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Summary: The majority of human genomic research studies have been conducted in European-ancestry cohorts, reducing the likelihood of detecting potentially novel and globally impactful findings. Here, we present mid-pass whole-genome sequencing data and a genome-wide association study in a cohort of 264 self-reported Malagasy individuals from three locations on the island of Madagascar. We describe genetic variation in this Malagasy cohort, providing insight into the shared and unique patterns of genetic variation across the island. We observe phenotypic variation by location and find high rates of hypertension, particularly in the Southern Highlands sampling site, as well as elevated self-reported malaria prevalence in the West Coast site relative to other sites. After filtering to a subset of 214 minimally related individuals, we find a number of genetic associations with body composition traits, including many variants that are only observed in African populations or populations with admixed African ancestry from the 1000 Genomes Project. This study highlights the importance of including diverse populations in genomic research for the potential to gain novel insights, even with small cohort sizes. This project was conducted in partnership and consultation with local stakeholders in Madagascar and serves as an example of genomic research that prioritizes community engagement and potentially impacts our understanding of human health and disease.

Transformation of forests into agricultural lands threatens biodiversity and ecosystem functions globally. In the biodiversity hotspot Madagascar, key ecosystem functions along with highly endemic flora and fauna are under threat. Comprehensive studies identifying determinants of biodiversity and ecosystem function losses are lacking, with no studies accounting for endemic species richness across multiple taxa. We assess how plot-scale stand structural attributes (basal area, leaf area index, diameter diversity, and tree species richness) and landscape-scale forest cover influence biodiversity (species richness of butterflies, ants, birds, reptiles, amphibians, herbaceous plants, and multidiversity) and ecosystem functions (soil organic carbon, predation rate, acoustic diversity, and multifunctionality) in the tropical mosaic landscape of northeastern Madagascar. Complexly structured stands with a larger basal area and/or a higher tree species richness promoted greater endemic multidiversity (R² = 0.70), soil organic carbon, and acoustic diversity. However, our models did not indicate significant explanatory variables for multidiversity (R² = 0.25) and multifunctionality (R² = 0.43). Landscape-scale forest cover significantly favored endemic bird species richness. Our findings highlight that a simplified stand structure, resulting from land-use change, substantially reduces endemic biodiversity and ecosystem functions in this historically forested region. Conservation actions should aim at maintaining complex stand structure in forests and agroforests, while restoration interventions should focus on re-building such structures.

Introduction A prototype lateral flow device detecting cytokine biomarkers interleukin (IL)-1α and IL-1β has been developed as a point-of-care test—called the Genital InFlammation Test (GIFT)—for detecting genital inflammation associated with sexually transmitted infections (STIs) and/or bacterial vaginosis (BV) in women. In this paper, we describe the rationale and design for studies that will be conducted in South Africa, Zimbabwe and Madagascar to evaluate the performance of GIFT and how it could be integrated into routine care.Methods and analysis We will conduct a prospective, multidisciplinary, multicentre, cross-sectional and observational clinical study comprising two distinct components: a biomedical (‘diagnostic study’) and a qualitative, modelling and economic (‘an integration into care study’) part. The diagnostic study aims to evaluate GIFT’s performance in identifying asymptomatic women with discharge-causing STIs (Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), Trichomonas vaginalis (TV) and Mycoplasma genitalium (MG)) and BV. Study participants will be recruited from women attending research sites and family planning services. Several vaginal swabs will be collected for the evaluation of cytokine concentrations (ELISA), STIs (nucleic acid amplification tests), BV (Nugent score) and vaginal microbiome characteristics (16S rRNA gene sequencing). The first collected vaginal swab will be used for the GIFT assay which will be performed in parallel by a healthcare worker in the clinic near the participant, and by a technician in the laboratory. The integration into care study aims to explore how GIFT could be integrated into routine care. Four activities will be conducted: user experiences and/or perceptions of the GIFT device involving qualitative focus group discussions and in-depth interviews with key stakeholders; discrete choice experiments; development of a decision tree classification algorithm; and economic evaluation of defined management algorithms.Ethics and dissemination Findings will be reported to participants, collaborators and local government for the three sites, presented at national and international conferences, and disseminated in peer-reviewed publications.The protocol and all study documents such as informed consent forms were reviewed and approved by the University of Cape Town Human Research Ethics Committee (HREC reference 366/2022), Medical Research Council of Zimbabwe (MRCZ/A/2966), Comité d’Ethique pour la Recherche Biomédicale de Madagascar (N° 143 MNSAP/SG/AMM/CERBM) and the London School of Hygiene and Tropical Medicine ethics committee (LSHTM reference 28046).Before the start, this study was submitted to the Clinicaltrials.gov public registry (NCT05723484).Trial registration number NCT05723484.

Plague is a flea-borne fatal disease caused by the bacterium Yersinia pestis, which persists in rural Madagascar. Although fleas parasitizing rats are considered the primary vectors of Y. pestis, the human flea, Pulex irritans, is abundant in human habitations in Madagascar, and has been found naturally infected by the plague bacterium during outbreaks. While P. irritans may therefore play a role in plague transmission if present in plague endemic areas, the factors associated with infestation and human exposure within such regions are little explored. To determine the socio-ecological risk factors associated with P. irritans infestation in rural households in plague-endemic areas of Madagascar, we used a mixed-methods approach, integrating results from P. irritans sampling, a household survey instrument, and an observational checklist. Using previously published vectorial capacity data, the minimal P. irritans index required for interhuman bubonic plague transmission was modeled to determine whether household infestations were enough to pose a plague transmission risk. Socio-ecological risk factors associated with a high P. irritans index were then identified for enrolled households using generalized linear models. Household flea abundance was also modeled using the same set of predictors. A high P. irritans index occurred in approximately one third of households and was primarily associated with having a traditional dirt floor covered with a plant fiber mat. Interventions targeting home improvement and livestock housing management may alleviate flea abundance and plague risk in rural villages experiencing high P. irritans infestation. As plague-control resources are limited in developing countries such as Madagascar, identifying the household parameters and human behaviors favoring flea abundance, such as those identified in this study, are key to developing preventive measures that can be implemented at the community level.

BackgroundPlague, caused by the bacterium Yersinia pestis, remains an important disease in Madagascar, where the oriental rat flea, Xenopsylla cheopis, is a primary vector. To control fleas, synthetic pyrethroids (SPs) have been used for >20 years, resulting in resistance in many X. cheopis populations. The most common mechanisms of SP resistance are target site mutations in the voltage-gated sodium channel (VGSC) gene.Methodology/principal findingsWe obtained 25 collections of X. cheopis from 22 locations across Madagascar and performed phenotypic tests to determine resistance to deltamethrin, permethrin, and/or dichlorodiphenyltrichloroethane (DDT). Most populations were resistant to all these insecticides. We sequenced a 535 bp segment of the VGSC gene and identified two different mutations encoding distinct substitutions at amino acid position 1014, which is associated with knockdown resistance (kdr) to SPs in insects. Kdr mutation L1014F occurred in all 25 collections; a rarer mutation, L1014H, was found in 12 collections. There was a significant positive relationship between the frequency of kdr alleles and the proportion of individuals surviving exposure to deltamethrin. Phylogenetic comparisons of 12 VGSC alleles in Madagascar suggested resistant alleles arose from susceptible lineages at least three times. Because genotype can reasonably predict resistance phenotype, we developed a TaqMan PCR assay for the rapid detection of kdr resistance alleles.Conclusions/significanceOur study provides new insights into VGSC mutations in Malagasy populations of X. cheopis and is the first to report a positive correlation between VGSC genotypes and SP resistance phenotypes in fleas. Widespread occurrence of these two SP resistance mutations in X. cheopis populations in Madagascar reduces the viability of these insecticides for flea control. However, the TaqMan assay described here facilitates rapid detection of kdr mutations to inform when use of these insecticides is still warranted to reduce transmission of plague.

Resolving ecological-economic trade-offs is a challenge in agriculture. Here, Wurz et al. find that in Malagasy vanilla agroforests, vanilla yield is generally not related to tree, herbaceous plant, bird, amphibian, reptile and ant biodiversity, creating opportunities for conservation outside protected areas.

Abstract Background and Aim Beta blockers combined with endoscopic variceal band ligation (EVL) is the most effective means for the prevention of variceal rebleeding. No data are available on the efficacy of carvedilol in the secondary prophylaxis of variceal bleeding in hepatosplenic schistosomiasis. The aim of this study was to evaluate the efficacy and safety of carvedilol compared to propranolol as secondary prophylaxis of variceal bleeding in hepatosplenic schistosomiasis. Methods This was a prospective, randomized study over a period of 14 months from February 2019 to March 2020. All patients with portal hypertension due to schistosomiasis with at least one episode of variceal bleeding were included and randomized to the propranolol and carvedilol groups. EVL protocol was continued in both groups. Results Sixty‐one patients were eligible and randomized to propranolol (n = 30) and carvedilol (n = 31) groups. There was no significant difference in hemorrhagic recurrence between the carvedilol (n = 1) and propranolol (n = 3) groups (3.33 vs 10%; P = 0.30). At 4 months, there was a significant reduction in mean arterial pressure (−4.13 mm Hg; 95% CI: −6.27 to −1.99; P

Blue Ventures (BV) works holistically with communities in Madagascar, developing transformative approaches to catalyse and sustain locally led marine conservation. In response to the coronavirus disease 2019 (COVID-19) pandemic, BV’s priority was to safeguard the immediate wellbeing and livelihoods of as many communities as possible, recognising that livelihoods are integral to broader well-being. This article describes in detail BV’s health response and the perceptions of BV’s Madagascar team regarding the successes and challenges of this effort. As a result of the combined efforts of BV teams across Madagascar and in the United Kingdom, the existing healthcare services at BV’s sites were maintained, and messages about recognising and dealing with COVID-19 and the importance of vaccination were conveyed to communities that might otherwise not have received comprehensive information. Data were also collected on suspected cases in areas where testing was not available, and outbreaks of suspected COVID-19 cases were managed. Because BV’s teams are embedded within the communities where they work, they maintain strong relationships with communities and conveyed important messages around reducing the spread of COVID-19, not only via activities in response to the pandemic but also through activities for other programmes such as fisheries and livelihoods. Blue Ventures’ holistic approach ensured that the organisation had a multidimensional understanding of the impacts of the pandemic on communities, facilitating the development of more relevant messaging that considered both safety and the need for continued income-generating activities. Staff felt that an effective public health response was facilitated by strong in-country partnerships and BV’s long-standing presence in communities. Contribution: The challenges in responding to the pandemic and in implementing and maintaining effective behaviour change are discussed. Although not an objective study of the effectiveness of the response or a comparison with other approaches, the lessons learned from this process are shared in the hope that they may inform responses to future shocks in low-income countries.

The genus Copelatus Erichson, 1832 (Coleoptera, Dytiscidae, Copelatinae) of Madagascar is revised in two parts. This review is restricted to the Copelatus species that have fewer than ten elytral + one submarginal stria, including all species except those of the erichsonii species group. Both morphological and molecular (mitochondrial COI) data are used in an integrative taxonomic approach. Thirteen species are recognised, of which five are described as new: Copelatus ankaratra sp. nov., Copelatus kely sp. nov., Copelatus pseudostriatus sp. nov., Copelatus safiotra sp. nov. and Copelatus vokoka sp. nov. Copelatus unguicularis Régimbart, 1903 and Copelatus apicalis Fairmaire, 1898 are both transferred to the genus Madaglymbus Shaverdo & Balke, 2008 (comb. nov.). Copelatus mimetes Guignot 1957 is a junior synonym of the widespread Afrotropical–Arabian Copelatus pulchellus (Klug, 1834) (syn. nov.). Copelatus marginipennis (Laporte, 1835) is reinstated (stat. nov.) as a valid species with Copelatus aldabricus Balfour-Browne, 1950 and Copelatus aldabricus var. simplex Guignot, 1952 as junior synonyms (syn. nov.). We designate lectotypes for Colymbetes marginipennis Laporte, 1835 and Copelatus obtusus Boheman, 1848. Copelatus peridinus Guignot, 1955 is recorded for Madagascar for the first time and Copelatus nodieri Régimbart, 1895 is rejected as a species present in Madagascar.

Several dozen stones of an ordinary chondrite meteorite fell in and around the town of Benenitra in southwestern Madagascar during the early evening of 27 July 2018, minutes after a widely observed meteor fireball (bolide) transit and detonation. The event was confirmed by low-frequency infrasound recordings received at ~17h15 UTC (Coordinated Universal Time; 19h15 local time) at the Comprehensive Nuclear Test Ban Treaty Organization (CTBTO) infrasound station I33MG near Antananarivo, 542 km north-northeast of Benenitra. An energy release equivalent to 2.038 kt of TNT was calculated from the infrasound signals. Seismograph readings at the SKRH station 77 km north-northwest of Benenitra recorded a twostage signal consistent with the arrivals of an initial air-coupled ground wave at 16h48:08 UTC and a stronger pulse at 16h49:22 UTC linked directly to the atmospheric pressure wave. The infrasound and seismic signal arrival times suggest that the bolide entry and detonation occurred at approximately 18h46 local time (16h46 UTC), entry was from the northwest, and the detonation hypocentre was located within ~20 km of Benenitra. Despite meteorite debris being found among buildings within Benenitra, there was no damage to structures or injuries reported. Eyewitness accounts and photographic records indicate that approximately 75 mostly intact stones were collected; however, the remoteness of the area, the rugged nature of the terrain and sales of fragments to meteorite collectors have limited scientific analysis of the fall and the extent of the strewn field. The total mass of recovered stones is estimated at between 20 kg and 30 kg, with one fragment of 11.2 kg and several of ~1 kg. Petrographic and mineral chemical analyses indicate that the stones belong to the L6 class of ordinary chondrites. Cosmogenic radionuclide analysis confirms that the fall is linked to the bolide event. The name Benenitra has been officially accepted by the Meteoritical Bulletin Database. Significance: • Eyewitness reports, CTBTO infrasound records, seismograph records and cosmogenic radionuclide analysis confirm a meteorite fall over Benenitra on 27 July 2018. • Petrographic and geochemical analyses confirm that the meteorite is an L6 ordinary chondrite. • Recovery of meteorite falls is rare; this is Madagascar’s second known meteorite fall and the first that can be linked to a bolide. • Regional and global science monitoring networks can be interrogated to improve the understanding of bolide events. • Interaction of scientists with local communities is important to dispel misunderstandings around scientific phenomena, and can improve collection of data.

Abstract We report new P and S wave velocity models of the upper mantle beneath southern Africa using data recorded on seismic stations spanning the entire subcontinent. Beneath most of the Damara Belt, including the Okavango Rift, our models show lower than average velocities (−0.8% Vp; −1.2% Vs) with an abrupt increase in velocities along the terrane's southern margin. We attribute the lower than average velocities to thinner lithosphere (~130 km thick) compared to thicker lithosphere (~200 km thick) immediately to the south under the Kalahari Craton. Beneath the Etendeka Flood Basalt Province, higher than average velocities (0.25% Vp; 0.75% Vs) indicate thicker and/or compositionally distinct lithosphere compared to other parts of the Damara Belt. In the Rehoboth Province, higher than average velocities (0.3% Vp; 0.5% Vs) suggest the presence of a microcraton, as do higher than average velocities (1.0% Vp; 1.5% Vs) under the Southern Irumide Belt. Lower than average velocities (−0.4% Vp; −0.7% Vs) beneath the Bushveld Complex and parts of the Mgondi and Okwa terranes are consistent with previous studies, which attributed them to compositionally modified lithosphere resulting from Precambrian magmatic events. There is little evidence for thermally modified upper mantle beneath any of these terranes which could provide a source of uplift for the Southern African Plateau. In contrast, beneath parts of the Irumide Belt in southern and central Zambia and the Mozambique Belt in central Mozambique, deep‐seated low velocity anomalies (−0.7% Vp; −0.8% Vs) can be attributed to upper mantle extensions of the African superplume structure.

The new coronavirus disease 2019 (COVID-19) could be associated with elevated inflammatory cytokine levels, suggesting the involvement of cytokine release syndrome. This syndrome is characterized by release of interleukin 6 correlated with COVID-19 severity and mortality. Targeting IL-6 with Tocilizumab treatment could be a potential therapeutic option for old patients. We report the case of an 88-year-old man with COVID-19 disease who presented at the admission with anemia, fever, oxygen desaturation (92%), and inflammatory syndrome (C-reactive protein (CRP) at 182.5 mg/L; reference range

Background: The West Malagasy dry forests support numerous endemic species and experience heavy anthropogenic pressures, yet remain very poorly studied. Further research is required to understand species distributions and overall diversity in these threatened forest ecosystems. Objectives: We aimed to provide a description of the avifaunal community of a particular dry forest, Mariarano forest, north-western Madagascar, as well as other habitats that are heavily integrated with these Forests. The study site possesses a highly endemic bird community and is under severe environmental pressure, but remains poorly explored. Method: We compiled all records from a 9-year (2010–2018) bird survey data set (the most extensive compiled from a Madagascan dry forest to date), which yielded data from a combination of point count and mist-netting protocols. This was further supplemented by approximately 4384 h of opportunistic observation effort. Results: In total, 95 species were detected, including 63 regional endemics (66.3% of all species), 2 local endemics and 7 Threatened or Near-Threatened species. Conclusion: We highlight the forest mosaic habitats of Mariarano as a potential new Important Bird Area, given the regional importance of its endemic avifauna.

Two words, Malagasy and Madagascan, have emerged in the literature as English terms to refer to the people, the culture, and other animate and inanimate objects from Madagascar, the choice of which has left room for confusion for users (e.g. Malagasy art or Madagascan art, Malagasy rice or Madagascan rice, Malagasy Republic or Madagascan Republic, and so forth). This article has two aims: (1) understanding the sources of such confusion, and (2) subsequently proposing a unified English term (noun and adjective) that will avoid further misperceptions in written and verbal communications accounting for Madagascar. The results from investigating the Web of Science, from historical documents, and from viewpoints from online survey combine to suggest that the term ‘Malagasy’ must have unintentionally been substituted by the term ‘Madagascan’ from the earliest documented usage until now. These two words have been used interchangeably, and the usage has never been applied consistently. This could have been influenced by the simple assumption that ‘Madagascan’ is an intuitive form, derivative of Madagascar. The word “Malagasy” is not simply a straightforward English–Malagasy translation but there is much meaning to it that relate to the history and the culture of Madagascar. ‘Malagasy’ is unique to Madagascar, and in future usage in the English language, we recommend everyone to use it as a word qualifier for different objects, animals, plants, and the people of Madagascar. Keywords: Malagasy, Madagascan, Madagascar, Terminology misconception

The ‘D. bakoue species complex’ Rafael, 1984 (‘D. montium species group’ Da Lage et al., 2007) comprises seven Afrotropical species. Using complete mitochondrial genome sequences and detailed morphological analysis, we revised the phylogenetic relationships between these species including two new ones. We found the ‘D. bakoue species complex’ to be a junior synonym of the ‘D. seguyi species complex’ Lachaise, 1971 and its seven species polyphyletic. We thus classified the species into three complexes, the ‘D. seguyi species complex’ comprises D. seguyi Smart, 1945, D. malagassya Tsacas & Rafael, 1982, D. curta Chassagnard & Tsacas, 1997 and D. chocolata sp. nov., the new ‘D. tsacasi species complex’ comprises D. tsacasi Bock & Wheeler, 1972 and D. seguyiana Chassagnard & Tsacas, 1997, and the new ‘D. vulcana species complex’ comprises D. vulcana Graber, 1957 and D. mylenae sp. nov. Drosophila bakoue Tsacas & Lachaise, 1974 could not be assigned to any of the defined complexes. The two new species are endemic to Madagascar and we report the presence of D. seguyi and D. curta in Mayotte and Madagascar, respectively. The results hence represent a significant step towards understanding the diversity and evolution of this species group in Africa and the islands of the Western Indian Ocean.

L'endocardite de Libman-Sacks constitue une manifestation cardiaque peu fréquente de la maladie lupique au cours de laquelle il existe une végétation non infectieuse au niveau des valves cardiaques. Il y a un risque important d'endocardite infectieuse. Notre patiente était une femme de 38 ans, présentant une fièvre persistante et une polyarthralgie inflammatoire au niveau des poignets et des chevilles. Elle présentait un souffle systolique mitral 2 sur 6 et une tuméfaction douloureuse des poignets et des chevilles. Nous avions objectivé un syndrome inflammatoire biologique. Le dosage des anticorps anti-nucléaire était positif avec un aspect moucheté, ainsi que les anticorps anti-DNA natifs. La recherche de syndrome des anti-phospholipides (SAPL) était négative. L'échographie doppler cardiaque avait objectivé des végétations au niveau des valves mitrales et aortiques. Les améliorations clinique, biologique et morphologique n'avaient été obtenues qu'après association antibiothérapie et corticothérapie. Nous pouvons conclure que l'endocardite de Libman-Sacks est d'évolution favorable en l'absence d'un syndrome des anti-phospholipides associé. Il faut toujours craindre dans tous les cas une greffe bactérienne. Le traitement est basé sur l'association antibiothérapie-corticothérapie-antipaludéen de synthèse.

In Madagascar, soil erosion is significant even when it is compared to world averages. A resulting special geomorphic feature is a form of gully erosion known as lavaka that appears in the highlands of the country. Lavakization (the generation and development of these features) is due to rather unique multifactorial environmental conditions. Among many factors (geology, soil composition, human activities, etc.), the spatial and temporal distribution of precipitation is a key factor influencing the behaviour of lithology and the vegetation cover of the island. The inter-annual variability in precipitation seems to be responsible for the enhanced generation of small cracks that might eventually lead to the development of a gully. However, the way of the development of such gullies is unknown. To what extent the actual precipitation pattern contributes to the aforementioned phenomenon has not yet been studied in great detail. This paper aims to analyze lavaka distribution with GIS methods and to study the relation between lavaka density and climatic conditions. Study areas have been designated throughout the country and lavakas have been identified using satellite imagery. Archive climate data of the study areas have been used to understand the influence of the weather on gully density. Data show that the spatial distribution of precipitation is connected to the appearance of lavakas to a given extent and its effect is further strengthened by the tropical cyclones. However, neither the amount of the precipitation, nor its variability alone can explain the high variation found in the spatial distribution of lavakas. Further multidisciplinary studies are necessary to draw conclusions about lavaka formation and to describe the process of lavaka development.

Mathematical models are effective tools for evaluating the impact of predicted climate change on agricultural production, but it is difficult to test their applicability to future weather conditions. We applied the SWAP model to assess its applicability to climate conditions, differing from those, for which the model was developed. We used a database obtained from a winter wheat drought stress experiment. Winter wheat was grown in six soil columns, three having optimal water supply (NS), while three were kept under drought-stressed conditions (S). The SWAP model was successfully calibrated against measured values of potential evapotranspiration (PET), potential evaporation (PE) and total amount of water (TSW) in the soil columns. The Nash-Sutcliffe model efficiency coefficient (N-S) for TWS for the stressed columns was 0.92. For the NS treatment, we applied temporally variable soil hydraulic properties because of soil consolidation caused by regular irrigation. This approach improved the N-S values for the wetting-drying cycle from -1.77 to 0.54. We concluded that the model could be used for assessing the effects of climate change on soil water regime. Our results indicate that soil water balance studies should put more focus on the time variability of structuredependent soil properties.

Objective: To evaluate the potential efficacy of seed extracts of Annona squamosa and Annona muricata used as natural insecticides to control adult and larvae of the vectors Aedes albopictus and Culex quinquefasciatus under laboratory conditions. Methods: Aqueous and oil extracts of the two plants were prepared from dried seeds. Preliminary identifications of the chemical components of each seed extracts were performed using micro-reactional and GCP techniques. Larvae and adults of Aedes albopictus and Culex quinquefasciatus were collected from the breeding sites in coastal and highlands regions of Madagascar. WHO standardized tests of susceptibility for larvae and imaginal stage of mosquitoes were realized to determine mortality and LC50 of mosquitoes. Results: Chemical identifications showed that these extracts contain alkaloids and flavonoids compounds that probably confer their biological insecticidal proprieties. CPG analysis showed also the presence of various fatty acids. On adult mosquitoes, significant insecticidal effects were observed with both aqueous and oil extracts of the two plant seeds compared to mortality induced by deltamethrin, an insecticide used as reference. Extracts of Annona muricata induced high mortality rate to both species of mosquito compared to extracts of Annona squamosa at all concentrations tested. The LC50 of seed extracts ranged from 1% to 5% for adults and 0.5% to 1% for larvae. Conclusions: The seed extracts of these two plants may be used as mosquito controlling agents and offer a new approach to a less costly, practical and environmentally friendly control of vector borne diseases.