Although today the forest cover is continuous in Central Africa this may have not always been the case, as the scarce fossil record in this region suggests that arid conditions might have significantly reduced tree density during the Ice Ages. Our aim was to investigate whether the dry ice-age periods left a genetic signature on tree species that can be used to infer the date of the past fragmentation of the rainforest. We sequenced reduced representation libraries of 182 samples representing five widespread Legume trees and seven outgroups. Phylogenetic analyses identified an early divergent lineage for all species in West Africa (Upper Guinea), and two clades in Central Africa: Lower Guinea-North and Lower Guinea-South. As the structure separating the Northern and Southern clades -congruent across species- cannot be explained by geographic barriers, we tested other hypotheses with demographic model testing using ∂a∂I. The best estimates indicate that the two clades split between the Upper Pliocene and the Pleistocene, a date compatible with forest fragmentation driven by ice-age climatic oscillations. Furthermore, we found remarkably older split dates for the shade-tolerant tree species with non-assisted seed dispersal than for light-demanding species with long-distance wind dispersal. Different recolonisation abilities after recurrent cycles of forest fragmentation seem to explain why species with long-distance dispersal show more recent genetic admixture between the two clades than species with limited seed dispersal. Despite their old history, our results depict the African rainforests as a dynamic biome where tree species have expanded relatively recently after the last glaciation.

vcf and fasta files of Genotyping By Sequencing data of five Legume tree species widespread in the rainforests of West and Central Africa Pericopsis elata (Harms) Meeuwen, Distemonanthus benthamianus Baill., Erythrophleum ivorense A. Chev., Erythrophleum suaveolens (Guill. & Perr.) Brenan,and Scorodophloeus zenkeri Harms. Seven outgroup species (OUT) were also sequenced: Pericopsis laxiflora (Benth. Ex Baker) Meewen, Dicorynia guianensis Amshoff, Dialium guianense (Aubl.) Sandwith, Erythrophleum africanum (Welw. Ex Benth.) Harms, Erythrophleum chlorostachys Baill., Calpocalyx brevibracteatus Harms, and Hymenostegia afzelii (Oliv.) Harms. The genetic clusters were Upper Guinea (UG), Dahomey Gap, (DG), Lower Guinea North (LG-North), Lower Guinea South (LG-South), Lower Guinea East (LG-East), and Congo.