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 encompassing around 200 individuals loci for more than 200,000 base pairs. Opposite to previous reconstructions, most species appear as monophyletic groups even if high levels of gene tree conflict between the species trees and individual gene trees are reported, suggesting either incomplete lineage sorting (ILS) and/or reticulate evolution. Introgressed plastomes, and signature of ILS and reticulation for nuclear genes when species are nevertheless relatively well delineated by nuclear genome support to some extent that Brachystegia may behave a group of interfertile but still relatively well-delineated species (i.e. syngameon). Molecular dating analysis supports a Pliocene origin for the genus, with most of the diversification events occurring during the Plio-Pleistocene. We also conducted preliminary investigations to explore the potential of the genomics approaches used in this thesis to delineate problematic species or to reconstruct the past spatial dynamic of Brachystegia in current miombo regions.Overall, through this thesis, we clarified many aspects of the taxonomically complex Brachystegia genus. Genomic data support hybridization and plastid introgression on large spatial scales, giving credit to a Brachystegia syngameon that remains yet to be furthered characterised and validated. Moreover, results indicate a fairly recent origin of dominant species of the miombo congruently with their spatial expansion documented by plastid data, giving possibly insights into the temporal and spatial evolution of the miombo woodlands / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

dissertation submitted in fulfilment of the academic requirements for the degree of Master of Science in the School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg. May 2015 / In this study I investigated the climate ecology and population biology of Brachystegia spiciformis (miombo) woodland at the distributional range edge in southern Africa. The main aim of the study was to exploit miombo relict populations, isolated well beyond contemporary distribution, to establish likely spatial and population dynamic response to future global climate change. Miombo woodlands have expanded and contracted across the central African plateau over geological time, with palynological evidence supporting an extensive latitudinal range during the Holocene altithermal. It is hypothesised that small shifts in climate may have major impacts on woodland dynamics and distribution. However, miombo relict populations in southern Africa, one in Mozambique and one in South Africa, suggest refugia; physiographic settings that support a once prevalent regional climate that has been lost (or is being lost) due to climatic shifts. Inclusion of relict populations has been shown to improve the performance of model-based projections elsewhere and have value as natural laboratories for investigating how populations react to on-going climatic change. This study aims to contribute to a better understanding of miombo woodland - an ecologically and economically significant savanna community - response to global climate change in southern Africa. A niche modelling approach was used to produce present-day and select future B. spiciformis woodland ecological niche models. Precipitation of the wettest quarter and temperature seasonality were identified as the two most important bioclimatic variables explaining B. spiciformis woodland distribution in southern Africa. Both variables displayed a relatively narrow range of optimal suitability for the species; 422 - 576 mm and 2.6 - 3.0 °C, respectively. In addition, significantly high temperature seasonality and maximum temperature of the warmest month were identified as limiting factors at the periphery of the contemporary miombo woodland distribution. Considering future regional climate change projections, it is suggested that the B. spiciformis climate niche could retract by between 30.6 - 47.3% in southern Africa by 2050. v In addition, a meta-population analysis of miombo woodland at the southern distributional range edge was carried out to elucidate patterns in population dynamics that could validate theorized climate response. Whilst the continuous miombo woodlands occurring to the north of the southern African range edge are internally relatively homogenous in community composition, relict populations reflected a loss of natural biota and a restructuring of the vegetation unit resulting in clear divergence from the core and range edge communities, and from each other. Although B. spiciformis reproduction, population density and structural dimensions were significantly low at the recently discovered relict population in South Africa relative to populations occurring to the north, we suggest that the medium-term persistence of this population is plausible based on the longevity of genets, their historic resilience, and a traditional management regime. The vicariant B. spiciformis relict population located in southern Mozambique is greater in extent than its South African counterpart and data suggest suitable reproduction dynamics for medium-term persistence. However, this population is currently heavily impacted by unsustainable habitat transformation under a lack of formal ecological or conservation protection. This study uniquely highlights B. spiciformis woodland as a climate (precipitation) sensitive component of savanna ecosystems in southern Africa and provides important baseline data for population dynamics at the distributional range edge.