PT  - JOURNAL ARTICLE
AU  - Mathieu Groussin
AU  - Bastien Boussau
AU  - Gergely Szöllősi
AU  - Laura Eme
AU  - Manolo Gouy
AU  - Céline Brochier-Armanet
AU  - Vincent Daubin
TI  - Origins of major archaeal clades do not correspond to gene acquisitions from bacteria
AID  - 10.1101/019851
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 019851
4099  - http://biorxiv.org/content/early/2015/05/27/019851.short
4100  - http://biorxiv.org/content/early/2015/05/27/019851.full
AB  - In a recent articxle, Nelson-Sathi et al. [NS] report that the origins of Major Archaeal Lineages [MAL] correspond to massive group-specific gene acquisitions via horizontal gene transfer (HGT) from bacteria (Nelson-Sathi et al., 2015, Nature 517(7532):77-80). If correct, this would have fundamental implications for the process of diversification in microbes. However, a re-examination 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 re-analysis 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.