title: Extending the conserved phylogenetic core of archaea disentangles the evolution of the third domain of life.
abstract: Initial studies of the archaeal phylogeny relied mainly on the analysis of the RNA component of the small subunit of the ribosome (SSU rRNA). The resulting phylogenies have provided interesting but partial information on the evolutionary history of the third domain of life because SSU rRNA sequences do not contain enough phylogenetic signal to resolve all nodes of the archaeal tree. Thus, many relationships, and especially the most ancient ones, remained elusive. Moreover, SSU rRNA phylogenies can be heavily biased by tree reconstruction artifacts. The sequencing of complete genomes allows using a variety of protein markers as an alternative to SSU rRNA. Taking advantage of the recent burst of archaeal complete genome sequences, we have carried out an in-depth phylogenomic analysis of this domain. We have identified 200 new protein families that, in addition to the ribosomal proteins and the subunits of the RNA polymerase, form a conserved phylogenetic core of archaeal genes. The accurate analysis of these markers combined with desaturation approaches shed new light on the evolutionary history of Archaea and reveals that several relationships recovered in recent analyses are likely the consequence of tree reconstruction artifacts. Among others, we resolve a number of important relationships, such as those among methanogens Class I, and we propose the definition of two new superclasses within the Euryarchaeota: Methanomada and Diaforarchaea.
authors: UMR CNRS 8079, Unité d'Ecologie, Systématique et Evolution, Université Paris-Sud, Orsay, France.
authors: Céline
authors: C
authors: Petitjean
authors: UMR CNRS 8079, Unité d'Ecologie, Systématique et Evolution, Université Paris-Sud, Orsay, France.
authors: Philippe
authors: P
authors: Deschamps
authors: UMR CNRS 8079, Unité d'Ecologie, Systématique et Evolution, Université Paris-Sud, Orsay, France.
authors: Purificación
authors: P
authors: López-García
authors: UMR CNRS 8079, Unité d'Ecologie, Systématique et Evolution, Université Paris-Sud, Orsay, France david.moreira@u-psud.fr celine.brochier-armanet@univ-lyon1.fr.
authors: David
authors: D
authors: Moreira
authors: Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France david.moreira@u-psud.fr celine.brochier-armanet@univ-lyon1.fr.
authors: Céline
authors: C
authors: Brochier-Armanet
mesh_terms: D001105:Archaea / Q000235:genetics; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D020745:Genome, Archaeal; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000235:genetics*; D012269:Ribosomal Proteins / Q000235:genetics; D054679:Ribosome Subunits, Small / Q000235:genetics*; D012270:Ribosomes / Q000235:genetics
chemical_list: D012335:RNA, Ribosomal; D012269:Ribosomal Proteins
keywords: Diaforarchaea; Methanomada; Methanopyrus kandleri; Phylogeny; Slow–Fast method; horizontal gene transfer