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

Mathieu Groussin (1) , Bastien Boussau (2) , Gergely J Szollosi (3) , Laura Eme , Manolo Gouy (2) , Céline Brochier-Armanet (2) , Vincent Daubin (2)

1 LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
2 BPGE - Bioinformatique, phylogénie et génomique évolutive
3 ELTE - Eötvös Loránd University

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.

Mots clés: ancestral genome reconstruction; Archaea; horizontal gene transfer

Domaines: Sciences de l'environnement; Biodiversité et Ecologie; Evolution [q-bio.PE]; Systématique, phylogénie et taxonomie; Ecologie, Environnement; Génétique; Statistiques [stat]

Mathieu Groussin, Bastien Boussau, Gergely J Szollosi, Laura Eme, Manolo Gouy, et al.. Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated. Molecular Biology and Evolution, 2016, 33 (2), pp.305 - 310. ⟨10.1093/molbev/msv249⟩. ⟨hal-01913926⟩