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We explored the effects of Quaternary climate changes on the campos rupestre sky island ecosystem in central and eastern Brazil studying the phylogeography of Richterago discoidea (Asteraceae) to better understand the effect of historical biogeographic processes on species diversification in this region. DNA sequences of nuclear (ITS) and plastid (psbA-trnH, rpl32-trnL(UAG), trnK(UUU)-rps16 and ycf3-trnS) markers and 83 AFLP loci were used to genotype up to 90 individuals from 19 populations of R. discoidea. We investigated intraspecific genetic structure, demographic history and spatiotemporal diversification. Also, ecological niche modelling was used to infer palaeodistribution. Three lineages (without strong geographical structure) were identified in the Bayesian genetic structure analysis of 25 haplotypes, whereas AFLPs revealed two lineages with considerable levels of admixture. The origin of diversification of R. discoidea is on the Diamantina Plateau (Espinhaco Meridional, Minas Gerais), from where lineages expanded to the central highlands of Brazil during glacial periods in the Mid-Pleistocene. The current disjunct distribution is a relict of an ancient wide distribution, resulting from retraction during interglacial periods, confining populations to mountain-top sky islands that acted as refugia (Espinhaco Range and Goias highlands). Expansion within refugium sites during the LGM blurred deeper genetic structure, and pressure of selection in ecological outliers favoured high genetic diversity outside refugia. (c) 2018 The Linnean Society of London, Biological Journal of the Linnean Society, 2018, YY, 000-000