Figure 6

The chlamydial aaxABC genes have been vertically inherited and maintained under selective pressure. The phylogeny of chlamydial 16S ribosomal RNA genes (shown at the upper left) was inferred by the maximum likelihood method using the PhyML program to analyze aligned sequences from the ribosomal database project (RDP) [33, 54]. Bootstrap values from 1000 replicates are shown in red for each lineage supported by a plurality of trees, and this tree was rooted using the Parachlamydia sp. UWE25 rRNA sequence. A tree calculated by the weighbor method has the same topology (phylogram from RDP not shown). The phylogenies of the aaxA, aaxB and aaxC genes and d _N /d _S values for each lineage (shown in red) were inferred using maximum likelihood methods, as described in the text. No d _N /d _S values are shown for lineages with fewer than 0.05 nucleotide substitutions per codon. For each tree, the scale bar indicates the number of nucleotide substitutions per position.