Supporting Information Table S1. PCR primers used in this project. Target gene Primer pair (5’ to 3’) (Fragment Annealing Target group (ºC) size) 10F: AGTTTGATCATGGCTCAGATTGa 16S rRNA Most bacteria 1507R: TACCTTGTTACGACTTCACCCCAGa (~1500 bp) 27F: GAGAGTTTGATCCTGGCTCAGb 16S rRNA 1492R: GGTTACCTTGTTACGACTTb (~1470 bp) Most bacteria 559F: CGTGCCAGCAGCCGCGGTAATACc temp 16S-ITS-35R Most bacteria (>1000 bp) (not Wolbachia) 60 55 58 35R: CCTTCATCGCCTCTGACTGCd p58IV_F: AAAGGTTTACATTCACCAAGTCGe P58 Spiroplasma p58IV_R: ATTGTTCATTAACTTTATCTTGTGGe 53 (362 bp) wspF: TGGTCCAATAAGTGATGAAGAAACTAGCTAf wsp Touchdown Wolbachia wspR: (~600 bp) 65–55 AAAATTAAACGCTACTCCAGCTTCTGCACf HCO2198: TAAACTTCAGGGTGACCAAAAAAT g COI Most LCO1490: GGTCAACAAATCATAAAGATATTGg (~709 bp) invertebrates 45 a Munson et al. (1991) b Lane (1991) c Russell et al. (2003) d Mateos et al. (2006) e Xie et al. (2010) f Jeyaprakash & Hoy (2000) g Folmer et al. (1994) 1 Table S1 Number of flies per isoline, Spiroplasma-infection state, and sex used to stock the initial generation of each bottle (replicate). Isoline ID Spiroplasma infection state Sex No. individuals in S+ population No. individuals in S-population … 1 S– S+ 5 S– S+ Total S– S+ F M F M F M F M F M F M 5 5 5 5 5 5 5 100 10 10 100 5 5 5 10 10 10 10 2 5 5 Figure S1. Experimental Setting. Columns indicate fly vials and circles represent population bottles. S = Spiroplasma infection treatment; Lh = Leptopilina heterotoma treatment. 3 4 Figure S2. Vertical transmission efficiency of Spiroplasma in females from the S+Lh+ and S+Lhtreatments in all generations. S = Spiroplasma, Lh = Leptopilina heterotoma treatment. Error bar: standard error. Note: G4 is lacking data because the selected replicate used for this generation had lost Spiroplasma infection. References Folmer O, Black M, Hoeh W, Lutz R & Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3: 294-299. 5 Jeyaprakash A & Hoy MA (2000) Long PCR improves Wolbachia DNA amplification: wsp sequences found in 76% of sixty-three arthropod species. Insect Mol Biol 9: 393–405. Lane DJ (1991) 16S/23S rRNA sequencing. Nucleic acid techniques in bacterial systematics,(Stackebrandt E & Goodfellow M, eds.), pp. 115-175. John Wiley and Sons, New York, NY. Mateos M, Castrezana SJ, Nankivell BJ, Estes AM, Markow TA & Moran NA (2006) Heritable endosymbionts of Drosophila. Genetics 174: 363-376. Munson MA, Baumann P, Clark MA, Baumann L, Moran NA, Voegtlin DJ & Campbell BC (1991) Evidence for the establishment of aphid-eubacterium endosymbiosis in an ancestor of four aphid families. J Bacteriol 173: 6321-6324. Russell JA, Latorre A, Sabater-Munoz B, Moya A & Moran NA (2003) Side-stepping secondary symbionts: widespread horizontal transfer across and beyond the Aphidoidea. Mol Ecol 12: 1061-1075. Xie J, Vilchez I & Mateos M (2010) Spiroplasma bacteria enhance survival of Drosophila hydei attacked by the parasitic wasp Leptopilina heterotoma. PLoS ONE 5: e12149. 6