FIG 5.

Phylogenetic analysis of closely related Rickettsia rickettsii strains. The evolutionary history was inferred by using a maximum likelihood method based on the Tamura-Nei model (45). The tree with the highest log likelihood (−58,350.3501) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. The initial tree(s) for the heuristic search was obtained automatically by applying neighbor joining and BioNJ algorithms to a matrix of pairwise distances estimated using the maximum composite likelihood approach and then selecting the topology with the superior log likelihood value. A discrete gamma distribution was used to model evolutionary rate differences among sites (five categories [+G, parameter = 0.0500]). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 10-nucleotide sequences. Codon positions included were 1st, 2nd, 3rd, and noncoding. There were a total of 42,243 positions in the final data set. Evolutionary analyses were conducted in MEGA, version 5 (46).