Table 3.
Results of the evolutionary pathways method (Nei and Gojobori 1986) to estimate values of d S, d N and their standard errors for antigen (ABS) or non-antigen (non-ABS) binding sites defined by homology with HLA (Bondinas et al. 2007) and for codon sites identified as positively selected sites (PSS) or as non-positively selected sites (non-PSS) within the 61 Mimu-DRB and the 60 Mimu-DQB sequences
| Positions | n | d N | d S | ω | Z (P) |
|---|---|---|---|---|---|
| Mimu-DRB | |||||
| ABS | 11 | 0.49 ± 0.09 | 0.07 ± 0.04 | 6.84 | 5.22 (0.00) |
| Non-ABS | 45 | 0.04 ± 0.01 | 0.03 ± 0.02 | 1.30 | 0.50 (0.62) |
| PSS | 11 | 0.52 ± 0.06 | 0.12 ± 0.08 | 4.20 | 4.08 (0.00) |
| Non-PSS | 45 | 0.04 ± 0.01 | 0.02 ± 0.01 | 2.08 | 1.32 (0.19) |
| All | 54 | 0.12 ± 0.02 | 0.04 ± 0.02 | 3.02 | 2.87 (0.05) |
| Mimu-DQB | |||||
| ABS | 11 | 0.37 ± 0.10 | 0.01 ± 0.01 | 26.84 | 3.33 (0.01) |
| Non-ABS | 45 | 0.07 ± 0.02 | 0.05 ± 0.02 | 1.37 | 0.71 (0.48) |
| PSS | 3 | 0.59 ± 0.27 | 0.03 ± 0.01 | 22.17 | 2.12 (0.04) |
| Non-PSS | 51 | 0.04 ± 0.02 | 0.10 ± 0.02 | 0.43 | 2.05 (0.04) |
| All | 54 | 0.12 ± 0.03 | 0.04 ± 0.02 | 2.82 | 2.51 (0.01) |
n — number of codons in each category; ω — d N/d S; P — probability that d N and d S are similar using a Z-test of selection