Search

Aim: How spatial, historical and ecological processes drive diversity patterns remains one of the main foci of island biogeography. We determined how beta diversity varies across spatial scales and among organisms, disentangled the drivers of this variation, and examined how, consequently, biogeographic affinities within and among archipelagos vary among land plants., J.P. is funded by the Ministerio de Ciencia e Innovación (MICINN) through the Ramón y Cajal program (RYC-2016-20506) and the grant (ASTERALIEN -PID2019-110538GA-I00) and by the Fundación BBVA (INVASION -PR19_ECO_0046). OH and AV are research director of the Belgian Funds for Scientific Research (FRS-FNRS). No permits were needed to perform this study.

Influence de l’ecartement et du semencier sur la croissance des plants de Pericopsis elata durant les vingt premiers mois d’un essai de plantation Description du sujet. Pericopsis elata (Fabaceae) est un arbre heliophile des forets tropicales africaines qui produit du bois de grande valeur economique. Ses populations naturelles souffrent de surexploitation et presentent un deficit de regeneration naturelle. Les plantations pourraient augmenter sa production et limiter la pression sur les forets naturelles. Cependant, les connaissances sur l'influence de l'ecartement et du semencier sur la croissance des arbres font encore defaut pour les protocoles de plantation. Objectifs. Cette etude evalue l'influence de la densite de plantation et du semencier sur les croissances en diametre et en hauteur des plants de P. elata, 20 mois apres la plantation. Methode. Les graines ont ete collectees sur 19 semenciers dans un peuplement naturel de 400 ha pres de Kisangani (RDC). En octobre 2017, les plantules ont ete transplantees dans une plantation suivant le dispositif de Nelder en trois repetitions, pour comparer la croissance de 540 plants en plein decouvert suivant 10 densites differentes. Les accroissements en diametre et en hauteur ont ete analyses en fonction de la competition locale et du semencier, a l'aide des modeles additifs generalises. Resultats. Vingt mois apres la plantation, les croissances etaient maximales, en hauteur (165,6 ± 39,2 cm·an-1) a une densite intermediaire de 47 000 tiges·ha-1, en diametre (24,6 ± 8,3 mm·an-1) a une faible densite de 4 200 tiges·ha-1. L’origine genetique des plants a affecte leur croissance, les coefficients de variation entre semenciers ont atteint 7,6 % et 6,4 % pour les accroissements en diametre et en hauteur, respectivement. Le diametre initial a influence positivement la croissance diametrique mais la hauteur initiale n'a pas affecte la croissance en hauteur. Conclusions. Le dispositif de Nelder s'est avere utile pour confirmer la dependance de la croissance des plants vis-a-vis de l’ecartement et mettre en evidence l’influence de facteurs genetiques sur la croissance.

BACKGROUND In Western countries, COVID-19 has been particularly deadly for care home residents. OBJECTIVE To understand the role of age and sex structures, health frailty, and contamination dynamics in COVID-19 mortality in populations living inside and outside care homes. METHODS We compared COVID-19 death data recorded in March-June 2020 in Wallonia (southern Belgium) for populations living inside and outside care homes, using annual death data (all-cause mortality in 2017) to assess the health condition of each population. RESULTS Sixty-four percent of COVID-19 deaths were residents in care homes, where the outbreak started after that in the external population, but at a faster pace. The death rate varied between 0 parts per thousand and 340 parts per thousand (mean 43 parts per thousand) per care home, increasing with the number of both residents and staff. All-cause and COVID-19 mortality rates increased exponentially with age but were much higher in care homes. The ratio of male (M) to female (F) death rates was 1.6 for all-cause mortality and 2.0 for COVID-19 mortality (both confirmed and suspected). The COVID-19 mortality reached 24% (M) and 18% (F) of the all-cause mortality rate in care homes, compared to 5% (M) and 4% (F) outside care homes. CONCLUSIONS The COVID-19 mortality rate was 130x higher inside than outside care homes, due to the near multiplicative effects of differences in the residents' age and sex structure (11x), health frailty (3.8x), and infection risk (probably 3.5x). CONTRIBUTION Care homes should be treated as a very specific population in epidemiological studies due to their extreme vulnerability to COVID-19.

The responses of tropical forests to environmental change are critical uncertainties in predicting the future impacts of climate change. The positive phase of the 2015–2016 El Niño Southern Oscillation resulted in unprecedented heat and low precipitation in the tropics with substantial impacts on the global carbon cycle. The role of African tropical forests is uncertain as their responses to short-term drought and temperature anomalies have yet to be determined using on-the-ground measurements. African tropical forests may be particularly sensitive because they exist in relatively dry conditions compared with Amazonian or Asian forests, or they may be more resistant because of an abundance of drought-adapted species. Here, we report responses of structurally intact old-growth lowland tropical forests inventoried within the African Tropical Rainforest Observatory Network (AfriTRON). We use 100 long-term inventory plots from six countries each measured at least twice prior to and once following the 2015–2016 El Niño event. These plots experienced the highest temperatures and driest conditions on record. The record temperature did not significantly reduce carbon gains from tree growth or significantly increase carbon losses from tree mortality, but the record drought did significantly decrease net carbon uptake. Overall, the long-term biomass increase of these forests was reduced due to the El Niño event, but these plots remained a live biomass carbon sink (0.51 ± 0.40 Mg C ha −1 y −1 ) despite extreme environmental conditions. Our analyses, while limited to African tropical forests, suggest they may be more resistant to climatic extremes than Amazonian and Asian forests., info:eu-repo/semantics/published

The consequences of the Cretaceous–Paleogene (K–Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic. [Allopolyploidy; Cretaceous–Paleogene (K–Pg) boundary; Fabaceae, Leguminosae; paleopolyploidy; phylogenomics; whole genome duplication events], info:eu-repo/semantics/published

Background: Comparative phylogeographic studies on rainforest species that are widespread in Central Africa often reveal genetic discontinuities within and between biogeographic regions, indicating (historical) barriers to gene flow, possibly due to repeated and/or long-lasting population fragmentation during glacial periods according to the forest refuge hypothesis. The impact of forest fragmentation seems to be modulated by the ecological amplitude and dispersal capacities of each species, resulting in different demographic histories. Moreover, while multiple studies investigated the western part of Central Africa (Lower Guinea), few have sufficiently sampled the heart of the Congo Basin (Congolia). In this study, we look for genetic discontinuities between populations of the widespread tropical tree Scorodophloeus zenkeri Harms (Fabaceae, Detarioideae) in Central Africa. Additionally, we characterize genetic diversity, selfing rate and fine-scale spatial genetic structure within populations to estimate the gene dispersal capacity of the species. Results: Clear intraspecific genetic discontinuities occur throughout the species’ distribution range, with two genetic clusters in Congolia and four in Lower Guinea, and highest differentiation occurring between these bioregions. Genetic diversity is higher in Lower Guinea than Congolia. A spatial genetic structure characteristic of isolation by distance occurs within the genetic clusters. This allowed us to estimate gene dispersal distances (σg) for this outcrossing species with ballistic seed dispersal, which range between 100 and 250 m in areas where S. zenkeri occurs in high densities, and are in the low range of σg values compared to other tropical trees. Gene dispersal distances are larger in low density populations, probably due to extensive pollen dispersal capacity. Conclusions: Fragmentation of S. zenkeri populations seems to have occurred not only in Lower Guinea but also in the Congo Basin, though not necessarily according to previously postulated forest refuge areas. The lower genetic diversity in Congolia compared to Lower Guinea parallels the known gradient of species diversity, possibly reflecting a stronger impact of past climate changes on the forest cover in Congolia. Despite its bisexual flowers, S. zenkeri appears to be mostly outcrossing. The limited dispersal observed in this species implies that genetic discontinuities resulting from past forest fragmentation can persist for a long time before being erased by gene flow., SCOPUS: ar.j, info:eu-repo/semantics/published

Secondary metabolites are essential for plant survival and reproduction. Wild undomesticated and tropical plants are expected to harbor highly diverse metabolomes. We investigated the metabolomic diversity of two morphologically similar trees of tropical Africa, Erythrophleum suaveolens and E. ivorense, known for particular secondary metabolites named the cassaine-type diterpenoids. To assess how the metabolome varies between and within species, we sampled leaves from individuals of different geographic origins but grown from seeds in a common garden in Cameroon. Metabolites were analyzed using reversed phase LC-HRMS(/MS). Data were interpreted by untargeted metabolomics and molecular networks based on MS/MS data. Multivariate analyses enabled us to cluster samples based on species but also on geographic origins. We identified the structures of 28 cassaine-type diterpenoids among which 19 were new, 10 were largely specific to E. ivorense and five to E. suaveolens. Our results showed that the metabolome allows an unequivocal distinction of morphologically-close species, suggesting the potential of metabolite fingerprinting for these species. Plant geographic origin had a significant influence on relative concentrations of metabolites with variations up to eight (suaveolens) and 30 times (ivorense) between origins of the same species. This shows that the metabolome is strongly influenced by the geographical origin of plants (i.e. genetic factors)., info:eu-repo/semantics/published

In the pantropical mimosoid legume genus Parkia, taxonomic classification has remained controversial in Africa due to clinal phenotypic variations. Three species (P. biglobosa, P. bicolor, and P. filicoidea) are currently recognized, ranging from West to East Africa, with partially overlapping ranges across different floristic regions. However, additional taxa (species or varieties) have been suggested by different authors. To assess species boundaries of African Parkia and phylogeographic patterns within species, we genotyped 889 individuals using 10 microsatellite markers and compared our results with existing morphological descriptions. Bayesian genetic clustering confirmed the species boundaries assessed from morphological traits and did not reveal introgression but identified genetic discontinuities within each species. Six moderately differentiated genetic clusters were recovered in P. biglobosa (pairwise FST: 0.05–0.19), while P. bicolor and P. filicoidea, each, displayed four well-differentiated clusters (FST: 0.18–0.41 and 0.11–0.34, respectively). Within each species, genetic clusters occurred in parapatry. Parkia biglobosa clusters were congruent with the longitudinal clinal variation in leaflets sizes but 26% of individuals presented admixed genotypes. Genetic clusters in P. bicolor and P. filicoidea followed environmental gradients as well as phytogeographic subdivisions. They were also largely congruent with morphological discontinuities described in previous taxonomic studies and < 10% individuals showed admixed genotypes. We conclude that only one species (P. biglobosa) should be considered in the Guineo-Sudanian savanna. However, P. bicolor and P. filicoidea might each represent a complex of (sub)species. Thus, the hypotheses of cryptic species within P. bicolor and P. filicoidea should be further investigated by testing reproductive barriers., SCOPUS: ar.j, info:eu-repo/semantics/published

BACKGROUND AND AIMS: Afromontane forests host a unique biodiversity distributed in isolated high-elevation habitats within a matrix of rain forests or savannahs, yet they share a remarkable flora that raises questions about past connectivity between currently isolated forests. Here, we focused on the Podocarpus latifolius-P. milanjianus complex (Podocarpaceae), the most widely distributed conifers throughout sub-Saharan African highlands, to infer its demographic history from genetic data. METHODS: We sequenced the whole plastid genome, mitochondrial DNA regions and nuclear ribosomal DNA of 88 samples from Cameroon to Angola in western Central Africa and from Kenya to the Cape region in eastern and southern Africa to reconstruct time-calibrated phylogenies and perform demographic inferences. KEY RESULTS: We show that P. latifolius and P. milanjianus form a single species, whose lineages diverged during the Pleistocene, mostly between approx, 200 000 and 300 000 years BP, after which they underwent a wide range expansion leading to their current distributions. Confronting phylogenomic and palaeoecological data, we argue that the species originated in East Africa and reached the highlands of the Atlantic side of Africa through two probable latitudinal migration corridors: a northern one towards the Cameroon volcanic line, and a southern one towards Angola. Although the species is now rare in large parts of its range, no demographic decline was detected, probably because it occurred too recently to have left a genetic signature in our DNA sequences. CONCLUSIONS: Despite the ancient and highly fluctuating history of podocarps in Africa revealed by palaeobotanical records, the extended distribution of current P. latifolius/milanjianus lineages is shown to result from a more recent history, mostly during the mid-late Pleistocene, when Afromontane forests were once far more widespread and continuous., SCOPUS: ar.j, info:eu-repo/semantics/published

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., SCOPUS: ar.j, info:eu-repo/semantics/published

Plant translocations allow the restoration of genetic diversity in inbred and depauperate populations and help to prevent the extinction of critically endangered species. However, the successes of plant translocations in restoring genetically viable populations and the possible associated key factors are still insufficiently evaluated. To fill this gap, we carried out a thorough genetic monitoring of three populations of Arnica montana that were created or reinforced by the translocation of plants obtained from seeds of two large natural source populations from southern Belgium. We genotyped nine microsatellite markers and measured fitness quantitative traits over two generations (transplants, F1 seed progeny and newly established F1 juveniles). Two years after translocation, the genetic restoration had been effective, with high genetic diversity and low genetic differentiation across generations, extensive contemporary pollen flow, admixture between seed sources in the F1 generation and recruitment of new individuals from seeds. We detected site, seed source and maternal plant effects on plant fitness. The results also suggest that phenotypic plasticity may favour short-term individual survival and long-term adaptive capacity and enhance the evolutionary resilience of the populations to changing environmental conditions. We found no sign of heterosis or outbreeding depression at early life stages in the F1 generation. Our findings emphasize the importance of the translocation design (700 transplants of mixed sources, planted at high density) as well as the preparatory site management for the successful outcome of the translocations, which maximized flowering, random mating, and recruitment from seeds in the first years after translocation., SCOPUS: ar.j, info:eu-repo/semantics/published

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., SCOPUS: ar.j, info:eu-repo/semantics/published

Phylogenies are a central and indispensable tool for evolutionary and ecological research. Even though most angiosperm families are well investigated from a phylogenetic point of view, there are far less possibilities to carry out large-scale meta-analyses at order level or higher. Here, we reconstructed a large-scale dated phylogeny including nearly 1/8th of all angiosperm species, based on two plastid barcoding genes, matK (incl. trnK) and rbcL. Novel sequences were generated for several species, while the rest of the data were mined from GenBank. The resulting tree was dated using 56 angiosperm fossils as calibration points. The resulting megaphylogeny is one of the largest dated phylogenetic tree of angiosperms yet, consisting of 36,101 sampled species, representing 8,399 genera, 426 families and all orders. This novel framework will be useful for investigating different broad scale research questions in ecological and evolutionary biology., info:eu-repo/semantics/published

How the Central African rain forests have been affected by climatic fluctuations of the Quaternary remains debated. Phylogeographical studies have shown that tree species from western Central Africa often display spatially congruent genetic discontinuities, supporting the hypothesis that the forest was previously fragmented. Extensive seed dispersal is expected to accelerate the admixture between gene pools but most of the species studied so far have presumably limited seed dispersal abilities. Here, we genotyped 15 nuclear and three plastid microsatellite markers in a low-density Central African tree species with long-distance seed dispersal: Baillonella toxisperma (Sapotaceae). While plastid markers revealed a weak structure in Cameroon, nuclear markers highlighted three genetic clusters: two distributed in Cameroon and separating Atlantic coastal forests from the inland forests, and one cluster occurring in Gabon. Substantial genetic differentiation with a phylogeographical signal was detected only between Cameroonian and Gabonese populations, suggesting two major genetic clusters located approximately North and South of the equatorial climatic hinge. Genetic differentiation was very low between the clusters within Cameroon. This pattern could be partially explained by the climate niche distribution modelling applied on the Last Glacial Maximum (LGM) which predicts a unique remnant population per country. The deep North-South differentiation in a species with long-distance seed dispersal supports the hypothesis that Central African rain forests have been fragmented at the height of the equator during a substantial part of the Quaternary.

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 vegetation (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 populations (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, molecular 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/expanding events during successive glacial periods might explain why similar phylogeographic patterns can be generated over contrasting timescales.

Background and aims – Most tree species with aril-covered seeds are assumed to be dispersed by frugivores. However, the number of studied African rainforest plant species remains low. This study focused on Afzelia bipindensis, an important timber species, which produces seeds partly covered by an aril. Specifically, this study aimed to: (1) identify the dispersers and the predators of A. bipindensis seeds, (2) characterize the role of those dispersers and predators in the regeneration process, and (3) understand the role of the aril in seed germination in relation to the feeding behaviour of the identified dispersers. Methods – The study took place in a Gabonese evergreen rainforest in 2015 and in a Cameroonian semi-deciduous rainforest in 2016 and 2017. We conducted more than 100 hours of direct observations, and used camera traps to monitor animal activities for 3000 hours within the canopy and 10 000 hours on the ground under fruiting trees. Key results – Three rodent taxa (Cricetomys emini, Funisciurus isabella and an undetermined species of Muridae) were mainly observed interacting with the seeds but neither birds nor monkeys were observed. Rodents removed more than 90% of the seeds, after detaching the aril, to probably cache them in burrows or superficial caches. Seeds from which we manually removed the aril (mimicking rodent behaviour) had a higher germination rate.Conclusions – Rodents may play a more important role than expected in the dynamics of tree species producing aril-covered seeds., info:eu-repo/semantics/published

Detarioideae is well known for its high diversity of floral traits, including flower symmetry, number of organs, and petal size and morphology. This diversity has been characterized and studied at higher taxonomic levels, but limited analyses have been performed among closely related genera with contrasting floral traits due to the lack of fully resolved phylogenetic relationships. Here, we used four representative transcriptomes to develop an exome capture (target enrichment) bait for the entire subfamily and applied it to the Anthonotha clade using a complete data set (61 specimens) representing all extant floral diversity. Our phylogenetic analyses recovered congruent topologies using ML and Bayesian methods. Anthonotha was recovered as monophyletic contrary to the remaining three genera (Englerodendron, Isomacrolobium and Pseudomacrolobium), which form a monophyletic group sister to Anthonotha. We inferred a total of 35 transitions for the seven floral traits (pertaining to flower symmetry, petals, stamens and staminodes) that we analyzed, suggesting that at least 30% of the species in this group display transitions from the ancestral condition reconstructed for the Anthonotha clade. The main transitions were towards a reduction in the number of organs (petals, stamens and staminodes). Despite the high number of transitions, our analyses indicate that the seven characters are evolving independently in these lineages. Petal morphology is the most labile floral trait with a total of seven independent transitions in number and seven independent transitions to modification in petal types. The diverse petal morphology along the dorsoventral axis of symmetry within the flower is not associated with differences at the micromorphology of petal surface, suggesting that in this group all petals within the flower might possess the same petal identity at the molecular level. Our results provide a solid evolutionary framework for further detailed analyses of the molecular basis of petal identity. © 2019 Elsevier Inc., SCOPUS: ar.j, info:eu-repo/semantics/published

Phylogenomics is increasingly used to infer deep-branching relationships while revealing the complexity of evolutionary processes such as incomplete lineage sorting, hybridization/introgression and polyploidization. We investigate the deep-branching relationships among subfamilies of the Leguminosae (or Fabaceae), the third largest angiosperm family. Despite their ecological and economic importance, a robust phylogenetic framework for legumes based on genome-scale sequence data is lacking. We generated alignments of 72 chloroplast genes and 7,621 homologous nuclear encoded proteins, for 157 and 76 taxa, respectively. We analysed these with Maximum Likelihood, Bayesian Inference, and a multi-species coalescent summary method, and evaluated support for alternative topologies across gene trees. We resolve the deepest divergences in the legume phylogeny despite lack of phylogenetic signal across all chloroplast genes and the majority of nuclear genes. Strongly supported conflict in the remainder of nuclear genes is suggestive of incomplete lineage sorting. All six subfamilies originated nearly simultaneously, suggesting that the prevailing view of some subfamilies as "basal" or "early-diverging" with respect to others should be abandoned, which has important implications for understanding the evolution of legume diversity and traits. Our study highlights the limits to phylogenetic resolution in relation to rapid successive speciation.

The rainforests of Tropical Africa have fluctuated over time. Although today the forest cover is continuous in Central Africa this may have not always been the case, as the scarce fossil record in this region suggests that more arid conditions might have significantly reduced the density of trees during the Ice Ages. Our aim was to investigate whether the dry ice-age periods left a genetic signature on tree species that can be used to date the past fragmentation of the rainforest. We sequenced reduced representation libraries of 182 samples representing five Legume tree species that are widespread in African rainforests and seven outgroups. Phylogenetic analyses identified an early divergent lineage for all species in West Africa (Upper Guinea), and two clades in Central Africa: Lower Guinea-North and Lower Guinea-South. As the structure separating the Northern and Southern clades cannot be explained by geographic barriers, we tested other hypotheses using demographic model testing. The best estimates recovered using ∂a∂I indicate that the two clades split between the Upper Pliocene and the Pleistocene, a date compatible with forest fragmentation driven by ice-age climatic oscillations. Furthermore, we found remarkably older split dates for the shade-tolerant tree species with non-assisted seed dispersal than for light-demanding long-distance wind-dispersed trees. We also show that the genetic diversity significantly declines with the distance from ice-age refugia in the two long-distance dispersed species only. Different recolonisation abilities after recurrent cycles of forest fragmentation seem to explain why we observe congruent genetic spatial structures across species with contrasted timescales.SIGNIFICANCE STATEMENTAlthough today the rainforest cover is continuous in Central Africa, the scarce fossil record suggests that arid conditions during the Ice Ages might have reduced the density of trees during the Ice Ages. However, the vast majority of the fossil pollen records preserved in Tropical Africa is too young to inform about this period. Investigating whether the past climate change left a genetic signature on trees can thus be useful to date past forest fragmentation. However, most genetic studies available to date lack resolution as they use limited numbers of loci. In this study we use modern DNA technology to study five Legume trees. Our results show significant differentiation of the populations of each species at a date compatible with forest fragmentation driven by ice-age climatic oscillations. Contrasted timescales were obtained for each species, which probably reflects their different recolonisation abilities after forest fragmentation.

Few studies have addressed the evolutionary history of tree species from African savannahs at large geographic scales, particularly in the southern hemisphere (Zambezian region).Afzelia(Fabaceae: Caesalpinioideae) contains economically important timber species, including two species widely distributed in African savannahs:A. africanain the Sudanian region andA. quanzensisin the Zambezian region. To characterize the population genetic diversity and structure of these two species across their distribution ranges, we used nuclear microsatellites (simple sequence repeats, SSRs) and genotyping-by-sequencing (GBS) markers. Six SSR loci were genotyped in 241A. africanaand 113A. quanzensisindividuals, while 2,800 and 3,841 high-quality single nucleotide polymorphisms (SNPs) were identified in 30A. africanaand 12A. quanzensisindividuals, respectively. Both species appeared to be outcrossing (selfing rate ~ 0%). The spatial genetic structure was consistent with isolation-by-distance expectations based on both SSR and SNP data, suggesting that gene dispersal is spatially restricted in both species (bLd (SSR)= −0.005and −0.007andbLd (SNP)= −0.008and −0.006 forA. africanaandA. quanzensis, respectively). Bayesian clustering of SSR genotypes failed to identify genetic structure within species. In contrast, SNP data resolved intraspecific genetic clusters in both species, illustrating the higher resolving power of GBS at shallow levels of divergence. However, the clusters identified by SNPs revealed low levels of differentiation and no clear geographical entities. These results suggest that, although gene flow has been restricted over short distances in both species, 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 past climate changes, in contrast to patterns commonly found in African rainforest trees.

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 São Tomé and Príncipe. 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 FST and RST 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 São Tomé and Príncipe 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., SCOPUS: ar.j, info:eu-repo/semantics/published

The consequences of the Cretaceous-Paleogene (K-Pg) boundary (KPB) mass extinction for the evolution of plant diversity are poorly understood, even although evolutionary turnover of plant lineages at the KPB is central to understanding the assembly of the Cenozoic biota. One aspect that has received considerable attention is the apparent concentration of whole genome duplication (WGD) events around the KPB, which may have played a role in survival and subsequent diversification of plant lineages. In order to gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the legume family, one of the most important angiosperm clades that rose to prominence after the KPB and for which multiple WGD events are found to have occurred early in its evolution. The legume family (Leguminosae or Fabaceae), with c. 20.000 species, is the third largest family of Angiospermae, and is globally widespread and second only to the grasses (Poaceae) in economic importance. Accordingly, it has been intensively studied in botanical, systematic and agronomic research, but a robust phylogenetic framework and timescale for legume evolution based on large-scale genomic sequence data is lacking, and key questions about the origin and early evolution of the family remain unresolved. We extend previous phylogenetic knowledge to gain insights into the early evolution of the family, analysing an alignment of 72 protein-coding chloroplast genes and a large set of nuclear genomic sequence data, sampling thousands of genes. We use a concatenation approach with heterogeneous models of sequence evolution to minimize inference artefacts, and evaluate support and conflict among individual nuclear gene trees with internode certainty calculations, a multi-species coalescent method, and phylogenetic supernetwork reconstruction. Using a set of 20 fossil calibrations we estimate a revised timeline of legume evolution based on a selection of genes that are both informative and evolving in an approximately clock-like fashion. We find that the root of the family is particularly difficult to resolve, with strong conflict among gene trees suggesting incomplete lineage sorting and/or reticulation. Mapping of duplications in gene family trees suggest that a WGD event occurred along the stem of the family and is shared by all legumes, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. We propose that the difficulty of resolving the root of the family is caused by a combination of ancient polyploidy and an alternation of long and very short internodes, shaped respectively by extinction and rapid divergence. Our results show that the crown age of the legumes dates back to the Maastrichtian or Paleocene and suggests that it is most likely close to the KPB. We conclude that the origin and early evolution of the legumes followed a complex history, in which multiple nested polyploidy events coupled with rapid diversification are associated with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic.

Questions: Do functional and phylogenetic diversity vary along a natural metal gradient? Do resources acquisition and metal tolerance-related traits show the same patterns of variation? Is the ability to grow on metal-enriched soil phylogenetically conserved or the result of functional convergence? Location: Fungurume V hill (10°37′03″ S, 26°17′22″ E), Upper Katanga, Democratic Republic of Congo. Methods: In 21 communities along a natural copper gradient, we quantified the variation of species richness and turnover as well as the phylogenetic diversity. We assessed the variation of three univariate functional indices — community-weighted mean, functional richness and functional dispersion — for ten functional traits related to resources acquisition, conservation, dispersal and metal tolerance strategy. Results and Conclusions: Along a gradient of increasing soil Cu concentration, we found a decrease in species number and a strong species turnover. On metal-poor soils, phylogenetic clustering and overdispersion of functional traits indicated selection for certain clades (e.g. Fabaceae) with many different trait combinations suggesting niche partitioning. On metal-enriched soils, contrary to expectations, we found functional convergence towards trait values associated with rapid resource use, lower stature and smaller seeds in several clades. Conversely, metal tolerance strategy showed a clear overdispersion on metal-rich soils reflecting the presence of several strategies to cope with the excess of metal in the soil. This suggests that some extreme toxicity gradients, such as this one, do not always impose strong functional convergence towards a stress tolerance strategy, as is often assumed., SCOPUS: ar.j, info:eu-repo/semantics/published

Resolving phylogenetic relationships allows the investigation of how species diversity has evolved in various ecosystems. The genera Entandrophragma and Khaya consist of tree species distributed in different African biomes (lowland rain forest, dry forest and savanna, montane forest), and are suitable to examine how (single or multiple events) and when the processes of diversification led to biome transitions. Based on the sequencing of plastome (pDNA: c. 160,000 bp), ribosomal DNA (rDNA: c. 5300 bp), and habitat characteristic data for each species, we have: (i) reconstructed phylogenetic relationships between species and estimated the divergence period between the main lineages, and (ii) reconstructed ancestral states regarding biome preferences. The phylogenetic trees obtained with both markers support monophyly of the five sections of Entandrophragma previously defined based on fruit and floral characters. Nevertheless, the position of some species from the pDNA and rDNA tree topologies varied within sections. In Khaya, pDNA and rDNA show very divergent topologies, possibly due to a more recent diversification involving incomplete lineage sorting and/or recurrent hybridization events. Khaya diversified during the Pliocene and Pleistocene according to both markers; whereas, according to rDNA data, the Entandrophragma sections diverged during the early Miocene and species within sections diverged from the late Miocene to the Pleistocene. Divergence date estimates tended to be more recent using pDNA data. Biome transitions could not be reconstructed in Khaya as the species tree remains unresolved. Contrarily, three independent biome transitions were inferred in Entandrophragma. The first transition from rain to dry forests occurred during the Miocene and two other transitions were inferred during the Pleistocene, one from rain forest to dry forest and another from rain forest to mountain forest. Overall, we demonstrate that multiple biome transitions occurred, starting from a rain forest biome, possibly reflecting the global trend of aridification of Africa throughout the Cenozoic. © 2019 Elsevier GmbH, SCOPUS: ar.j, info:eu-repo/semantics/published

International audience; Despite significant progress made in recent years toward developing an infrafamilial classification of Orchidaceae, our understanding of relationships among and within tribal and subtribal groups of epidendroid orchids remains incomplete. To reassess generic delimitation among one group of these epidendroids, the African angraecoids, phylogenetic relationships were inferred from DNA sequence data from three regions, ITS, matK, and the trnL-trnF intergenic spacer, obtained from a broadly representative sample of taxa. Parsimony and Bayesian analyses yielded highly resolved trees that are in clear agreement and show significant support for many key clades within subtribe Angraecinae s.l. Angraecoid orchids comprise two well-supported clades: an African/American group and an Indian Ocean group. Molecular results also support many previously proposed relationships among genera, but also reveal some unexpected relationships. The genera Aerangis, Ancistrorhynchus, Bolusiella, Campylocentrum, Cyrtorchis, Dendrophylax, Eurychone, Microcoelia, Nephrangis, Podangis and Solenangis are all shown to be monophyletic, but Angraecopsis, Diaphananthe and Margelliantha are polyphyletic. Diaphananthe forms three well-supported clades, one of which might represent a new genus, and Rhipidoglossum is paraphyletic with respect to Cribbia and Rhaesteria, and also includes taxa currently assigned to Margelliantha. Tridactyle too is paraphyletic as Eggelingia is embedded within it. The large genus Angraecum is confirmed to be polyphyletic and several groups will have to be recognized as separate genera, including sections Dolabrifolia and Hadrangis. The recently segregated genus Pectinariella (previously recognized as A. sect. Pectinaria) is polyphyletic and its Continental African species will have to be removed. Similarly, some of the species recently transferred to Angraecoides that were previously placed in Angraecum sects. Afrangraecum and Conchoglossum will have to be moved and described as a new genus.

Restriction associated DNA sequencing was conducted on two genetically independent individuals of Iroko, Milicia excelsa, for the discovery of nuclear SNPs. Ninety-four samples, well-distributed over the natural range and including timber DNA, were screened at 138 loci on a MassARRAY iPLEX system. Amplification success was high and 77 loci were selected to design a set of markers for genetic timber tracking purposes.

Aim We sought to test the refuge hypothesis as a major driver of genetic differentiation to explain the development of distinct phytogeographical domains in tropical Central African rain forest. To address this aim, we studied the phylogeographical pattern of a pair of sister plant species, Haumania danckelmaniana and H. liebrechtsiana (Marantaceae), distributed across the two phytogeographical domains: Lower Guinea and Congolia. Location Tropical Central Africa including the phytogeographical domains Lower Guinea and Congolia., Methods Seven polymorphic microsatellite loci were genotyped in a total of 513 individuals from both species. The dataset was analysed for population genetic structure and demographic change and the results compared to the geographical pattern of plastid DNA sequences from a previous publication and other sympatric species., Results Based on the microsatellite dataset, three distinct homogeneous genetic clusters were detected in H. danckelmaniana and two in H. liebrechtsiana. These clusters corresponded geographically with the patterns found in the plastid DNA sequences. Genetic diversity and endemism were unevenly distributed between clusters in the two species. Most clusters exhibited signals of population expansion., Main conclusions The phylogeographical data based on microsatellites and plastid DNA revealed a complex history involving (1) allopatric differentiation with each species originating in a different phytogeographical domain, potentially resulting from past forest fragmentation, followed by (2) population expansion and interspecific introgression, which probably occurred during a phase of forest expansion. Moreover, phylogeographical patterns within each species provided evidence of (3) past population fragmentation followed by partial population admixture in H. danckelmaniana, and deep differentiation between Lower Guinea and Congolia in H. liebrechtsiana. The observed patterns were globally consistent with the refuge hypothesis and the presented scenario illustrates evolutionary processes that likely have contributed to shaping the African phytogeographical domains., Furthermore, the first author acknowledges a 2-year postdoctoral fellowship by the Germany Research Foundation (DFG) and a SYNTHESYS grant visiting the Real Jardíın Botánico-CSIC, Madrid., The second author acknowledges a Ramóon y Cajal Fellowship (RYC2009-04537) from the Spanish Ministry for Science and Innovation (MICINN), a Marie Curie Intra-European Fellowship (PIEF-GA-2012-329088) and a research grant (CGL2012- 40129-C02-02) from the Spanish Ministry of Economy and Competitiveness (MINECO).

Aim: Our aim was to document African rain forest tree diversity patterns to test whether they support one of the following hypotheses: the structure of tree species diversity is at equilibrium and mostly driven by neutral processes (H0); the structure of tree species diversity results from Pleistocene forest cover dynamics (H1); or the structure of tree species diversity results from ecological sorting along environmental gradients (H2). Location: West Central Africa: the hilly region of Gabon, a putative Pleistocene forest refuge, and the adjacent flat littoral region, putatively colonized by forests from the hilly region after the last glaciation. Methods: We used 103 standardized 0.1-ha tree plots distributed among five landscapes in the two regions. We partitioned the tree diversity within and among plots at a local and regional scale using the Hurlbert effective number of species framework. The explanatory power of geographical and elevational distances on species turnover was tested. At the landscape scale, we partitioned the beta diversity into nestedness and turnover components. Results: Mean alpha and gamma diversities were much higher in the hilly region, where differences in elevation explained a significant part of species turnover. Substantial species turnover correlated with geographical distance also occurred in the littoral region despite its low elevational heterogeneity. Floristic turnover between plots from different regions remained stable whatever the elevational/geographical distances. At the regional scale, species replacement remained the main contributor to beta diversity (low nestedness values). Main conclusions: The heterogeneous distribution of alpha and gamma diversity, similar levels of species turnover among plots and the low contribution of the nestedness component to beta diversity between hilly and littoral landscapes do not support hypotheses H0 and H1. The combined impacts of limited dispersal and ecological sorting along environmental gradients (H2) can explain patterns within regions. The marked floristic discontinuity between regions could reflect contrasting histories (two distinct refugia) although the role of contrasting environments cannot be discounted.

Mating system and gene flow are major influencing factors of species population dynamics and evolution. These factors are often not characterized in tropical tree species, yet they constitute basic information that must be considered to implement sustainable management practices. In particular, as logging implies a reduction of the density of congeneric mates, the connectivity through pollination between individuals has to be well characterized (selfing versus outcrossing rates, distances between mates). We conducted a genetic-based analysis (using 10 nuclear microsatellites) to determine the mating system and gene flow characteristics of an emblematic timber tree species from lowland rain forests of the Congo Basin, Baillonella toxisperma (Sapotaceae). The species, which is frequently exploited for its wood and for a number of non-timber forest products, naturally occurs at low densities (ca. 0.01–0.1 individuals/ha). It is supposedly an entomophilous species whose seeds are probably dispersed by mammals. We have shown that the species presents a mixed-mating system (about 20–40% of selfing depending on analysis method). However, the comparison of inbreeding parameters among cohorts suggests that inbred individuals die between seedling and mature tree stages. The mean pollen dispersal distance was relatively low for such a low-density population species (estimated to be 690 or 777 m depending on analysis method) and, together with a low mean number of pollen donors (NEP = 2.76), it suggests a pattern of nearest-neighbour mating where allo-pollen could be a limiting factor. However, B. toxisperma presents a relatively weak genetic structure (Sp statistic = 0.0095) indicative of long gene dispersal distance (σg = 3–5 km according to the assumed effective population density). Overall, this would indicate that gene flow occurs mainly by extensive seed dispersal in this species. These results suggest that mammals and local populations involved in the dispersal of the species play a key role by lowering biparental inbreeding effects. Sustainable population management might require assisted regeneration using unrelated planting material., SCOPUS: ar.j, info:eu-repo/semantics/published

International audience; Species delimitation within Angraecum section Dolabrifolia is problematic due to morphological variability coupled with overlap in many of the characters traditionally used to distinguish species. Recent molecular phylogenetic studies of the genus included three of the five currently described species of the Dolabrifolia group, placing them as sister to continental African species of Angraecum sect. Pectinaria. In preparation for a taxonomic revision of section Dolabrifolia, we analyzed morphological and molecular data to re-assess the circumscription of each of the five currently described species, examined the relationships among members of the section, and assessed their position within the genus. We used 172 alcohol-preserved specimens to perform multivariate analyses on 15 morphological characters. We also collected molecular sequence data from 16 taxa including all members of the section using six DNA regions, and analyzed these data with parsimony and Bayesian methods. The morphometric study revealed five distinct groups, of which four correspond to currently recognized species, while the fifth represents a taxonomic novelty. Angraecum podochiloides is the most distinctive morphologically, recognizable by its narrow leaves bearing white-yellowish flowers. The often confused species Angraecum distichum and Angraecum bancoense are clearly distinguishable by flower size. Molecular phylogenetic analyses indicated that section Dolabrifolia forms a well-supported clade related to the continental African members of section Pectinaria. Four species are well delimited, while the accessions of Angraecum aporoides formed two well-supported clades corresponding to two subclusters revealed by the morphometric study. The recently published Angraecum poppendickianum is shown to be a synonym of A. distichum.