Table 2 Phylogenetic analysis by ML estimation for SARS S gene sequences from different epidemic groups.
Epidemic phases | Model code | lnL | dN/dS | Estimates of parameters | 2Δl | Positive selection |
|---|---|---|---|---|---|---|
02–04 interspecies epidemic group | M0 (one-ratio) | -5339.90 | 0.64 | ω = 0.64 | 40.23 | Yes |
|  | M3 (discrete) | -5319.78 | 0.77 | p0 = 0.00000, = p1 = 0.99407 (p2 = 0.00593), ω0 = 0.00, ω1 = 0.38, ω2 = 66.02 | (13.28) |  |
| Â | M1a (NearlyNeutral) | -5334.74 | 0.35 | p0 = 0.65391 (p1 = 0.34609) | 29.92 | Yes |
|  | M2a (PositiveSelection) | -5319.78 | 0.77 | p0 = 0.99407, p1 = 0.00000 (p2 = 0.00593), ω2 = 66.01 | (9.21) |  |
| Â | M7 (beta) | -5336.08 | 0.30 | p = 0.01702, q = 0.03977 | 32.23 | Yes |
|  | M8 (beta&v) | -5319.97 | 0.80 | p0 = 0.99405 (p1 = 0.00595), p0 = 0.01217, q = 0.01714 ω = 67.24 | (9.21) |  |
03-early-mid epidemic group | M0 (one-ratio) | -5194.47 | 0.94 | ω = 0.94 | 24.25 | Yes |
|  | M3 (discrete) | -5182.34 | 1.10 | p0 = 0.05053, p1 = 0.92251 (p2 = 0.02696), ω0 = ω1 = 0.00, ω2 = 40.88 | (13.28) |  |
| Â | M1a (NearlyNeutral) | -5192.6 9 | 0.45 | p0 = 0.54981 (p1 = 0.45019) | 20.70 | Yes |
|  | M2a (PositiveSelection) | -5182.34 | 1.10 | p0 = 0.97303, p1 = 0.00000 (p2 = 0.02696), ω2 = 40.88 | (9.21) |  |
| Â | M7 (beta) | -5192.73 | 0.40 | p = 0.00510, q = 0.00776 | 20.78 | Yes |
|  | M8 (beta&v) | -5182.34 | 1.10 | p0 = 0.97303 (p1 = 0.02697), p = 0.00500, q = 1.39962, ω = 40.87 | (9.21) |  |
03-late epidemic group | M0 (one-ratio) | -5121.66 | 0.26 | ω = 0.26 | NA | No |
|  | M3 (discrete) | -5121.66 | 0.26 | p0 = 0.43056, p1 = 0.37490 (p2 = 0.19455), ω0 = 0.25, ω1 = 0.26, ω2 = 0.26 | (13.28) |  |
| Â | M1a (NearlyNeutral) | -5121.66 | 0.26 | p0 = 1.00000 (p1 = 0.00000) | NA | No |
|  | M2a (PositiveSelection) | -5121.66 | 0.26 | p0 = 1.00000, p1 = 0. 00000 (p2 = 0.00000), ω0 = 0.26, ω1 = ω2 = 1.00 | (9.21) |  |
| Â | M7 (beta) | -5121.66 | 0.25 | p = 33.88884, q = 99.00000 | NA | No |
|  | M8 (beta&v) | -5121.68 | 0.26 | p0 = 1.00000 (p1 = 0.00000), p = 0.64576, q = 1.83663, ω = 2.08 | (9.21) |  |