Table 3. Log likelihood values and parameter estimates under the site models and branch-site models.

Model	Para a	ln l b	Estimates of parameters	2Δl c	Positively selected sitesd
M0 (one-ratio)	1	−1369.71	ω0 = 0.3856		not allowed
Site models
M1a (Nearly Neutral)	2	−1366.56	p 0 = 0.7704 (p 1 = 0.2296); ω0 = 0.2110 (ω1 = 1)		not allowed
M2a (Positive Selection)	4	−1366.22	p 0 = 0.9032; p 1 = 0 (p 2 = 0.0968); ω0 = 0.2736 (ω1 = 1), ω2 = 1.7797	(M1a vs. M2a) 0.68	none
M7 (beta)	2	−1367.06	p = 0.6432; q = 0.9806		not allowed
M8 (beta & ω)	5	−1366.23	p 0 = 0.9054; p = 37.7260; q = 99.0000 (p 1 = 0.0947); ω = 1.7952	(M7 vs. M8) 1.66	none
Branch-site models
M1a	2	−1366.56	p 0 = 0.7704 (p 1 = 0.2296); ω0 = 0.2110 (ω1 = 1)
Model A	4	−1363.55	p 0 = 0; p 1 = 0.7632 (p 2 = 0.2368); ω0 = 0.1827 (ω1 = 1), ω2 = Inf	(M1a vs. Model A) 6.02**	544A, 551H, 556G, 661V, 681S

^aThe number of parameters estimated in the model.

^bLog likelihood values.

^cLRT to detect positive selection ^** P<0.01.

^dAmino acid sites under positive selection based on a Bayes Empirical Bayes (BEB) probability >95%. No amino acids sites under the model M2a and M8 were shown to be under positive selection.