Phylogenetic network with concatenated 16S rRNA, 23S rRNA, <i>GroEL</i>, <i>rpoB</i> and <i>dnaK</i> sequences (3009 unambiguously aligned bp), including 71 <i>Coxiella</i>-like strains of ticks, 15 <i>C</i>. <i>burnetii</i> reference strains, and bacterial outgroups.

<p>The four <i>Coxiella</i> clades are labeled A to D. A zoom on the A clade which contains <i>C</i>. <i>burnetii</i> isolates is shown in Supplementary Fig C in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004892#ppat.1004892.s001" target="_blank">S1 Text</a>. Each number corresponds to one tick species as detailed in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004892#ppat.1004892.t001" target="_blank">Table 1</a>. Blue—<i>Coxiella</i>-like organisms; red—<i>C</i>. <i>burnetii</i>; green—<i>Rickettsiella</i>; black- other bacteria. All multi-locus typing of <i>Coxiella</i> and <i>Rickettsiella</i> of ticks are new sequences from this study. The scale bar is in units of substitution/site.</p

List of tick species and populations included in the analysis, with details on their origin, the population sample size, and the prevalence of <i>Coxiella</i> spp. and <i>Rickettsiella</i> spp.

<p>List of tick species and populations included in the analysis, with details on their origin, the population sample size, and the prevalence of <i>Coxiella</i> spp. and <i>Rickettsiella</i> spp.</p

Characterization of new <i>Coxiella</i> strains derived from whole-genome sequencing (WGS) of the cattle tick <i>Rhipicephalus microplus</i>.

<p>(a) Percent identity of 50 genes uniquely attributable to <i>Coxiella</i> from <i>R</i>. <i>microplus</i> WGS versus 15 sequenced <i>C</i>. <i>burnetii</i> genomes and other reference genomes. (b) Bacterial phylogeny, comprising the <i>Coxiella</i> found in the <i>R</i>. <i>microplus</i> WGS data, reconstructed from the concatenated sequences of Fig 3A (19,304 unambiguously aligned bp) using maximum-likelihood (ML). Branch numbers indicate percent bootstrap support for major branches (1,000 replicates; only bootstrap values >90% are shown). The scale bar is in units of substitution/site.</p

Geographic origin of the sampled ticks and distribution of <i>Coxiella</i> and <i>Rickettsiella</i> infections.

<p>Square size indicates the number of populations sampled per geographic area. Numbers refer to the tick species whereas letters discriminate the different populations screened within a species; this nomenclature is detailed in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004892#ppat.1004892.t001" target="_blank">Table 1</a>. The colors within squares indicate the infection status of populations. Two tick species were infected by both <i>Coxiella</i> and <i>Rickettsiella</i> at the species level, but not at individual and population levels.</p

Genetic estimates for 85 <i>Coxiella</i>-like strains and for 15 <i>Coxiella burnetii</i> reference strains.

<p>Analyses are based on nucleotide sequences of five housekeeping genes, excluding sites with alignment gaps and/or missing data. L, sequence fragment length in base pairs; N_i, Number of examined strains; P_nsi, Pairwise nucleotide sequence identity (%); N_a, number of alleles; P_s, number of polymorphic sites; A_d, allelic diversity; π, nucleotide diversity; D, average number of nucleotide differences between sequences.</p><p>Genetic estimates for 85 <i>Coxiella</i>-like strains and for 15 <i>Coxiella burnetii</i> reference strains.</p