Table III. Evidence for adaptive evolution of genes located in the S-locus region.
M0 is the dN/dS ratio averaged across all sites and lineages. M7 versus M8 indicates the outcome of the likelihood test. −1 means that the value of 2Δℓ (twice the log likelihood difference between two models) is 0 or less than 0.0001 and there is no significant difference between the two models. Estimates of parameters indicate the proportion of amino acids predicted to be under adaptive evolution (and their corresponding dN/dS ratio) from model M8. NA indicates not applicable because there is no significant difference between the positive selection model and the neutral model. Positively selected sites are amino acids under positive selection with Bayesian posterior P > 0.95 based on model M8 using the Bayes Empirical Bayes method. Ns is the number of sequences in the analysis. LA indicates the codon in the alignment. For the SRK gene, Aly-S16 is the reference sequence, and for the SCR gene, Ath-Cvi is the reference sequence. For ARK3 and other genes, Ath-Col is the reference. * P < 0.05, ** P < 0.001, *** P < 0.0001.
| Gene | M0 | M7 Versus M8 (2Δℓ) | Estimates of Parameters | Positively Selected Sites | Ns | LA |
| At4g21326 | 0.198 | −1 | NA | NA | 8 | 700 |
| At4g21330 | 0.217 | 3.894 | NA | NA | 8 | 210 |
| At4g21340 | 0.312 | 0.069 | NA | NA | 8 | 309 |
| At4g21350 (PUB8) | 0.106 | −1 | NA | NA | 8 | 374 |
| SCR | 1.210 | 7.896* | 44.2% (ω = 2.955) | 32L, 34K, 43T, 48R, 58H, 63K, 67V | 4 | 95 |
| At4g21370 (SRK) | 0.340 | 26.137*** | 4.3% (ω = 3.300) | 275R | 5 | 868 |
| At4g21380 (ARK3) | 0.198 | 11.882* | 0.3% (ω = 9.127) | None with P > 0.95 | 8 | 854 |
| At4g21390 | 0.113 | −1 | NA | NA | 8 | 851 |
| At4g21400 | 0.325 | −1 | NA | NA | 7 | 718 |
| At4g21410 | 0.185 | 0.195 | NA | NA | 7 | 680 |
| At4g21430 | 0.314 | 2.965 | NA | NA | 8 | 940 |