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Creevey C.;Fitzpatrick D.;Philip G.;Kinsella R.;O'Connell M.;Pentony M.;Travers S.;Wilkinson M.;McInerney J.
Proceedings of the Royal Society B: Biological Sciences
Does a tree-like phytogeny only exist at the tips in the prokaryotes?
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Molecular evolution Phylogenetic supertrees Phylogenomics Prokaryotic phylogeny Taxonomic congruence
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. © 2004 The Royal Society.
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