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Table 4 Genes under positive selection (using FDR < 0.05) across the whole phylogeny (4 taxa tree)

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

OrthoDB group id a

Gene b

Classification sites c

Total ratio d

Likelihood

p-value q-value e

BH-corrected sites f

Positively selected

EOG66DJHX-2

dscam

Immunoglobulin

777

186.607

0.00000

0.00000

4L, 6R, 8S, 11D, 13G, 14D, 20Q, 22A, 24M, 26A, 30T, 35A, 37T, 43E, 44P, 52R, 54T, 56I, 58T, 60P, 63K, 65I, 66H

EOG6HHMH6

serpin-23

Scavenger receptor

2066

15.366

0.00046

0.00987

36S, 87S, 90Q, 92K, 288P, 334S, 397N, 431S, 490D, 761P, 772R, 811K, 815T, 816Y, 824S, 877S, 1782K, 1788E

EOG66DJHQ

aubergine

Small RNA regulatory path-members

787

15.955

0.00034

0.00858

219K, 269K, 287A, 342S, 348D, 359G, 397R, 410E, 415P, 431G, 436D, 621K

EOG64B8H5

CLIP-A10

CLIP serine protease

816

29.218

0.00000

0.00003

1I, 3H, 21V, 25P, 37P, 291K, 333T, 335T, 344S, 457S

EOG6KKWHX

argonaute-2

Small RNA regulatory pathway members

896

20.248

0.00004

0.00150

24W, 27N, 43S, 48Q, 58S, 59N, 81D, 103I, 519F

EOG6J3TZ2

cardinal

Peroxidase

1203

14.276

0.00079

0.01489

35M, 46S, 538A, 711A, 742E, 743T, 882D, 931V

EOG6VX0M3

ark

Caspase

1263

17.732

0.00014

0.00423

67G, 386G, 752T, 1028G, 1078T, 1112F

EOG6JQ2CF

LOC100642575 (B. terr)

Scavenger receptor

924

22.212

0.00002

0.00075

75S, 78P, 111I, 112P, 647S

EOG6W9GK1-3

rm62-B1

Small RNA regulatory pathway members

431

11.766

0.00279

0.04179

425A, 430S, 431E

EOG634TNR

pellino

Toll pathway

431

12.386

0.00204

0.03407

1P, 2S

  1. aGroup identifiers are from OrthoDB 6 (http://cegg.unige.ch/orthodb6).
  2. bUnless otherwise specified, gene names are taken from the A. mellifera or D. melanogaster orthologs.
  3. cTotal number of codons in the alignment after trimming with Gblocks.
  4. dComparison of model M7 versus M8.
  5. eMultiple test correction by the method of Benjamini and Hochberg to control the false discovery rate (only groups where FDR < 0.05 are shown).
  6. fSites are classified as under positive selection if the Bayesian posterior probability > 0.75 (>0.95 in bold italic). Sites where \( E\left[\omega \right]-\sqrt{\mathrm{Var}\left(\omega \right)}>1.25 \) are italic.
  7. Reference sequence taken from A. mellifera.