Table 3.
Test for variable selection pressures on different codons based on ML-based codon substitution models of Yang et al. (2000)
| Model | Free parameters | Parameter estimates | Likelihood scores | Model comparison (2Δl, d.f., p) | Positively selected sites | ω ± S.E. |
|---|---|---|---|---|---|---|
| Lineage 1a | ||||||
| M0: One-ratio | 1 | ω = 0.6152 | −2510.069374 | None | ||
| M1a: Nearly neutral | 1 | ω0 = 0.1, ω1 = 1, (p0 = 0.62, p1 = 0.38) | −2473.399503 | Not allowed | ||
| M2a: Positive selection | 3 | ω0 = 0, ω1 = 1, ω2 = 7.31; (p0 = 0.62, p1 = 0.32, p2 = 0.06) | −2444.710131 | (M1a vs. M2a), 57.378744, d.f. = 2, p = 0.0000 | 93-H(0.989) | 7.523 ± 1.614 |
| 105-Y (0.987) | 7.504 ± 1.640 | |||||
| 106-F (1.000) | 7.595 ± 1.464 | |||||
| 143-K (0.748) | 5.832 ± 3.077 | |||||
| 154-P (1.000) | 7.594 ± 1.466 | |||||
| 155-R(0.667) | 5.263 ± 3.239 | |||||
| 158-S (0.980) | 7.456 ± 1.718 | |||||
| 171-R(0.958) | 7.323 ± 1.953 | |||||
| 173-T (0.971) | 7.380 ± 1.805 | |||||
| 176-T (0.583) | 4.674 ± 3.305 | |||||
| 188-T (0.973) | 7.393 ± 1.788 | |||||
| M7: β | 2 | p = 0.1085, q = 0.1183 | −2474.985643 | Not allowed | ||
| M8: β + ωs > 1 | 4 | p0 = 0.94, p1 = 0.06, p = 0.36716, q = 0.47347, ω = 6.83 | −2444.453952 | (M7 vs. M8), 61.063382, d.f. = 2, p = 0.0000 | 93-H (0.993) | 7.265 ± 1.428 |
| 105Y (0.993) | 7.264 ± 1.426 | |||||
| 106-F (1.000) | 7.307 ± 1.332 | |||||
| 143-K (0.814) | 6.055 ± 2.779 | |||||
| 154-P (1.000) | 7.306 ± 1.332 | |||||
| 155-R (0.744) | 5.575 ± 3.020 | |||||
| 156-T (0.649) | 4.762 ± 2.999 | |||||
| 158-S (0.990) | 7.242 ± 1.468 | |||||
| 171-R(0.970) | 7.119 ± 1.718 | |||||
| 173-T (0.989) | 7.228 ± 1.480 | |||||
| 176-T (0.664) | 5.028 ± 3.191 | |||||
| 188-T (0.991) | 7.239 ± 1.460 | |||||
| M8a: β + ωs = 1 | 3 | p0 = 0.62, p1 = 0.38, p = 11.37, q = 99, ω = 1 | −2473.400411 | (M8 vs. M8a), 57.892918, d.f. = 1, p = 0.0000 | Not allowed | |
| Lineage 1b | ||||||
| M0: One-ratio | 1 | ω = 0.4649 | −3088.137934 | None | ||
| M1a: Nearly neutral | 1 | ω0 = 0.166, ω1 = 1, (p0 = 0.72, p1 = 0.28) | −3048.588195 | Not allowed | ||
| M2a: Positive selection | 3 | ω0 = 0.179, ω1 = 1, ω2 = 9.729; (p0 = 0.696, p1 = 0.289, p2 = 0.013) | −3028.791341 | (M1a vs. M2a), 39.593708, d.f. = 2, p = 0.0000 | 146-P (1.00) | 8.326 ± 1.713 |
| 183-F (1.00) | 8.325 ± 1.714 | |||||
| 196-L (0.999) | 8.316 ± 1.732 | |||||
| M7: β | 2 | p = 0.393, q = 0.546 | −3054.125576 | Not allowed | ||
| M8: β + ωs > 1 | 4 | p0 = 0.89, p1 = 0.11p = 1.777, q = 4.03, ω = 2.84 | −3034.377594 | (M7 vs. M8), 39.495964, d.f. = 2, p = 0.0000 | 146-P (1.000) | 5.183 ± 1.880 |
| 157-F (0.718) | 3.601 ± 2.137 | |||||
| 183-F (1.000) | 5.183 ± 1.880 | |||||
| 196-L (0.999) | 5.181 ± 1.882 | |||||
| 199-S (0.573) | 2.935 ± 2.110 | |||||
| M8a: β + ωs = 1 | 3 | p0 = 0.72, p1 = 0.28, p = 19.98, q = 99, ω = 1 | −3048.6126 | (M8 vs. M8a), 28.470012, d.f. = 1, p = 0.0000 | Not allowed | |
| Lineage 2a | ||||||
| M0: One-ratio | 1 | ω = 0.6898 | −2927.296491 | None | ||
| M1a: Nearly neutral | 1 | ω0 = 0.248, ω1 = 1, (p0 = 0.565, p1 = 0.435) | −2913.654666 | Not allowed | ||
| M2a: Positive selection | 3 | ω0 = 0.382, ω2 = 4.487; (p0 = 0.69, p1 = 0.23, p2 = 0.073) | −2898.698295 | (Mla vs. M2a), 29.912742, d.f. = 2, p = 0.0000 | 85-L (1.000) | 5.340 ± 1.570 |
| 93-Q (0.888) | 4.839 ± 2.038 | |||||
| 105-L (0.878) | 4.694 ± 1.966 | |||||
| 109-S(0.913) | 4.898 ± 1.899 | |||||
| 113-L (0.732) | 3.959 ± 2.193 | |||||
| 121-P (0.510) | 2.849 ± 2.078 | |||||
| 180-L (0.535) | 3.024 ± 2.228 | |||||
| 202-S (0.508) | 2.890 ± 2.196 | |||||
| 232-Y (0.989) | 5.295 ± 1.627 | |||||
| 239-P (0.975) | 5.226 ± 1.690 | |||||
| M7: β | 2 | p = 0.606, q = 0.379 | −2917.092133 | Not allowed | ||
| M8: β + ωs > 1 | 4 | p0 = 0.89, p1 = 0.11, p = 28.418, q = 31.77, ω = 3.65 | −2898.947133 | (M7 vs. M8), 36.29, d.f. = 2, p = 0.0000 | 85-L (1.000) | 5.381 ± 1.324 |
| 93-Q (0.900) | 4.945 ± 1.872 | |||||
| 105-L (0.920) | 4.988 ± 1.751 | |||||
| 109-S (0.939) | 5.093 ± 1.673 | |||||
| 113-L (0.777) | 4.282 ± 2.179 | |||||
| 121-P (0.528) | 3.028 ± 2.275 | |||||
| 180-L (0.546) | 3.173 ± 2.375 | |||||
| 202-S (0.519) | 3.038 ± 2.358 | |||||
| 232-Y (0.992) | 5.351 ± 1.376 | |||||
| 239-P (0.983) | 5.306 ± 1.439 | |||||
| M8a: β + ωs = 1 | 3 | p0 = 0.57, p1 = 0.43, p = 33.25, q = 99, ω = 1 | −2913.719868 | (M8 vs. M8a), 29.54547 d.f. = 1, p = 0.0000 | Not allowed | |
| Lineage 2b | ||||||
| M0: One-ratio | 1 | ω = 0.7065 | −1855.459267 | None | ||
| M1a: Nearly neutral | 1 | ω0 = 0, ω1 = 1, (p0 = 0.49, p1 = 0.51) | 840.547215 | Not allowed | ||
| M2a: Positive selection | 3 | ω0 = 0, ω1 = 1, ω2 = 10.0195; (p0 = 0.45, p1 = 0.52, p2 = 0.03) | −1829.903873 | (M1a vs. M2a), 21.286684, d.f. = 2, p = 0.00002 | 100-E (0.999) | 7.607 ± 2.041 |
| 105-P (0.971) | 7.432 ± 2.288 | |||||
| 109-P (0.911) | 6.994 ± 2.703 | |||||
| 213-R (0.682) | 5.477 ± 3.516 | |||||
| M7: β | 2 | p = 0.00517, q = 0.005 | −1840.570751 | Not allowed | ||
| M8: β + ωs > 1 | 4 | p0 = 0.97, p1 = 0.03, p = 0.005, q = 0.005, ω = 9.6 | 830.002479 | (M7 vs. M8), 21.136554, d.f. = 2, p = 0.00003 | 100-E (1.000) | 6.823 ± 2.093 |
| 105-P (0.985) | 6.745 ± 2.196 | |||||
| 109-P (0.958) | 6.561 ± 2.375 | |||||
| 114-Y (0.515) | 3.679 ± 3.226 | |||||
| 116-G (0.572) | 4.071 ± 3.293 | |||||
| 162-E (0.606) | 4.080 ± 3.052 | |||||
| 201-T (0.500) | 3.579 ± 3.206 | |||||
| 213-R (0.770) | 5.424 ± 3.159 | |||||
| 220-P (0.629) | 4.385 ± 3.236 | |||||
| M8a: β + ωs = 1 | 3 | p0 = 0.49, p1 = 0.51, p = 0.005, q = 2.785, ω = 1 | 840.547213 | (M8 vs. M8a), 21.089468, d.f. = 1, p = 0.0000 | Not allowed | |
Null models (M1a, M7, and M8a) are compared with their respective alternative models (M2a, M8) that allow ω > 1. Proportion of positively selected sites and their corresponding ω-values in M2a and M8 models are in bold. The posterior probability of each positively selected amino acid site is in parenthesis. Posterior probabilities are estimated based on Bayes Empirical bayes analyses (Yang et al., 2005).