rpl36 tree and alignment. The M3 codon model in MrBayes was used to calculate the tree using the alignment shown. Nodes with posterior probability <0.95 are collapsed. Posterior probabilities (left) and PROML BP values >50% (right) are shown on the remaining nodes. The PROML bootstraps were run with four rate categories (estimated with PUZZLE) and global rearrangements. Nucleotide and amino-acid based ML analyses using PAUP* and MrBayes also gave 100% support for the division between the c-type and p-type rpl36 genes. This support is maintained when all positions containing gaps are removed. Because the 3' extension unique to some c-type rpl36 genes (see Additional File 2) was excluded from this phylogenetic analysis, it is not shown in the alignment. In the alignment, each base is colored according to the key. Taxa in red include the red algae and their secondary plastid containing relatives. A subset of the many proteobacterial species which contain both the p-type and c-type genes is shown in purple. The p-type Pseudomonas, Photobacterium, and Vibrio genes are not shown here.