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Table 6 Genes under positive selection (using FDR < 0.05) on the branch to Apis (5 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
EOG6VX0M3 ark Caspase 1128 9.974 0.00079 0.02812 412N, 484N, 593S, 862P, 941N, 953L
EOG66Q57J LOC100642902 (B. terr) Serine protease inhibitor 1189 9.555 0.00100 0.02812 425D, 452I, 540S, 622S, 721M
EOG634TN0 drosha Small RNA regulatory pathway members 1290 8.884 0.00144 0.03380 58A, 94N, 155M, 278V
EOG6XWDCW rm62-C Small RNA regulatory pathway members 492 10.537 0.00058 0.02812 32S, 130I, 151S, 269S
EOG6DV43B immune deficiency IMD pathway 249 9.882 0.00083 0.02812 139V, 141S
EOG6RV16R-1 BGRP-1 GNBP 459 9.619 0.00096 0.02812 151L
  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.