Does a tree-like phylogeny only exist at the tips in the prokaryotes?

Christopher J. Creevey, David A. Fitzpatrick, Gayle K. Philip, Rhoda J. Kinsella, Mary J. O'Connell, Melissa M. Pentony, Simon A. Travers, Mark Wilkinson, James O. McInerney*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

102 Citations (Scopus)


The extent to which prokaryotic evolution has been influenced by horizontal gene transfer (HGT) and therefore might be more of a network than a tree is unclear. Here we use supertree methods to ask whether a definitive prokaryotic phylogenetic tree exists and whether it can be confidently inferred using orthologous genes. We analysed an 11-taxon dataset spanning the deepest divisions of prokaryotic relationships, a 10-taxon dataset spanning the relatively recent γ-proteobacteria and a 61-taxon dataset spanning both, using species for which complete genomes are available. Congruence among gene trees spanning deep relationships is not better than random. By contrast, a strong, almost perfect phylogenetic signal exists in γ-proteobacterial genes. Deep-level prokaryotic relationships are difficult to infer because of signal erosion, systematic bias, hidden paralogy and/or HGT. Our results do not preclude levels of HGT that would be inconsistent with the notion of a prokaryotic phylogeny. This approach will help decide the extent to which we can say that there is a prokaryotic phylogeny and where in the phylogeny a cohesive genomic signal exists.

Original languageEnglish
Pages (from-to)2551-2558
Number of pages8
JournalProceedings of the Royal Society B: Biological Sciences
Issue number1557
Publication statusPublished - 22 Dec 2004
Externally publishedYes


  • Molecular evolution
  • Phylogenetic supertrees
  • Phylogenomics
  • Prokaryotic phylogeny
  • Taxonomic congruence

ASJC Scopus subject areas

  • Medicine(all)
  • Immunology and Microbiology(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Environmental Science(all)
  • Agricultural and Biological Sciences(all)


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