Spreadsheet: 2d118c60-3035-4e12-8f0d-70197d2e10cc
Sheet: Sheet1

Table S3. Genes Tested for Selection with PAML M8 vs. [NAME] | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6
 |  | Pairwise | M8 vs. [NAME] | M8 vs. [NAME] | M8 dN/dS | [NAME] Under
Gene | Functional Info | dN/dS | Species Used | p-value** | (% codons) | Selection (BEB P > 0.9)
Acp24A4 | serine protease inhibitor | 1.0906 | [NAME], sim, sec, ere | 0.00986009214277795 | 10.02 (0.200) | 14K, 26N, 38S, 40E
Acp26Aa | hormone, induces ovulation | 1.2415 | [NAME], sim, sec, yak, ere | 3.011650493092155e-08 | 4.22 (0.338) | 26L, 39T, 79I, 82L, 91R, 97S, 101D, 102L, 106P, 107F, 114F, 115P, 118-, 119K, 121K, 124G, 146L, 191G, 208S, 212S, 217A, 241S, 246N, 254-, 261E, 272L
Acp29AB | galactose binding, sperm competition | 0.3352 | [NAME], sim, sec | 0.438578032670934 | n.s. | n.s.
Acp36DE | glycoprotein, sperm storage | 0.5821 | [NAME], sim, sec | 0.1244822250514295 | n.s. | n.s.
Acp53C14c | unknown function | 0.6902 | [NAME], sim, sec, yak, ere | 0.05312445788169122 | n.s. | n.s.
Acp62F | serine protease inhibitor | 0.3716 | [NAME], sim, sec, yak, ere | 3.73798186755076e-05 | 8.08 (0.076) | 42E, 99L, 103S, 113N, 115S
Acp63F | unknown function | 0.7997 | [NAME], sim, sec, yak | 0.02060377574410105 | 3.45 (0.314) | 10F, 24I, 25Y, 45P, 47Y, 68P, 73H, 79S, 80L
[NAME] | defense response | 1.6747 | [NAME], sim, sec, yak, ere | 0.1512102420027701 | n.s. | n.s.
CG10862 | ubiquitin ligase activity | 0.9159 | [NAME], sim, sec, yak, ere | 0.7772974108728412 | n.s. | n.s.
CG15031 | unknown function | 0.9078 | [NAME], sec, yak, ere | 0.4165599438190531 | n.s. | n.s.
CG1701-PB | unknown function | 0.2617 | [NAME], sim, sec, yak, ere | 0.4165599438189728 | n.s. | n.s.
CG17242 | serine protease | 0.3662 | [NAME], sim, sec, yak, ere | 0.4310472862990055 | n.s. | n.s.
CG17472* | unknown function | 0.8777 | [NAME], sim, sec, yak, ere | 0.006378989637741676 | 3.56 (0.161) | 37N, 41Y, 77V, 81Q, 84L, 132E, 136V, 139L, 146P, 148A, 151E, 160L, 162G
CG18284 | lipase activity | 0.2368 | [NAME], sim, yak | 0.1593904698266834 | n.s. | n.s.
CG31418 | unknown function | 0.3126 | [NAME], sim, sec | 0.006378989637741676 | infinity (0.005) | 98G
CG31515 | unknown function | 0.94 | [NAME], sim, sec, yak | 0.001106676774171895 | 8.88 (0.059) | 95T, 107M, 146E
CG31704 | serine protease inhibitor | 0.6626 | [NAME], sim, sec, yak, ere | 0.04828611613883998 | 4.79 (0.110) | 23F, 24Q, 27S, 54L
CG31758 | serine protease inhibitor | 0.3445 | [NAME], sim, sec, yak, ere | 0.841480581133695 | n.s. | n.s.
CG31872 | triacylglycereol lipase | 0.5431 | [NAME], sim, sec, yak | 1.188335865793262e-07 | 2.11 (0.428) | 88S, 94V, 102G, 107F, 108S, 109R, 110G, 120K, 124S, 132G, 141Q, 142Y, 146A, 158Q, 164S, 169Q, 171Q, 174L, 186P, 187Y, 194S, 197R, 198N, 200D, 215S, 227G, 232D, 236S, 246L, 249G, 256S, 258I, 264G, 265L, 347A, 350L, 362Q, 384K, 392K, 467D, 468K, 499T, 501I, 521S, 533S, 537A, 542Q, 543R, 549S, 555I, 556L, 557T, 566Q, 574V, 669S, 679S, 689D, 704L, 706E, 709A, 716C, 720S, 1000A, 1022L
CG4815 | serine protease | 0.519 | [NAME], sim, sec, yak, ere | 0.01207379834940886 | 4.77 (0.046) | 254K, 261N
CG5402 | unknown function | 0.4356 | [NAME], sim, sec, ere | 0.09909804632958175 | n.s. | n.s.
CG6289 | serine protease inhibitor | 0.8152 | [NAME], sec, yak | 1.125825374440599e-06 | 2.28 (0.594) | 19I, 24V, 42S, 43L, 49D, 50A, 64T, 90E, 94T, 104A, 107V, 117E, 126N, 143V, 144G, 150K, 158E, 161G, 163G, 165V, 168R, 169E, 181D, 183D, 184Q, 185G, 188I, 196D, 197K, 200H, 201A, 202K, 204F, 209R, 214S, 216V, 218V, 237S, 250S, 256E, 283G, 285H, 297S, 298Q, 305K, 309N, 310L, 314R, 317E, 338R, 340V, 342S, 344E, 348Y, 356R, 358E, 364G, 369P, 370T, 371G, 410I, 427H
CG9029 | defense response | 0.8633 | [NAME], sim, sec | 0.7290344901853953 | n.s. | n.s.
[NAME] | cysteine protease inhibitor | 0.3589 | [NAME], sim, sec, yak, ere | 0.5967012180891057 | n.s. | n.s.
Dup99B | hormone, post-mating behavior | 0.4964 | [NAME], sim, sec, yak | 0.9999997476867478 | n.s. | n.s.
lectin-29Ca | lectin, galactose binding | 0.3658 | [NAME], sim, sec, yak, ere | 0.4708416843455674 | n.s. | n.s.
lectin-30A | lectin, galactose binding | 0.5639 | [NAME], sim, sec, yak, ere | 0.06136884029979092 | n.s. | n.s.
[NAME] | defense response, lysozyme activity | infinity | [NAME], sim, sec, yak, ere | 1 | n.s. | n.s.
Met75Ca/Cb | unknown function | 2.7802 | [NAME], sim, sec, yak, ere | 4.359281263032835e-06 | 32.27 (0.064) | 30S, 38H, 39A
Mst57Db | unknown function | 0.7191 | [NAME], sim, sec, yak, ere | 0.03350083599634831 | 6.95 (0.076) | 7L
Mst57Dc | unknown function | 0.9137 | [NAME], sim, sec | 0.0003656555788308318 | infinity (0.015) | 55V
Obp22a | odorant binding protein | 0.466 | [NAME], sec, yak, ere | 4.871723638335156e-09 | infinity (0.047) | 112R, 113D, 114S, 115A, 118R
Obp56f | odorant binding protein | 0.3321 | [NAME], sim, sec, yak, ere | 0.4976239741582525 | n.s. | n.s.
Obp56i | odorant binding protein | 0.4162 | [NAME], sim, sec, yak, ere | 0.6891565168366232 | n.s. | n.s.
Spn2 | serine protease inhibitor | 0.8133 | [NAME], sim, ere, yak | 9.635563614458247e-14 | 7.07 (0.120) | 110S, 127D, 155S, 160S, 184L, 188R, 208S, 210R, 276A, 281V, 292E, 293K, 294S, 298K, 305N, 307H, 309K, 310K, 334F, 338S, 339M, 341M, 342P, 344S, 345Q
Spn7 | serine protease inhibitor | 0.3786 | [NAME], sim, sec, yak, ere | 0.2116653141285382 | n.s. | n.s.
 |  |  |  |  |  | position refers to Dmel sequence; - indicates a gap in Dmel
 |  |  |  |  |  | plain = BEB > 0.9
 |  |  |  |  |  | bold = BEB > 0.95
 |  |  |  |  |  | underline = BEB > 0.99
*comparison in this table includes only one of two duplicate copies from each of D. simulans and D. sechellia
**After [NAME] correction, p < 0.00139 remains significant in the [NAME] vs. M8 likelihood ratio test