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Proceedings of the Royal Society B: Biological Sciences logoLink to Proceedings of the Royal Society B: Biological Sciences
. 2004 Dec 22;271(1557):2551–2558. doi: 10.1098/rspb.2004.2864

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

Christopher J Creevey 1, David A Fitzpatrick 1, Gayle K Philip 1, Rhoda J Kinsella 1, Mary J O'Connell 1, Melissa M Pentony 1, Simon A Travers 1, Mark Wilkinson 1, James O McInerney 1
PMCID: PMC1691901  PMID: 15615680

Abstract

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.

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Selected References

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