Phylogenetic trees for selected TT genes with apparent XGD involving an ortholog from a thermophilic species. Maximum-likelihood unrooted trees were constructed and bootstrap probabilities were computed using the MOLPHY program. Branches with bootstrap probability >70% are marked by black circles. Each leaf is denoted by the standard gene identifier (for the the complete list of correspondence between genes and species, see Additional file 1: "Gene identifiers and species names for figure 6"). The DR and TT genes are boxed. Genes from thermophilic species are shown in red. A. Ribosomal protein L30. B. Ribosomal protein L15. C. Thiamin biosynthesis protein ThiC. D. tRNA thiolation enzyme TtcA.