Table 2. Parameter estimates and likelihood scores for the PR gene under different branch-site models.

Codon model	Hypothesis	Estimates of ω parameters	Positive selection
M3 k = 2	H0: BG = G-FG = B-FG	p0 = 0.81, ω0 = 0.02	None	-6176.81
		(p1 = 0.18), ω1 = 0.33
Model B, ω2 = 1	H1: BG = B-FG ≠ G-FG	p0 = 0.50, ω0 = 0.02	G-FG: not allowed	-6167.16
		p1 = 0.12, ω1 = 0.31
		(p2+3 = 0.38), (ω2 = 1)	BG+B-FG: none
	H2: BG = G-FG ≠ B-FG	p0 = 0.78, ω0 = 0.03	B-FG: not allowed	-6164.15
		p1 = 0.13, ω1 = 0.38
		(p2+3 = 0.08), (ω2 = 1)	BG+G-FG: none
	H3: BG ≠ G-FG = B-FG	p0 = 0.75, ω0 = 0.03	FG1 + FG2: not allowed	-6153.40
		p1 = 0.13, ω1 = 0.36
		(p2+3 = 0.12), (ω2 = 1)	BG: none
Model B	H1: BG = B-FG ≠ G-FG	p0 = 0.78, ω0 = 0.02	G-FG: 5 sites	-6159.24
		p1 = 0.18, ω1 = 0.31
		(p2+3 = 0.03), ω2 = 76	BG+B-FG: none
	H2: BG = G-FG ≠ B-FG	p0 = 0.82, ω0 = 0.03	B-FG: 10 sites	-6156.29
		p1 = 0.13, ω1 = 0.39
		(p2+3 = 0.05), ω2 = 99	BG+G-FG: none
	H3: BG ≠ G-FG = B-FG	p0 = 0.80, ω0 = 0.03	FG1+FG2: 16 sites	-6142.67
		p1 = 0.13, ω1 = 0.37
		(p2+3 = 0.06), ω2 = 14	BG: none

Tree topology, BG, G-FG, and B-FG are presented in Fig 1. , log likelihood score. Boldface indicates an estimate value >1. Parentheses indicate a parameter value obtained by subtraction.