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Sci Adv. 2017 Jul 5;3(7):e1603195. doi: 10.1126/sciadv.1603195. eCollection 2017 Jul.

Revisiting ancestral polyploidy in plants.

Author information

1
Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany.
2
Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium.
3
VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium.
4
Bioinformatics Institute Ghent, Technologiepark 927, 9052 Ghent, Belgium.
5
Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.
6
Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria, South Africa.
7
School of Biosciences, University of Melbourne, Parkville, Victoria 3010, Australia.

Abstract

Whole-genome duplications (WGDs) or polyploidy events have been studied extensively in plants. In a now widely cited paper, Jiao et al. presented evidence for two ancient, ancestral plant WGDs predating the origin of flowering and seed plants, respectively. This finding was based primarily on a bimodal age distribution of gene duplication events obtained from molecular dating of almost 800 phylogenetic gene trees. We reanalyzed the phylogenomic data of Jiao et al. and found that the strong bimodality of the age distribution may be the result of technical and methodological issues and may hence not be a "true" signal of two WGD events. By using a state-of-the-art molecular dating algorithm, we demonstrate that the reported bimodal age distribution is not robust and should be interpreted with caution. Thus, there exists little evidence for two ancient WGDs in plants from phylogenomic dating.

KEYWORDS:

BEAST; Genome evolution; Phylogenomics; Plant polyploidy; molecular dating; r8s; whole genome duplication

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