Table 5

Results of codon based Z- test of selection for group 1 and group 2
n dN dS Z P
Group 1
ABS 18 0.171 ± 0.135 0.016 ± 0.03 1.244 0.108
Non-ABS 194 0.067 ± 0.014 0.112 ± 0.034 −1.218 1
PSS 9 0.152 ± 0.101 0.038 ± 0.039 1.493 0.069
Non-PSS 203 0.065 ± 0.014 0.115 ± 0.036 −1.254 1
All 212 0.075 ± 0.015 0.103 ± 0.032 −0.788 1
Group 2
ABS 18 0.578 ± 0.132 0.134 ± 0.068 3.694 <0.001
Non-ABS 203 0.054 ± 0.011 0.128 ± 0.032 −2.106 1
PSS 27 0.492 ± 0.092 0.069 ± 0.051 5.801 <0.001
Non-PSS 194 0.043 ± 0.009 0.136 ± 0.034 −2.686 1
All 221 0.085 ± 0.017 0.126 ± 0.029 −1.158 1

The rates of non-synonymous mutations (dN) and synonymous mutations (dS) were computed using Nei-Gojobari method and Jukes-Cantor correction. The standard errors were obtained through 1000 bootstraps replicates. Z test of selection estimated dN-dS (indicated as Z) and computed a1-tailed test to determine whether dN > dS (indicated as P). n is the number of nucleotides representing antigen binding sites (ABS), non antigen binding sites (Non-ABS), positively selected sites (PSS), non positively selected sites (Non-PSS) and all sites in Group 1 and Group 2. ABS were detected by superimposing the chicken Mhc class I sequences and assuming concordance. Significant p-values are bold.

Sepil et al.

Sepil et al. BMC Evolutionary Biology 2012 12:68   doi:10.1186/1471-2148-12-68

Open Data