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. 2024 Apr 4;133(5-6):643–648. doi: 10.1093/aob/mcae041

Preface to the Special Issue on African Flora in a Changing World: Integrating multiple dimensions of diversity

A Muthama Muasya 1,✉, Jasper A Slingsby 2,3, G Anthony Verboom 4,5,6
PMCID: PMC11082513

Africa is home to globally important biodiversity. Straddling the equator and extending to temperate latitudes (at 37°N and 34°S; not including oceanic islands such as Marion and Prince Edward), the continent accommodates a variety of ecosystems and biomes, including tropical and temperate forests, savanna and montane grasslands, deserts, and Mediterranean-type ecosystems (Olson et al., 2011; Linder, 2014). The continent has remained relatively stable in the Cenozoic period (66 to 2.5 million years ago, Ma), despite dramatic geological events, including shifting coastlines, volcanism and formation of the rift valley (Couvreur et al., 2021). Africa has a rich diversity of vascular plants, with over 65 000 species recorded on the continent and its surrounding islands (Qian et al., 2021). This equates to approximately 18.5% of plant species recorded globally (Antonelli et al., 2023). However, efforts to catalogue African plant diversity and composition are uneven, with certain regions (e.g. tropical east and central Africa) being relatively well catalogued and others (e.g. Sudan) being barely explored (Marshal et al., 2016). At the same time, increased ecological and evolutionary research points to varied patterns of diversification and assembly of the flora; however, there is a lack of wider consolidation of the disparate knowledge. This Special Issue aims to bring together pan-African research and build a holistic synthesis of knowledge on the ecology and evolution of African plants. The 17 research papers cover broad themes in biogeography and macroevolution (Dagallier et al., 2024; Lamont et al., 2024; Lopes et al., 2024; Masters et al., 2024; Swart et al., 2024; Xue et al., 2024); patterns and determinants of species richness and composition in tropical- (Bello et al., 2024; Courtenay et al., 2024; Karimi and Hanes, 2024; Wieczorkowski et al., 2024) and temperate- (Cramer and Verboom, 2024; Verboom et al., 2024; Zhigila et al., 2024) areas; and ecological and genetic processes structuring population patterns (Chumová et al., 2024; Escudero et al., 2024; Kafuti et al., 2024; Rincón Barrado et al., 2024). These contributions focus on vascular plants in open and closed habitats (Fig. 1), with a bias towards the Cenozoic. Furthermore, the specific role of fire and its impact on the African Flora is featured in several papers (i.e. Courtenay et al., 2024; Cramer and Verboom, 2024; Verboom et al., 2024; Wieczorkowski et al., 2024).

Fig. 1.

Fig. 1.

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Examples of plants and habitat included in this study: (A) Monodora angolensis, Annonaceae; (B) Platycerium stemeria, Polypodiaceae; (C) Dicerothamnus rhinocerotis (Asteraceae); (D) Carex heloides (Cyperaceae); (E) Euphorbia balsaminifera (Euphorbiaceae); (F) Lannea edulis (Anacardiaceae) growing in miombo woodlands; (G) Grewia androyensis (Malvaceae); (H) quartz field in Overberg; (I) fynbos vegetation in Vogelgat.

Photo credits: A - https://www.inaturalist.org/observations/68804647, Warren McCleland; B - https://www.inaturalist.org/observations/198810883, bureaubenjamin; C - https://www.inaturalist.org/observations/198579046, geoffnichols; D—Marcial Escudero; E - https://www.inaturalist.org/observations/122922188, Pål A. Olsvik; F—Anya Courtenay, G—Porter P. Lowry, H, I—A. Muthama Muasya.

Inferring the deep biogeographic history of African plants is hampered by a lack of fossil evidence. Africa is generally poor in plant macrofossils; some of the best representatives include the Middle Eocene miombo woodland deposits in Tanzania (46 Ma; Jacobs, 2004). While multiple proxies (e.g. carbon isotope signatures, phytoliths) have been used to examine the evolution of iconic taxa, such as hominids, since the late Miocene (Bonnefille, 2010; Peppe et al., 2023), reconstruction of past vegetation and species distribution has relied on molecular phylogenetic reconstructions. Previously, the Cape and African Proteaceae were hypothesised to have an Australian origin (Barker et al., 2007). In this Issue, however, Lamont et al., (2024) synthesize insights from fossil pollen, molecular phylogenies, plate tectonics, and ocean circulation models to find stronger support for an African origin of Proteaceae. While there are many instances of pre-Miocene long distance dispersal (LDD) of flowering plants from Australia to Africa (e.g. Bergh and Linder, 2009; Elliott et al, 2023) and late Miocene LDD from Africa to Australia (e.g. Bergh and Linder, 2009; Viljoen et al., 2022), the ubiquity of Triorites africaensis fossils in tropical Africa 107–94 Ma (Lamont et al., 2024) supports a widespread occurrence of Proteaceae subfamily Proteoideae in Africa well before they arrived in Australia.

Another approach to deducing the biogeographic origin and diversification of lineages is to focus on species-, habitat-, or vegetation- type affinities. Pan-African forests, for example, are thought to have been widespread in the Palaeocene (56 Ma; Fine and Ree, 2006; Korasidis et al., 2022), notwithstanding evidence of ongoing contraction and expansion through the Cenozoic (Couvreur et al., 2021). The inferred age of forest-restricted lineages in Africa, such as the ancestor of the Poaceae, corroborate this picture, pointing to the presence of forests in Africa since at least 60 Ma (Elliott et al., 2023). Similarly, the Annonaceae, a shade-adapted family shown to have originated in African forests based on palynological and fossil evidence (Couvreur et al., 2011), is a model organism for understanding the biogeography and evolution of forest-restricted lineages. In this Issue, Lopes et al., (2024) report on the biogeographic history of Annonaceae tribe Bocageeae, which has a disjunct distribution in African and South American tropical forests. They show that Bocageeae arose in Africa around 55 Ma and dispersed to South America via a boreotropical land bridge through the northern latitudes at a time when the climate was warmer. Similar geodispersal from Africa to the Neotropics via a boreotropical connection (from 52–50 to 34 Ma; Wolfe, 1975) has been invoked to explain the observed disjunction of forest plant lineages in Sapotaceae (Smedmark and Anderberg, 2007) and Rubiaceae (Antonelli et al., 2009). Evidence in support of dispersal via a Northern Hemisphere, boreotropical land bridge, versus LDD across the Atlantic Ocean, include the presence of fossil evidence for Annonaceae in the Northern Hemisphere (Chandler, 1964; Manchester, 1994) since the unique fruits of the Bocageeacae are borne on the trunks of the trees and are unsuited for wind or bird dispersal typically associated with LDD.

In a second paper on the Annonaceae in this Issue, Dagallier et al., (2024) determine a late Oligocene origin (~25 Ma) of Annonaceae tribe Monodoreae (Fig. 1A) within the same ancestral area as that of Bocageeae in East Africa. This group, occurring in lowland forests which are separated into eastern and western blocks, speciated rapidly in the late Miocene in response to forest fragmentation caused by the mid-Miocene Climate Transition and regional uplifting which promoted aridification (Sepulchre et al., 2006; Couvreur et al., 2021). A subtly different diversification scenario is observed in lineages of epiphytes such as orchids (Zhang et al., 2023) and ferns (Polypodiaceae; Sundue et al., 2015), which are inferred to have originated after the Palaeocene-Eocene Thermal Maximum (PETM, ca. 56 Ma; Huurdeman et al., 2021) and diversified as the expanding forests created new vertical (arboreal) niches. In this Issue, Xue et al., (2024), sampling all the epiphytic staghorn fern (Platycerium; Fig. 1B) species for a plastome phylogenomic study, determine a stem node in East African forest during the Eocene-Oligocene boundary (~35.2 Ma), followed by Miocene diversification (15–10 Ma) and ‘out of Africa’ LDD to Asia and South America, where they diversified further. Overall, there is evidence that climatically-forced contraction and expansion of the forest habitats in Africa throughout the Cenozoic stimulated lineage diversification within these habitats.

Tectonic uplift and volcanism in the Miocene fragmented the lowland pantropical forest, in the process generating novel niches for Afromontane forests and Afroalpine plant communities. These high elevation ecosystems, aptly named the Afromontane archipelago (White, 1978), are separated by low-lying savannas which harbour a distinct biota. The Afroalpine islands have been colonised by plant species from temperate niches in the northern hemisphere (e.g. Kandziora et al., 2022) and from the Cape region (e.g. Galley et al., 2007) since the late Miocene, pointing to the role of LDD in traversing areas of unsuitable habitat. In this Issue, Swart et al., (2024) study six Afromontane forest blocks, from the equator (Mt Kenya) to temperate (Cape) forests, to evaluate whether latitudinal variation in species richness is linked to reproductive traits. While they find no direct relationship between latitude and reproductive traits (flower and fruits), they show that taller trees are more likely to be wind or insect pollinated and to bear larger fruits, with tree taxonomic diversity decreasing with increasing latitude. Dispersal syndrome also shows a biogeographic affinity, with palaeotropical tree genera displaying a relatively high incidence of black-purple fruit colour (bird dispersed) compared to pantropical genera, and Afrotropical genera having a high incidence of abiotic seed dispersal. Regardless of these findings, vertebrates are known to disperse seeds in African plants, for example, the forest dwelling Monodora myristica (Annonaceae) has its seeds dispersed by primates and elephants (Chapman and Durham, 2018).

Open habitats are extensive in Africa, being found in areas whose climate is unsuitable for forests, such as the deserts and arid savannas, and in areas in which disturbance (e.g. fire or herbivory) promotes growth of a continuous, shade-intolerant ground layer, largely comprised of C4 grasses and sedges in tropical latitudes (Bond, 2019). Fire is a key driver of African and global biodiversity (He et al., 2019) whose effect depends on return frequency and seasonality, driving feedback mechanisms. Among iconic open habitats are the miombo woodlands (Fig. 1F), which represents one of the largest savanna systems in the world (Frost, 1996), and being a habitat in which multiple fires return within a decade (Archibald et al., 2010). Using a long-term fire experiment in three treatments (Late-season, Early-season, No-fire) spanning over 60 years, Wieczorkowski et al., (2024, in this Issue) assess the impact of fire on miombo woodland diversity, finding the ground layer (C4 grasses and sedges, geoxyles) to be most diverse under a late-season fire treatment, and to have the least unique species under a no-fire treatment. Geoxyles are plants which have large woody underground parts, bearing ephemeral or short-lived above-ground stems, that resprout from buds located at ground level (Pausas et al., 2018). The growth-form of the geoxylic suffrutex, whose congeners are frequently growing in forests and woodlands, termed underground forest (White, 1976; Maurin et al., 2014), occurs in over 40 plant families in Africa. Fire is hypothesised to be the key driver in the independent evolution of geoxylic suffrutices among plant groups which have congeners that are trees. However, frost (Meller et al., 2022) and waterlogging (White, 1976) have been proposed as alternative drivers of geoxylic lifeforms in tropical Africa. Furthermore, Courtenay et al., (2024, in this Issue) quantify variability in the niche of underground tree species, finding that they occupy distinct and extreme environments relative to open and closed ecosystem congeners. There is low niche overlap among the four lineages studied (including Lannea; Fig. 1F), confirming the multiplicity of extreme environments (fire, frost, herbivory, waterlogging) that underground trees occupy.

In addition, fire-driven open habitats in Africa are ancestral areas for C4 grasses and sedges (PACMAD and Cypereae clades; Elliott et al., 2023), including important crop and fodder species. Masters et al., (2024, in this Issue) use phylogenomic data to infer the phylogenetic relations and ancestral traits of important forage species in the C4 grass genus Urochloa, finding five independent origins of forage species. These African grasses are preferred in tropical and subtropical parts of the world, and are widely grown to feed the beef industry in Brazil as they are highly palatable and nutrient dense yet tolerant of low-quality soils (Jank et al., 2014). Current trends in fire management such as fire exclusion and tree planting for carbon sequestration are likely having negative impacts on this diversity that thrives in regularly burned ecosystems (Veldman et al., 2015). Threatened species include fodder grasses that support iconic African wildlife and provide essential ecosystem services and livelihoods for the local human economy. Caution is needed in efforts to restore and manage African grasslands and other open habitats (Buisson et al., 2022), as this may threaten lineages which tolerate disturbance (including fire) but are intolerant of shade.

Drivers of species richness and diversity vary widely in Africa and globally. Mediterranean type ecosystems display exceptional richness, with the Greater Cape Floristic Region (GCFR) hosting nearly one fifth of Africa’s species richness within less than 0.5% of its continental area (Linder et al., 2010). Several factors are thought to influence species richness, including resource availability (e.g. water and temperature), spatial and temporal environmental heterogeneity, disturbance regime (e.g. fire), and biotic feedbacks. In this Issue, Cramer and Verboom, (2024) quantify drivers of species richness in the GCFR by evaluating richness variation at the quarter degrees square scale, and testing its dependence on climatic, edaphic, and biotic variables. They find species richness to be most strongly associated with spatial heterogeneity of climatic (mean annual precipitation, precipitation in coldest quarter), edaphic and biotic variables. Contrary to expectation, however, soil edaphic properties have no direct effect on species richness despite numerous previous studies linking edaphic turnover with beta diversity in the GCFR (see Cramer and Verboom, 2017). This edaphic paradox in the GCFR is further examined by Verboom et al., (2024, this Issue) who test the role of episodic fire on vegetation structure and composition in two discreet vegetation types with low and high nutrient soils (fynbos and renosterveld respectively) in the Cape Peninsula. They find that in the initial years after fire, both vegetation types are dominated by a common set of plant families with high foliar nutrient concentrations, but the fynbos communities (Fig. 1I) show declining species richness with time after fire in families with high foliar nutrient concentrations. No such pattern is apparent in species from families with low foliar nutrient concentrations, or in renosterveld growing on more fertile soils. Based on these data, they identify a role for fire-modulated nutrient release in stimulating species turnover and richness in fynbos vegetation.

A unique feature of the GCFR is rapid turnover of edaphic niches. This is well exemplified by quartz field habitats, which are found within both the renosterveld and succulent Karoo vegetation (Schmiedel and Jürgens, 1999). Quartz fields are edaphic islands which differ in nutrient and water availability from the intervening vegetation matrix, and which support a distinct flora. Zhigila et al., (2024, in this Issue) examine species diversity and phylogenetic structure within and among quartz fields, and between quartz fields and the surrounding vegetation. They show that Aizoaceae, Asteraceae, Crassulaceae and Fabaceae are over-represented on quartz fields, but quartz specialists are often more similar to species in surrounding communities, yet there is no clear phylogenetic community structure. The quartz fields (Fig. 1H) are dominated by low growing plants (nano chamaephytes), which tend to be succulents that use crassulacean acid metabolism photosynthesis (CAM; Gilman et al., 2023; Sage et al., 2023), thus explaining the high species richness of the succulent families (Aizoaceae and Crassulaceae). These nuanced diversity patterns are observed when the studies scale to continental levels, as seen in the palaeotropical woody genus, Grewia (Fig. 1G, Malvaceae), growing in over 40 countries in Africa (POWO, 2024). Grewia attains its greatest species richness in Madagascar, together with coastal Tanzania/Kenya and in tropical southern Africa (Zambezian ecoregion, sensuLinder et al., 2012); its richness is best predicted by parameters related to aridity (potential evapotranspiration) (Karimi and Hanes, 2024, in this Issue). Fine scale patterns in Madagascar show highest species richness in the northwest and southwest ecoregions, where co-occurring species are morphologically divergent, and species turnover between ecoregions is hypothesised to be driven by biotic (birds, small mammals) dispersal agents. The above studies on species richness assume thorough effort in plant collection in the regions. Despite botanical collection on the continent gaining momentum in the 19th century, new species continue to be discovered in remote areas and effort is uneven across the continent. For instance, Bello et al., (2024, in this Issue) find over 20 vascular plant species new to science are described annually in Nigeria, Africa’s most populous country and one where taxonomic expertise is lacking. They predict that nearly 1000 species will be described in the next 50 years. Two of the 32 global diversity darkspots are in Africa, namely the Cape Provinces and Madagascar (Antonelli et al., 2023). Diversity darkspots are regions predicted to lack information about their species diversity and distribution, and are often recognized as also being biodiversity hotspots, as is the case with the two African darkspots (Myers et al., 2000). In such areas, accelerated plant species documentation is urgently needed for the implementation of conservation actions.

Population level processes are fundamental in driving macroevolution. Phylogeographic studies, incorporating detailed sampling and rapidly evolving molecular markers, are lagging in African plants science, where most effort has focussed on crops and other economically important species. Chumová et al., (2024, in this Issue) studied the flagship renosterveld species, Dicerothamnus rhinocerotis (Fig. 1C, renosterbos; Asteraceae), to determine whether recognized morphotypes differ in terms of cytotype, genetics, and environmental niche. Two ploidy types coincide with known morphotypes (Levyns, 1929), and tend to occur in distinct areas but are genetically similar, with tetraploids arising independently in the four genetic clusters, and the cytotypes differ in their niche optima for water availability and temperature. Similar patterns occur in the Mediterranean sedge Carex heloides (Fig. 1D; Escudero et al., 2024, in this Issue), whose disjunct populations differ in levels of heterogeneity and karyotype, with a Moroccan population derived out of an Iberian Peninsula population during the Pleistocene. Limited studies have focused on chromosomal and genome features of the African flora, but a recent global review shows relatively low proportion of polyploids and smaller genomes except in the mediterranean Cape and northern African floras (Bureš et al., 2024).

Biogeographic disjunctions are observed within and between species in Africa. The aridity adapted flora in North Africa, the Rand flora, has been subject to recent studies aiming to explain the origin of sister taxa that are geographically separated between western and eastern regions (e.g. Pokorny et al., 2015). Most striking is the phylogeography of sweet tabaiba, Euphorbia balsaminifera (Fig. 1E; Euphorbiaceae), a dioecious succulent dendroid shrub which occurs in the Canary Islands and northwestern Africa and has its sister species distributed on the eastern side of the Sahara Desert into the Horn of Africa and Socotra. Rincón Barrado et al., (2024, in this Issue) test a hypothesis of climatic extinction of the Rand flora (Sanmartín et al., 2010, Pokorny et al., 2015) by densely sampling populations of E. balsaminifera across its range. Their results show a Canary Island origin of the species, with east-to-west island colonisation and admixture of eastern island and northwest African populations. This led to the conclusion that the northwestern African populations are not remnants of an ancestral population, but instead are recent migrants. A different scenario is hypothesised to explain the phylogeographic structure among timber species from the African lowland forests. In several co-occurring species, population level studies show genetic clustering centred in five regions, interpreted to represent refugia (Maley, 1996). This clustering apparently preserves evidence of Pleistocene fragmentation (Piñeiro et al., 2021). Several economically important species show variability in regeneration history and population dynamics (Bhasin et al., 2024), and ecophysiological conditions for heartwood formation within their geographic range and under different land use regimes (Kafuti et al., 2024, this Issue). Spatially explicit phylogeographical studies, especially among widespread species, need to be integrated into decision making towards sustainable management of timber trees and other species.

Overall, the 17 papers presented in this Special Issue advance current understanding on the ecology and evolution of Africa’s rich plant diversity, the latter spanning different dimensions of diversity, from the population to the ecosystem level. This diversity, which has evolved over a long period, under the influence of geomorphic and climate change, is under increasing conservation threat due to overexploitation of the plant resources and/or their habitats. Of particular concern is the adoption of paradigms of biodiversity conservation developed on other continents, especially in the temperate north, in which the historical and contemporary processes responsible for present day plant diversity differ from those which have shaped the African flora. The historical dynamism of the northern Eurasian and northern North American climates, for example, has produced a flora having lower endemism and greater mobility than is the case for much of the African flora, and whose floristic uniqueness is consequently less threatened by contemporary climate change (Dynesius and Jansson, 2000). Furthermore, much of these regions are dominated by forests, and there is most focus on the conservation and restoration of forests, whereas most of Africa is comprised of open savanna-grasslands and shrublands. We acknowledge that anthropogenic climate change (Parmesan and Hanley, 2015) is likely to impact the African flora in variously ways, the most evident being bush encroachment into African savannas which is attributed to tree seedlings vigorously growing to escape the fire trap (Devine et al., 2017). The present Issue advances our knowledge and understanding of the African flora, showcasing some of the key processes that underpin its floristic diversity and so providing a foundation for conservation actions that are more appropriate in an African context. However, in demonstrating the improved understanding gained from the application of modern scientific methods it also reveals gaps, highlighting, for example, the urgent need for expanded specimen collection and the development of densely sampled phylogenomic and phylogeographic datasets towards a more complete description of African plant diversity.

Contributor Information

A Muthama Muasya, Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa.

Jasper A Slingsby, Centre for Statistics in Ecology, Environment and Conservation, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa; Fynbos Node, South African Environmental Observation Network, Observatory 7925, South Africa.

G Anthony Verboom, Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa; Department of Biological & Environmental Sciences, University of Gothenburg, PO Box 463, 40530 Gothenburg, Sweden; Gothenburg Botanical Garden (Botaniska), Carl Skottsberg Gata 22A, 41319 Gothenburg, Sweden.

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