Table 5 Maximum likelihood (ML) estimates for 56 merged 3'-end ORFs 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 | 108 | M0 (one ratio) ω = 0.170 | Free Ratio ω = 0~∞ | -9142.692 (-9055.881) | 173.623 | < 0.001 | Not allowed |
Site Model M0 vs. M3 | 4 | M0 (one ratio) ω = 0.170 | M3 (discrete, K = 3) p0= 0, ω0= 0 p1= 0.866, ω1= 0.058 (p2= 0.134),ω2= 0.986 | -9142.692 (-9093.135) | 99.114 | < 0.001 | None |
Branch-site model A | |||||||
BSL group as foreground MA' vs. MA | 1 | MA' (fix ω2= 1) p0= 0.868, ω0= 0.059 p1= 0.132 (p2a+p2b = 0) | MA p0= 0.868, ω0= 0.059 p1= 0.132, ω2= 1.000 (p2a+p2b = 0) | -9093.137 (-9093.137) | 0 | 1.000 | None |
PC03 group as foreground MA' vs. MA | 1 | MA' (fix ω2= 1) p0= 0.868, ω0= 0.059 p1= 0.132 (p2a+p2b = 0) | MA p0= 0.868, ω0= 0.059 p1= 0.132, ω2 = 1.000 (p2a+p2b = 0) | -9093.137 (-9093.137) | 0 | 1.000 | None |
HPEM group as foreground MA' vs. MA | 1 | MA' (fix ω2= 1) p0= 0.855, ω0= 0.059 p1= 0.130 (p2a+p2b = 0.015) | MA p0= 0.861, ω0= 0.059 p1= 0.131, ω 2= 4.300 (p2a+p2b = 0.008) | -9093.127 (-9093.088) | 0.078 | 0.780 |  |
HPML group as foreground MA' vs. MA | 1 | MA' (fix ω2= 1) p0= 0.125, ω0= 0.047 p1= 0.017 (p2a+p2b = 0.858) | MA p0= 0.772, ω0= 0.046 p1= 0.106, ω 2= 9.863 (p2a+p2b = 0.122) | -9069.427 (-9065.120) | 8.614 | 0.003 | 11, 29, 85, 129, 136, 222, 279, 280, 304, 319, 377, 388, 418, 423, 436, 449, 463, 469, 504, 584, 696, 850, 932, 954, 993 |
PCHP04 group as foreground MA' vs. MA | 1 | MA' (fix ω2= 1) p0= 0.690, ω0= 0.055 p1= 0.097 (p2a+p2b = 0.213) | MA p0= 0.862, ω0 = 0.057 p1= 0.119, ω 2= 22.447 (p2a+p2b = 0.019) | -9087.427 (-9076.176) | 22.502 | < 0.001 | 25, 259, 609, 1184 |
SARS group as foreground MA' vs. MA | 1 | MA' (fix ω2 = 1) p0 = 0.664, ω0= 0.033 p1= 0.066 (p2a+p2b = 0.270) | MA p0= 0.804, ω0= 0.037 p1= 0.074, ω 2= 3.138 (p2a+p2b = 0.122) | -9058.932 (-9051.231) | 15.402 | < 0.001 | 11, 15, 81,117, 120, 121, 171, 193, 259, 355, 361, 560, 609, 628, 830, 850, 1184 |