Table 4 Maximum likelihood (ML) estimates for 35 merged replicase 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 | 66 | M0 (one ratio) ω = 0.024 | Free Ratio ω = 0~∞ | -14460.634 (-14354.549) | 212.17 | < 0.001 | Not allowed |
Site Model M0 vs. M3 | 4 | M0 (one ratio) ω = 0.024 | M3 (discrete, K = 3) p0= 0, ω0= 0 p1= 0.972, ω1= 0.016 (p2= 0.028), ω2 = 0.360 | -14460.634 (-14447.201) | 26.866 | < 0.001 | None |
Branch-site model A | |||||||
BSL group as foreground MA' vs. MA | 1 | MA' (fix ω2= 1) p0 = 0.993, ω0 = 0.020 p1 = 0.007 (p2a+p2b = 0) | MA p0 = 0.993, ω0 = 0.020 p1 = 0.007, ω2 = 1.000 (p2a+p2b = 0) | -14449.205 (-14449. 205) | 0 | 1.000 | None |
PC03 group as foreground MA' vs. MA | 1 | MA' (fix ω2 = 1) p0 = 0.993, ω0 = 0.020 p1 = 0.007 (p2a+p2b = 0) | MA p0 = 0.993, ω0 = 0.020 p1 = 0.007, ω2 = 1.000 (p2a+p2b = 0) | -14449. 205 (-14449. 205) | 0 | 1.000 | None |
HP03 group as foreground MA' vs. MA | 1 | MA' (fix ω2= 1) p0 = 0.322, ω0 = 0.015 p1 = 0.002 (p2a+p2b = 0.676) | MA p0= 0.913, ω0= 0.015 p1= 0.006, ω 2= 11.093 (p2a+p2b = 0.081) | -14389.596 (-14386.122) | 6.948 | 0.008 | 23, 123, 222, 236, 237, 250, 266, 375, 377, 409, 504, 563, 646, 654, 884, 1234, 1259, 1482, 1491, 1786, 1866, 1869, 1878, 1963, 1995, 2010, 2032, 2034 |
PCHP04 group as foreground MA' vs. MA | 1 | MA' (fix ω2= 1) p0= 0.761, ω0= 0.018 p1= 0.006 (p2a+p2b = 0.234) | MA p0= 0.760, ω0= 0.018 p1= 0.006, ω2 = 1.000 (p2a+p2b = 0.234) | -14435.921 (-14435.921) | 0 | 1.000 | None |
SARS group as foreground MA' vs. MA | 1 | MA' (fix ω2= 1) p0 = 0.850, ω0 = 0.012 p1 = 0.005 (p2a+p2b = 0.145) | MA p0 = 0.857, ω0 = 0.012 p1 = 0.005, ω2= 1.061 (p2a+p2b = 0.138) | -14405.997 (-14405.994) | 0.006 | 0.938 |  |