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

Research output: Contribution to journalArticlepeer-review

107 Citations (SciVal)


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 gamma-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 gamma-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


  • phylogenetic supertrees
  • prokaryotic phylogeny
  • taxonomic congruence
  • phylogenomics
  • molecular evolution


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