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.
Does a tree-like phylogeny only exist at the tips in the
Proceedings of The Royal Society of London, Biology Series, 271 (1557).
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.
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