Quaternary climatic oscillations profoundly impacted temperate biodiversity. For many diverse yet undersampled areas, however, the consequences of this impact are still poorly known. In Europe, particular uncertainty surrounds the role of Balkans, a major hotspot of European diversity, in postglacial recolonization of more northerly areas, and the Carpathians, a debatable candidate for a northern 'cryptic' glacial refugium. Using genome-wide SNPs and microsatellites, we examined how the interplay of historical processes and niche shifts structured genetic diversity of diploid Arabidopsis arenosa, a little-known member of the plant model genus that occupies a wide niche range from sea level to alpine peaks across eastern temperate Europe. While the northern Balkans hosted one isolated endemic lineage, most of the genetic diversity was concentrated further north in the Pannonian Basin and the Carpathians, where it likely survived the last glaciation in northern refugia. Finally, a distinct postglacial environment in northern Europe was colonized by populations of admixed origin from the two Carpathian lineages. Niche differentiation along altitude-related bioclimatic gradients was the main trend in the phylogeny of A. arenosa. The most prominent niche shifts, however, characterized genetically only slightly divergent populations that expanded into narrowly defined alpine and northern coastal postglacial environments. Our study highlights the role of eastern central European mountains not only as refugia for unique temperate diversity but also sources for postglacial expansion into novel high-altitude and high-latitude niches. Knowledge of distinct genetic substructure of diploid A. arenosa also opens new opportunities for follow-up studies of this emerging model of evolutionary biology.

Center for Ecological Research Kyoto University Kyoto JP 520 2113 Japan

Center for Ecological Research Kyoto University Kyoto JP 520 2113 Japan Faculty of Agriculture Ryukoku University Shiga JP 612 8577 Japan JST PRESTO Saitama JP 332 0012 Japan

Department of Botany Faculty of Science Charles University Prague Prague CZ 128 01 Czech Republic

Department of Botany Faculty of Science Charles University Prague Prague CZ 128 01 Czech Republic Institute of Botany Slovak Academy of Sciences Bratislava SK 845 23 Slovak Republic

Department of Botany Faculty of Science Charles University Prague Prague CZ 128 01 Czech Republic Institute of Botany The Czech Academy of Sciences Průhonice CZ 252 43 Czech Republic

Institute of Botany University of Innsbruck Innsbruck AT 6020 Austria

Natural History Museum University of Oslo PO Box 1172 Blindern Oslo NO 0318 Norway Department of Botany Faculty of Science Charles University Prague Prague CZ 128 01 Czech Republic Institute of Botany The Czech Academy of Sciences Průhonice CZ 252 43 Czech Republic

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