Understanding the evolutionary dynamics of genetic diversity is fundamental for species conservation in the face of climate change, particularly in hyper-diverse biomes. Species in a region may respond similarly to climate change, leading to comparable evolutionary dynamics, or individualistically, resulting in dissimilar patterns. The second largest expanse of continuous tropical rain forest (TRF) in the world is found in Central Africa. Here, present-day patterns of genetic structure are thought to be dictated by repeated expansion and contraction of TRFs into and out of refugia during Pleistocene climatic fluctuations. This refugia model implies a common response to past climate change. However, given the unrivalled diversity of TRFs, species could respond differently because of distinct environmental requirements or ecological characteristics. To test this we generated genome-wide sequence data for >750 individuals of seven co-distributed plants from Lower Guinea in Central Africa. We inferred species’ evolutionary and demographic histories within a comparative phylogeographic framework. Levels of genetic structure varied among species and emerged primarily during the Pleistocene, but divergence events were rarely concordant. Demographic trends ranged from repeated contraction and expansion to continuous growth. Furthermore, patterns in genetic variation were linked to disparate environmental factors including climate, soil and habitat stability. Using a strict refugia model to explain past TRF dynamics is too simplistic. Instead, individualistic evolutionary responses to Pleistocene climatic fluctuations have shaped patterns in genetic diversity. Predicting the future dynamics of TRFs under climate change will be challenging and more emphasis is needed on species ecology to better conserve TRFs worldwide.

Please refer to the methods section of the main text for an overview of how data was used. Detailed methods for each analysis can be found in the supplementary materials. Associated scripts can be found at https://github.com/ajhelmstetter/afrodyn.

Note: in some cases Monanthotaxis enghiana may be referred to as Friesodielsia enghiana or 'fries' for short. This is due to a recent taxonomic revision.

amova.zip Data from Analysis of Molecular Variance including location data, VCFs and Rdata from a previous run of the analyses. Two different AMOVAs were conducted to assess importance of (1) North-South barrier and (2) Refugia.

backbone_annonaceae.zip Runs and trees associated with the Annonaceae backbone tree.

backbone_palms.zip Runs and trees associated with the Arecaceae backbone tree.

clustering.zip DAPC and TESS3 clustering results for each species. Also included are results from DAPC sensitivity runs.

db_rda.zip Data from distance-based Redundancy analyses.

denim.zip Runs and trees from DENIM analyses.

enm.zip Input data and results of ecological niche modelling analyses using biomod2.

enm_locations.xlsx Location data used in ENM.

genetic_diversity.zip Data associated with analyses of genetic diversity in relation to distance from refugia.

mantel.zip Rdata for Mantel tests for patterns of genetic structure.

raxml.zip Input data and results of RAxML phylogenetic tree inference for each species.

sequenced_specimens.xlsx A list of the specimens sequences including names, sequencing indexes and locations. 

stable_areas.zip Data associated with the calculation of climatically stable areas.

stairwayplot.zip Input data and output for stairwayplot analyses.

starbeast.zip Runs and trees from STARBEAST analyses.