FIGURE 5.

Maximum-likelihood phylogenies of Cardinium strains and outgroup species. (A) Tree generated from 37 protein coding genes comprising 72,194 nucleotide alignment positions generated with RAxML under the GTR model, showing bootstrap values (1,000 replicates) and posterior probabilities from MrBayes. (B) Tree generated from 16S rRNA and gyrB genes comprising 2,426 nucleotide positions calculated as described for (A). Shading indicates major Cardinium groups. For both (A,B), similar analyses with varied alignment filtering stringency in Gblocks, different outgroups, different models, or using amino acid sequences, produced similar supported clades. (List of 37 genes in Supplementary Table 2; accession numbers in Supplementary Table 4; additional phylogenies in Supplementary Figures 1, 2.)