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Nat Genet. 2016 Sep;48(9):1077-82. doi: 10.1038/ng.3617. Epub 2016 Jul 18.

Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism.

Author information

1
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
2
Vienna Graduate School of Population Genetics, Institut für Populationsgenetik, Vetmeduni, Vienna, Austria.
3
Centre for Organismal Studies Heidelberg, University of Heidelberg, Heidelberg, Germany.
4
Department of Plant Physiology, Ruhr-Universität Bochum, Bochum, Germany.
5
Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.
6
Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
7
Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany.
8
Institute of Biology, Karelian Research Center of the Russian Academy of Sciences, Petrozavodsk, Russia.
9
Faculty of Science, Technology and Media, Department of Natural Sciences, Mid Sweden University, Sundsvall, Sweden.
10
Department of Biology, Lund University, Lund, Sweden.
11
Institut für Populationsgenetik, Vetmeduni, Vienna, Austria.
12
Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.
13
Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia.
14
Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.
15
Max Planck Institute for Developmental Biology, Tübingen, Germany.

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.

PMID:
27428747
DOI:
10.1038/ng.3617
[Indexed for MEDLINE]
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