Fig. 2

Phylogenetic tree of 16S RNA gene (rrs) of Candidatus Orientia chiloensis (OC) from trombiculid mites and patients with scrub typhus, as well as Orientia tsutsugamushi strains (OT), Candidatus Orientia chuto, and other bacteria. The evolutionary history was inferred by using the maximum likelihood method and Tamura-Nei model [18]. The tree with the highest log likelihood (−2747.08) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the maximum composite likelihood (MCL) approach, and then selecting the topology with superior log likelihood value. A discrete Gamma distribution was used to model evolutionary rate differences among sites [five categories (+ G, parameter = 0.1974)]. This analysis involved 42 nucleotide sequences. All positions with less than 95% site coverage were eliminated, i.e., fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position (partial deletion option). There was a total of 859 positions in the final dataset. Evolutionary analyses were conducted in MEGA X [19]. Red circles indicate the sequences from trombiculid mites of this study. Sequences retrieved from GenBank have the genus, followed by the species, strain, and GenBank accession number. Sequences from the different Orientia tsutsugamushi strains are named OT, followed by the strain