title: Does a tree-like phylogeny only exist at the tips in the prokaryotes?
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.
authors.affiliation: Bioinformatics and Pharmacogenomics Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Creevey
authors.forename: David A
authors.initials: DA
authors.lastname: Fitzpatrick
authors.forename: Gayle K
authors.initials: GK
authors.lastname: Philip
authors.forename: Rhoda J
authors.initials: RJ
authors.lastname: Kinsella
authors.forename: Mary J
authors.initials: MJ
authors.lastname: O'Connell
authors.forename: Melissa M
authors.initials: MM
authors.lastname: Pentony
authors.forename: Simon A
authors.initials: SA
authors.lastname: Travers
authors.forename: Mark
authors.initials: M
authors.lastname: Wilkinson
authors.forename: James O
authors.initials: JO
authors.lastname: McInerney
mesh_terms: D001419:Bacteria / Q000235:genetics*; D002965:Classification / Q000379:methods*; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D016680:Genome, Bacterial; D016013:Likelihood Functions; D008957:Models, Genetic; D010802:Phylogeny