Table 3.
Amino acid sites under positive selection pressure and likelihood ratio tests comparing positive selection models vs neutral models for different IBV gene segments
Positive selection models: M2a, M3, M8; neutral models: M0, M1a, M7. Positive selection pressure was defined as dN/dS > 1, where dN = number of non-synonymous substitutions per site and dS = number of synonymous substitutions per site. Positive selection site was determined by probability in Bayes empirical Bayes (BEB) analysis. ω, dN/dS ratio; L, log likelihood; M0, one ratio model; M1, nearly neutral model; M2, positive selection model; M3, discrete model; M7, beta model; M8, beta and ω model. na, Not analyzed; nf, not found. *P≤0.05; **P≤0.01.
| Protein | M0 (ω) | Likelihood test (2△LnL) | Positive selection site (aa) | ||
|---|---|---|---|---|---|
| M0 vs M3 | M1a vs M2a | M7 vs M8 | |||
| S1 | 0.37080 | 2243.276376** | 277.436402** | 306.1185** | 19L; 23K; 57T; 64S; 65D; 72Y; 96P; 98A; 101S; 105A; 130Q; 132S; 141Q; 174K; 301S; 307S; 316Q; 357N; 406R; 409T; 410R; 417R; 421T; 550F; 566S |
| E | 0.19028 | 89.030374** | 0.369408 | 8.355172* | 3L; 25V; 79S |
| M | 0.19238 | 331.734492** | 10.425006** | 51.90527** | 5E; 12S; 47L |
| N | 0.17251 | 754.57614** | 40.22616** | 60.60845** | 64S; 300R; 337P |
| 3a | 0.44618 | 40.87654** | 1.05086 | 2.37579 | nf |
| 3b | 0.41865 | 78.455836** | 10.71828** | 11.38464** | nf |
| 5a | 0.30974 | 97.822628** | 5.329922 | 19.34628** | 61D |
| 5b | 0.60993 | 152.690428** | 29.47067** | 31.11947** | 23E; 39P; 57I; 58D; 73S; 81S |
| Nsp2 | 0.19536 | 462.915408** | 0 | na | nf |
| Nsp3 | 0.15092 | 145.411142** | 0 | 1.962352 | 264N |
| Nsp4 | 0.16252 | 506.51592** | 0 | 17.12271** | 8W; 387T; 456A; 498I |
| Nsp5 | 0.16082 | 423.24087** | 21.774806** | 26.65132** | 66T; 177T; 221L |
| Nsp6 | 0.15092 | 145.411142** | 0 | 1.962352 | nf |
| Nsp7 | 0.11175 | 6.597726 | 0.000714 | 0.098472 | nf |
| Nsp8 | 0.14546 | 101.37074** | 0 | 14.46742** | nf |
| Nsp9 | 0.09007 | 31.338902** | 0.010186 | 6.5499* | nf |
| Nsp10 | 0.06749 | 85.882382** | 0 | 10.37397** | nf |
| Nsp12 | 0.06939 | 458.716066** | 17.618464** | 70.96948** | 22Q; 45C; 64A |
| Nsp13 | 0.06920 | 183.729002** | 0.000162 | 5.99636 | nf |
| Nsp14 | 0.07150 | 272.803576** | 0.061184 | 8.457994* | nf |
| Nsp15 | 0.09815 | 303.64197** | 0 | 4.891118 | nf |
| Nsp16 | 0.09701 | 484.788486** | 6.245764* | 32.88781** | 209I; 275F; 294T; 297S |