The world’s second largest expanse of tropical rain forest is in Central Africa and it harbours enormous species diversity. Population genetic studies have consistently revealed significant structure across central African rain forest plants, in particular a North-South genetic discontinuity around the equatorial line, in a continuous expanse of rain forest but where a climatic inversion is documented. Here, we took a phylogeographic approach by sequencing 351 nuclear markers in 112 individuals across the distribution of the African rain forest tree species Annickia affinis (Annonaceae). We showed for the first time that the North-South divide is the result of a single, major colonisation event across the climatic inversion from an ancestral population located in Gabon. We suggested that differences in ecological niche of populations located on either side of this inversion may have contributed to this phylogenetic discontinuity. We found evidence for inland dispersal, predominantly in northern areas, and variable demographic histories among genetic clusters, indicating that populations responded differently to past climate change. We show how newly-developed genomic tools can provide invaluable insights into our understanding of tropical rain forest evolutionary dynamics.

Included in this data repository are:

• Splitstree analysis file
• RAxML phylogenetic tree (rooted)
• ASTRAL phylogenetic tree
• SNAPP MCC tree and posterior distribution of trees
• Additional tables summarising MaxEnt modelling
• Stairway plot blueprints