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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)
l 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
  1. * Positively selected sites are identified with posterior probability p > 90%. In boldface, p > 95%.