Insights into the onset of African Miombo woodlands & Exploring diversification tempos and evolutionary histories from African rain to montane forests


Monday, November 6, 2023 - 10:00 to 12:00


OIST Main Campus (Lab 3 C700) and Online


Zoom link:
Meeting ID: 984 2599 0760, Password: 590538

1. Insights into the onset of African Miombo woodlands: Phylogenomics of the keystone genus Brachystegia (Fabaceae, Detarioideae)

Arthur F. Boom

Royal Museum for Central Africa, Biology Department, Section Vertebrates, Tervuren, Belgium.


Miombo woodlands are vast wooded savannas covering around 2 million square kilometers in eastern and southern Africa. The main feature of these landscapes with closed but not overly dense canopy is the dominance of legume trees of genera Brachystegia, Isoberlina, and Julbernardia. The timing of the onset of such vegetation remains unclear. Dated molecular phylogenies for those genera have the potential to provide insights regarding the origin of species that dominate the current woodlands. In this presentation, we will discuss mainly the diversification history of Brachystegia, a taxonomically difficult genus with 21 savanna species and eight Guineo-Congolian rainforest species in Africa. We reconstruct first a Brachystegia phylogeny using plastome DNA sequences obtained using a genome-skimming approach. In this plastid phylogeny, species represented by multiple specimens appear rarely monophyletic while plastid clades display strong geographical structuring, independently of the species. The strong spatial structure detected in this phylogeny suggests hybridization among the different species leading to recurrent chloroplast captures. We then reconstructed the evolutionary history of the genus using targeted enrichment sequencing of nuclear genes, encompassing around 200 loci. Opposite to previous reconstructions, most species appear as monophyletic groups. Introgressed plastomes, the signature of ILS, and/or reticulation for nuclear genes when species are nevertheless relatively well delineated by nuclear genome support to some extent that Brachystegia may behave as a group of interfertile but still relatively well-delineated species (syngameon). Molecular dating analysis supports a Pliocene origin for the genus, with most of the diversification events occurring during the Plio-Pleistocene. Our results indicate a recent origin of the dominant species of the miombo congruently with their spatial expansion documented by plastid data, giving insights into the temporal and spatial evolution of the miombo woodlands.

About Arthur:

Arthur F. Boom conducted his master's and Ph.D. degrees in the Evolutionary Biology and Ecology unit at the Université libre de Bruxelles (Belgium) under the supervision of Olivier J. Hardy. He started working on developing metabarcoding approaches to investigate the insitu diet of Bonobos (Pan paniscus). He then worked on the phylogeography and biogeography of African trees using genomic approaches to dissect their evolutionary history. Currently, his main research is conducted on aquatic organisms. He is looking at species delineation and phylogeographic patterns for African freshwater fish species, with a specific focus on the ichthyofauna of the lakes in the Albertine Rift. This current research is conducted with different partners at the Royal Museum for Central Africa (Belgium) under the supervision of Jos Snoeks (

2. Exploring diversification tempos and evolutionary histories from African rain to montane forests


Muséum départemental du Var, Toulon, FRANCE

Université Libre de Bruxelles, Evolutionary Biology and Ecology unit, Brussels, BELGIUM



Exploring what we know about the evolutionary history of African forests is a prerequisite to predict their potential response and resilience capacity to ongoing and future perturbations. According to palaeoecological proxies, the story of African forests is closely linked to Pliocene and Pleistocene climate oscillations: the contraction of forest cover during cold and dry glacial periods was counterbalanced by its expansion during warmer and wetter interglacial episodes. However, the role of climate as motor of evolution of tree species is difficult to assess with palaeoecology at a fine taxonomical scale, and there is still much uncertainty regarding the spatio-temporal species turnover, the intensity of past forest fragmentation, the size and location of forest refugia during glacial maxima and their role on diversification. One key proxy to address these questions consists in studying the genetic diversity and structure of forest-dwelling trees and disentangling the singular and repeated evolutionary trajectories of their constituent tree species through integrative phylogeography.

The development of high throughput sequencing through the capture of chloroplast genomes (pDNA) at deep multiplexing levels has been undertaken on three key trees belonging to three distinct functional groups. Plastomes were sequenced for 80 to 145 samples representative of (i) the rainforest long-living and shade-tolerant tree Greenwayodendron suaveolens (Annonaceae) (ii) the pioneer and short-living tree Musanga cecropioides (Urticaceae), and (iii) the afromontane Podocarpus milanjianus/latifolius (Podocarpaceae) conifers with a fragmented distribution above 1500-2000 m elevation in central, eastern and southern Africa. The polymorphism found on almost whole plastomes (several hundreds of SNPs along c. 100,000 bp) provides a very detailed phylogeographical signal to infer the evolutionary history of populations. At a population scale, nuclear microsatellite genotyping was also undertaken to better estimate gene flow and demographic history.

Distinct pDNA phylogroups with well-delimited geographical ranges were found for each species. Populations of Musanga and Greenwayodendron could have been fragmented into a restricted number of refugial areas in the past that seems display diverse demographic signatures. By contrast, fragmentation is under progress for Podocarpus trees where past extensive gene flow could be used to track the response of vegetation belts to past climate changes, and to compare to palaeoecological reconstructions. Molecular dating provide a more precise temporal framework for comparing speciation and the diversification of each phylogroup, and the role of their life history traits in terms of resilience during glacial/interglacial oscillations. Finally, patterns of genetic diversity will be discussed to better understand the mechanisms driving the current distribution of trees populations and their future persistence in a changing environmental context.

About Jérémy:

Jérémy Migliore is a molecular ecologist interested in evolutionary biogeography, phylogeography, population genetics, and conservation genetics of plants from the Mediterranean and Sahara, to Tropical Africa. One of his main professional objective is to provide scientific knowledge to societal actors in the field of biodiversity evolution for a sustainable conservation of life beings and their habitats.

Working as vice Curator in a Natural History Museum in Southern France (Muséum départemental du Var), in close collaboration with the Université Libre de Bruxelles (Evolutionary Biology and Ecology group), Jérémy is focusing on the origin, evolution and persistence of biodiversity towards a better understanding of the imprints left by past environmental changes on plants history. Now, he is developing research programs and biodiversity monitoring activities, promoting natural history collections and science dissemination.

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