Does a tree-like phylogeny only exist at the tips in the prokaryotes?
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.
Creevey
Christopher J
CJ
Bioinformatics and Pharmacogenomics Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland.
Fitzpatrick
David A
DA
Philip
Gayle K
GK
Kinsella
Rhoda J
RJ
O'Connell
Mary J
MJ
Pentony
Melissa M
MM
Travers
Simon A
SA
Wilkinson
Mark
M
McInerney
James O
JO
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