SupportinglnformationS2

S2. Maximum parsimony tree using seven parsimony informative (synapomorphic) SNPs with loci shared with closest outgroup species. Only one SNP locus (out of 11,386 total SNPs among C. burnetii genomes) was present in all genomes. The remaining six loci were found by relaxing the requirement that all loci are shared among all C. burnetii genomes as they were not present in the Q177 genome. All seven SNP loci were present in Pseudomonas syringae and Legionella pneumophila. Four of the seven loci were present in Ricketsiella grylli. Consistency index = 1.0. Numbers on branches indicate bootstrap support percentages from 1000 bootstrap replicates.