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Severe/critical Coronavirus Virus Disease 2019 (COVID-19) patients face increased risk of pulmonary embolism (PE) and other thromboembolic events. This risk exists even in patients who are on prophylactic and therapeutic doses of anticoagulant. We present three cases of Severe/critical COVID-19 patients who developed PE despite being placed on prophylactic doses of anticoagulants. Clinicians should be keenly aware of this and urgently institute appropriate diagnostic measures if PE is suspected

Tropical forests store 40–50 per cent of terrestrial vegetation carbon 1. However, spatial variations in aboveground live tree biomass carbon (AGC) stocks remain poorly understood, in particular in tropical montane forests 2. Owing to climatic and soil changes with increasing elevation 3, AGC stocks are lower in tropical montane forests compared with lowland forests 2. Here we assemble and analyse a dataset of structurally intact old-growth forests (AfriMont) spanning 44 montane sites in 12 African countries. We find that montane sites in the AfriMont plot network have a mean AGC stock of 149.4 megagrams of carbon per hectare (95% confidence interval 137.1–164.2), which is comparable to lowland forests in the African Tropical Rainforest Observation Network 4 and about 70 per cent and 32 per cent higher than averages from plot networks in montane 2,5,6 and lowland 7 forests in the Neotropics, respectively. Notably, our results are two-thirds higher than the Intergovernmental Panel on Climate Change default values for these forests in Africa 8. We find that the low stem density and high abundance of large trees of African lowland forests4 is mirrored in the montane forests sampled. This carbon store is endangered: we estimate that 0.8 million hectares of old-growth African montane forest have been lost since 2000. We provide country-specific montane forest AGC stock estimates modelled from our plot network to help to guide forest conservation and reforestation interventions. Our findings highlight the need for conserving these biodiverse 9,10 and carbon-rich ecosystems.

Paleo-environmental data show that the distribution of African rain forests was affected by Quaternary climate changes. In particular, the Dahomey Gap (DG) - a 200 km wide savanna corridor currently separating the West African and Central African rain forest blocks and containing relict rain forest fragments - was forested during the mid-Holocene and possibly during previous interglacial periods, whereas it was dominated by open vege-tation (savanna) during glacial periods. Genetic signatures of past population fragmentation and demographic changes have been found in some African forest plant species using nuclear markers, but such events appear not to have been synchronous or shared across species. To better understand the colonization history of the DG by rain forest trees through seed dispersal, the plastid genomes of two widespread African forest legume trees, Anthonotha macrophylla and Distemonanthus benthamianus, were sequenced in 47 individuals for each species, providing unprecedented phylogenetic resolution of their maternal lineages (857 and 115 SNPs, respectively). Both species exhibit distinct lineages separating three regions: 1. Upper Guinea (UG, i.e. the West African forest block), 2. the area ranging from the DG to the Cameroon volcanic line (CVL), and 3. Lower Guinea (LG, the western part of the Central African forest block) where three lineages co-occur. In both species, the DG popu-lations (including southern Nigeria west of Cross River) exhibit much lower genetic diversity than UG and LG populations, and their plastid lineages originate from the CVL, confirming the role of the CVL as an ancient forest refuge. Despite the similar phylogeographic structures displayed by A. macrophylla and D. benthamianus, mo-lecular dating indicates very contrasting ages of lineage divergence (UG diverged from LG since c. 7 Ma and 0.7 Ma, respectively) and DG colonization (probably following the Mid Pleistocene Transition and the Last Glacial Maximum, respectively). The stability of forest refuge areas and repeated similar forest shrinking/ex-panding events during successive glacial periods might explain why similar phylogeographic patterns can be generated over contrasting timescales.

Premise Few studies have addressed the evolutionary history of tree species from African savannahs. Afzelia contains economically important timber species, including two species widely distributed in African savannahs: A. africana in the Sudanian region and A. quanzensis in the Zambezian region. We aimed to infer whether these species underwent range fragmentation and/or demographic changes, possibly reflecting how savannahs responded to Quaternary climate changes. Methods We characterized the genetic diversity and structure of these species across their distribution ranges using nuclear microsatellites (SSRs) and genotyping-by-sequencing (GBS) markers. Six SSR loci were genotyped in 241 A. africana and 113 A. quanzensis individuals, while 2800 high-quality single nucleotide polymorphisms (SNPs) were identified in 30 A. africana individuals. Results Both species appeared to be mainly outcrossing. The kinship between individuals decayed with the logarithm of the distance at similar rates across species and markers, leading to relatively small Sp statistics (0.0056 for SSR and 0.0054 for SNP in A. africana, 0.0075 for SSR in A. quanzensis). The patterns were consistent with isolation by distance expectations in the absence of large-scale geographic gradients. Bayesian clustering of SSR genotypes did not detect genetic clusters within species. In contrast, SNP data resolved intraspecific genetic clusters in A. africana, illustrating the higher resolving power of GBS. However, these clusters revealed low levels of differentiation and no clear geographical entities, so that they were interpreted as resulting from the isolation by distance pattern rather than from past population fragmentation. Conclusions These results suggest that populations have remained connected throughout the large, continuous savannah landscapes. The absence of clear phylogeographic discontinuities, also found in a few other African savannah trees, indicates that their distribution ranges have not been significantly fragmented during the climatic oscillations of the Pleistocene, in contrast to patterns commonly found in African rainforest trees.

Aim: The Guineo‐Congolian region in Africa constitutes the second largest area of tropical rainforest (TRF) in the world. It covered an estimated 15–22 million km² during the late Miocene (55–11 Ma) and it has experienced since a declining trend, currently reaching 3.4 million km², associated with increasing aridification and the replacement of TRF by savanna habitats. Here, we examine whether rainforest area contraction led to a decrease in net diversification rates linked to increasing extinction, or if it is associated with increasing opportunities for allopatric or ecological speciation during periods of forest fragmentation. Location: Tropical Africa, Guineo‐Congolian region. Taxon: Anthonotha, Englerodendron, Berlinia clade (Leguminosae). Methods: We used a target enrichment approach combined with a complete data set representing all genera within the Berlinia clade. We combined phylogenomic, dating estimates, habitat reconstruction and diversification rate analyses to infer the effect of change in rainforest area coverage at two taxonomic levels: among genera, and within Anthonotha and Englerodendron. Results: We recovered fully resolved and well‐supported relationships among all genera and among species within the two genera. Most genera (87.5%) diverged before the Pleistocene, but Anthonotha and Englerodendron diversified recently, during the most recent cycles of forest contraction and expansion of the Pleistocene. Main conclusions: Our results suggest that the Berlinia clade displays an overall trend of accumulation of species over evolutionary time, suggesting the reduction in TRF area has not decreased net diversification rates. Most habitat shifts to savanna occurred in the Miocene, with no major habitat shifts during the most recent phases of forest expansion–contraction in the Pleistocene. Shifts in habitat from lowland forest to savanna did not trigger diversification rates, but habitat fragmentation might have increased diversification rates through allopatric speciation.

To highlight plant adaptive traits, we have observed the metabolome from leaves of wild type tropical Erythrophleum genus that includes the set of particular metabolites present in an organ at a certain time. To answer those ecological questions, genetic approaches as neutral genetic markers (like microsatellites) are usually used to evaluate how evolutionary forces interact to shape phenotypic variations observed among natural populations. As metabolites are the result of a complex network of gene expression, protein expression and interactions and other regulatory processes, they are therefore closer to the phenotype than transcriptome or proteome. Secondary metabolites resulting from specific biosynthetic pathways possess characteristic structural features depending on the specific allelic forms of enzymes involved in their biosynthesis. One example of such phylogenetic signature is found in the Erythrophleum (Fabaceae, Caesalpinioideae) which contains original cassane diterpenes, restricted to various Fabaceae genera. We have studied two species with various geographical origins: (i) E. Ivorense that grows in the rainforests of Guinea, Gabon and Congo, forming wide stands; and (ii) E. Suaveolens that grows in mountainous semi-humid areas and is found in the Guinean savannah, on the strip of land that runs from Gambia in the northwest to Kenya in the east, and from Mozambique in the southeast to the People’s Republic of the Congo in the southwest. For this study, all individuals were cultivated and collected in a common garden in Cameroun. After a metabolomic exploration by LC-HRMS and multi-block correlation of genotype with metabolome &[DT1] for the exploration of the phenotype based on the metabolome, we have developed a molecular networking dereplication pipeline based on MS/MS focusing on cassane diterpenes family. For molecular network construction the user-friendly Metgem software has been used. Principal results of dereplication will be presented. [DT1]???, Pour mettre en évidence les caractères d’adaptation des plantes, nous avons observé le métabolome de feuilles du genre Erythrophleum tropical de type sauvage comprenant l’ensemble des métabolites particuliers présents dans un organe à un moment donné. Pour répondre à ces questions écologiques, des approches génétiques en tant que marqueurs génétiques neutres (tels que les microsatellites) sont généralement utilisées pour évaluer la manière dont les forces évolutives interagissent pour façonner les variations phénotypiques observées au sein de populations naturelles. Les métabolites étant le résultat d’un réseau complexe d’expression génique, d’expression de protéines, d’interactions et de processus de régulation, ils sont donc plus proches du phénotype que le transcriptome ou le protéome. Les métabolites secondaires résultant de voies de biosynthèse spécifiques possèdent des caractéristiques structurelles caractéristiques en fonction des formes alléliques spécifiques des enzymes impliquées dans leur biosynthèse. Un exemple de cette signature phylogénétique se trouve dans l'Erythrophleum (Fabaceae, Caesalpinioideae) qui contient des diterpènes de cassane originaux, limités à divers genres de Fabaceae. Nous avons étudié deux espèces aux origines géographiques variées: (i) E. Ivorense qui pousse dans les forêts tropicales humides de Guinée, du Gabon et du Congo, formant de larges peuplements; et (ii) E. Suaveolens qui pousse dans les zones montagneuses semi-humides et se trouve dans la savane guinéenne, sur la bande de terre allant de la Gambie au nord-ouest au Kenya à l'est et du Mozambique au sud-est au peuple. République du Congo au sud-ouest. Pour cette étude, tous les individus ont été cultivés et rassemblés dans un jardin commun au Cameroun. Après une exploration métabolomique par LC-HRMS et une corrélation multi-blocs du génotype avec le métabolome et pour l'exploration du phénotype basé sur le métabolome, nous avons développé un pipeline de déréplication en réseaux moléculaires basé sur MS / MS et centré sur la famille des diterpènes de cassane. Le logiciel convivial Metgem a été utilisé pour la construction de réseaux moléculaires. Les principaux résultats de la déréplication seront présentés.

Aim Palaeoecological records indicate that Pleistocene glaciations affected the African rain forest, probably causing its fragmentation, which could explain phylogeographical breaks documented in many tree species. This refuge hypothesis was further tested through species distribution models, hindcasting persistence during the Last Glacial Maximum. However, previous studies failed to estimate with sufficient precision the divergence time between phylogeographical entities to confirm their Pleistocene origin. Developing genomic tools on a representative tree of mature rain forests, we test if parapatric genetic clusters documented in widespread tree species can be interpreted as the legacy of past population fragmentation during the last glacial period(s). Location Tropical Africa, Guineo-Congolian forests. Taxon Greenwayodendron (Annonaceae). Methods To further test the Pleistocene refuge hypothesis by molecular dating, we sequenced the plastome of 145 individuals of the shade-tolerant rain forest tree Greenwayodendron suaveolens and congeneric species, and genotyped the same samples using nuclear microsatellites to identify genetic clusters. Results Five plastid phylogroups of G. suaveolens occur in parapatry throughout Central Africa, following a spatial pattern generally congruent with genetic clusters. Four of them diverged 3.5-4.5 Ma, whereas the fifth one, located in the Cameroon volcanic line (CVL), diverged 8.3 Ma, in the range of divergence times between Greenwayodendron species, highlighting the key role of the CVL in hosting ancient lineages. Within phylogroups, most nodes were dated from 0.9 to 3.2 Myr and a correlation between haplotype divergence and spatial distance was still perceptible, indicating a slow population dynamic. Main conclusions The phylogeographical structures of Central African trees probably established during the Pliocene or early Pleistocene, and while they might have been reinforced during subsequent glacial-interglacial cycles, interglacial phases did not lead to genetic homogenization. Therefore, interpreting phylogeographical patterns of African trees must account for a much deeper past than previously assumed, and cannot be limited to the last glacial period.

Determining where species diversify (cradles) and persist (museums) over evolutionary time is fundamental to understanding the distribution of biodiversity and for conservation prioritization. Here, we identify cradles and museums of angiosperm generic diversity across tropical Africa, one of the most biodiverse regions on Earth. Regions containing nonrandom concentrations of young (neo-) and old (paleo-) endemic taxa were identified using distribution data of 1719 genera combined with a newly generated time-calibrated mega-phylogenetic tree. We then compared the identified regions with the current network of African protected areas (PAs). At the generic level, phylogenetic diversity and endemism are mainly concentrated in the biogeographically complex region of Eastern Africa. We show that mountainous areas are centres of both neo- and paleo-endemism. By contrast, the Guineo-Congolian lowland rain forest region is characterized by widespread and old lineages. We found that the overlap between centres of phylogenetic endemism and PAs is high (> 85%). We show the vital role played by mountains acting simultaneously as cradles and museums of tropical African plant biodiversity. By contrast, lowland rainforests act mainly as museums for generic diversity. Our study shows that incorporating large-scale taxonomically verified distribution datasets and mega-phylogenies lead to an improved understanding of tropical plant biodiversity evolution.

Combining genetic and morphological markers is a powerful approach for species delimitation, much needed in tropical species complexes. Greenwayodendron (Annonaceae) is a widespread genus of trees distributed from West to East African rainforests. Two species and four infra-specific taxa are currently recognized. However, preliminary genetic studies and morphological observations suggested the occurrence of additional species, undescribed to date. We tested species delimitation within Greenwayodendron by combining morphological and population genetics data. First, a visual inspection of about a thousand specimens suggested the existence of seven morphogroups: four of them occur in Central Africa and overlap in Gabon while three others are allopatric, occurring respectively in West Africa, East Africa, and the islands of Sao Tome and Principe. Their morphological differentiation was confirmed by analysis of 27 morphological characters coded from 233 herbarium specimens. Second, after genotyping 800 samples at eight nuclear microsatellites, Bayesian clustering analyses (STRUCTURE) identified four genetic clusters corresponding to the well-sampled morphogroups but failed to separate the three remaining morphogroups represented by few samples. However, we show that this is an inherent limit of the STRUCTURE algorithm, whereas factorial correspondence analysis (FCA) and pairwise F-ST and R-ST measures confirmed the genetic differentiation of all morphogroups. We considered that a clear genetic differentiation occurring between sympatric populations advocates for recognizing distinct species following the biological species concept. Our analyses highlight that the current taxonomic treatment of Greenwayodendron underestimates the total number of species. We identified two new species and support separation at the rank of species of two varieties (G. suaveolens subsp. suaveolens var. gabonica, G. suaveolens subsp. suaveolens var. suaveolens) and one subspecies (G. suaveolens subsp. usambaricum). The taxonomic status of specimens collected in Sao Tome and Principe remains inconclusive, partly due to the limited fertile material available. Our study highlights the strength of combining morphological and population genetics data for discovering new taxa. Guidelines for using genetic clustering approaches in species delimitation are provided.

Interpreting morphological variability in terms of species delimitation can be challenging. However, correcting species delineation can have strong implications for the sustainable management of exploited species. Up to now, species delimitation between two putative timber species from African forests, Entandrophragma congoense and E. angolense, remained unclear. To investigate their differences, we applied an integrated approach which combines morphological traits and genetic markers. We defined 13 morphological characters from 81 herbarium specimens and developed 15 new polymorphic microsatellite markers to genotype 305 samples (herbarium samples and specimens collected in the field across the species distribution ranges). Principal component analysis (PCA) of morphological data and the Bayesian clustering analyses of genetic data were used to assess differentiation between putative species. These analyses support two well-differentiated groups (F (ST) = 0.30) occurring locally in sympatry. Moreover, these two groups present distinct morphological characters at the level of the trunk, leaflets, and seeds. Our genetic markers identified few individuals (4%) that seem to be hybrids, though there is no evidence of genetic introgression from geographic patterns of genetic variation. Hence, our results provide clear support to recognize E. congoense as a species distinct from E. angolense, with a much lower genetic diversity than the latter, and that should be managed accordingly. This work highlights the power of microsatellite markers in resolving species boundaries.

Pollen and seed dispersal are key processes affecting the demographic and evolutionary dynamics of plant species and are also important considerations for the sustainable management of timber trees. Through direct and indirect genetic analyses, we studied the mating system and the extent of pollen and seed dispersal in an economically important timber species, Entandrophragma cylindricum (Meliaceae). We genotyped adult trees, seeds and saplings from a 400-ha study plot in a natural forest from East Cameroon using eight nuclear microsatellite markers. The species is mainly outcrossed (t=0.92), but seeds from the same fruit are often pollinated by the same father (correlated paternity, r(p)=0.77). An average of 4.76 effective pollen donors (N-ep) per seed tree contributes to the pollination. Seed dispersal was as extensive as pollen dispersal, with a mean dispersal distance in the study plot approaching 600m, and immigration rates from outside the plot to the central part of the plot reaching 40% for both pollen and seeds. Extensive pollen- and seed-mediated gene flow is further supported by the weak, fine-scale spatial genetic structure (Sp statistic=0.0058), corresponding to historical gene dispersal distances (sigma(g)) reaching approximately 1,500m. Using an original approach, we showed that the relatedness between mating individuals (F-ij=0.06) was higher than expected by chance, given the extent of pollen dispersal distances (expected F-ij=0.02 according to simulations). This remarkable pattern of assortative mating could be a phenomenon of potentially consequential evolutionary and management significance that deserves to be studied in other plant populations.

Background and aims - There is increasing recognition that plant traits mediate environmental influence on species distribution, justifying non-random community assembly. We studied the influence of local scale edaphic factors on the distribution of functional traits in a tropical rainforest of Cameroon with the aim to find correlations between the main edaphic gradient and community functional trait metrics (weighted mean trait, functional divergence and intraspecific variation). Methods - Within the Korup Forest Dynamics Plot (50 ha), we randomly selected 44 quadrats of 0.04 ha each, collected soils and analysed 11 topography and soil variables. Leaves were harvested from all 98 tree species found in the quadrats to calculate community trait metrics [quadrat-level weighted mean (q(k)) and functional divergence (FDiv(k))] for leaf area (LA), specific leaf area (SLA), leaf phosphorus (LPC), leaf nitrogen concentration (LNC) and nitrogen to phosphorus ratio (N:P ratio). We examined relationships between the main edaphic gradient with q(k), with FDiv(k) and with intraspecific variation and interpreted correlations as the effects of abiotic filtering and competitive interaction. Key results - Soil fertility was the main edaphic gradient and was significantly correlated with q(k) for LPC, LNC and LA and with FDiv(k) for LPC, N: P ratio, LA and SLA, confirming the influence of abiotic filtering and competitive interaction by the soil fertility gradient, respectively. For a given trait, quadrats were either over-dispersed or under-dispersed, accounting for 7-33 % of non-random trait distribution along the soil fertility gradient. Trends in intraspecific traits variation were consistently lower than quadrat-level mean traits along the soil fertility gradient. Conclusions - This study demonstrates the influence of soil fertility gradient on local scale community trait distribution and its contribution to non-random community assembly.

Polyploidy has rarely been documented in rain forest trees but it has recently been found in African species of the genus Afzelia (Leguminosae), which is composed of four tetraploid rain forest species and two diploid dry forest species. The genus Afzelia thus provides an opportunity to examine how and when polyploidy and habitat shift occurred in Africa, and whether they are associated. In this study, we combined three plastid markers (psbA, trnL, ndhF), two nuclear markers (ribosomal ITS and the single-copy PEPC E7 gene), plastomes (obtained by High Throughput Sequencing) and morphological traits, with an extensive taxonomic and geographic sampling to explore the evolutionary history of Afzelia. Both nuclear DNA and morphological vegetative characters separated diploid from tetraploid lineages. Although the two African diploid species were well differentiated genetically and morphologically, the relationships among the tetraploid species were not resolved. In contrast to the nuclear markers, plastid markers revealed that one of the diploid species forms a well-supported Glade with the tetraploids, suggesting historical hybridisation, possibly in relation with genome duplication (polyploidization) and habitat shift from dry to rain forests. Molecular dating based on fossil-anchored gene phylogenies indicates that extant Afzelia started diverging c. 14.5 or 20 Ma while extant tetraploid species started diverging c. 7.0 or 9.4 Ma according to plastid and nuclear DNA, respectively. Additional studies of tropical polyploid plants are needed to assess whether the ploidy-habitat association observed in African Afzelia would reflect a role of polyploidization in niche divergence in the tropics.

Greenwayodendron is a genus of rainforest trees endemic to tropical Africa. Eight nuclear microsatellite loci, amplifiable in two multiplexed reactions, were developed in G. suaveolens and cross-amplified in the second species of the genus, G. oliveri, as well as in all subspecies and varieties recognised by current taxonomic treatments. Characterisation of the microsatellite markers in one population of G. suaveolens from Cameroon revealed polymorphism levels suitable for characterisation of the spatial genetic variation (7 to 16 alleles per locus and expected heterozygosity ranging from 0.57 to 0.89). The eight microsatellite loci optimised could help estimate genetic diversity levels in populations of G. suaveolens, G. oliveri and new local endemic species of Greenwayodendron in rainforests from western and central Africa., SCOPUS: ar.j, info:eu-repo/semantics/published

Angraecum, the largest genus of the angraecoid orchids, has long been regarded as a natural group possessing a common overall floral morphology, although recent molecular studies have called into question its monophyly. No recent taxonomic revision is available for the genus or its sections, and previous studies (whether based on morphology or DNA sequences) have suffered from a paucity of material from continental Africa. An earlier study suggested that the section Pectinaria was polyphyletic, with one clade, containing the type species, centered in Madagascar and the other in continental Africa. Our recent morphometric and molecular study confirmed the polyphyly of this section, clarified the circumscription of its continental African species, and assessed their monophyly. Here we present a comprehensive taxonomic revision of the five continental African members of Angraecum section Pectinaria, including an identification key, distribution maps, and an assessment of their conservation status (two are threatened, one could become threatened in the near future, and two do not meet the criteria for threatened status). Species richness is highest in Atlantic Central Africa, and A. gabonense is reported for the first time from Equatorial Guinea. Lectotypffications are made for A. pungens, A. subulatum and its synonym, A. canaliculatiem.

1. Niche theory proposes that species differences underlie both coexistence within communities and the differentiation in species composition among communities via limiting similarity and environmental filtering. However, it has been difficult to extend niche theory to species-rich communities because of the empirical challenge of quantifying niches for many species. This has motivated the development of functional and phylogeny-based approaches in community ecology, which represent two different means of approximating niche attributes. 2. Here, we assess the utility of plant functional traits and phylogenetic relationships in predicting community assembly processes using the largest trait and phylogenetic data base to date for any set of species-rich communities. 3. We measured 17 functional traits for all 4672 individuals of 668 tree species co-occurring in nine tropical rain forest plots in French Guiana. Trait variation was summarized into two ordination axes that reflect species niche overlap. 4. We also generated a dated molecular phylogenetic tree based on DNA sequencing of two plastid loci (rbcL and matK) comprising 97% of the individuals and 91% of the species in the plots. 5. We found that, on average, co-occurring species had greater functional and, to a lesser extent, phylogenetic similarity than expected by chance. 6. We also found that functional traits and their ordination loadings showed significant, albeit weak, phylogenetic signal, suggesting that phylogenetic distance provides pertinent information on niche overlap in tropical tree communities. 7. Synthesis. We provide the most comprehensive examination to date of the relative importance of environmental filtering and limiting similarity in structuring tropical tree communities. Our results confirm that environmental filtering is the overriding influence on community assembly in these species-rich systems.