Phylogeny of Gammaproteobacteria

The phylogeny of the large bacterial classGammaproteobacteria has been difficult to resolve. Here we apply a telescoping multiprotein approach to the problem for 104 diverse gammaproteobacterial genomes, based on a set of 356 protein families for the whole class and even larger sets for each of four cohesive subregions of the tree. Although the deepest divergences were resistant to full resolution, some surprising patterns were strongly supported. A representative of theAcidithiobacillales routinely appeared among the outgroup members, suggesting that in conflict with rRNA-based phylogenies this order does not belong toGammaproteobacteria ; instead, it (and, independently, “Mariprofundus ”) diverged after the establishment of theAlphaproteobacteria yet before the betaproteobacteria/gammaproteobacteria split. None of the ordersAlteromonadales ,Pseudomonadales , orOceanospirillales were monophyletic; we obtained strong support for clades that contain some but exclude other members of all three orders. Extreme amino acid bias in the highly A+T-rich genome ofCa ndidatus Carsonella prevented its reliable placement withinGammaproteobacteria , and high bias caused artifacts that limited the resolution of the relationships of other insect endosymbionts, which appear to have had multiple origins, although the unbiased genome of the endosymbiontSodalis acted as an attractor for them. Instability was observed for the root of theEnterobacteriales , with nearly equal subsets of the protein families favoring one or the other of two alternative root positions; the nematode symbiontPhotorhabdus was identified as a disruptor whose omission helped stabilize theEnterobacteriales root.