Research ArticlePLANT SCIENCES

Revisiting ancestral polyploidy in plants

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Science Advances  05 Jul 2017:
Vol. 3, no. 7, e1603195
DOI: 10.1126/sciadv.1603195
  • 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 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 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.

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/3/7/e1603195/DC1

    Differences in duplication age estimates between (ME)(ME), (ME)(E), and (ME)(M) trees

    Timing and phylogenetic placement of the WGD derived from the Amborella synteny data

    table S1. Statistical analyses of modality of duplication age distributions

    table S2. Bayesian information criterion values from the EMMIX analysis to estimate the number of significant components in the duplication age distributions

    fig. S1. Phylogenetic gene trees with (ME)(E) and (ME)(M) topology.

    fig. S2. Distribution of duplication estimates in the (ME)(M) and (ME)(E) trees.

    fig. S3. Correlation of the gene tree topology with the duplication estimate.

    fig. S4. Correlation of the gene tree topology with the duplication estimate.

    fig. S5. Identification of significant components using SiZer.

    fig. S6. Replacing all ME node calibrations does not change the general pattern of the distribution of gene duplication ages estimated by BEAST.

    References (1722)

  • Supplementary Materials

    This PDF file includes:

    • Differences in duplication age estimates between (ME)(ME), (ME)(E), and (ME)(M) trees
    • Timing and phylogenetic placement of the WGD derived from the Amborella synteny data
    • table S1. Statistical analyses of modality of duplication age distributions
    • table S2. Bayesian information criterion values from the EMMIX analysis to estimate the number of significant components in the duplication age distributions
    • fig. S1. Phylogenetic gene trees with (ME)(E) and (ME)(M) topology.
    • fig. S2. Distribution of duplication estimates in the (ME)(M) and (ME)(E) trees.
    • fig. S3. Correlation of the gene tree topology with the duplication estimate.
    • fig. S4. Correlation of the gene tree topology with the duplication estimate.
    • fig. S5. Identification of significant components using SiZer.
    • fig. S6. Replacing all ME node calibrations does not change the general pattern of the distribution of gene duplication ages estimated by BEAST.
    • References (17–22)

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