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Inferring ancient divergences requires genes with strong phylogenetic signals

Author

Listed:
  • Leonidas Salichos

    (Vanderbilt University)

  • Antonis Rokas

    (Vanderbilt University)

Abstract

To tackle incongruence, the topological conflict between different gene trees, phylogenomic studies couple concatenation with practices such as rogue taxon removal or the use of slowly evolving genes. Phylogenomic analysis of 1,070 orthologues from 23 yeast genomes identified 1,070 distinct gene trees, which were all incongruent with the phylogeny inferred from concatenation. Incongruence severity increased for shorter internodes located deeper in the phylogeny. Notably, whereas most practices had little or negative impact on the yeast phylogeny, the use of genes or internodes with high average internode support significantly improved the robustness of inference. We obtained similar results in analyses of vertebrate and metazoan phylogenomic data sets. These results question the exclusive reliance on concatenation and associated practices, and argue that selecting genes with strong phylogenetic signals and demonstrating the absence of significant incongruence are essential for accurately reconstructing ancient divergences.

Suggested Citation

  • Leonidas Salichos & Antonis Rokas, 2013. "Inferring ancient divergences requires genes with strong phylogenetic signals," Nature, Nature, vol. 497(7449), pages 327-331, May.
    • Handle: RePEc:nat:nature:v:497:y:2013:i:7449:d:10.1038_nature12130
    DOI: 10.1038/nature12130
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    Cited by:

    1. Justin C Havird & Scott R Santos, 2014. "Performance of Single and Concatenated Sets of Mitochondrial Genes at Inferring Metazoan Relationships Relative to Full Mitogenome Data," PLOS ONE, Public Library of Science, vol. 9(1), pages 1-10, January.
    2. Md Shamsuzzoha Bayzid & Siavash Mirarab & Bastien Boussau & Tandy Warnow, 2015. "Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-40, June.
    3. Ruriko Yoshida & Kenji Fukumizu & Chrysafis Vogiatzis, 2019. "Multilocus phylogenetic analysis with gene tree clustering," Annals of Operations Research, Springer, vol. 276(1), pages 293-313, May.

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