Data from: Vanishing refuge? Testing the forest refuge hypothesis in coastal East Africa using genome-wide sequence data for seven amphibians

High-throughput sequencing data have greatly improved our ability to
understand the processes that contribute to current biodiversity patterns.
The “vanishing refuge” diversification model is speculated for the coastal
forests of eastern Africa, whereby some taxa have persisted and
diversified between forest refugia, while others have switched to becoming
generalists also present in non-forest habitats. Complex arrangements of
geographical barriers (hydrology and topography) and ecological gradients
between forest and non-forest habitats may have further influenced the
region’s biodiversity, but elucidation of general diversification
processes has been limited by lack of suitable data. Here, we explicitly
test alternative diversification modes in the coastal forests using
genome-wide single nucleotide polymorphisms, mtDNA, spatial and
environmental data for three forest (Arthroleptis xenodactyloides,
Leptopelis flavomaculatus and Afrixalus sylvaticus) and four generalist
(Afrixalus fornasini, A. delicatus, Leptopelis concolor, L. argenteus)
amphibians. Multiple analyses provide insight about divergence times,
spatial population structure, dispersal barriers, environmental stability
and demographic history. We reveal highly congruent intra-specific
diversity and population structure across taxa, with most divergences
occurring during the late Pliocene and Pleistocene. Although stability
models support the existence of some forest refugia, dispersal barriers
and demographic models point toward idiosyncratic diversification modes
across taxa. We identify a consistent role for riverine barriers in the
diversification of generalist taxa, but mechanisms of diversification are
more complex for forest taxa and potentially include topographical
barriers, forest refugia and ecological gradients. Our work demonstrates
the complexity of diversification processes in this region, which vary
between forest and generalist taxa, but also for ecologically similar
species with shared population boundaries.