Maximum-likelihood (ML) tree of known PylRS homologs. Branch colors depict the taxonomy of PylRS lineages, with Euryarchaeota (red), Firmicutes (blue) and Deltaproteobacteria (magenta). The different observed protein subunit configurations are depicted on the right, using the same color scheme. Absent protein regions within some groups is represented by whitespace. More narrow taxonomic designations are bracketed and labeled. The tree is rooted by an outgroup consisting of aligned regions from other class II aaRS representatives from different subclasses. Dotted lines represent branches with <50% bootstrap (BS) support; major clades with >80% BS support are labeled with respective BS support values. Italic numbers represent posterior probability (PP) support values from tree reconstruction in Phylobayes3.3 (PB). Significant conflict between the ML and PB trees is shown by an alternative diagonal branching. The alignment contains 37 taxa with alignment length of 475 amino acids. Branch lengths depict substitutions/site. (*)PP support value in the alternative PB topology; (**)PP support was not recovered for the rooting of PylRS using PB, as this node remained unresolved.