Aim The aim of this study was to understand the origin of the forest flora currently found in the Dahomey Gap (DG), a 200‐km‐wide forest‐savanna mosaic separating the West African and Central African rain forest blocks. More specifically, using a widespread rain forest tree species, Distemonanthus benthamianus (Fabaceae), we will test the hypothesis that the DG populations are remnants of a population dating back from the African Humid Period of the Holocene, when West African and Central African rain forests were supposedly connected. Location Tropical forests of Upper Guinea (West Africa) and Lower Guinea (Atlantic Central Africa) and the forest‐savanna mosaic of the DG extending from eastern Ghana to Benin. Methods Four hundred and twenty‐nine D. benthamianus samples from West to Central Africa were genotyped with 11 nuclear microsatellite markers. After detecting geographically coherent gene pools, their genetic diversity and differentiation were estimated and their demographic histories were inferred using coalescent simulations and approximate Bayesian computation (ABC) tests. Results Five parapatric gene pools were identified: three in Lower Guinea, one in Upper Guinea and one in the DG. ABC tests indicate that the DG gene pool probably originates from the admixture of adjacent Upper and Lower Guinean gene pools, with a higher contribution from Upper Guinea, at a timeframe consistent with the early Holocene (around 13–7 ka). The lower genetic diversity documented in the DG could result from a founder effect and/or from a demographic decline consistent with the Holocene climatic pejoration documented around 3 ka. Main conclusions This phylogeographical study inferring the history of the DG populations of D. benthamianus is consistent with palaeovegetation data that suggest that the forest flora of the DG might be essentially relicts of the early Holocene period when the Guineo‐Congolian forest reached its maximum geographical distribution.

Paleo-environmental reconstructions show that the distribution of tropical African rain forests was affected by Quaternary climate changes. They suggest that the Dahomey Gap (DG)—the savanna corridor that currently separates Upper Guinean (UG, West Africa) and Lower Guinean (LG, western Central Africa) rain forest blocks—was forested during the African Humid Holocene period (from at least 9 ka till 4.5 ka), and possibly during other interglacial periods, while an open vegetation developed in the DG under drier conditions, notably during glacial maxima. Nowadays, relics of semi-deciduous forests containing UG and LG forest species are still present within the DG. We used one of these species, the pioneer tree Terminalia superba (Combretaceae), to study past forest fragmentation in the DG and its impact on infraspecific biodiversity. A Bayesian clustering analysis of 299 individuals genotyped at 14 nuclear microsatellites revealed five parapatric genetic clusters (UG, DG, and three in LG) with low to moderate genetic differentiation (Fst from 0.02 to 0.24). Approximate Bayesian Computation analyses inferred a demographic bottleneck around the penultimate glacial period in all populations. They also supported an origin of the DG population by admixture of UG and LG populations around 54,000 (27,600–161,000) years bp, thus before the Last Glacial Maximum. These results contrast with those obtained on Distemonanthus benthamianus where the DG population seems to originate from the Humid Holocene period. We discuss these differences in light of the ecology of each species. Our results challenge the simplistic view linking population fragmentation/expansion with glacial/interglacial periods in African forest species.

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Resolving phylogenetic relationships allows the investigation of how species diversity has evolved in various ecosystems. The genera Entandrophragma and Khaya consist of tree species distributed in different African biomes (lowland rain forest, dry forest and savanna, montane forest), and are suitable to examine how (single or multiple events) and when the processes of diversification led to biome transitions. Based on the sequencing of plastome (pDNA: c. 160,000 bp), ribosomal DNA (rDNA: c. 5,300 bp), and habitat characteristic data for each species, we have: (i) reconstructed phylogenetic relationships between species and estimated the divergence period between the main lineages, and (ii) reconstructed ancestral states regarding biome preferences. The phylogenetic trees obtained with both markers support monophyly of the five sections of Entandrophragma previously defined based on fruit and floral characters. Nevertheless, the position of some species from the pDNA and rDNA tree topologies varied within sections. In Khaya, pDNA and rDNA show very divergent topologies, possibly due to a more recent diversification involving incomplete lineage sorting and/or recurrent hybridization events. Khaya diversified during the Pliocene and Pleistocene according to both markers; whereas, according to rDNA data, the Entandrophragma sections diverged during the early Miocene and species within sections diverged from the late Miocene to the Pleistocene. Divergence date estimates tended to be more recent using pDNA data. Biome transitions could not be reconstructed in Khaya as the species tree remains unresolved. Contrarily, three independent biome transitions were inferred in Entandrophragma. The first transition from rain to dry forests occurred during the Miocene and two other transitions were inferred during the Pleistocene, one from rain forest to dry forest and another from rain forest to mountain forest. Overall, we demonstrate that multiple biome transitions occurred, starting from a rain forest biome, possibly reflecting the global trend of aridification of Africa throughout the Cenozoic.

Paleo-environmental data show that the distribution of African rain forests was affected by Quaternary climate changes. In particular, the Dahomey Gap (DG)a 200 km wide savanna corridor currently separating the West African and Central African rain forest blocks and containing relict rain forest fragmentswas forested during the mid-Holocene and possibly during previous interglacial periods, whereas it was dominated by open vegetation (savanna) during glacial periods. Genetic signatures of past population fragmentation and demographic changes have been found in some African forest plant species using nuclear markers, but such events appear not to have been synchronous or shared across species. To better understand the colonization history of the DG by rain forest trees through seed dispersal, the plastid genomes of two widespread African forest legume trees, Anthonotha macrophylla and Distemonanthus benthamianus, were sequenced in 47 individuals for each species, providing unprecedented phylogenetic resolution of their maternal lineages (857 and 115 SNPs, respectively). Both species exhibit distinct lineages separating three regions: 1. Upper Guinea (UG, i.e. the West African forest block), 2. the area ranging from the DG to the Cameroon volcanic line (CVL), and 3. Lower Guinea (LG, the western part of the Central African forest block) where three lineages co-occur. In both species, the DG populations (including southern Nigeria west of Cross River) exhibit much lower genetic diversity than UG and LG populations, and their plastid lineages originate from the CVL, confirming the role of the CVL as an ancient forest refuge. Despite the similar phylogeographic structures displayed by A. macrophylla and D. benthamianus, molecular dating indicates very contrasting ages of lineage divergence (UG diverged from LG since c. 7 Ma and 0.7 Ma, respectively) and DG colonization (probably following the Mid Pleistocene Transition and the Last Glacial Maximum, respectively). The stability of forest refuge areas and repeated similar forest shrinking/expanding events during successive glacial periods might explain why similar phylogeographic patterns can be generated over contrasting timescales. Piñeiro et al., 2017). Environmental barriers (e.g. dry corridors separating wet ecosystems) can impede the homogenization of species pools while favoring genetic divergence between conspecific populations, as recently shown for the Dahomey Gap (Demenou et al., 2017; Demenou et al., 2016; Iloh et al., 2017). The Dahomey Gap (hereafter DG) is a c. 200 km wide corridor (Demenou, 2018) dominated by open vegetation in eastern Ghana, Togo, Benin, and western Nigeria, which separates two major Guineo-Congolian forest blocks: Upper Guinea (hereafter UG), which extends from Sierra Leone to Ghana, and Lower Guinea