Skip to main content

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.