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Inferring ancient divergences requires genes with strong phylogenetic signals

Naturevolume 497, pages327–331 (2013)Cite this article

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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.

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Figure 1: The yeast species phylogeny recovered from the concatenation analysis of 1,070 genes disagrees with every gene tree, despite absolute bootstrap support.
Figure 2: Differences in yeast phylogenies inferred from different phylogenomic practices.
Figure 3: Incongruence is more prevalent in shorter internodes located deeper on the phylogeny.

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Acknowledgements

We thank K. Polzin for providing a script that identified alignment sites that contained single substitutions between amino acids that differ in their physicochemical properties. We thank members of the Rokas laboratory and B. O’Meara for valuable comments on this work. This work was conducted in part using the resources of the Advanced Computing Center for Research and Education at Vanderbilt University. This work was supported by the National Science Foundation (DEB-0844968).

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Authors and Affiliations

  1. Department of Biological Sciences, Vanderbilt University, Nashville, 37235, Tennessee, USA

    Leonidas Salichos & Antonis Rokas

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  1. Leonidas Salichos

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  2. Antonis Rokas

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Contributions

L.S. and A.R. conceived and designed experiments; L.S. carried out experiments; L.S. and A.R. analysed data and wrote the paper.

Corresponding author

Correspondence toAntonis Rokas.

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The authors declare no competing financial interests.

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This file contains Supplementary Tables 1-2 and Supplementary Figures 1-17. (PDF 1109 kb)

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Salichos, L., Rokas, A. Inferring ancient divergences requires genes with strong phylogenetic signals.Nature497, 327–331 (2013). https://doi.org/10.1038/nature12130

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Editorial Summary

Calling time on phylogenetic analysis

Evolutionary events that happened close together, but long ago, present particular challenges to those seeking to reconstruct evolutionary history. The usual method relies on brute force — simply concatenate as much genetic information as possible and see what comes out. But how good are the data used to make such concatenations? Leonidas Salichos and Antonis Rokas asked this question of a 1,070-gene data set from 23 yeast genomes, and discovered that none of the 1,070 gene trees was identical to the phylogeny that received 100% support from the concatenation analysis. Incongruence severity increased for shorter internodes located deeper on the phylogeny. The researchers untied the knot by giving most credence to genes or internodes with high average clade support. They argue that abolishing incongruence in the data should be a first step for anyone seeking to unravel evolutionary events in deep time.

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