Phylogenetic reconstruction of ATPF0A.

<p>The tree shown is the best Bayesian topology, based on 215 sequences and 232 amino acid positions (length after trimming; median sequence length before trimming: 254). Numerical values at the nodes of the tree (x/y/z) indicate statistical support by MrBayes, PhyML and RAxML (posterior probability, bootstrap and bootstrap, respectively). Values for highly supported nodes have been replaced by symbols, as indicated. Species names are colour-coded based on their bioenergetic mode as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003821#pcbi-1003821-g001" target="_blank">Figure 1</a>. Full details and accession numbers for all protein sequences used are given in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003821#pcbi.1003821.s008" target="_blank">Table S1</a>. The tree is rooted at the N-ATPase clade, previously reported to be the result of horizontal gene transfer in a variety of species, all of which also contain a canonical ATPF₀F₁ (apart from the two <i>Methanosarcina</i> species shown, which also have a canonical ATPV). The tree confidently separates the major bacterial taxonomic lineages, but with limited support for their branching order: strong support is provided for a subgroup containing the verrucomicrobia and chloroflexi, while another subgroup containing the alpha-proteobacteria, actinobacteria, chlorobi, bacteroidetes and planctomycetes also has reasonable support. This group also includes the spirochaete <i>Leptospira interrogans</i> and the gemmatimonadete <i>Gemmatimonas aurantiaca</i>, as well as <i>Candidatus Nitrospira defluvii</i> which groups with the alpha-proteobacteria. Reasonable support is also provided for the grouping of dictyoglomi and cyanobacteria, and for a subgroup containing the fusobacteria, firmicutes, tenericutes, thermotogae, and beta-gamma-proteobacteria. Two species-specific duplications (in <i>Saccharopolyspora erythraea</i> and <i>Pelobacter carbinolicus</i>) are highlighted with a red “>”. Two further duplications are highlighted with a red “-” after the species name; in <i>Photobacterium profundum</i> the duplication either occurred before the split from other closely-related species or represents HGT from other gamma-proteobacteria; the duplication in <i>Desulfococcus oleovorans</i> possibly represents HGT from thermotogae (also see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003821#pcbi.1003821.s001" target="_blank">Figures S1</a> and <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003821#pcbi.1003821.s002" target="_blank">S2</a>).