pubmed.ncbi.nlm.nih.gov

Inferring ancient divergences requires genes with strong phylogenetic signals - PubMed

  • ️Tue Jan 01 2013

. 2013 May 16;497(7449):327-31.

doi: 10.1038/nature12130. Epub 2013 May 8.

Affiliations

Inferring ancient divergences requires genes with strong phylogenetic signals

Leonidas Salichos et al. Nature. 2013.

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.

PubMed Disclaimer

Similar articles

Cited by

References

    1. Nature. 2006 Nov 2;444(7115):85-8 - PubMed
    1. Proc Natl Acad Sci U S A. 2010 Jan 26;107(4):1476-81 - PubMed
    1. Nature. 2006 Feb 23;439(7079):965-8 - PubMed
    1. Mol Biol Evol. 2006 Feb;23(2):254-67 - PubMed
    1. G3 (Bethesda). 2011 Jun;1(1):11-25 - PubMed

Publication types

MeSH terms

LinkOut - more resources