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

Revisiting ancestral polyploidy in plants

Colin Ruprecht  1 , Rolf Lohaus  2   3   4 , Kevin Vanneste  2   3 , Marek Mutwil  1 , Zoran Nikoloski  1   5 , Yves Van de Peer  2   3   4   6 , Staffan Persson  1   7
Affiliations

Revisiting ancestral polyploidy in plants

Colin Ruprecht et al. Sci Adv. .

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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Figures

Fig. 1
Fig. 1. Duplication and calibration nodes in the phylogenetic gene tree topologies.
Example of a gene tree with (ME)(ME) topology, tree RAxML_1111 from Jiao et al. (5), in which both paralogs were retained in both monocots (M) and eudicots (E) after the duplication event. Age estimates of nodes were extracted from the original r8s output file of Jiao et al. (5) and are given in parentheses for colored nodes. The nodes for the split of bryophytes (AL node), lycophytes (PL node), monocots and eudicots (ME and MEO nodes), and rosids (RO node) were also extracted from the original r8s output file. The green MEO node was the uncalibrated ME node in the r8s analysis of Jiao et al. (5) (indicated by the absence of square brackets in the small schematic tree at the top right). M and E nodes represent the crown nodes of monocots and eudicots, respectively. m and e nodes are additional calibration nodes that were used when testing the potentially too young upper constraint for the ME nodes (see Methods for details). Examples of gene trees with (ME)(M) and (ME)(E) topologies can be found in fig. S1
Fig. 2
Fig. 2. The two duplication peaks correspond to two distinct classes of gene tree topologies.
Age estimates of nodes were extracted from the original r8s output file of Jiao et al. (5). (A) Age estimates of gene duplication nodes in all trees (n = 777). (B) Age estimates of ME nodes (blue) and MEO nodes (green) in (ME)(ME) trees (n = 283). (C) Age estimates of gene duplication nodes in (ME)(ME) trees (n = 283). (D) Age estimates of gene duplication nodes in (ME)(E) and (ME)(M) trees (n = 494). In all panels, the small schematic trees illustrate the general topology of the corresponding trees with color of nodes matching color of age estimates showed in the histograms (yellow circle indicates the gene duplication node; blue and green circles indicate ME and MEO nodes, respectively). Square brackets indicate which node/clade had been calibrated.
Fig. 3
Fig. 3. Distribution of gene duplication estimates using BEAST for phylogenomic dating.
Top row: Age estimates of gene duplication nodes in trees with calibration of only one ME node [the same as in Jiao et al. (5); illustrated by blue node with square brackets in small schematic trees]. (A) Age estimates in (ME)(ME) trees (n = 285). (B) Age estimates in (ME)(E) and (ME)(M) trees (n = 487). (C) Age estimates in all trees (n = 772). Bottom row: Age estimates of gene duplication nodes in trees with calibration of both child nodes of a gene duplication node (illustrated by colored nodes with square brackets in small schematic trees). (D) Age estimates in (ME)(ME) trees; calibration of both ME and MEO nodes (n = 285). (E) Age estimates in (ME)(E) and (ME)(M) trees; calibration of both ME and E or M nodes (if this node exists), respectively (n = 487). (F) Age estimates in all trees; calibration of both ME and MEO, E, or M nodes (n = 772). For comparison, the distribution of the original data of Jiao et al. (5) is given in light yellow in the background. In all panels, the small schematic trees illustrate the general topology of the corresponding trees (yellow circle indicates the gene duplication node). Square brackets indicate which node/clade has been calibrated.
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