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Manipulation of Ploidy in Caenorhabditis elegans
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Revisiting ancestral polyploidy in plants.

Colin Ruprecht1, Rolf Lohaus2,3,4, Kevin Vanneste2,3

  • 1Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany.

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|July 12, 2017
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Summary

Reanalyzing plant phylogenomic data challenges previous findings of two ancient whole-genome duplications (WGDs). New molecular dating methods suggest the bimodal gene duplication pattern is not robust evidence for these early polyploidy events.

Keywords:
BEASTGenome evolutionPhylogenomicsPlant polyploidymolecular datingr8swhole genome duplication

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Area of Science:

  • Plant evolutionary biology
  • Phylogenomics
  • Molecular evolution

Background:

  • Whole-genome duplications (WGDs) are significant evolutionary events in plants.
  • A widely cited study proposed two ancient WGDs predating flowering and seed plants based on gene duplication age distributions.
  • This hypothesis relied on the bimodal age distribution of gene duplication events from phylogenetic analyses.

Purpose of the Study:

  • To re-evaluate the phylogenomic data used to support two ancient plant WGDs.
  • To investigate the robustness of the bimodal gene duplication age distribution.
  • To reassess the evidence for ancient polyploidy events in early plant evolution.

Main Methods:

  • Reanalysis of existing phylogenomic data from Jiao et al.
  • Application of a state-of-the-art molecular dating algorithm.
  • Examination of gene duplication age distributions derived from phylogenetic gene trees.

Main Results:

  • The strong bimodality in gene duplication age distribution may stem from technical and methodological issues.
  • The previously reported bimodal distribution is not robust when analyzed with advanced molecular dating techniques.
  • Evidence for two ancient WGDs in plants, based on phylogenomic dating, is weak.

Conclusions:

  • The interpretation of the bimodal age distribution as evidence for two ancient WGDs requires caution.
  • Current phylogenomic dating methods provide limited support for the existence of these two specific ancient polyploidy events in plants.
  • Further research is needed to clarify the history of whole-genome duplication events in early plant evolution.