Table 6.
Genes under positive selection (using FDR < 0.05) on the branch to Apis (5 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 |
|---|---|---|---|---|---|---|---|
| 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 |
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.