Table 4.
Maximum likelihood (ML) estimates for 35 merged replicase genes of SARS-CoV
| 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 | |
* Positively selected sites are identified with posterior probability p > 90%. In boldface, p > 95%.