There is still limited consensus on the evolutionary history of species-rich temperate alpine floras due to a lack of comparable and high-quality phylogenetic data covering multiple plant lineages. Here we reconstructed when and how European alpine plant lineages diversified, i.e., the tempo and drivers of speciation events. We performed full-plastome phylogenomics and used multi-clade comparative models applied to six representative angiosperm lineages that have diversified in European mountains (212 sampled species, 251 ingroup species total). Diversification rates remained surprisingly steady for most clades, even during the Pleistocene, with speciation events being mostly driven by geographic divergence and bedrock shifts. Interestingly, we inferred asymmetrical historical migration rates from siliceous to calcareous bedrocks, and from higher to lower elevations, likely due to repeated shrinkage and expansion of high elevation habitats during the Pleistocene. This may have buffered climate-related extinctions, but prevented speciation along elevation gradients as often documented for tropical alpine floras.

Center for Theoretical Study Charles University and the Academy of Sciences of the Czech Republic CZ 11000 Prague Czech Republic

CNRS Lautaret Jardin du Lautaret Université Grenoble Alpes FR 38000 Grenoble France

Czech Academy of Sciences Institute of Botany CZ 25243 Průhonice Czech Republic

Department of Botany Faculty of Science Charles University CZ 12801 Prague Czech Republic

Génomique Métabolique Genoscope Institut François Jacob CEA CNRS Université Evry Université Paris Saclay FR 91057 Evry France

Swiss Federal Research Institute WSL CH 8903 Birmensdorf Switzerland

Systematics and Evolution of Vascular Plants Associated Unit to CSIC Departament de Biologia Animal Biologia Vegetal i Ecologia Facultat de Biociències Universitat Autònoma de Barcelona ES 08193 Bellaterra Spain

UiT The Arctic University of Norway The Arctic University Museum of Norway N 9037 Tromsø Norway

Univ Grenoble Alpes Univ Savoie Mont Blanc CNRS LECA FR 38000 Grenoble France

Université Paris Saclay CEA CNRS Institute for Integrative Biology of the Cell FR 91190 Gif sur Yvette France

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