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Mol Biol Evol. 2016 Feb;33(2):305-10. doi: 10.1093/molbev/msv249. Epub 2015 Nov 4.

Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated.

Author information

1
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA.
2
Université de Lyon, Lyon, France Université Lyon 1, Villeurbanne, France CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France.
3
ELTE-MTA "Lendület" Biophysics Research Group, Budapest, Hungary.
4
Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada.
5
Université de Lyon, Lyon, France Université Lyon 1, Villeurbanne, France CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France vincent.daubin@univ-lyon1.fr.

Abstract

In a recent article, Nelson-Sathi et al. (NS) report that the origins of major archaeal lineages (MAL) correspond to massive group-specific gene acquisitions via HGT from bacteria (Nelson-Sathi et al. 2015. Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature 517(7532):77-80.). If correct, this would have fundamental implications for the process of diversification in microbes. However, a reexamination of these data and results shows that the methodology used by NS systematically inflates the number of genes acquired at the root of each MAL, and incorrectly assumes bacterial origins for these genes. A reanalysis of their data with appropriate phylogenetic models accounting for the dynamics of gene gain and loss between lineages supports the continuous acquisition of genes over long periods in the evolution of Archaea.

KEYWORDS:

Archaea; ancestral genome reconstruction; horizontal gene transfer

PMID:
26541173
PMCID:
PMC4866543
DOI:
10.1093/molbev/msv249
[Indexed for MEDLINE]
Free PMC Article

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