Table 1.

Amino acid sites under positive selection (d_N/d_S > 1) and Likelihood ratio tests of IBV N gene between models that allow positive selection (M2a, M3, M8) and neutral models (M0, M1a, M7).

Parameter	M0	M3	M1a	M2a	M7	M8
-L	6185.85	6095.77	6114.53661	6097.91	6119.18	6098.87
2(L1 − L0)	180.16 (comparison between M0 and M3)		33.25322 (comparison between M1a and M2a)		40.62 (comparison between M7 and M8)
chi-square test	p < 0.001		p < 0.001		p < 0.001
d.f. (between 2 models)	4		2		2
Parameter estimates	ω = 0.10026	ω0 = 0.02378, p0 = 0.76904; ω1 = 0.34981, p1 = 0.22444; ω2 = 1.84622, p2 = 0.00652	Not allow	ω0 = 0.02948, p0 = 0.80713; ω1 = 1, p1 = 0.01564; ω2 = 0.4, p2 = 0.17724	ω0 = 0, p0 = 0.5; ω1 = 0.24135, p1 = 0.5	ω0 = 0, p0 = 0.47944; ω1 = 0.15589, p1 = 0.47944; ω2 = 1, p2 = 0.04111
Positive selected sites	Not allow	64 Q, pa = 0.997; 123 V, pa = 0.995	Not allow	64 Q, pb = 0.846; 123 V, pb = 0.808	Not allow	64 Q, pb = 0.981; 123 V, pb = 0.972; 223 M, pb = 0.635; 350 G, pb = 0.572; 360 P, pb = 0.532

a: probability in naive empirical bayes (NEB) analysis; b: probability in bayes empirical bayes (BEB) analysis; d.f: degree of freedom; ω: d_N/d_S ratio; p: proportion; L: log likelihood; M0: one ratio model; M1a: nearly neutral model; M2a: positive selection model; M3: discrete model; M7: beta model; M8: beta and ω model.