Baobab Index

Artemisinin-resistant Plasmodium falciparum has emerged in several East African countries neighbouring Madagascar. Despite the island's substantial malaria burden, recent data on artemisinin partial resistance are limited, raising concerns about the potential emergence of resistant parasites. This study provides an updated overview of the prevalence and diversity of P. falciparum Kelch13 (pfkelch13) polymorphisms in Madagascar. During a nationally representative, cross-sectional survey conducted between January and May 2024, dried blood samples were collected from 4850 febrile patients at 65 health facilities. Pfkelch13 genotyping was performed using a targeted amplicon deep sequencing approach. Of the 1944 P. falciparum-positive samples, 963 (49.5%) pfkelch13 sequences were successfully obtained, and 885 (91.9%) corresponded to the 3D7 wild-type. Non-synonymous and synonymous mutations were detected in 1.8% (17/963) and 6.2% (60/963) of isolates, respectively, whereas one isolate (0.1%) carried double mutations. Of the 18 mutations identified, 5 had not been previously reported. The two most frequent polymorphisms in Madagascar were the synonymous mutations C469C (3.0%, 29/963) and P417P (2.8%, 27/963). None of the WHO-validated artemisinin partial resistance markers were detected. This study provides an updated baseline of pfkelch13 polymorphisms in Madagascar, with no evidence of artemisinin partial resistance emergence. Importantly, no parasites harbouring a validated artemisinin resistance marker were detected across the regions sampled, suggesting that resistant parasites have not yet become established. These findings provide a valuable baseline for future genomic surveillance efforts aimed at the early detection of mutations associated with artemisinin partial resistance.

Given that some DNA viruses have been found to exhibit virus-host co-evolution and establish lifelong infection, mammals with unique evolutionary histories in island ecosystems likely host exceptionally diverse viruses. Madagascar is inhabited by endemic non-human primate and rodent lineages interacting with expansive populations of introduced non-native rodents across the island. Using a viral metagenomic workflow on 189 oral swabs of lemurs and rodents in southeastern Madagascar, we characterized genomic sequences of DNA viruses in the families

In this prospective multicentre study, we analysed 1296 non-duplicate Carbapenem-resistant

Respiratory illness contributes to substantial global morbidity and mortality. In Madagascar, an island nation off the southeastern coast of the African continent, hospital-based public health surveillance for respiratory pathogens screens for common respiratory viruses. However, many cases remain undiagnosed. We conducted metagenomic Next Generation Sequencing (mNGS) to identify the pathogen profile of 102 undiagnosed febrile patients who presented to public hospitals with respiratory symptoms and screened negative on a 14-virus multiplex RT-qPCR. We analyzed the diversity of the respiratory microbiome of each patient from mNGS data and identified viral infections potentially linked to undiagnosed fever. We assembled whole genome consensus sequences of viruses with sufficient read depth and coverage, characterized each phylogenetically, and identified any discrepancies with the primers used in the multiplex RT-qPCR panel. Finally, we compared all whole genome sequences against publicly available global databases in a phylogenetic analysis. We identified evidence of infection by a wide range of known human viruses in approximately two thirds (64.7%) of study participants from nine different families of viruses and generated 30 complete or nearly complete consensus sequences of known respiratory viruses including orthopneumoviruses, metapneumoviruses, rhinoviruses, coronaviruses, parainfluenza virus, and bocaparvovirus. mNGS-attributed evidence of infection was predominantly due to orthopneumovirus (also called respiratory syncytial virus [RSV]; n = 24; n = 8 previously diagnosed) and rhinovirus (n = 18) detections, despite previous negative RT-qPCR results for the majority of these cases. Finally, phylogenetic analysis identified two distinct phylogenetic clusters of RSV subtype A, suggesting local transmission following distinct international introductions for this virus. mNGS provides a sensitive pan-pathogenic tool for virus detection. We demonstrate the diversity of viruses associated with undiagnosed respiratory fevers in Madagascar, emphasize the importance and relevance of the existing respiratory surveillance in the country, and highlight the interconnectedness of regional respiratory infection dynamics with global networks of respiratory pathogen transmission.

Understanding plant adaptation is critical under intensifying global aridification. Succulence, a key drought-resistance innovation, has evolved repeatedly across plant lineages, yet its intrinsic genomic drivers remain underexplored. Integrating comprehensive evidence from genomics, ecology, and morphology, we investigate adaptation to aridity in the tree grape genus, Cyphostemma (Vitaceae), whose species span environmental gradients from rainforests to deserts and exhibit wide genomic and phenotypic variation. Utilising genome assemblies of representative Cyphostemma species, we demonstrate that specific long terminal repeat retrotransposon (LTR-RT) lineages thrived through the radiation of Cyphostemma and led to substantial intron expansion, a phenomenon rarely studied in eudicots. The intronic LTR-RT insertions likely enhanced tolerance of genome structural changes, facilitating succulence evolution. Genomes of succulents were further expanded by intergenic LTR-RTs, which exhibit recurrent evolutionary advantages in arid and seasonal habitats. Our study reveals how genomic landscapes are shaped by both intrinsic LTR-RT dynamics and extrinsic environmental forces. Critically, we suggest that stochastic dynamics of LTR-RT communities enhance genomic evolvability, enabling adaptive evolution in plants.

Climate change is impacting biodiversity worldwide at an accelerating pace. Traditionally, Ecological Niche Models (ENMs) have been widely used to infer the likely impacts of climate change on species, while accounting for their potential dispersal towards climatically suitable habitats. More recently, Genotype-environment association (GEA) approaches applied to genomic data have opened the possibility to investigate local adaptation underlying species' genetic adaptive capacity, allowing quantification of maladaptation risk under future climatic conditions. In this study, we integrate ENMs with GEAs to assess climate change impacts on

Biologging and telemetry have transformed our understanding of marine megafauna movement ecology. Yet, methodological constraints continue to limit data quality and deployment duration. Devices recording whale shark ( Whale shark researcher responses to the survey highlighted clamp-based systems as a practical and more widely applicable approach than drill-based methods, which are often used to secure tags to other large sharks. They also noted that clamps have greater retention potential and are suitable for a wider range of tags compared to dart-based methods, but are still constrained by design, placement, and deployment conditions. Researchers used a variety of materials and designs to build their own clamps, often facilitated by direct collaboration with each other or key manufacturers. Clamps produced highly variable outcomes, ranging from successful long-term satellite transmissions over 200 days and short-term biologging for 48 h at 20 Hz, to premature detachment and cases of fin damage. For long-term clamps, changes in position on the fin allowed for more stable satellite transmissions over time. Some clamp designs achieved data quantity and quality close to that of drilled deployments, demonstrating their potential to rival traditional methods while offering a less invasive approach. Results emphasised the ongoing need for technological refinement and rigorous evaluation of clamp performance and associated impacts. Based on collective insights, we present a unified approach to clamp design and positioning, and identify key priorities for advancing this attachment technology, such as aiming for positions b-2 and c-2 on the fin and ensuring the clamp bridge distance (always between 30 and 50 mm) and tension are matched to shark size. Optimising clamp systems could substantially improve our ability to generate high-quality, long-duration movement data while minimising tagging impacts on the animal where possible. This could enhance ecological and conservation research outcomes for endangered whale sharks, with broader implications for tagging other large-bodied marine megafauna. The online version contains supplementary material available at 10.1186/s40317-026-00462-4.

Freshwater biodiversity is declining at a pace that outstrips the capacity of existing monitoring approaches both in temporal and spatial dimensions, highlighting the urgent need for rapid and scalable assessment and attribution of biodiversity states and changes. Here we present a global assessment and unified analysis of riverine fish biodiversity using environmental DNA collected from 1,818 sites across 113 river systems spanning 5 continents. We quantified species richness, functional redundancy, phylogenetic diversity and genetic sequence diversity, and related them to drainage characteristics. Our results showed that environmental DNA effectively captured global patterns of multi-faceted riverine fish biodiversity and disentangled the roles of climate and different aspects of human activities in shaping biodiversity-area relationships. The accumulation of biodiversity with catchment area was consistently enhanced in warmer climates, while human activities weakened this scaling. Further, species richness, functional and genetic sequence diversity exhibited stronger negative responses to human activities in larger catchments. In contrast, phylogenetic diversity was negatively affected by human activities, yet this effect diminished as catchment area increased, highlighting the facet-dependent nature of biodiversity responses to environmental gradients and catchment characteristics. Our findings demonstrate the power of environmental-DNA-based datasets for harmonized, multi-faceted biodiversity assessments, offering a scalable approach for detecting and attributing biodiversity change and informing conservation strategies under accelerating global change.

Using an

Naegleria fowleri is a highly lethal free-living protozoan responsible for primary amoebic meningoencephalitis (PAM), a rapidly progressive central nervous system infection with a mortality rate exceeding 95%, for which no licensed vaccine or effective preventive therapy currently exists. The absence of prophylactic strategies demands development of novel immunopharmacological interventions. In this study, a comprehensive pan-genomic and structure-guided immunoinformatics approach was employed to design a multi-epitope vaccine candidate against N. fowleri. Four genomes of N. fowleri were subjected to an integrative pan-genomic-immunoinformatics pipeline involving orthologous clustering, subtractive genomics, and immunological relevance screening. From 1427 predicted membrane proteins, 885 antigenic, non-allergenic, and non-toxic candidates were identified. Epitope prediction yielded 7 B-cell epitopes, 26 MHC class I-restricted CTL epitopes, and 22 MHC class II-restricted HTL epitopes, which were assembled into a multi-epitope vaccine construct with immunostimulatory adjuvants. The resulting 320-amino acid construct demonstrated high antigenicity and global population coverage of 91.75%. Structural validation confirmed 98.9% of residues in favorable Ramachandran regions and an ERRAT quality score of 92.484. Molecular docking with Toll-like receptor 3 (TLR3) revealed a highly stable complex with a weighted energy score of - 1475.4 kcal/mol, featuring 24 hydrogen bonds and 5 salt bridges. Molecular dynamics simulations over 100 ns demonstrated structural stability with low RMSD and RMSF values, indicating dynamic stability and coordinated residue motions. Immune simulations predicted strong humoral and cellular immune responses with sustained antibody levels and memory cell generation. Codon optimization achieved a CAI of 0.99 and 53.4% GC content, supporting heterologous expression in Escherichia coli. This multi-epitope vaccine candidate exhibits strong immunogenic potential, structural stability, and favorable interactions with innate immune receptors, positioning it as a promising candidate for experimental validation against N. fowleri infection.