title: The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon.
abstract: BACKGROUND
  The tree of life is usually rooted between archaea and bacteria. We have previously presented three arguments that support placing the root of the tree of life in bacteria. The data have been dismissed because those who support the canonical rooting between the prokaryotic superkingdoms cannot imagine how the vast divide between the prokaryotic superkingdoms could be crossed.
  
  
  RESULTS
  We review the evidence that archaea are derived, as well as their biggest differences with bacteria. We argue that using novel data the gap between the superkingdoms is not insurmountable. We consider whether archaea are holophyletic or paraphyletic; essential to understanding their origin. Finally, we review several hypotheses on the origins of archaea and, where possible, evaluate each hypothesis using bioinformatics tools. As a result we argue for a firmicute ancestry for archaea over proposals for an actinobacterial ancestry.
  
  
  CONCLUSIONS
  We believe a synthesis of the hypotheses of Lake, Gupta, and Cavalier-Smith is possible where a combination of antibiotic warfare and viral endosymbiosis in the bacilli led to dramatic changes in a bacterium that resulted in the birth of archaea and eukaryotes.
  
  
  METHODS
  This article was reviewed by Patrick Forterre, Eugene Koonin, and Gáspár Jékely.
authors.affiliation: Bioinformatics Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. rvalas@ucsd.edu
authors.forename: Ruben E
authors.initials: RE
authors.lastname: Valas
authors.forename: Philip E
authors.initials: PE
authors.lastname: Bourne
mesh_terms: D001105:Archaea / Q000145:classification / Q000235:genetics*; D005075:Biological Evolution; D006094:Gram-Positive Bacteria / Q000145:classification / Q000235:genetics*; D010802:Phylogeny