MBE Advance Access originally published online on September 8, 2005
Molecular Biology and Evolution 2006 23(1):74-85; doi:10.1093/molbev/msj009
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Research Article |
Genome Phylogenies Indicate a Meaningful 
-Proteobacterial Phylogeny and Support a Grouping of the Mitochondria with the Rickettsiales
Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland
E-mail: james.o.mcinerney{at}may.ie.
Placement of the mitochondrial branch on the tree of life has been problematic. Sparse sampling, the uncertainty of how lateral gene transfer might overwrite phylogenetic signals, and the uncertainty of phylogenetic inference have all contributed to the issue. Here we address this issue using a supertree approach and completed genomic sequences. We first determine that a sensible 
-proteobacterial phylogenetic tree exists and that it can confidently be inferred using orthologous genes. We show that congruence across these orthologous gene trees is significantly better than might be expected by random chance. There is some evidence of horizontal gene transfer within the -proteobacteria, but it appears to be restricted to a minority of genes (
23%) most of whom (74%) can be categorized as operational. This means that placement of the mitochondrion should not be excessively hampered by interspecies gene transfer. We then show that there is a consistently strong signal for placement of the mitochondrion on this tree and that this placement is relatively insensitive to methodological approach or data set. A concatenated alignment was created consisting of 15 mitochondrion-encoded proteins that are unlikely to have undergone any lateral gene transfer in the timeline under consideration. This alignment infers that the sister group of the mitochondria, for the taxa that have been sampled, is the order Rickettsiales.
Key Words: -proteobacterial phylogeny • supertree • mitochondria • removing fast-evolving sites
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