title: Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated.
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.
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Groussin
authors.affiliation: Université de Lyon, Lyon, France Université Lyon 1, Villeurbanne, France CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France.
authors.forename: Bastien
authors.initials: B
authors.lastname: Boussau
authors.affiliation: ELTE-MTA "Lendület" Biophysics Research Group, Budapest, Hungary.
authors.forename: Gergely
authors.initials: G
authors.lastname: Szöllõsi
authors.affiliation: Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada.
authors.forename: Laura
authors.initials: L
authors.lastname: Eme
authors.affiliation: Université de Lyon, Lyon, France Université Lyon 1, Villeurbanne, France CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France.
authors.forename: Manolo
authors.initials: M
authors.lastname: Gouy
authors.affiliation: Université de Lyon, Lyon, France Université Lyon 1, Villeurbanne, France CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France.
authors.forename: Céline
authors.initials: C
authors.lastname: Brochier-Armanet
authors.affiliation: 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.
authors.forename: Vincent
authors.initials: V
authors.lastname: Daubin
mesh_terms: D001105:Archaea / Q000145:classification / Q000235:genetics*; D001419:Bacteria / Q000235:genetics*; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D019766:Genes, Archaeal; D005798:Genes, Bacterial; D023281:Genomics; D005838:Genotype; D010802:Phylogeny
keywords: Archaea; ancestral genome reconstruction; horizontal gene transfer