title: Toward automatic reconstruction of a highly resolved tree of life.
abstract: We have developed an automatable procedure for reconstructing the tree of life with branch lengths comparable across all three domains. The tree has its basis in a concatenation of 31 orthologs occurring in 191 species with sequenced genomes. It revealed interdomain discrepancies in taxonomic classification. Systematic detection and subsequent exclusion of products of horizontal gene transfer increased phylogenetic resolution, allowing us to confirm accepted relationships and resolve disputed and preliminary classifications. For example, we place the phylum Acidobacteria as a sister group of delta-Proteobacteria, support a Gram-positive origin of Bacteria, and suggest a thermophilic last universal common ancestor.
authors.affiliation: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany.
authors.forename: Francesca D
authors.initials: FD
authors.lastname: Ciccarelli
authors.forename: Tobias
authors.initials: T
authors.lastname: Doerks
authors.forename: Christian
authors.initials: C
authors.lastname: von Mering
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Creevey
authors.forename: Berend
authors.initials: B
authors.lastname: Snel
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
mesh_terms: D000604:Amino Acyl-tRNA Synthetases / Q000235:genetics; D000818:Animals; D001105:Archaea / Q000145:classification* / Q000235:genetics; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D005075:Biological Evolution; D019295:Computational Biology; D005057:Eukaryotic Cells; D022761:Gene Transfer, Horizontal; D016678:Genome; D007448:Invertebrates / Q000145:classification* / Q000235:genetics; D010802:Phylogeny; D010944:Plants / Q000145:classification* / Q000235:genetics; D014176:Protein Biosynthesis; D012269:Ribosomal Proteins / Q000235:genetics; D014714:Vertebrates / Q000145:classification* / Q000235:genetics
chemical_list: D012269:Ribosomal Proteins; D000604:Amino Acyl-tRNA Synthetases