The spiny thicket of southwestern Madagascar represents an extreme and ancient landscape with extraordinary levels of biodiversity and endemism. Few hypotheses exist for explaining speciation in the region and few plant studies have explored hypotheses for species diversification. Here we investigate three species in the endemic genus Megistostegium (Malvaceae) to evaluate phylogeographic structure and explore the roles of climate, soil and paleoclimate oscillations on population divergence and speciation throughout the region. We combine phylogenetic and phylogeographic inference of RADseq data with ecological niche modeling across space and time. Population structure is concurrent with major rivers in the region and we identify a new, potentially important biogeographic break coincident with several landscape features. Our data further suggests that niches occupied by species and populations differ substantially across their distribution. Paleodistribution modelling provide evidence that past climatic change could be responsible for the current distribution, population structure and maintenance of species in Megistostegium.

RAD-sequencing derived SNP variants called in 40 samples of Megistostegium microphyllum

MM30.snps.hdf5.zip

RAD-sequencing derived SNP variants called in 33 samples of Megistostegium nodulosum

MN30.snps.hdf5.zip