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Inferring ancient divergences requires genes with strong phylogenetic signals

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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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.

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Correspondence to Antonis Rokas.

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Salichos, L., Rokas, A. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497, 327–331 (2013). https://doi.org/10.1038/nature12130

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