A multiple sequence alignment of the 16S genes was generated with Muscle v3.41 [47] using default values for maximum iterations and maximum time. A distance matrix was generated from the aligned sequences with 4SC-202 the dnadist program from the Phylip suite v3.68 using the Kimura 2-parameter distance model. For each orthologous cluster, we extracted the taxon IDs of the taxa included in the

cluster. Using the calculated distances between taxa based on aligned 16S sequences as edge weights between the taxon nodes, a minimum spanning tree (MST) was generated using Prim’s algorithm [48]. Each MST was scored based on the sum of edge weights included in the tree. Table 5 16S rRNA gene sequence sources Refseq ID Taxon Coordinates

Species name NC_012026.1 320483 246283-247795 Anaplasma marginale str. Florida, Fosbretabulin price complete genome NC_004842.2 234826 247468-248989 Anaplasma marginale str. St. Maries NC_007797.1 212042 1057470-1058902 Anaplasma phagocytophilum HZ NC_007205.1 335992 511358-512831 Candidatus Pelagibacter ubique HTCC1062 NC_007354.1 269484 285955-287439 Ehrlichia canis str. Jake NC_007799.1 205920 check details 942218-943726 Ehrlichia chaffeensis str. Arkansas NC_006831.1 302409 303748-305256 Ehrlichia ruminantium str. Gardel NC_006832.1 254945 306928-308437 Ehrlichia ruminantium str. Welgevonden NC_005295.2 254945 326964-328421 Ehrlichia ruminantium str. Welgevonden NC_007798.1 222891 36268-37765 Neorickettsia sennetsu str. Miyayama

to NC_009488.1 357244 1322598-1324120 Orientia tsutsugamushi str. Boryong NC_010793.1 334380 379135-380647 Orientia tsutsugamushi str. Ikeda, complete genome NC_009881.1 293614 864179-865686 Rickettsia akari str. Hartford NC_009883.1 391896 1008161-1009668 Rickettsia bellii OSU 85-389 NC_007940.1 336407 537796-539303 Rickettsia bellii RML369-C NC_009879.1 293613 385940-387447 Rickettsia canadensis str. McKiel] NC_003103.1 272944 884601-886108 Rickettsia conorii str. Malish 7 NC_007109.1 315456 456383-457890 Rickettsia felis URRWXCal2 NC_009900.1 416276 968391-969898 Rickettsia massiliae MTU5 NC_000963.1 272947 772263-773769 Rickettsia prowazekii str. Madrid E NC_009882.1 392021 876489-877996 Rickettsia rickettsii str. ‘Sheila Smith’ NC_010263.1 452659 887263-888750 Rickettsia rickettsii str. Iowa NC_006142.1 257363 779669-781167 Rickettsia typhi str. Wilmington NC_010981.1 570417 1136001-1137446 Wolbachia endosymbiont of Culex quin-quefasciatus Pel, complete genome NC_002978.6 163164 1167943-1169389 Wolbachia endosymbiont of Drosophila melanogaster NC_006833.1 292805 634569-636083 Wolbachia endosymbiont strain TRS of Brugia malayi NC_012416.1 66084 1289969-1291473 Wolbachia sp. wRi complete genome MST distances for each cluster containing a wBm gene were rounded to 2 decimal places and scaled to integers between 0 and 100.