Baobab Index

Species' traits and environmental conditions determine the abundance of tree species across the globe. The extent to which traits of dominant and rare tree species differ remains untested across a broad environmental range, limiting our understanding of how species traits and the environment shape forest functional composition. We use a global dataset of tree composition of >22,000 forest plots and 11 traits of 1663 tree species to ask how locally dominant and rare species differ in their trait values, and how these differences are driven by climatic gradients in temperature and water availability in forest biomes across the globe. We find three consistent trait differences between locally dominant and rare species across all biomes; dominant species are taller, have softer wood and higher loading on the multivariate stem strategy axis (related to narrow tracheids and thick bark). The difference between traits of dominant and rare species is more strongly driven by temperature compared to water availability, as temperature might affect a larger number of traits. Therefore, climate change driven global temperature rise may have a strong effect on trait differences between dominant and rare tree species and may lead to changes in species abundances and therefore strong community reassembly.

Genomic analysis of parasites can deepen our understanding of their transmission, population structure, and important biological characteristics. Onchocerciasis (river blindness), caused by the parasitic nematode Onchocerca volvulus, involves adult worms residing in subcutaneous nodules that produce larval-stage microfilariae (mf), which are routinely detected in the skin for diagnosis. Whole-genome studies of mf are limited; most analyses have focused on the mitochondrial genome. We conducted a genome-wide analysis with 94% median nuclear genome coverage, analyzing 171, 37, and 98 mf from 16, 3, and 5 individuals from Ghana, Liberia, and the Democratic Republic of Congo, respectively. These data were used to investigate population differentiation, estimate the number of reproductive adult worms, and analyze genetic variation across chromosomes. Population genetic analyses across hosts and countries showed that nuclear genome diversity can reveal fine-scale genetic structure, even between geographically close countries, providing more resolution than mitochondrial haplotype data. By reconstructing maternal and paternal sibships, we estimated the number of reproductively active adult filariae. Comparisons between adult worm estimates from genetic data and nodule observations showed that genetics-based estimates were higher or equal to observed worm counts in 8 out of 9 hosts for female worms and 7 out of 9 hosts for male worms. Our analysis also revealed lower-than-expected X chromosome diversity, consistent with neo-X chromosome fusions in filarial species. This study represents an important step in using nuclear genome data from mf to support onchocerciasis elimination efforts and in developing genetic tools that could inform mass drug administration programs.

Mangroves are vital for climate change adaptation and mitigation due to their efficient carbon sequestration and coastal protection roles providing often untapped opportunities for countries to enhance their national climate commitments (including the so-called Nationally Determined Contributions) under the Paris Agreement adopted at the United Nations Framework Convention on Climate Change (UNFCCC) COP21 in 2015. In Africa, several countries possess mangroves and have signed the Paris Agreement, however, the level of integration of mangrove actions into the Nationally Determined Contributions (NDCs) has not been adequately explored. Using a systematic review methodology, 33 African countries possessing mangroves were selected and their NDCs were reviewed, scored, and ranked to assess their level of integration of mangrove ecosystems into their NDCs. Countries like Equatorial Guinea, Nigeria, Senegal, and Sudan demonstrate commendable progress and leadership in integrating mangroves within their NDCs. However, gaps in budgetary commitments, spatial planning, and temporal specificity for mangrove actions among a majority of the countries hinder broader mangrove inclusion. The study also revealed a disconnect between research outputs and policy frameworks, where countries with increased mangrove research output in Africa failed to integrate mangrove actions into their NDCs. To increase African countries' resilience to climate risks and contributions to global climate goals, there is a need to increase effective collaboration between mangrove researchers, local communities, and policymakers in mangrove-possessing countries. This will bolster public education on mangroves and their inclusion of mangrove actions in their NDCs, ultimately enhancing the implementation of mangrove actions on the ground.

The John Dory Zeus faber is a commercially exploited demersal fish species with a known distribution ranging from the Northeast Atlantic to parts of the Indian and Pacific oceans. A previous genetic survey using cytochrome c oxidase subunit I (COI) DNA barcodes suggested the presence of two geographically segregated taxonomic units within Z. faber. We revisit this hypothesis by expanding the number and geographic coverage of DNA barcodes, addressing a major data gap along parts of the Atlantic coast of Africa and conducting a comprehensive phylogeographic analysis. Our findings consolidated the existence of two highly divergent mitochondrial clades, Clade A and Clade B (mean K2P distance: 7.4%), with the transition zone between them located along the Atlantic coast of Morocco. Clade A exhibited no phylogeographic structure, with haplotypes shared between Northeast Atlantic and Mediterranean populations. Conversely, four geographically structured subclades (mean K2P distance: 0.9%) were detected within Clade B, extending south and eastward from Morocco to Japan and New Zealand. Historical demographic events driving allopatric divergence, along with oceanographic and environmental factors, likely shaped the current geographic distribution of the two clades. These findings not only prompt the need to re-evaluate the taxonomic status of Z. faber but also highlight the probable existence of multiple evolutionarily significant units (ESUs) that must be considered in the scope of stock assessment, fisheries management and conservation purposes.

Liberia (West Africa) has an extensive (co)burden of urogenital and intestinal schistosomiasis; each largely restricted to more inland areas. Where urogenital schistosomiasis is endemic, as both disease surveillance and case management are nascent, many women may unknowingly be living with Female Genital Schistosomiasis (FGS). Using a recently developed FGS score card, we appraised FGS score card valuations with point-of-care gynaecological and molecular parasitological evaluations as undertaken within typical primary care settings of four Liberian counties. A total of 400 women, 100 participants from each of four endemic inland counties, underwent a cursory gynaecological examination using a speculum for visible FGS lesions, undertaken by a midwife, and provided a urine sample that was examined by centrifugation with microscopy for Schistosoma ova. Urine-sediments in ethanol were later analysed with a high-resolution melt (HRM) real-time (rt) PCR assay to screen for Schistosoma genetic markers. Using a combination of clinical and parasitological information, overall prevalence of UGS and FGS was <10% and a single case of putative FGS-associated co-infection with Schistosoma mansoni was observed. Participant interviews with the FGS score cards provided an insight into at-risk lifestyle and environmental factors, e.g. women who fished regularly were more likely to present with FGS whereas those who lived > 15 km from a local river were less likely to present with FGS. In this resource-poor setting of Liberia, active surveillance for FGS with either clinical or parasitological methods remains challenging such that sole future use of the FGS score card is most pragmatic for primary care.

Flooding is a dominant constraint to rice production in lowland and floodplain ecosystems, where stress intensity, timing, and duration vary widely across agroecological zones. This review synthesizes current knowledge on flooding typologies affecting rice, including anaerobic germination failure, flash flooding, stagnant flooding, and deep-water submergence, and critically examines how rice plants respond at physiological, anatomical, and molecular levels. We integrate evidence on key adaptive mechanisms, including anaerobic metabolism during germination, SUB1-mediated quiescence under short-term submergence, SNORKEL-driven internode elongation in deep-water environments, aerenchyma development, leaf gas films, and antioxidant defense systems. Particular emphasis is placed on the genetic architecture underpinning these responses, highlighting the successes and limitations of the SUB1 locus and the necessity of multitrait pyramiding to address prolonged, deep, or sequential flooding events. Drawing on case studies from Africa and Asia, the review demonstrates that flooding impacts are strongly context-specific, shaped by rainfall variability, hydrology, soil properties, and water management infrastructure, with disproportionate socioeconomic consequences for smallholder farmers. We argue that reliance on single-gene solutions is insufficient under climate change scenarios that intensify flood unpredictability. Instead, resilient rice systems require an integrated strategy combining stress-tolerant varieties, adaptive crop and nutrient management, and climate-informed decision-making. By consolidating physiological insights, breeding advances, and regional flood dynamics, this review provides a targeted framework for developing rice varieties and management options tailored to diverse flooding regimes, with direct implications for food security in flood-prone regions.

DNA barcoding for timber species identification requires comprehensive reference datasets, informative DNA barcodes, and cost-effective protocols. We developed a workflow leveraging Hyb-Seq (target capture sequencing and genome skimming) to address these challenges, and we tested it on four genera from the mahogany family (Meliaceae). We sequenced up to 350 nuclear and 177 plastid loci from 132 herbarium specimens representing leaf samples of 22 species. We determined the DNA barcoding potential of each locus by looking at species recovery and monophyly in gene trees. We then selected 13 short regions (candidate barcodes) within high-potential loci and tested their PCR amplification and Sanger sequencing on wood DNA. Three candidate barcodes emerged as the most reliably sequenced from wood DNA and as providing the most accurate species-level identifications, with species monophyly rates above 80%. Failure to obtain sequences from some wood DNA extracts was more often associated with potential DNA impurity (as inferred from DNA color) than with DNA degradation. Our reference data and candidate barcodes provide a foundation to support the DNA barcoding of mahogany and its relatives. Our workflow illustrates how the wealth of Hyb-Seq data currently generated from global herbaria may be leveraged to monitor plant diversity.

Yellow fever virus (YFV), a mosquito-borne orthoflavivirus that causes severe hemorrhagic disease, is endemic in parts of South America and Africa, yet genomic data from Sierra Leone is lacking despite ongoing case-based surveillance. Using hybrid-capture metagenomic sequencing, we generated a complete 10,611 nt YFV genome (98% coverage) from an adult male patient who reported to the Kailahun Government Hospital with fever and muscle pain. Phylogenetic analysis assigned the genome to the West African II genotype via the YFV Nextstrain build. The Sierra Leone genome showed 57 substitutions, three of which were non-synonymous (NS2B: N79S, NS3: V515I, and NS5 (RdRp domain): A643V), relative to its most recent common ancestor with other genomes from Senegal and the Netherlands. Bayesian phylogenetics estimated the time to the most recent common ancestor with these genomes as January 14, 2001 (95% HPD: December 17, 1987 - April 28, 2009), potentially indicative of long-standing transmission within West Africa that has not been genomically characterized, rather than specific localization to Sierra Leone. Together, these findings underscore the need for expanded genomic surveillance to monitor YFV spread and evolution.

The 2023 iteration of the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) estimated prevalence, incidence, and health burden for 375 diseases and injuries, including 12 mental disorders. We assess past, current, and emerging trends in the prevalence and burden of mental disorders across sexes and age groups, for 21 regions, 204 countries and territories, and by Socio-demographic Index (SDI) quintile, from 1990 to 2023. Mental disorders included in GBD 2023 were anxiety disorders, major depressive disorder, dysthymia, bipolar disorder, schizophrenia, autism spectrum disorders, conduct disorder, attention-deficit hyperactivity disorder, anorexia nervosa, bulimia nervosa, idiopathic developmental intellectual disability, and a residual category of other mental disorders. A literature review identified epidemiological data for each disorder. These were analysed via a Bayesian meta-regression to estimate prevalence by disorder, sex, age, location, and year. Disorder-specific prevalence was multiplied by disability weights representing the severity of health loss associated with each disorder to estimate years lived with disability (YLDs). Deaths due to anorexia nervosa were assessed with a Cause of Death Ensemble modelling strategy to estimate deaths by sex, age, location, and year, and then multiplied by the standard life expectancy at age of death to estimate years of life lost (YLLs). YLDs equalled disability-adjusted life-years (DALYs) for all mental disorders except anorexia nervosa (the only mental disorder considered as an underlying cause of death in GBD), for which DALYs represented the sum of YLDs and YLLs. We presented prevalence, deaths, YLDs, YLLs, and DALYs as counts, age-specific rates per 100 000 population, and age-standardised rates per 100 000 population. We estimated 1·17 billion (95% uncertainty interval 1·06-1·31) prevalent cases of mental disorders globally in 2023, equivalent to an age-standardised prevalence rate of 14 210·7 cases (12 849·5-15 940·1) per 100 000 population. These estimates represented a 95·5% (75·0-121·2) increase in prevalent cases and 24·2% (11·4-41·4) increase in age-standardised prevalence rate between 1990 and 2023. All mental disorders showed increases in prevalent cases between 1990 and 2023, while notable increases were seen in age-standardised prevalence rates for anxiety disorders, major depressive disorder, dysthymia, anorexia nervosa, bulimia nervosa, schizophrenia, and conduct disorder. There were an estimated 171 million (127-228) DALYs due to mental disorders globally across sex and age in 2023, equivalent to an age-standardised DALY rate of 2070·5 DALYs (1519·1-2750·5) per 100 000 population. Mental disorders contributed to 6·1% (4·8-7·6) of all-cause DALYs in 2023, making them the fifth leading cause of global DALYs (up from 12th in 1990). DALYs were almost entirely composed of YLDs. Mental disorders were the leading cause of YLDs in 2023 (up from second in 1990), explaining 17·3% (14·8-20·6) of all-cause global YLDs. Leading causes of mental disorder DALYs were anxiety disorders (ranked 11th among the 304 diseases and injuries at Level 4 of the GBD cause hierarchy), major depressive disorder (15th), and schizophrenia (41st). Globally in 2023, mental disorder age-standardised DALY rates were higher among females (2239·6 [1643·7-3014·1] per 100 000) than among males (1900·2 [1399·8-2510·8] per 100 000), and peaked in the 15-19 years age group (2617·3 [1850·6-3696·8] per 100 000). All locations showed increased mental disorder DALY rates in 2023 compared with 1990, ranging across countries and territories from 1302·4 (952·7-1683·7) per 100 000 in Viet Nam to 3555·8 (2661·9-4715·0) per 100 000 in the Netherlands. Across SDI quintiles, DALY rates ranged from 1853·0 (1352·1-2469·3) per 100 000 for middle SDI to 2184·1 (1606·1-2890·3) per 100 000 for high SDI. A significant health burden was imposed by mental disorders in all countries and territories in 2023, irrespective of the health resources available. In some instances, this burden has increased over time and is unevenly distributed across populations. Stronger surveillance systems, particularly in low-income and middle-income countries, are required. Additionally, we need more coordinated and inclusive policies to reduce the burden through early treatment and prevention, tailored to sex and age differences across locations. Responding to the mental health needs of our global population, especially those most vulnerable, is an obligation, not a choice. Gates Foundation, Queensland Health, and University of Queensland.