Skip to main content

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