Table 2 Maximum likelihood (ML) estimates for 59 S genes of SARS-CoV
From: Differential stepwise evolution of SARS coronavirus functional proteins in different host species
Models | d.f. | Parameters under null model | Parameters under alternative model | lnL0 (lnL1) | 2Δl | P-value | Positively selected sites* |
|---|---|---|---|---|---|---|---|
Branch Model M0 vs. FR | 114 | M0 (one ratio) ω = 0.081 | Free Ratio ω = 0~∞ | -12834.110 (-12656.604) | 355.006 | < 0.001 | Not allowed |
Site Model M0 vs. M3 | 4 | M0 (one ratio) ω = 0.081 | M3 (discrete, K = 3) p0 = 0.732, ω0 = 0.015 p1 = 0.255, ω1 = 0.285 p2 = 0.013, ω 2= 3.214 | -12834.110 (-12616.008) | 436.204 | < 0.001 | 142,311, 430, 462, 479, 540 609, 626, 665 |
Branch-site model A | |||||||
BSL group as foreground MA' vs. MA | 1 | MA' (fix ω2= 1) p0 = 0.912, ω0 = 0.047 p1 = 0.088 (p2a+p2b = 0) | MA p0 = 0.912, ω0 = 0.047 p1 = 0.088, ω2 = 1.000 (p2a+p2b = 0) | -12661.687 (-12661.687) | 0 | 1.000 | None |
PC03 group as foreground MA' vs. MA | 1 | MA' (fix ω2= 1) p0 = 0.707, ω0 = 0.046 p1 = 0.069 (p2a+p2b = 0.224) | MA p0 = 0.782, ω0 = 0.046 p1 = 0.076, ω 2= 1.592 (p2a+p2b = 0.142) | -12658.258 (-12658.246) | 0.024 | 0.877 | None |
HPEM group as foreground MA' vs. MA | 1 | MA' (fix ω2= 1) p0 = 0.587, ω0 = 0.044 p1 = 0.055 (p2a+p2b = 0.358) | MA p0 = 0.885, ω0 = 0.045 p1 = 0.083, ω 2= 28.756 (p2a+p2b = 0.032) | -12646.115 (-12638.329) | 15.572 | < 0.001 | 49, 75, 344, 360, 501, 778 794, 860, 861 1001, 1148, 1163 1179, 124 |
HPL group as foreground MA' vs. MA | 1 | MA' (fix ω2 = 1) p0= 0.400, ω0 = 0.045 p1= 0.038 (p2a+p2b = 0.562) | MA p0 = 0.400, ω0 = 0.045 p1= 0.038, ω2 = 1.000 (p2a+p2b = 0.562) | -12650.732 (-12650.732) | 0 | 1.000 |  |
PCHP04 group as foreground MA' vs. MA | 1 | MA' (fix ω2= 1) p0= 0.718, ω0 = 0.045 p1= 0.057 (p2a+p2b = 0.225) | MA p0= 0.901, ω0= 0.045 p1= 0.072, ω 2= 57.205 (p2a+p2b = 0.027) | -12626,601 (-12569.700) | 113.802 | < 0.001 | 78, 91, 108, 113, 147, 227, 243, 425, 440, 462, 479, 609, 613, 632, 743, 765, 839, 844, 856, 900, 1052 1080 |
SARS group as foreground MA' vs. MA | 1 | MA' (fix ω2= 1) p0= 0.753, ω0 = 0.024 p1= 0.035 (p2a+p2b = 0.212) | MA p0= 0.792, ω0= 0.027 p1= 0.034, ω 2= 1.989 (p2a+p2b = 0.174) | -12498.107 (-12488.470) | 19.274 | < 0.001 | 2, 7, 9, 12, 14, 20, 27, 33, 37, 43, 58, 68, 70, 75, 84, 107, 108, 131, 134, 137, 139 147, 151, 154, 163, 165, 167, 169, 174, 199, 201, 214, 227, 230, 237, 239 242, 243, 244, 248, 249, 294, 333, 336, 344, 353, 391, 392, 426, 431, 440, 442, 457, 459, 462, 479, 480, 487, 488,494, 607, 613, 644, 729, 732, 743, 754, 758, 765, 778, 1052, 1080, 1148, 1163 |