DOI: 10.5061/dryad.1rn8pk0rk
title: Data from: Individualistic evolutionary responses of central African rain forest plants to Pleistocene climatic fluctuations

description: 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
 &gt;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.
description: 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 <em>Monanthotaxis enghiana</em> may be referred to
 as <em>Friesodielsia enghiana</em> or 'fries' for
 short. This is due to a recent taxonomic revision.
 <strong>amova.zip</strong> 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.
 <strong>backbone_annonaceae.zip </strong>Runs and
 trees associated with the Annonaceae backbone tree.
 <strong>backbone_palms.zip </strong>Runs and trees
 associated with the Arecaceae backbone tree.
 <strong>clustering.zip</strong> DAPC and TESS3
 clustering results for each species. Also included are results from DAPC
 sensitivity runs.
 <strong>db_rda.zip</strong> Data from distance-based
 Redundancy analyses.
 <strong>denim.zip</strong> Runs and trees from DENIM
 analyses. <strong>enm.zip</strong> Input
 data and results of ecological niche modelling analyses using
 biomod2.
 <strong>enm_locations.xlsx</strong> Location data
 used in ENM.
 <strong>genetic_diversity.zip</strong> Data
 associated with analyses of genetic diversity in relation to distance from
 refugia. <strong>mantel.zip</strong> Rdata
 for Mantel tests for patterns of genetic structure.
 <strong>raxml.zip </strong>Input data and results of
 RAxML phylogenetic tree inference for each species.
 <strong>sequenced_specimens.xlsx</strong> A list of
 the specimens sequences including names, sequencing indexes and
 locations. 
 <strong>stable_areas.zip</strong> Data associated
 with the calculation of climatically stable areas.
 <strong>stairwayplot.zip</strong> Input data and
 output for stairwayplot analyses.
 <strong>starbeast.zip</strong> Runs and trees from
 STARBEAST analyses.