ECR Feature: Arthur Boom unravels the history of miombo woodlands through study of Brachystegia plastid genomes

Arthur Boom is a PhD student at the Université Libre de Bruxelles. He is interested in the biogeography of African plants and the application of genomic approaches to study their evolutionary. Arthur shares his recent work on trees from the Brachystegia genus to understand the history of miombo woodlands in Africa through sequencing of their plastid genomes.

Arthur Boom

Personal links. ResearchGate | GoogleScholar

Institute. Evolutionary Biology & Ecology unit, Université Libre de Bruxelles (Belgium)

Academic life stage. PhD student.

Research themes. Phylogenomics, Phylogeography, and Biogeography of African plant taxa.

Current study system. My co-authors and I are currently studying the evolutionary history of Brachystegia tree species. This genus is particularly emblematic of southern African savannas and woodlands. With roughly twenty species, it is one of the most dominant tree genera in the vegetation belt stretching from Angola to Tanzania: the miombo woodlands (c. 2.7 million km²). Additionally, eight Brachystegia species are also distributed in the African Guineo-Congolian rain forests. This spatial distribution and diversity of species allow the investigation of global biogeographical questions. Namely, how, and when, tree species diversified in African biomes and how plant lineages may have shifted between biomes. Consequently, Brachystegiaas as a broadly distributed genus is a useful system to explore the onset of current African biodiversity. However, Brachystegia is also a taxonomically challenging taxon to work with, as several species are morphologically variable in addition to having blurred species boundaries. Little is known about what influences patterns of morphological variation for these species and may be due either to hybridization, ecotypic differentiation, or phenotypic plasticity.

Recent paper in JBI. Boom, AF, Migliore, J, Kaymak, E, Meerts, P, Hardy, OJ. Plastid introgression and evolution of African miombo woodlands: New insights from the plastome‐based phylogeny of Brachystegia trees. J Biogeogr. 2021; 48: 933– 946.

Motivation behind this paper. Molecular-dated phylogenies using either large taxonomic coverage, or focusing on some key plant taxa, are essential to understand the tempo and modalities of species diversification. In plants, such phylogenetic investigations have been extensively conducted in Europe and northern America, such that generation of major phylogeographic hypotheses on factors affecting lineage diversification in plants are geographically biased. In the Afrotropics, we are increasingly testing these hypotheses developed on other continents to determine their global generality. In comparison to Europe/northern America, African woodlands and savannas are still poorly investigated despite their wide spatial distribution, their functional properties and unique biodiversity, and their key role in Hominid evolution. Brachystegia genus is typical, dominant, and diverse in the miombo woodlands of Africa and is a potentially useful system to gain new insights on the history African savannas and woodlands. We aimed to explore the phylogenetic relationships and corresponding divergence timing at the genus scale among Brachystegia species.

Some of the specimens that were collected in the frame of this study (A, B, and C: Brachystegia spiciformisB. longifolia and B. boehmii). In addition to herbarium vouchers, we also collected leaflets and dried them using silica gel (in D, left to right: B. spiciformisB. longifolia and B. taxifolia). DNA is generally better conserved using the latter approach.

Key methodologies. Our approach used African field collections and herbarium vouchers in combination with high-throughput sequencing technologies. We took advantage of recent advances in molecular biology to extract DNA from ancient plant material and to assemble plastid genomes of 25 different Brachystegia tree taxa. Bioinformatic tools were thus essential to reconstruct the Brachystegia plastid phylogeny, using Bayesian and Maximum-Likelihood methods. To infer the temporal dynamics of Brachystegia diversification, we conducted a two-step dating approach. Firstly, a dated phylogeny covering the Fabaceae family allowed the use of multiple fossils for time calibrations and to estimate the divergence time between Brachystegia and a near-relative genus, Julbernardia. We then applied this divergence time estimate to calibrate the Brachystegia plastid phylogeny.

Major results. Our main contribution is a proposed scenario for the past history of Brachystegia settlements, allowing us to better understand the history of miombo woodlands. In our JBI paper, plastid genomes proved to be very informative for tracking the past dynamics of the genus Brachystegia. In southern Africa, Brachystegia plastid clades appear older in eastern regions than in western ones, suggesting a possible historical westwards expansion of miombo vegetation, during the Plio-Pleistocene. Our results bring explicit insights of the past distribution of one of the largest African woodland types.

Unexpected outcomes. We were particularly surprised that the Brachystegia clades revealed by the plastid phylogeny exhibited a strong geographical structuring independently of their species delineation. Specimens from the same species were rarely monophyletic, except when they were geographically close. This unexpected tree topology could be explained by hybridisation with subsequent backcrosses. This highlights possible cytoplasmic introgression between species that co-occur in the same area and share closely related plastid genomes. To our knowledge, our study is one of the first to report such a phenomenon of spatially dependent introgression in a tree genus from the Afrotropics, but such introgression has been observed in Quercus and Eucalyptus trees in Neartic, Paleartic and Australasian realms.

(left) Miombo woodlands have a closed but not overly dense canopy, allowing the growth of an herbaceous layer. They are dominated by trees such as Brachystegia, Isoberlina, and Julbernardia (Lubumbashi surroundings, Democratic Republic of Congo). (right) Collection of branches and leaves from a Brachystegia tree using a long-reach pruner.

Next steps? Using plastid genomes, we now have a better view about the miombo spatial and temporal dynamics. However, further investigations are needed to provide a dated species phylogenetic tree of the Brachystegia species. We are thus currently sequencing several hundred low-copy nuclear genes, using a targeted enrichment genomic approach. Additionally, by increasing our geographical cover, we would like to deeply investigate the Brachystegia genus developing continuous phylogeographic and phylodynamic inferences using additional plastid sequences. Such investigations would be conducted in a comparative framework using other emblematic trees from miombo woodlands such as Julbernardia and Isoberlina.

If you could study any organism on Earth, what would it be?Without surprise, if I could study any organism on Earth, it would be trees! Through my ongoing PhD thesis, I was particularly surprised by the large knowledge gaps in the phylogeographic history of trees! I am especially interested in tropical trees, which are poorly studied despite their ecosystem engineer role in most of the hotspots of biodiversity. Among the questions coming to my mind: how do tropical and dominant trees diversify? How is such diversity maintained through time? These questions reflect a more global interest on hybridisation and the concepts of plant species. Oaks are particularly interesting in this context as recent genomic and ecological investigations have broader implications on how dominant trees diversify, coexist, cooperate and compete. I am also convinced that tropical taxa can be very promising in evolutionary ecology. Apart from plants, I am also fond of jellyfish, bumblebees, and dinosaurs!

Anything else to add? Collecting plant materials from tropical African species, like Brachystegia, distributed on such a wide spatial scale (18 countries), including narrowly and disjunctly distributed taxa was definitively a challenging aspect of this study. It was also a unique opportunity to discover unforgettable landscapes in Democratic Republic of Congo, to explore precious herbarium collections (BR, BRLU, FHO & LISC), and to develop innovative genome skimming sequencing. Even fairly old vouchers can be of use with such an approach. Indeed, one of the samples used in this study was collected in 1933! Finally, we were helped in many ways during this study, and I’d like to take the opportunity to thank all the people that made this study feasible, researchers, those involved in the field collections, curators and lab colleagues.

Published by jbiogeography

Contributing to the growth and societal relevance of the discipline of biogeography through dissemination of biogeographical research.

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