Data from: Genomics of the divergence continuum in an African plant biodiversity hotspot, I: drivers of population divergence in Restio capensis (Restionaceae)

Understanding the drivers of population divergence, speciation and species persistence is of great interest to molecular ecology, especially for species-rich radiations inhabiting the world’s biodiversity hotspots. The toolbox of population genomics holds great promise for addressing these key issues, especially if genomic data are analyzed within a spatially and ecologically explicit context. We have studied the earliest stages of the divergence continuum in the Restionaceae, a species-rich and ecologically important plant family of the Cape Floristic Region (CFR) of South Africa, using the widespread CFR endemic Restio capensis (L.) H.P. Linder & C.R. Hardy as an example. We studied diverging populations of this morphotaxon for chloroplast (cp) DNA sequences and >14 400 nuclear DNA polymorphisms from Restriction site Associated DNA (RAD) sequencing and analyzed the results jointly with spatial, climatic, and phytogeographic data, using a Bayesian generalized linear mixed modeling (GLMM) approach. The results indicate that population divergence across the extreme environmental mosaic of the CFR is driven by isolation-by-environment (IBE) rather than isolation-by-distance (IBD) for both neutral and non-neutral markers, consistent with genome hitchhiking during early stages of divergence. Mixed modeling of cpDNA and single highly divergent outlier loci from a Bayesian genome scan confirmed the predominant role of climate and pointed to additional drivers of divergence, such as drift and ecological agents of selection captured by phytogeographic zones. Our study demonstrates the usefulness of population genomics for disentangling the effects of IBD and IBE along the divergence continuum often found in species radiations across heterogeneous ecological landscapes.