The notion of species as reproductively isolated units related through a bifurcating tree implies that gene trees should generally agree with the species tree and that sister taxa should not share polymorphisms unless they diverged recently and should be equally closely related to outgroups. It is now possible to evaluate this model systematically. We sequenced multiple individuals from 27 described taxa representing the entire Arabidopsis genus. Cluster analysis identified seven groups, corresponding to described species that capture the structure of the genus. However, at the level of gene trees, only the separation of Arabidopsis thaliana from the remaining species was universally supported, and, overall, the amount of shared polymorphism demonstrated that reproductive isolation was considerably more recent than the estimated divergence times. We uncovered multiple cases of past gene flow that contradict a bifurcating species tree. Finally, we showed that the pattern of divergence differs between gene ontologies, suggesting a role for selection.

Artificial Intelligence Research Center National Institute of Advanced Industrial Science and Technology Tokyo Japan

Centre for Organismal Studies Heidelberg University of Heidelberg Heidelberg Germany

Department of Biology Lund University Lund Sweden

Department of Botany Faculty of Science Charles University Prague Czech Republic

Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland

Department of Plant Physiology Ruhr Universität Bochum Bochum Germany

Faculty of Science Technology and Media Department of Natural Sciences Mid Sweden University Sundsvall Sweden

Gregor Mendel Institute Austrian Academy of Sciences Vienna Biocenter Vienna Austria

Institut für Populationsgenetik Vetmeduni Vienna Austria

Institute of Biology Karelian Research Center of the Russian Academy of Sciences Petrozavodsk Russia

Institute of Botany Slovak Academy of Sciences Bratislava Slovakia

Institute of Integrative Biology ETH Zurich Zurich Switzerland

Institute of Plant Breeding Seed Science and Population Genetics University of Hohenheim Stuttgart Germany

Max Planck Institute for Developmental Biology Tübingen Germany

Vienna Graduate School of Population Genetics Institut für Populationsgenetik Vetmeduni Vienna Austria

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