobacterium tuberculosis complex (MTBC) are thought to have expanded from a common progenitor in Africa. However, the molecular events that accompanied this emergence remain largely unknown. Here, we describe two MTBC strains isolated from patients with multidrug resistant tuberculosis, representing an as-yet-unknown lineage, named Lineage 8 (L8), seemingly restricted to the African Great Lakes region. Using genome-based phylogenetic reconstruction, we show that L8 is a sister clade to the known MTBC lineages. Comparison with other complete mycobacterial genomes indicate that the divergence of L8 preceded the loss of the cobF genome region - involved in the cobalamin/vitamin B12 synthesis - and gene interruptions in a subsequent common ancestor shared by all other known MTBC lineages. This discovery further supports an East African origin for the MTBC and provides additional molecular clues on the ancestral genome reduction associated with adaptation to a pathogenic lifestyle. The human- and animal-adapted lineages of the Mycobacterium tuberculosis complex (MTBC) are thought to be evolved from a common progenitor in Africa. Here, the authors identify two MTBC strains isolated from patients with multidrug-resistant tuberculosis, representing an as-yet-unknown lineage further supporting an East African origin for the MTBC. [ABSTRACT FROM AUTHOR]

Africa contains some of the most vulnerable ecosystems to fires. Successful seasonal prediction of fire activity over these fire-prone regions remains a challenge and relies heavily on in-depth understanding of various driving mechanisms underlying fire evolution. Here, we assess the seasonal environmental drivers and predictability of African fire using the analytical framework of Stepwise Generalized Equilibrium Feedback Assessment (SGEFA) and machine learning techniques (MLTs). The impacts of sea-surface temperature, soil moisture, and leaf area index are quantified and found to dominate the fire seasonal variability by regulating regional burning condition and fuel supply. Compared with previously-identified atmospheric and socioeconomic predictors, these slowly evolving oceanic and terrestrial predictors are further identified to determine the seasonal predictability of fire activity in Africa. Our combined SGEFA-MLT approach achieves skillful prediction of African fire one month in advance and can be generalized to provide seasonal estimates of regional and global fire risk. Fire is an important component of many African ecosystems, but prediction of fire activity is challenging. Here, the authors use a statistical framework to assess the seasonal environmental drivers of African fire, which allow for a better prediction of fire activity. [ABSTRACT FROM AUTHOR]

Accurate and comprehensive measurements of economic well-being are fundamental inputs into both research and policy, but such measures are unavailable at a local level in many parts of the world. Here we train deep learning models to predict survey-based estimates of asset wealth across ~ 20,000 African villages from publicly-available multispectral satellite imagery. Models can explain 70% of the variation in ground-measured village wealth in countries where the model was not trained, outperforming previous benchmarks from high-resolution imagery, and comparison with independent wealth measurements from censuses suggests that errors in satellite estimates are comparable to errors in existing ground data. Satellite-based estimates can also explain up to 50% of the variation in district-aggregated changes in wealth over time, with daytime imagery particularly useful in this task. We demonstrate the utility of satellite-based estimates for research and policy, and demonstrate their scalability by creating a wealth map for Africa's most populous country. It is generally difficult to scale derived estimates and understand the accuracy across locations for passively-collected data sources, such as mobile phones and satellite imagery. Here the authors show that their trained deep learning models are able to explain 70% of the variation in ground-measured village wealth in held-out countries, outperforming previous benchmarks from high-resolution imagery with errors comparable to that of existing ground data. [ABSTRACT FROM AUTHOR]

Urban land expansion is one of the most visible, irreversible, and rapid types of land cover/land use change in contemporary human history, and is a key driver for many environmental and societal changes across scales. Yet spatial projections of how much and where it may occur are often limited to short-term futures and small geographic areas. Here we produce a first empirically-grounded set of global, spatial urban land projections over the 21st century. We use a data-science approach exploiting 15 diverse datasets, including a newly available 40-year global time series of fine-spatial-resolution remote sensing observations. We find the global total amount of urban land could increase by a factor of 1.8–5.9, and the per capita amount by a factor of 1.1–4.9, across different socioeconomic scenarios over the century. Though the fastest urban land expansion occurs in Africa and Asia, the developed world experiences a similarly large amount of new development. Here the authors develop a set of global, long-term, spatial projections of urban land expansion for understanding the planet's potential urban futures. The global total amount of urban land increases by a factor of 1.8-5.9 over the 21st century, and the developed world experiences as much new urban development as the developing world. [ABSTRACT FROM AUTHOR]

Diogenites are a group of meteorites that are derived from the interior of the largest protoplanet Vesta. They provide a unique opportunity to understanding together the internal structure and dynamic evolution of this protoplanet. Northwest Africa (NWA) 8321 was suggested to be an unbrecciated noritic diogenite meteorite, which is confirmed by our oxygen and chromium isotopic data. Here, we find that olivine in this sample has been partly replaced by orthopyroxene, troilite, and minor metal. The replacement texture of olivine is unambiguous evidence of sulfur-involved metasomatism in the interior of Vesta. The presence of such replacement texture suggests that in NWA 8321, the olivine should be of xenolith origin while the noritic diogenite was derived from partial melting of pre-existing rocks and had crystallized in the interior of Vesta. The post-Rheasilvia craters in the north-polar region on Vesta could be the potential source for NWA 8321. The authors here analyse the petrology of the meteorite NWA 8321 (parent body Vesta). They find sulfidation processes of olivine suggesting metasomatism in the Vestan interior and a partial melting origin for the host noritic diogenite. [ABSTRACT FROM AUTHOR]