Toward automatic reconstruction of a highly resolved tree of life

Science. 2006 Mar 3;311(5765):1283-7. doi: 10.1126/science.1123061.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acyl-tRNA Synthetases / genetics
  • Animals
  • Archaea / classification*
  • Archaea / genetics
  • Bacteria / classification*
  • Bacteria / genetics
  • Biological Evolution
  • Computational Biology
  • Eukaryotic Cells
  • Gene Transfer, Horizontal
  • Genome*
  • Invertebrates / classification*
  • Invertebrates / genetics
  • Phylogeny*
  • Plants / classification*
  • Plants / genetics
  • Protein Biosynthesis
  • Ribosomal Proteins / genetics
  • Vertebrates / classification*
  • Vertebrates / genetics


  • Ribosomal Proteins
  • Amino Acyl-tRNA Synthetases