Table 8.

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

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

^aGroup identifiers are from OrthoDB 6 (http://cegg.unige.ch/orthodb6).

^bNumber of codons remaining in the alignment after trimming with Gblocks.

^cComparison of Branch-site model A versus a constrained version with ω ₂ = 1.

^eMultiple test correction by the method of Benjamini and Hochberg to control the false discovery rate (only groups where FDR < 0.05 are shown).

^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.