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Premise: Phylogenetic approaches can provide valuable insights on how and when a biome emerged and developed using its structuring species. In this context, Brachystegia Benth, a dominant genus of trees in miombo woodlands, appears as a key witness of the history of the largest woodland and savanna biome of Africa. Methods: We reconstructed the evolutionary history of the genus using targeted-enrichment sequencing on 60 Brachystegia specimens for a nearly complete species sampling. Phylogenomic inferences used supermatrix (RAxML-NG) and summary-method (ASTRAL-III) approaches. Conflicts between species and gene trees were assessed, and the phylogeny was time-calibrated in BEAST. Introgression between species was explored using Phylonet. Results: The phylogenies were globally congruent regardless of the method used. Most of the species were recovered as monophyletic, unlike previous plastid phylogenetic reconstructions where lineages were shared among geographically close individuals independently of species identity. Still, most of the individual gene trees had low levels of phylogenetic information and, when informative, were mostly in conflict with the reconstructed species trees. These results suggest incomplete lineage sorting and/or reticulate evolution, which was supported by network analyses. The BEAST analysis supported a Pliocene origin for current Brachystegia lineages, with most of the diversification events dated to the Pliocene-Pleistocene. Conclusions: These results suggest a recent origin of species of the miombo, congruently with their spatial expansion documented from plastid data. Brachystegia species appear to behave potentially as a syngameon, a group of interfertile but still relatively well-delineated species, an aspect that deserves further investigations., SCOPUS: ar.j, info:eu-repo/semantics/published

Helichrysum arenarium (L.) Moench (Asteraceae) is a self‐compatible, insect‐pollinated herb occurring in sand grasslands, and is declining and endangered in many parts of its European distribution range. A recovery plan of H. arenarium has been conducted in southern Belgium, involving plant translocations. We developed multiplex genotyping protocol for nine microsatellite markers previously published for Helichrysum italicum and two newly developed microsatellite markers for H. arenarium .Eleven polymorphic loci were associated (pooled) in two multiplex panels, to assess the genetic status of the only small remaining population in Belgium and of three large German populations used as seed source for propagating transplants. The small Belgian population was characterized by high clonality, with only two, however heterozygous, genets detected. The three large German populations showed high genetic diversity ( H e ranging from 0.635 to 0.670) and no significant inbreeding coefficient values, despite expectations of geitonogamous selfing. Management practices (grazing livestock) increasing seed dispersal distances, inbreeding depression at early stages of development, and mechanisms preventing or delaying selfing might be hypothesized to explain the observed patterns. The two Belgian genotypes remained within genetic variation range of German populations so that the high genetic differentiation between Belgian and German populations ( F ST values ranging from 0.186 to 0.206) likely resulted from genetic drift effects and small sample size. Transplants obtained from seeds sampled from the three large source populations from Germany constitute a highly diverse, noninbred gene pool, and are thus of high genetic quality for plant translocations., SCOPUS: ar.j, info:eu-repo/semantics/published

Premise of the study: Coula edulis Baill (Coulaceae) is a common tree species in the Guineo-Congolian forests producing an edible fruit known as African walnut, which is an important food and income resource for rural populations. However, the species suffers from a deficit of natural regeneration. We developed here nuclear microsatellite markers for C. edulis to be able to study the genetic structure of its natural populations and gene flow. Methods and results: A genomic library was obtained using the Illumina platform, and 21 polymorphic microsatellite loci were developed. The polymorphic microsatellites displayed eight to 22 alleles per locus (average: 14.2), with a mean expected heterozygosity ranging from 0.33 to 0.72 in five populations from Central and West Africa. Conclusions: The high polymorphism of the nuclear microsatellite markers developed makes them useful to investigate gene flow and the organization of genetic diversity in C. edulis, and to assess whether particular genetic resources require conservation efforts., SCOPUS: ar.j, info:eu-repo/semantics/published

This Ph.D thesis explores the complex dynamics of Central African rainforest ecosystems, focusing on the gene flow and insect pollination of canopy-emergent timber tree species such as Cylicodiscus gabunensis Harms and other important timber species. These selected species represent a wide range of flower types, indicative of diverse pollination syndromes. Additionally, some have been the subject of previous genetic research, providing insights into pollen dispersal distances. Special attention is given to C. gabunensis due to its significant importance and the challenges it faces, including low population density and limited natural regeneration within dense forests. Data on gene dispersal within its population are scarce, highlighting the need for immediate attention in developing sustainable management strategies.The first step was focused on developing 24 polymorphic microsatellite markers to study the genetic diversity, structure, and gene flow within C. gabunensis populations. This toolkit subsequently enabled an in-depth exploration of the complex interactions influencing regeneration in C. gabunensis, including human activities, mating systems, and seed/pollen dispersal processes. Spatial and genetic analyses provided insight into population-specific characteristics, highlighting the necessity for context-specific and nuanced management strategies to ensure the long-term sustainability of the species.The focus then shifts to the often-overlooked role of insect-mediated pollination in tropical canopy trees. Exploring insect pollination within African canopy-emergent tree species using camera observations, the subsequent section offers insights into a diverse range of floral traits and pollination syndromes. This chapter challenges conventional assumptions regarding flower size, pollinator size, and pollen dispersal distances while also indicating that cross- pollination is not expected to be limited under selective logging based on extensive estimates of poll, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

Most Central African rainforest canopies consist of light-demanding tree species that hold high commercial value but also suffer locally from regeneration deficits, raising concerns about the sustainability of logging. Regeneration is influenced by factors such as past perturbations (including human activity), mating systems, and seed/pollen dispersal processes that impact demographic, spatial, and genetic structures within populations. To gain a better understanding of these interactions, we studied the spatial distribution and trunk diameter structure of Cylicodiscus gabunensis (Fabaceae) - a wind-dispersed, insect-pollinated, timber species - in three plots ranging from 400 to 839 ha situated in various environmental contexts (e.g. forest types and elephant densities) across Central Africa. We also genotyped adults and juveniles using microsatellite markers to analyze the spatial genetic structure of each population and infer the selfing rate, seed and pollen dispersal capacities and selection gradients using the ‘neighborhood model’. The selfing rate was low (3 – 4 %), and seed dispersal distances (ds = 184 m) were much shorter than pollen dispersal distances (dp > 2 km). The three populations displayed contrasted spatial, demographic and genetic structures. One population showed no spatial aggregation or genetic structure, and a multimodal diameter structure indicating pulses of regeneration events. Two populations showed strong spatial aggregation and genetic structures. One exhibited a unimodal diameter structure indicating one ancient pulse of regeneration, while the other displayed a 'reverse J-shaped' diameter structure, typical of ongoing regeneration. In the latter, reproductive success appeared leptokurtic, three mother trees accounting for over 90 % of the regeneration and no tree below the minimum cutting diameter implemented by logging companies had offspring. The idiosyncratic nature of population characteristics observed in C. gabunensis suggests t, SCOPUS: ar.j, info:eu-repo/semantics/published

Measuring impacts of non-native species is challenging, particularly for long-established invasions in poorly characterised native ecosystems. Recreating historical population dynamics using dendrochronological methods is a popular approach for addressing conservation and forest management questions. However, these tools are rarely applied for addressing questions of invasion. Classical dendrochronology is also not well suited to many tropical tree species as they do not produce growth rings. Here we test the validity of an alternative approach, based on the analysis of multiple morphological markers, that could allow for both the recreation of historical invasion dynamics as well as quantify the impacts of invasion on the recipient native ecosystem. We validate this method on the Cecropia peltata invasion in Cameroon and its potential impacts on a native tree, Musanga cecropioides. We were able to compare architectural development over time in a mixed secondary forest where the two species co-occur and revealed differences in performance (growth, branching and flower production) between the two tree species. Our results revealed more sustained growth during early establishment and an early sexual maturity for the non-native C. peltata, compared to its native counterpart. A lower density of M. cecropioides was observed in the region of co-occurrence, supporting a hypothesis of competitive exclusion of the native species at the juvenile stage. Our work provides a novel way to understand the impacts of plant invasions via retrospective analysis that could well be applied to other invasions globally, opening up more opportunities to prioritise management on an impact-focused basis., SCOPUS: ar.j, info:eu-repo/semantics/published

Malgré le consensus croissant sur la nécessité d'une transition vers des pratiques agricoles plus durables, les céréales et, en particulier, le froment, ont pris du retard dans la conversion à l'agriculture biologique. Parmi les facteurs contribuant à ce retard figure le manque de variétés adaptées à ces pratiques agricoles et à leurs spécificités. Dans cette thèse, nous nous concentrons sur l’une des principales alternatives variétales pour répondre à ce problème :les populations hétérogènes. Par populations hétérogènes, nous désignons ici tout type de diversité intraspécifique, allant des mélanges variétaux jusqu’aux variétés-populations. Un avantage essentiel de cette hétérogénéité est que la présence de contrastes entre plantes peut donner lieu à des mécanismes de facilitation susceptibles d'améliorer les performances des cultures et leur stabilité face à des conditions défavorables. Malgré ces propriétés prometteuses, nous manquons cependant encore de clés pour guider ce type de sélection. Il s’agit là du principal objet de cette thèse.Ces dernières années, la recherche académique semble avoir mis l’accent sur la recherche d'associations de traits pouvant conduire aux mécanismes de facilitation que nous mentionnions ci-dessus. Dans ce travail, nous avons choisi de nous intéresser également à un autre type d'interaction qui a lieu au sein des populations hétérogènes :la compétition. En particulier, nous avons émis l'hypothèse qu'un certain type de compétition, que nous appelons « compétition individualiste », pourrait avoir des effets négatifs sur la culture. En effet, il arrive parfois que la sélection naturelle nous joue des tours en favorisant des individus qui ont pourtant un moindre potentiel de rendement, ou qui contribuent moins à la facilitation. Par conséquent, plus que la seule facilitation, le principal déterminant de la performance des populations hétérogènes pourrait plus précisément être l'équilibre entre compétition et facilitation. Dans les chapi, Despite the growing consensus on the need for a transition to more sustainable farming practices, cereals and, in particular, common wheat, have been lagging behind in the conversion to organic farming. We argue that one of the reasons for this is the lack of varieties that are adapted to these farming practices and their specificities. In this thesis, we focus on a main varietal alternative to respond to this issue: intra-crop diversity. By intra-crop diversity, we mean anything from variety mixtures to evolutionary populations, which we hereafter refer to with the umbrella term “heterogeneous stands”. One main advantage of intra-crop diversity is that trait contrasts between crop plants can give rise to facilitative mechanisms which can enhance crop performance and its stability in the face of unpredictable adverse conditions. However, we still know little about how to breed these heterogeneous stands. This is the main question that we try to address in this thesis.In recent years, a primary focus in the literature has been to identify favorable trait associations that can lead to facilitation. Here, we chose to also lend an eye to another type of plant interaction that unfolds in heterogeneous stands: competition. Indeed, we hypothesized that a specific type of competition, which we call “selfish competition”, could lead to negative effects on the crop. Sometimes, natural selection can indeed play tricks on us and favor genotypes that have lower grain yield potential or contribute less to facilitation. Hence, more than simply facilitation, it is the balance between competition and facilitation that may actually be the main determinant of heterogeneous stand performance. In chapters II and III, we thus sought to assess if selfish competition could indeed hinder heterogeneous stand performance, and to identify some of its underlying causes (with a focus on trait contrasts and sowing density). In agronomic trials with 12 variety mixtures and 2 Composite-Cross Popula, Doctorat en Sciences agronomiques et ingénierie biologique, info:eu-repo/semantics/nonPublished

Prior to the pre-colonial period in Central Africa, human populations were dispersed throughout the forests, where they engaged in slash-and-burn agriculture. Starting in the 19th century, they gradually established permanent settlements in villages, resulting in vast areas of abandoned forest. In present-day southern Cameroon, the forest canopy is primarily composed of large emergent trees, which are often attributed to past human activities. The aim of this study is to assess the significance of past human activities on the current floristic composition. Throughout the study area, there were shards of pottery, burnt palm nuts, and charcoal, indicating widespread human occupation and fire. This human occupation dates back to 2200 to 1500 BP, and more recently, three centuries ago. The frequent occurrence of fire and the presence of oil palm, both of recent origin, suggest the use of slash-and-burn agricultural practices. This coincides with the age of the large emergent trees and the dry climate phases recorded in the early 17th century. Therefore, these findings support the hypothesis that these activities have influenced the current floristic composition of the Central African forest., SCOPUS: ar.j, info:eu-repo/semantics/published

La compréhension des mécanismes écologiques qui gouvernent l’assemblage des espèceset qui permettent leur coexistence dans les forêts naturelles est un objectif central de l’écologiedes communautés. La structuration des communautés implique des mécanismesdéterministes comme le filtrage environnemental abiotique et les interactions compétitivesmenant à une limitation de similarité ou à une dominance compétitive. Elle implique égalementdes mécanismes neutres et quasi-neutres comme la dérive écologique, la limitation dedispersion et la géométrie stochastique. La contribution relative de ces mécanismesd’assemblage varie en fonction des espèces, du stade de vie des individus et de l’échellespatiale considérée. Les motifs de distribution spatiale des espèces conservent une empreintedes mécanismes qui les sous-tendent et permettent donc de les inférer. Le développementrécent de techniques d’analyse spatiale de semis de points offre aujourd’hui de nouveauxoutils pour mieux relier les motifs de distribution spatiale des espèces et les mécanismesd’assemblage à l’œuvre. L’objectif général de cette thèse est d’identifier et de quantifierl’importance relative des mécanismes d’assemblage des espèces ligneuses au sein de deuxforêts tempérées belges. Les deux communautés étudiées sont des forêts de recolonisation,la première étant située sur le versant nord de la colline calcaire du Moessia (Calestienneoccidentale) et la seconde se situant en contexte urbain au Kauwberg (sud de Bruxelles).Le cadre méthodologique intègre l’analyse i) de la distribution spatiale des individus au seindes communautés et de leurs capacités de dispersion au moyen d’analyses spatiales de semisde points uni-, bi- et multivariées, ii) des liens entre les motifs de distribution des espèces et lavaleur de leurs traits fonctionnels et iii) d’un grand nombre de variables environnementales(édaphiques, topographiques, d’intensité lumineuse). Utilisés seuls, ces voletsméthodologiques ne permettent pas une interpré, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

Delimiting species is not only a central issue in evolutionary and systematic biology but also a prerequisite to physiological, ecological, and population genetic studies. However, species boundaries' delineation in highly diverse environments, such as shallow tropical coral reefs, remains challenging. Traditional hypotheses that separate lineages in corals have long been based on morphological traits that did not yield resolution at the species level. The plastic response of corals to environmental variations and reports of intermediate morphotypes in the field have also hindered this task, casting doubt on current species delimitations. Therefore, while anthropogenic disturbances threaten coral reef ecosystems, the taxonomy of vulnerable taxa that inhabits them remains obscure.The difficulty to navigate this intricate taxonomic landscape is epitomized by the coral genus Acropora, which exhibits more than a hundred morphospecies and provides an excellent training ground to test and validate new practices. Species delimitation attempts in Acropora corals have so far been unsuccessful due to widespread genealogical incongruence among genetic markers and between morphological groupings, mating trials, and molecular clades obtained in phylogenetic analyses. Consequently, this thesis aimed to test the current species delimitation in scleractinian corals, outlining an integrative approach and establishing a methodology that paves the way for a taxonomic revision using the Acropora genus as a case study.For this purpose, a historical overview highlighting the emergence of the main issues faced by coral taxonomy was compiled (Chapter I). Molecular approaches were then applied to delimitate sympatric species of ecologically important and closely related tabular Acropora species. The congruence of the resulting molecular species delineation with additional lines of evidence, such as mating trials and morphology, was then gauged to select the most robust taxonomic hypothesis, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

The role dispersal has for species diversification and dynamics of angiosperms is a topic that has been extensively discussed. However, studies have seldom attempted to investigate this on at a wider range of species scales. Thus, the aim of this thesis was to explore the effect dispersal has on diversification and species dynamics ranging from the family level down to local populations, using Staudtia kamerunensis Warb. (Myristicaceae) as our biological model. We collected genetic samples of S. kamerunensis and other Myristicaceae from multiple herbaria and from the field (Gabon and the Democratic Republic of Congo), and extracted their total genomic DNA to use in molecular analyses. We used a variety of sampling schemes, with an aim of obtaining a wider range of information. We performed Sanger sequencing, microsatellite genotyping and genome skimming. In Chapter 1, we explored the biogeography of Myristicaceae. We then reconstructed a dated phylogeny using plastid sequences and Bayesian inference. We found that the family has a Miocene crown age, with the African species bring the basal group. We consider that the family reached its current disjunct distribution at least partially through long-distance transoceanic dispersal.In Chapter 2, we reconstructed the plastid lineages of S. kamerunensis and their historical spread throughout Central Africa and estimated the crown age of the species. We identified five plastid lineages, and a stark difference in genetic diversity between the western and eastern lineages. We estimate that S. kamerunensis reached its current geographic range fairly recently and rapidly, indicating a potentially high dispersal capacity.In Chapter 3, we investigated the intraspecific genetic diversity of S. kamerunensis through the use of microsatellite markers and Sanger sequencing. We found traces of past fragmentation and identified five genetic clusters. We found that gene flow between genetic clusters is uninterrupted, with pollen likely, Doctorat en Sciences, info:eu-repo/semantics/nonPublished

In the last decades, illegal logging has posed a serious threat for the integrity of forest ecosystems and for biodiversity conservation in tropical Africa. Although international treaties and regulatory plans have been implemented to reduce illegal logging, much of the total timber volume is harvested and traded illegally from tropical African forest regions. As a result, the development and the application of analytical tools to enhance the traceability and the identification of wood and related products is critical to enforce international regulations. Among available techniques, DNA barcoding is a promising approach for the molecular identification of plant species. However, although it has been used successfully for the discrimination of animal species, no set of genetic markers is available for the universal identification of plant species. In this work, we firstly characterized the genetic diversity of 17 highly-valuable African timber species from five genera ( Afzelia ,Guibourtia ,Leplea ,Milicia ,Tieghemella ) across their distribution ranges in West and Central Africa using the genome skimming approach in order to reconstruct their chloroplast genomes and nuclear ribosomal DNA. Next, we identified single-nucleotide polymorphisms (SNPs) for the discrimination of closely-related species. In this way, we successfully developed and tested novel species-specific genetic barcodes for species identification., SCOPUS: ar.j, info:eu-repo/semantics/published

Documenting species and population diversity is becoming increasingly important as the destruction and degradation of natural ecosystems are leading to a worldwide biodiversity loss. Despite the rapid development of genetic tools, many species remain undocumented and little is known about the diversity of individuals and populations, especially for tropical African plants. In this study, we aim to identify putative hidden species and/or differentiated populations in the tropical African tree Staudtia kamerunensis Warb. (Myristicaceae), a widespread species characterized by a high morphological diversity and a complex taxonomical history. Historical herbarium vouchers were sampled and leaf or cambium samples were collected in the field, dried in silica gel, and subsequently genotyped at 14 microsatellite loci (SSRs), as well as sequenced for two nuclear genes ( At103 ,Agt1 ) and one plastid region ( psbA-trnH ). These genetic data were then analyzed using Bayesian clustering, population genetics, and the construction of haplowebs to assess genetic clustering patterns, the distribution of genetic diversity, and genetic differentiation among populations. Multiple genetically differentiated clusters were observed in parapatry throughout Central Africa. Genetic diversity was high and similar among these clusters, apart from the most differentiated populations in southeast Democratic Republic of the Congo (DR Congo), which showed lower levels of genetic diversity. The genetic breaks detected between S. kamerunensis populations are likely not indicative of hidden species but rather result from ancient rainforest fragmentation during cold and dry periods in the Pliocene and/or Pleistocene. The strong genetic divergence between populations in southeast DR Congo could be the result of an ongoing speciation linked to ecological niche differentiation., SCOPUS: ar.j, info:eu-repo/semantics/published

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. Location: Macaronesia. Taxon: Bryophytes, pteridophytes, spermatophytes. Methods: Species turnover and nestedness were compared within and among archipelagos across taxonomic groups. The relationship between species turnover and nestedness, climatic, geological and geographic factors was analysed using generalized dissimilarity models. Results: Species turnover, but not nestedness, increased with the geographic scale. This increment decreased from spermatophytes, pteridophytes and bryophytes, wherein the median turnover was less than half that in spermatophytes. Bryophytes exhibited a significantly higher nestedness and lower turnover than spermatophytes. Extant climatic conditions and island age contributed the most to all models but the importance of island age for bryophyte and pteridophyte turnover was marginal. Spermatophyte floras clustered by archipelago, whereas the clustering patterns in pteridophyte and bryophyte floras reflected macroclimatic conditions. Main Conclusions: The lower increment of species turnover with spatial scale and the higher nestedness in bryophytes and pteridophytes than in spermatophytes reflect the variation in dispersal capacities and distribution ranges among land plants. Accordingly, extant climatic conditions contributed more to explain turnover in bryophytes and pteridophytes than in spermatophytes, whereas factors associated with dispersal limitations, including island age, geographic distance and archipelago structure, exhibited the reverse trend. The differences in beta diversity patterns, caused by different responses of Macaronesian land plant lineages to the, SCOPUS: ar.j, info:eu-repo/semantics/published

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.