title: Origins of major archaeal clades correspond to gene acquisitions from bacteria.
abstract: The mechanisms that underlie the origin of major prokaryotic groups are poorly understood. In principle, the origin of both species and higher taxa among prokaryotes should entail similar mechanisms--ecological interactions with the environment paired with natural genetic variation involving lineage-specific gene innovations and lineage-specific gene acquisitions. To investigate the origin of higher taxa in archaea, we have determined gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes in the context of their homologues from 1,847 reference bacterial genomes. Archaeal-specific gene families define 13 traditionally recognized archaeal higher taxa in our sample. Here we report that the origins of these 13 groups unexpectedly correspond to 2,264 group-specific gene acquisitions from bacteria. Interdomain gene transfer is highly asymmetric, transfers from bacteria to archaea are more than fivefold more frequent than vice versa. Gene transfers identified at major evolutionary transitions among prokaryotes specifically implicate gene acquisitions for metabolic functions from bacteria as key innovations in the origin of higher archaeal taxa.
authors.affiliation: Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany.
authors.forename: Shijulal
authors.initials: S
authors.lastname: Nelson-Sathi
authors.affiliation: Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany.
authors.forename: Filipa L
authors.initials: FL
authors.lastname: Sousa
authors.affiliation: Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany.
authors.forename: Mayo
authors.initials: M
authors.lastname: Roettger
authors.affiliation: Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany.
authors.forename: Nabor
authors.initials: N
authors.lastname: Lozada-Chávez
authors.affiliation: Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany.
authors.forename: Thorsten
authors.initials: T
authors.lastname: Thiergart
authors.affiliation: Mathematisches Institut, Heinrich-Heine University, 40225 Düsseldorf, Germany.
authors.forename: Arnold
authors.initials: A
authors.lastname: Janssen
authors.affiliation: Department of Mathematics and Statistics, University of Otago, Dunedin 9054, New Zealand.
authors.forename: David
authors.initials: D
authors.lastname: Bryant
authors.affiliation: Genomic Microbiology Group, Institute of Microbiology, Christian-Albrechts-Universität Kiel, 24118 Kiel, Germany.
authors.forename: Giddy
authors.initials: G
authors.lastname: Landan
authors.affiliation: Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, 24118 Kiel, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Schönheit
authors.affiliation: Faculty of Chemistry, Biofilm Centre, Molecular Enzyme Technology and Biochemistry, University of Duisburg-Essen, 45117 Essen, Germany.
authors.forename: Bettina
authors.initials: B
authors.lastname: Siebers
authors.affiliation: Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland.
authors.forename: James O
authors.initials: JO
authors.lastname: McInerney
authors.affiliation: 1] Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany [2] Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.
authors.forename: William F
authors.initials: WF
authors.lastname: Martin
mesh_terms: D001105:Archaea / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D019843:Archaeal Proteins / Q000235:genetics; D001419:Bacteria / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D019766:Genes, Archaeal / Q000235:genetics*; D005798:Genes, Bacterial / Q000235:genetics*; D020745:Genome, Archaeal / Q000235:genetics; D010802:Phylogeny
chemical_list: D019843:Archaeal Proteins