Baobab Index

The genetic history of African indigenous pigs remains poorly documented due to scarce archaeological and genomic data. Here, we analyzed 473 mitogenomes and 202 Y chromosome sequences from indigenous pigs in Africa, alongside 901 published mitogenomes and 715 Y chromosome sequences from Eurasian pigs and wild boars. Our results reveal that African pigs predominantly descend from European (haplogroup E, 44.8%) and East Asian (haplogroup D, 53.3%) lineages. Interestingly, there was a novel detection of Asian wild boar haplogroup A∗ (1.9%) in Tanzania. This pattern is congruent with that of Y chromosome analysis. Further maternal analyses confirm a genetic link between western African and Iberian pigs dating to about 4.5 ka, and dispersal into eastern Africa coinciding with the Bantu expansion around 2 ka. Our findings demonstrate complex human-mediated dispersal routes, highlighting the role of Bantu societies in shaping the genetic architecture of African indigenous pigs.

This study reports novel 21 aSTR (autosomal Short Tandem Repeats) allele frequencies from 538 individuals, as well as 11 triallelic profiles, representing seven Bantu-speaking groups in Southern Africa (Ndebele, Pedi, Phuthi, Tsonga, Sotho, Swati, and Xhosa). These data contributed to a comprehensive representation of the Southern Bantu (SB). The defined SB reference database was evaluated for various forensic uses and applications: extant diversity, population structure, adequacy of alternative reference databases, and continental biogeographical ancestry prediction. Different analytical methods-including summary statistics, multivariate analyses (Multidimensional Scaling, MDS; Discriminant Analysis of Principal Components, DAPC), and Bayesian clustering-detected continental structure, identifying four major clusters: Southern, Eastern, Western, and Horn of Africa. This observation motivated the evaluation of two practical applications of this information: one methodological (alternative reference frequency database) and one predictive (biogeographic assignment). The adequacy of alternative reference databases for representing SB populations-STRidER South Africa, STRidER Africa, African American, and global datasets-was assessed by comparing reciprocal allelic coverage and shifts in random match probabilities (RMPs). Of the databases tested, the STRidER Africa database provided the closest representation of the SB. Population-level analyses evidenced the need for a stratification correction (θ = 0.005 or 0.01) for SB populations. Intracontinental biogeographic prediction was assessed using an XGBoost machine learning classification model across four major African regions. The model's predictive balanced accuracy ranged from 80 % to 94 % across African regions (94 % for the Horn of Africa, 87 % for Southern Africa, 84 % for Western Africa, and 80 % for Eastern Africa). The accuracy and limitations of this practice are discussed, along with its ethical implications. The assessment of reference databases can be extended to more general applications across Africa.

We aimed to establish an external quality assessment (EQA) programme for the yaws eradication campaign that would meet the needs of reference and district-level laboratories in low- and middle-income countries. We designed proficiency testing items (PTIs) using a plasmid containing gene target sequences for Treponema pallidum (TP) and Haemophilus ducreyi (HD). The storage stability of the plasmids under different environmental conditions was then tested. A proficiency testing panel of seven swabs loaded with different concentrations of plasmids in different combinations, as well as human HEK293 cells to simulate the sample background, was prepared and sent to participating reference (RL) and district (DL) laboratories in Ghana, Côte d'Ivoire and Cameroon followed by three rounds of blinded proficiency testing. We tested quantitative real-time PCR (qPCR) performance of reference laboratories and loop-mediated isothermal amplification (LAMP) performance of district laboratories and retested 20% of human field samples at the London School of Hygiene & Tropical Medicine laboratories to further assess qPCR quality. PTIs proved to be stable in dry conditions with no significant loss of copy number. Participating laboratories achieved qPCR results with a concordance of 95.0-100.0% (97.7% ± 5.2% (mean±standard deviation ((SD)) with the provider and a concordance of 76.0-100.0% (TP: 90.3 ± 13.7% and HD: 78.5 ± 7.5% (mean±SD)) for LAMP results, with inconsistencies, particularly in the detection of low HD plasmid DNA levels combined with high TP plasmid copies. Retesting of field samples resulted in 100% correct TP and HD sample identification by the African reference laboratories. We have developed a functional plasmid-based EQA programme specifically designed to meet the needs of resource-poor settings in the tropics. The programme is suitable as a blueprint for other disease programmes.

Lumpy skin disease (LSD) threatens cattle health and productivity in Ivory Coast, where limited resources for livestock management hinder disease control. Moreover, the lack of studies on its prevalence and genetic profile leaves critical gaps in understanding its epidemiology and local risk factors. This study addresses these gaps by investigating LSD viruses' prevalence, its molecular characteristic and the associated risk factors among cattle in the Poro Region of northern Ivory Coast. Using a cross-sectional design, nodule and nasal swab samples were collected from 405 cattle across 36 villages between September 2023 and December 2024 based on syndromic surveillance. The samples were analyzed PCR to confirm LSD virus presence, followed by sequencing of four viral genes: RPO30, GPCR, EEV glycoprotein, and B22R. Overall, LSD prevalence among cattle showing pox-like lesions and clinical symptoms was found to be 51.85% and varied significantly across localities, reaching 66.67% in M'bengué and 70.87% in Dikodougou. Larger herds (over 50 cattle) had a higher prevalence (76.51%) compared to smaller herds (34.72%), and transhumant herds showed increased prevalence ( The present study shows a notable regional difference in the prevalence of LSD in cattle in Ivory Coast, with big and transhumant herds having a higher prevalence rate making the herd size and movement a major risk factor. Molecular analysis demonstrated that Ivory Coast LSD strains are in the same group with other strains found in the African field, indicating that it is necessary to take control measures within the region and provide further surveillance.

Integrase mutations associated with dolutegravir resistance have been well characterized, but based on limited data from non-B subtypes. We aim to identify potential integrase mutations not currently classified as integrase strand transfer inhibitor (INSTI) resistance mutations (DRMs) in individuals with viremia on dolutegravir-based regimens. We included integrase sequences from DTG RESIST study sites in African countries. These were interpreted using Stanford HIVdb v9.8. We used a viral genome-wide association study-like approach restricted to the integrase region (INT-WAS) to identify mutations not classified as major or accessory INSTI DRMs but occurring more frequently in sequences carrying major INSTI DRMs than in those without major INSTI DRMs. We performed the same INT-WAS analysis with drug-naïve sequences from the Los Alamos HIV-1 database to test whether these identified mutations were enriched among sequences from individuals with viraemia whilst receiving DTG-based treatment. Among 382 sequences, 104 (27.2%) showed at least intermediate dolutegravir resistance. Twelve integrase mutations not classified as major or accessory DRMs (S39R, L45I, I72L, L74I, V79I, I113V, S119R, K156N, I208M, T218M, A265V, and R284G) were significantly associated with predicted DTG resistance. Among them, V79I [adjusted odds ratio (aOR) 167.1, 95% credible interval (CrI) 17.9-2947.6] and I72L (aOR 65.6, 95% CrI 6.6-1273.7) were strongly associated. S39R, L45I, V79I, S119R, and K156N were linked to established INSTI resistance pathways, and I72L, L74I, V79I, K156N, I208M, and R284G were overrepresented in sequences from viraemic individuals on DTG-based treatment relative to drug-naïve sequences. We identified several amino acid substitutions outside the established DRMs that are strongly associated with predicted dolutegravir resistance. Dolutegravir resistance evolution is complex and likely involves mutations not currently classified as DRMs.

Cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) are two viral diseases that threaten cassava production in the East and Central African countries. These diseases are spread by members of the cryptic species complex of the whitefly Bemisia tabaci sensu lato, and/or through the propagation of infected stem cuttings. This study aims to i) identify the B. tabaci s.l. species colonizing cassava in the north of the Democratic Republic of the Congo (DRC), ii) analyse their genetic diversity, and iii) examine how this diversity is geographically structured or influenced by invasions from neighbouring (eastern) countries with high CBSD prevalence. A comprehensive sampling survey was conducted across 43 sites from east to west in the DRC, spanning 1339 km. Both nuclear and mitochondrial markers were used to identify the species and study the genetic diversity and structuring of the populations. Three species of B. tabaci s.l. were found: B. tabaci SSA1-SG1 U SG2; B. tabaci SSA1-SG3, and B. tabaci SSA2 U SSA3. In the surveyed provinces, B. tabaci SSA1 SG1 U SG2 was the dominant species (94.91%). It was structured into two genetic clusters along the east-west transect, while B. tabaci SSA2 U SSA3 was restricted to the western provinces. The findings of this study confirm that B. tabaci SSA1-SG1 U SG2 is the most abundant and adapted species on cassava in the DRC. It is likely that this species is responsible for the spread of cassava virus diseases in the DRC. Furthermore, the results showed significant geographical structuring of B. tabaci SSA1-SG1 U SG2 populations, with potential movements of populations towards the west of the country. This highlights the increased risk of virus spread towards West Africa.

The critically endangered white-thighed colobus, Colobus vellerosus, is on the brink of extinction, necessitating the implementation of effective conservation management strategies. The population in Kikélé village serves as the primary remaining stronghold for this species in Benin, comprising around twenty-nine individuals in the small Kikélé Sacred Forest (KSF) and an additional eight individuals in the community-managed Okuta Kobunan Forest (OKF). The KSF is a well-established sacred forest managed by the Kikélé community and is situated an average of 7.5 km from the OKF, which is currently being developed as a community-managed forest. These two populations are believed to have descended from a single founding pair introduced to the Kikélé region circa 1800. Given the small population size and the possible severe genetic bottleneck at its foundation, the genetic diversity might be extremely low. In our study, we conducted a first analysis of the genetic diversity of the two populations using mitochondrial markers, the complete cytochrome b (cytb) and a segment of the hypervariable control region (D-loop, 750 bp). Our findings revealed only one cytb haplotype, along with two haplotypes that differ by just one site in the D-loop. We recommend a range-wide population genetic assessment of the species to explore the possibility of translocations as a potential genetic rescue strategy.

Soil eukaryotes, including fungi, protists, plants, and animals, are central to biosphere functioning and resilience. The Global Standardised Soil Eukaryome Dataset (GloSED) is the first dataset encompassing the entire spectrum of soil eukaryotes, covering 4,063 sampling sites in 121 countries on all continents, revealing nearly one million operational taxonomic units. All samples were collected and analysed using a standardised protocol minimizing technical biases. Long-read sequencing of full-length ITS and 18S-V9 regions provide broad taxonomic coverage and high-resolution identification supported by specialist curation of "dark taxa". A rigorous bioinformatic processing ensures against homopolymer errors, PCR-mediated chimeras, and index switching providing high data quality. The dataset is supported by raw sequences and an open-source containerised workflow for reproducible analyses. The samples are accompanied by land-cover description and directly measured soil pH, δ

Microbial ecology and microbiome science are increasingly central to global "One Health" efforts, a framework that recognizes the interconnected health of humans, animals, and the environment. In Africa, these fields are particularly important for addressing interconnected challenges in public health, agriculture, and ecosystem resilience. Discussions at the ISME Africa Morocco 2025 regional meeting highlighted both progress and persistent gaps in African microbiome research. Initiatives such as the African BioGenome Project and Human Heredity and Health in Africa demonstrate the feasibility of population-representative studies, regional training, networking, and open-science frameworks; however, the research landscape remains fragmented, with limited intra-African collaboration and continued reliance on external funding and leadership. The development of Africa-specific reference genomes, population-based microbiome datasets, is essential to address these gaps and ensure global representation. This perspective synthesizes current evidence and outlines strategic priorities to transition from toward coordinated pan-African research networks and flagship programs. Key recommendations include developing Africa-specific genome reference datasets, establishing pan-continental consortia, fostering equitable African-non-African partnerships, integrating microbiome science into policy frameworks, and adopting FAIR open-science practices. Strengthening bioinformatics and computational capacity will be essential to transform fragmented data into high-impact, coordinated insights. Advancing these priorities will accelerate translation into One Health outcomes, including antimicrobial resistance surveillance, food security, climate-resilient agriculture, and precision medicine. Africa's rich microbial diversity offers significant potential for antibiotic discovery, improved crop productivity, and sustainable agricultural systems. Collectively, strengthening Africa-led, collaborative microbiome research will enable the continent's microbial diversity to drive impactful solutions with regional and global relevance.

Human whipworm infections caused by Trichuris trichiura and Trichuris incognita remain a major public health problem, affecting over 400 million people globally and responding poorly to standard benzimidazole chemotherapy. Ivermectin-albendazole and moxidectin-albendazole have emerged as promising combination therapies, but recent in vitro evidence suggests that ivermectin and moxidectin may also affect gut bacteria. We therefore characterized their off-target effects on the gut microbiome in a randomized controlled trial including 204 Trichuris spp.-infected individuals in Côte d'Ivoire treated with albendazole (400 mg), ivermectin-albendazole (200 µg/kg/400 mg), or moxidectin-albendazole (8 mg/400 mg). By combining Illumina short reads and Nanopore long reads, we recovered over 800 high-quality metagenome-assembled genomes. Albendazole and moxidectin-albendazole induced taxonomic shifts with only mild functional consequences. In contrast, individuals receiving higher absolute ivermectin doses based on their bodyweight ( ≥ 15 mg) showed pronounced changes in taxonomic composition and microbial function, whereas the resistome remained largely stable. These findings confirm that ivermectin can exert antibacterial off-target effects in the human gut beyond those previously observed in vitro. Given its central role in parasite control, its broader microbiome effects warrant careful evaluation in future treatment strategies.