Species delimitation in closely related plant taxa can be challenging because (i) reproductive barriers are not always congruent with morphological differentiation, (ii) use of plastid sequences might lead to misinterpretation, (iii) rare species might not be sampled. We revisited molecular-based species delimitation in the African genus Milicia, currently divided into M. regia (West Africa) and M. excelsa (from West to East Africa). We used 435 samples collected in West, Central and East Africa. We genotyped SNP and SSR loci to identify genetic clusters, and sequenced two plastid regions (psbA-trnH, trnC-ycf6) and a nuclear gene (At103) to confirm species’ divergence and compare species delimitation methods. We also examined whether ecological niche differentiation was congruent with sampled genetic structure. West African M. regia, West African and East African M. excelsa samples constituted three well distinct genetic clusters according to SNPs and SSRs. In Central Africa, two genetic clusters were consistently inferred by both types of markers, while a few scattered samples, sympatric with the preceding clusters but exhibiting leaf traits of M. regia, were grouped with the West African M. regia cluster based on SNPs or formed a distinct cluster based on SSRs. SSR results were confirmed by sequence data from the nuclear region At103 which revealed three distinct ‘Fields For Recombination’ corresponding to (i) West African M. regia, (ii) Central African samples with leaf traits of M. regia, and (iii) all M. excelsa samples. None of the plastid sequences provide indication of distinct clades of the three species-like units. Niche modelling techniques yielded a significant correlation between niche overlap and genetic distance. Our genetic data suggest that three species of Milicia could be recognized. It is surprising that the occurrence of two species in Central Africa was not reported for this well-known timber tree. Globally, our work highlights the importance of collecting samples in a systematic way and the need for combining different nuclear markers when dealing with species complexes. Recognizing cryptic species is particularly crucial for economically exploited species because some hidden taxa might actually be endangered as they are merged with more abundant species.

Adaptive evolution is a major driver of organism diversification, but the links between phenotypic traits and environmental niche remain little documented in tropical trees. Moreover, trait‐niche relationships are complex because a correlation between the traits and environmental niches displayed by a sample of species may result from (a) convergent evolution if different environmental conditions have selected different sets of traits, and/or (b) phylogenetic inertia if niche and morphological differences between species are simply function of their phylogenetic divergence, in which case the trait‐niche correlation does not imply any direct causal link. Here, we aim to assess the respective roles of phylogenetic inertia and convergent evolution in shaping the differences of botanical traits and environmental niches among congeneric African tree species that evolved in different biomes. This issue was addressed with the tree genus Guibourtia Benn. (Leguminosae and Detarioideae), which contains 13 African species occupying various forest habitat types, from rain forest to dry woodlands, with different climate and soil conditions. To this end, we combined morphological data with ecological niche modelling and used a highly resolved plastid phylogeny of the 13 African Guibourtia species. First, we demonstrated phylogenetic signals in both morphological traits (Mantel test between phylogenetic and morphological distances between species: r = .24, p = .031) and environmental niches (Mantel test between phylogenetic and niche distances between species: r = .23, p = .025). Second, we found a significant correlation between morphology and niche, at least between some of their respective dimensions (Mantel's r = .32, p = .013), even after accounting for phylogenetic inertia (Phylogenetic Independent Contrast: r = .69, p = .018). This correlation occurred between some leaflet and flower traits and solar radiation, relative humidity, precipitations, and temperature range. Our results demonstrate the convergent evolution of some morphological traits in response to climatic factors in congeneric tree species and highlight the action of selective forces, along with neutral ones, in shaping the divergence between congeneric tropical plants.

La présente thèse s’intéresse aux mécanismes à l’origine de la diversification des espèces d’arbres tropicaux. Elle utilise le genre Guibourtia Benn. (Fabaceae-Detarioideae) comme modèle biologique afin de comprendre les mécanismes historiques, biologiques et environnementaux à l’origine de la diversité de ce genre. Plus particulièrement, elle vise, d’une part, à étudier, au niveau interspécifique, le rôle relatif des forces évolutives neutres et de sélection dans la diversification du genre Guibourtia et, d’autre part, au niveau intra-spécifique, à questionner les causes de la différenciation des populations de trois espèces de Guibourtia. Au niveau interspécifique, la phylogénie datée basée sur le séquençage du génome chloroplastique complet a globalement confirmé la taxonomie actuelle. Elle a montré une diversification au milieu du Miocène en trois clades qui sont décrits aujourd’hui comme des sous-genres (Guibourtia, Gorskia et Pseudocopaiva). Elle démontre en outre que deux espèces américaines sont issues d’une migration de l’Afrique vers l’Amérique à la fin du Miocène. Il est également apparu que certains traits morphologiques ont été sélectionnés de manière convergente au sein des différents clades du genre Guibourtia en fonction des niches climatiques des espèces. Ce dernier résultat a été consolidé au moyen d’une expérimentation écophysiologique prouvant que la lumière constitue un important facteur de sélection et de différenciation adaptative entre certaines espèces du genre. Au niveau intraspécifique, une étude de phylogéographie a permis de mettre en évidence que les barrières biogéographiques chez G. ehie et les gradients climatiques chez G. coleosperma auraient contribué à la différenciation génétique des populations. En outre, cette étude montre une forte différenciation entre les populations de G. ehie d’Afrique de l’Ouest et d’Afrique centrale, en lien avec quelques traits morphologiques, ce qui préjuge de l’existence d’une nouvelle espèce. Enfin, chez G. tessmannii, espèce aux fruits déhiscents et graines arillées, nous avons identifié les principaux disperseurs dont les calaos (Ceratogymna atrata) qui pourraient contribuer à une dispersion à longue distance, influençant la structure spatiale de la variation génétique des populations. Cette thèse, en utilisant le genre Guibourtia comme modèle d’étude, a apporté de nouveaux éléments à la compréhension des mécanismes qui génèrent la diversité au sein des espèces d’arbres.