Table 3.
Summary of MHC-IIB variants, genetic divergence and codon-based Z tests for selection in R. japonica, R. ornativentris, and R. t. tagoi
| Species | No. of variants | Range of divergence within individual | Mean distance (nucleotide, amino acid) | Z-tests for selection for exon 2; Z statistic (p-value) | Z-tests for selection for exon 3; Z statistic (p-value) | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Total | Per animal | Amino acid | Nucleotide | Amino acid | Exon 2 | Exon 3 | Neutrality | Purifying | Positive | Neutrality | Purifying | Positive | |
| dN - dS | dS - dN | dN - dS | dN - dS | dS - dN | dN - dS | ||||||||
| R. japonica | 9 | 2–3 | 62 | 0.001–0.128 | 0.004–0.233 | 0.089, 0.179 | 0.044, 0.063 | 3.648 (0.0003) | −3.669 (n.s.) | 3.641 (0.0002) | −2.543 (0.012) | 2.563 (0.006) | −2.573 (n.s.) |
| R. ornativentris | 11 | 1–2 | 74 | 0.001–0.158 | 0–0.262 | 0.107, 0.180 | 0.039, 0.044 | 0.746 (0.457) | −0.743 (n.s.) | 0.751 (0.227) | −3.377 (0.001) | 3.398 (0.0005) | −3.390 (n.s.) |
| R. t. tagoi | 13 | 2 | 113 | 0.011–0.258 | 0–0.391 | 0.143, 0.235 | 0.066, 0.082 | 0.888 (0.376) | −0.887 (n.s.) | 0.881 (0.190) | −3.247 (0.002) | 3.334 (0.0006) | −3.262 (n.s.) |
| R. t. tagoi (excl Rata-01) | 77 | 0.011–0.153 | 0–0.234 | 0.131, 0.220 | 0.037, 0.036 | 1.048 (0.297) | −1.049 (n.s.) | 1.054 (0.147) | −3.411 (0.001) | 3.438 (0.0004) | −3.386 (n.s.) | ||
#excluding insertions and deletions; n.s. – not significant, p = 1.000