Peer-Reviewed Journal Details
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Creevey C.;Fitzpatrick D.;Philip G.;Kinsella R.;O'Connell M.;Pentony M.;Travers S.;Wilkinson M.;McInerney J.
2004
December
Proceedings of the Royal Society B: Biological Sciences
Does a tree-like phytogeny only exist at the tips in the prokaryotes?
Published
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Optional Fields
Molecular evolution Phylogenetic supertrees Phylogenomics Prokaryotic phylogeny Taxonomic congruence
271
1557
2551
2558
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.
0962-8452
10.1098/rspb.2004.2864
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