Fitzpatrick, David A. and Creevey, Christopher J. and McInerney, James O.
Genome Phylogenies Indicate a Meaningful a-Proteobacterial Phylogeny
and Support a Grouping of the Mitochondria with the Rickettsiales.
Molecular Biology and Evolution, 23 (1).
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 a-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 a-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.
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