Diversification, evolution and population dynamics of the genus Brachystegia, a keystone tree of African miombo woodlands

Miombo woodlands are vast wooded savannas covering 2 million km2 in East and Southern Africa. The main feature of these landscapes with closed but not overly dense canopy is the dominance of Brachystegia, Isoberlina, and Julbernardia legume trees genera. The timing of the onset of such vegetation, mainly understood through pollen fossils remains unclear. Dated molecular phylogeny calibrated with fossils for the aforementioned genera has the potential to provide details regarding the origin of species that nowadays dominate the current woodlands and possibly of miombo vegetation as a whole. The Brachystegia is a taxonomically complex genus and is compared to the other aforementioned genera, rich in species with 21 savanna species and eight species in the African Guineo-Congolian rain forests. We aim through the thesis to identify the diversification history of Brachystegia using dated phylogenies.We first reconstruct the Brachystegia phylogeny using nearly full plastome sequences in addition to ribosomal DNA sequences. Both sequences were obtained using a genome- skimming approach. In plastid phylogeny, species represented by multiple specimens appear rarely monophyletic while plastid clades display strong geographical structuring, independently of the species. Ribosomal phylogeny conversely allowed to identify morphological clades, but the lack of DNA polymorphism prevents the reconstruction of a well-resolved Brachystegia phylogeny. The strong spatial structure detected in plastid phylogeny suggests hybridization among the different species leading to recurrent chloroplast captures. Plastomes proved very informative for tracking the past dynamics of the genus and suggest a historical westwards expansion of miombo Brachystegia during the Plio-Pleistocene. We subsequently reconstructed the evolutionary history of the genus using targeted enrichment sequencing. Phylogenetic inferences were conducted using supermatrix and summary-method approaches on a dataset encompas
Doctorat en Sciences
info:eu-repo/semantics/nonPublished