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

Creevey, Christopher J. and Fitzpatrick, David A. and Philip, Gayle K. and Kinsella, Rhoda J. and O'Connell, Mary J. and Pentony, Melissa M. and Travers, Simon A. and Wilkinson, Mark and McInerney, James O. (2004) Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proceedings of The Royal Society of London, Biology Series, 271 (1557). pp. 2551-2558.

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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 c-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 c-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.

Item Type: Article
Keywords: phylogenetic supertrees; prokaryotic phylogeny; taxonomic congruence; phylogenomics; molecular evolution
Subjects: Science & Engineering > Biology
Item ID: 414
Depositing User: Dr. James McInerney
Date Deposited: 23 Sep 2008
Journal or Publication Title: Proceedings of The Royal Society of London, Biology Series
Publisher: The Royal Society of London
Refereed: Yes
URI:

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