title: Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism.
abstract: 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.
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.|Vienna Graduate School of Population Genetics, Institut für Populationsgenetik, Vetmeduni, Vienna, Austria.
authors.forename: Polina Yu
authors.initials: PY
authors.lastname: Novikova
authors.affiliation: Centre for Organismal Studies Heidelberg, University of Heidelberg, Heidelberg, Germany.
authors.forename: Nora
authors.initials: N
authors.lastname: Hohmann
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
authors.forename: Viktoria
authors.initials: V
authors.lastname: Nizhynska
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
authors.forename: Takashi
authors.initials: T
authors.lastname: Tsuchimatsu
authors.affiliation: Department of Plant Physiology, Ruhr-Universität Bochum, Bochum, Germany.
authors.forename: Jamshaid
authors.initials: J
authors.lastname: Ali
authors.affiliation: Vienna Graduate School of Population Genetics, Institut für Populationsgenetik, Vetmeduni, Vienna, Austria.
authors.forename: Graham
authors.initials: G
authors.lastname: Muir
authors.affiliation: Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.
authors.forename: Alessia
authors.initials: A
authors.lastname: Guggisberg
authors.affiliation: Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
authors.forename: Tim
authors.initials: T
authors.lastname: Paape
authors.affiliation: Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany.
authors.forename: Karl
authors.initials: K
authors.lastname: Schmid
authors.affiliation: Institute of Biology, Karelian Research Center of the Russian Academy of Sciences, Petrozavodsk, Russia.
authors.forename: Olga M
authors.initials: OM
authors.lastname: Fedorenko
authors.affiliation: Faculty of Science, Technology and Media, Department of Natural Sciences, Mid Sweden University, Sundsvall, Sweden.
authors.forename: Svante
authors.initials: S
authors.lastname: Holm
authors.affiliation: Department of Biology, Lund University, Lund, Sweden.
authors.forename: Torbjörn
authors.initials: T
authors.lastname: Säll
authors.affiliation: Institut für Populationsgenetik, Vetmeduni, Vienna, Austria.
authors.forename: Christian
authors.initials: C
authors.lastname: Schlötterer
authors.affiliation: Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.|Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia.
authors.forename: Karol
authors.initials: K
authors.lastname: Marhold
authors.affiliation: Department of Plant Physiology, Ruhr-Universität Bochum, Bochum, Germany.
authors.forename: Alex
authors.identifier: 0000-0001-8253-5137
authors.initials: A
authors.lastname: Widmer
authors.affiliation: Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.
authors.forename: Jun
authors.initials: J
authors.lastname: Sese
authors.affiliation: Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
authors.forename: Kentaro K
authors.initials: KK
authors.lastname: Shimizu
authors.affiliation: Max Planck Institute for Developmental Biology, Tübingen, Germany.
authors.forename: Detlef
authors.initials: D
authors.lastname: Weigel
authors.affiliation: Department of Plant Physiology, Ruhr-Universität Bochum, Bochum, Germany.
authors.forename: Ute
authors.initials: U
authors.lastname: Krämer
authors.affiliation: Centre for Organismal Studies Heidelberg, University of Heidelberg, Heidelberg, Germany.
authors.forename: Marcus A
authors.identifier: 0000-0002-1693-6829
authors.initials: MA
authors.lastname: Koch
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
authors.forename: Magnus
authors.identifier: 0000-0001-7178-9748
authors.initials: M
authors.lastname: Nordborg
mesh_terms: D017360:Arabidopsis / Q000145:classification* / Q000235:genetics*; D051456:Gene Flow / Q000235:genetics*; D017343:Genes, Plant / Q000235:genetics*; D049810:Genetic Speciation; D011110:Polymorphism, Genetic / Q000235:genetics*