Table 3.

Parameter estimates and likelihood scores for glycoside hydrolase (GH16) gene under models of variable ω ratios.

Nested model pairs	dN/dSb	Parameter estimatesc	PSS (*P > 95%; **P > 99%)d	Likelihood
M0:one-ratio (1)a	0.0871	ω = 0.0871		−12,014.227
M3: discrete (5)	0.2194	p0 = 0.335, p1 = 0.353, (p2 = 0.298) ω0 = 0.011, ω1 = 0.082, ω2 = 0.251	3  I 0.999** 6 W 0.979* 9 I 0.999**	−11,619.479
M1: neutral (1)	0.3076	p0 = 0.764, p1 = 0.235 ω0 = 0.094, ω1 = 1		−11,844.804
M2: selection (3)	0.3076	p0 = 0.764, p1 = 0.085, (p2 = 0.149) ω0 = 0.094, (ω1 = 1), ω2 = 1	3 I 0.956* 6 W 0.730 9 I 0.945	−11,844.804
M7: beta (2)	0.1221	p = 0.605, q = 3.970		−11,628.839
M8: beta + ω > 1(4)	0.2225	p0 = 0.989, (p1 = 0.010) p = 0.628, q = 4.589, ω = 10.628	3 I 0.999** 6 W 0.972* 9 I 0.998**	−11,617.599
M8a: beta + ω = 1(4)	0.1281	p0 = 0.652, (p1 = 0.028) p = 0.652, q = 5.181, ω = 1		−11,621.768

Gene	Modele		P value
GH16	M3 vs M0		2.86508957212e−167
GH16	M2 vs M1		1
GH16	M8 vs M7		1.31253379663e−05
GH16	M8 vs M8a		0.00387888988444

^aThe number of free parameters in the ω distribution.

^bAverage ratio dN/dS of all sites for the GH16 gene alignment.

^cThe number in parentheses are not free parameters.

^dNumber of positively selected sites.

^eLikelihood ratio test statistics for models of variable selective pressure among codons.