[23]. All analyses were performed in three independent runs, each taking 5 million generations. Acknowledgements This work was supported by Ministry of Education, Czech Republic (grants LC06073 and MSM 60076605801), the Grant Agency of Academy of Sciences of the Czech Republic (Grant IAA601410708) and a National Science Foundation grant (0626716) to N.A. Moran (University of Arizona). We thank all of our collaborators for providing the samples. Electronic supplementary material Additional file 1:

Consensus tree derived from the Conservative matrix (284 positions) under MP criterion. Transversion/Elafibranor transition ratio was set to 1:3. Names of the taxa clustering within the Arsenophonus clade derived from Basic matrix are printed in colour: red for the long-branched taxa, dark orange for the short-branched taxa. (EPS 2 MB) Additional file 2: Tree

consensus derived from Sampling4 this website (1107 positions) matrix under the MP criterion. Transversion/transition ratio was set to 1:1. The type species A. nasoniae is designated by the orange asterisk. (EPS 759 KB) Additional file 3: Insertions MK-4827 in vivo within the sequences of P-like symbionts. (EPS 2 MB) Additional file 4: The 41 bp long motif inconsistently distributed among distinct bacterial taxa. Position of the sequence in alignment and 16S rDNA secondary structure is indicated by the arrows. Following records are not included in the Additional file 1: Sitophilus rugicollis [GenBank: AY126639], Drosophila paulistorum [GenBank: U20279, U20278], Polyrhachis foreli ever [GenBank: AY336986], Haematopinus eurysternus [GenBank: DQ076661]. (EPS 2 MB) Additional file 5: List of sequences included in Basic matrix. Dashed line separates members of the Arsenophonus clade from the outgroup taxa. Sequences

included into the Clock matrix are underlined. (DOC 142 KB) References 1. Huger AM, Skinner SW, Werren JH: Bacterial infections associated with the son-killer trait in the parasitoid wasp, Nasonia (= Mormoniella ) vitripennis (Hymenoptera, Pteromalidae). J Invertebr Pathol 1985, 46:272–280.CrossRefPubMed 2. Skinner SW: Son-killer – A 3rd extrachromosomal factor affecting the sex-ratio in the parasitoid wasp, Nasonia (= Mormoniella ) vitripennis. Nasonia 1985, 109:745–759. 3. Werren JH, Skinner SW, Huger AM: Male-killing bacteria in a parasitic wasp. Science 1986, 231:990–992.CrossRefPubMed 4. Gherna RL, Werren JH, Weisburg W, Cote R, Woese CR, Mandelco L, Brenner DJ:Arsenophonus nasoniae gen. nov., sp. nov., the causative agent of the son-killer trait in the parasitic wasp Nasonia vitripennis. Int J Syst Bacteriol 1991, 41:563–565.CrossRef 5. Hypša V: Endocytobionts of Triatoma infestans : distribution and transmission. J Invertebr Pathol 1993, 61:32–38.