>Background and Aims The relative role of Pleistocene climate changes in driving the geographic distribution and genetic diversity of South American species is not well known, especially from open biomes such as the Cerrado, the most diverse tropical savanna, encompassing high levels of endemism. Here the effects of Quaternary climatic changes on demographic history, distribution dynamics and genetic diversity of Dimorphandra mollis, an endemic tree species widely distributed in the Cerrado, were investigated.>Methods A total of 38 populations covering most of the distribution of D. mollis were analysed using internal transcribed spacer (ITS) sequences and nuclear microsatellite variation [simple sequence repeats (SSRs)]. The framework incorporated statistical phylogeography, coalescent analyses and ecological niche modelling (ENM).>Key Results Different signatures of Quaternary climatic changes were found for ITS sequences and SSRs corresponding to different time slices. Coalescent analyses revealed large and constant effective population sizes, with high historical connectivity among the populations for ITS sequences and low effective population sizes and gene flow with recent population retraction for SSRs. ENMs indicated a slight geographical range retraction during the Last Glacial Maximum. A large historical refugium across central Brazil was predicted. Spatially explicit analyses showed a spatial cline pattern in genetic diversity related to the paleodistribution of D. mollis and to the centre of its historical refugium.>Conclusions The complex genetic patterns found in D. mollis are the result of a slight geographical range retraction during the Last Glacial Maximum followed by population expansion to the east and south from a large refugium in the central part of the Cerrado. This historical refugium is coincident with an area predicted to be climatically stable under future climate scenarios. The identified refugium should be given high priority in conservation polices to safeguard the evolutionary potential of the species under predicted future climatic changes.
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