Dianne_et_al_Predation_tests

Dianne_et_al_Predation_test

Additional file 1: Table S1. of Reliability of molecular host-identification methods for ticks: an experimental in vitro study with Ixodes ricinus

Number of ticks measured in each treatment group of the experiment. Table S2. Description of statistical models used to analyse the influence of host type (“host”), time post-moult (“moult”), tick life stage (“stage”), bloodmeal life stage (“bloodmeal”) and method as explanatory fixed variable and tick as a random nested factor on detection threshold, detection rate and tick size. N gives the number of ticks included in each analysis. “Maximal model” gives the complete set of explanatory variables tested (and their interactions) included in the model. “Minimal model” gives the model containing only the significant variables and their interactions. (DOCX 16 kb

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

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

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