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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.