Table 3 Likelihood ratio test (LRT) statistics for models of variable selective pressure among branches.

From: The evolutionary history of genes involved in spoken and written language: beyond FOXP2

MAMMALS

Gene

Foreground branch (MA versus MA1) a

−2lnL b

pvalue (FDR corrected)

MEME-BEB Sites c

CNTNAP2, reg1

Chiroptera

8.948

2.778 × 10−3

–

DCDC2, reg2

Alpaca

18.546

1.658 × 10−5 (1.658 × 10−5)

–

Dolphin

23.572

1.204 × 10−6 (2.328 × 10−6)

E309, G310

Ruminantia

23.082

1.552 × 10−6 (2.328 × 10−6)

R379, Q417

AVES

Gene

Foreground branch (MA versus MA1) a

−2lnL b

p value (FDR corrected)

MEME-BEB Sites d

DCDC2, reg1

Pigeon

24.931

5.941 × 10−7

Q135, I140

FOXP2

Hoatzin

47.666

5.054 × 10−12 (1.516 × 10−11)

Q377, Q379

Adelie penguin

17.596

2.732 × 10−5 (4.098 × 10−5)

E385

Golden-collared manakin

11.781

5.985 × 10−4 (5.985 × 10−4)

H225

ROBO2

Chimney swift

15.853

6.846 × 10−5 (1.141 × 10−4)

–

Zebra Finch

36.886

1.252 × 10−9 (2.504 × 10−9)

A814, A815, S816,T817

  1. Notes:
  2. aMA and MA1 are branch-site models that assume four classes of sites: the MA model allows a proportion of codons to have ω ≥ 1 on the foreground branches, whereas the MA1 model does not.
  3. b2ΔlnL: twice the difference of the natural logs of the maximum likelihood of the models being compared.
  4. cPositions refer to the human sequence (see also Supplementary table 2)
  5. dPositions refer to the chicken sequence (see also Supplementary table 2).
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