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Table 8 Genes under positive selection (using FDR < 0.05) on the branch between Bombus and Apis (4 taxa tree)

From: A depauperate immune repertoire precedes evolution of sociality in bees

OrthoDB group id a Gene b Classification Total sites c Likelihood ratio d p-value BH-corrected q-value e Positively selected sites f
EOG6VDNFR dorsal Relish 476 36.202 0.00000 0.00000 121Q, 194S, 228S, 318L, 326R, 330W, 333K, 334I, 335S, 345D, 348N, 350Q, 351N, 353A, 358Y, 359P, 363D, 367K, 368S, 369N, 372D, 373T, 375A, 376K, 377L, 380A, 384Q, 386T, 387T, 390S, 392D, 394D, 396C, 397D, 398T, 400T, 401S, 403Q, 404M, 407F, 410L, 411S, 415K, 420T, 422P, 425P, 433K, 434Q, 440V, 441P, 443E, 446Q, 447S, 448L, 453N, 454T, 458S, 462S, 463P, 465E, 467G, 468K, 471S, 472E, 473K, 474K, 476T
EOG6ZPC96 nimrod-C2 Nimrod 1802 26.848 0.00000 0.00001 37Q, 47Q, 188M, 444H, 458K, 511M, 522V, 535V, 537E, 542Q, 550K, 576C, 582E, 599Y, 612P, 617T, 619V, 626P, 628V, 633R, 643V, 644N, 663R, 669S, 677E, 693S, 1010P
EOG66Q57J LOC100642902 (B. terr) Serine protease inhibitor 1327 39.488 0.00000 0.00000 40G, 213S, 287E, 291D, 299V, 334V, 341S, 452S, 503T, 507H, 508S, 509D, 577G, 597D, 631T, 666D, 704K, 708S, 710A, 743S, 758K, 759W, 775Q, 778S, 820K, 856M, 858Q
EOG6BG79T spindle-E Small RNA regulatory pathway members 1273 7.774 0.00265 0.03328 17H, 55Q, 157D, 175S, 254N, 391Q, 492G, 749T, 751S, 787I, 832F, 1026P, 1131S, 1237N, 1248T
EOG68SF83 tep23 Thioester-containing protein 1694 10.554 0.00058 0.01087 15T, 39Y, 84S, 204P, 288G, 652A, 683S, 1070S, 1092S, 1466L, 1467S, 1470E, 1482A, 1543L
EOG6QNKCB spatzle-1B Spaetzle 169 7.766 0.00266 0.03328 3S, 10C, 14E, 17S, 22A, 36S, 62S, 96A, 116T, 142S
EOG6866VT tube Toll pathway 298 8.801 0.00151 0.02258 24S, 30S, 45M, 195L, 267L, 287V, 295N
EOG6XWDDG-1 serpin-10A Serine protease inhibitor 385 11.507 0.00035 0.00743 88S, 253F, 335S, 341C, 344P
EOG6W3R35 belle Small RNA regulatory pathway members 683 14.230 0.00008 0.00303 134T, 278I, 602S, 633Q, 664S
EOG6KKWHX argonaute-2 Small RNA regulatory pathway members 896 12.187 0.00024 0.00665 44S, 49S, 746S
EOG6HHMH6 serpin-23 Scavenger receptor 2066 10.002 0.00078 0.01303 1459K
EOG66DJHX-1 dscam-like protein Immunoglobulin 1847 12.000 0.00027 0.00665 None
  1. aGroup identifiers are from OrthoDB 6 (http://cegg.unige.ch/orthodb6).
  2. bNumber of codons remaining in the alignment after trimming with Gblocks.
  3. cComparison of Branch-site model A versus a constrained version with ω 2 = 1.
  4. eMultiple test correction by the method of Benjamini and Hochberg to control the false discovery rate (only groups where FDR < 0.05 are shown).
  5. fSites are classified as under positive selection if the Bayesian posterior probability > 0.75 (> 0.95 in bold). The reference sequence is from A. mellifera.