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Table 1 Mean intra- and inter-specific diversity for chicken and zebra finch at all, immune, non-immune and McDonald-Kreitman tests outlier genes.

From: Evidence of the adaptive evolution of immune genes in chicken

Gene set

All

Immune

Non-immune

Genes with p < 0.051

Number

2,604

64

2540

26

ω 2

0.0963 ± 0.130

0.0826 ± 0.091

0.0967 ± 0.131

0.2950 ± 0.169

Chicken GC3

0.600 ± 0.173

0.652 ± 0.171

0.599 ± 0.173

0.518 ± 0.132

Zebra finch GC3

0.554 ± 0.159

0.608 ± 0.182

0.553 ± 0.158

0.507 ± 0.133

D N

94,635

1,504

93,131

1096

P N

1,293

17

1,276

0

D S

384,749

5,852

378,897

1439

P S

5,069

129

4,940

272

P N per kb3

0.459

0.327

0.464

0

P S per kb3

1.813

2.474

1.800

0.111

P N /P S

0.255

0.132

0.258

0

D N /D S

0.246

0.257

0.246

0.762

L N /L S 4

3.075

3.363

3.068

2.860

FI 5

0.964

1.950

0.952

0

eFI 6

1.056

0.945

1.060

1.377

α 7

-0.087

1.062

-0.102

-1.000

Coverage8

0.814

0.723

0.816

0.859

  1. 1 Genes whose McDonald-Kreitman test one tailed p values > 0.05 for D N /D S >P N /P S . 2 Calculation excluded non-immune gene XM_422655 that had d N > 0 and d S = 0. 3 Per kb of effective CDS nucleotide length. 4 Total number of synonymous (L S ) nonsynonymous (L N ) sites. 5 Observed fixation index, FI = (D N /D S )/(P N /P S ). 6 Expected fixation index, eFI. 7 Proportion of fixed nonsynonymous mutations driven by positive selection fixed in chicken, α = (FI - eFI)/eFI.8 Mean transcript coverage per base.