Table 1. Results of LRT for selection of the CYP3 family in Actinopterygii.

Model	np	Estimates of parameters	lnL	LRT pairs	df	2ΔlnL
M0: one ratio	1	ω = 0.22	−29204.69
M3: discrete	5	p0 = 0.28,p1 = 0.45,(p2 = 0.27), ω0 = 0.03, ω1 = 0.20, ω2 = 0.55	−28506.07	M0/M3	4	1394.24**
M1a: neutral	2	p0 = 0.75,(p1 = 0.25), ω0 = 0.17,(ω1 = 1.00)	−28832.23
M2a: selection	4	p0 = 0.75,p1 = 0.09,(p2 = 0.16), ω0 = 0.17,(ω1 = 1.00), ω2 = 1.00	−28832.23	M1a/M2a	2	0
M7: beta	2	p = 0.77, q = 2.25	−28496.45
M8: beta&ω	4	p0 = 0.98, p = 0.82,q = 2.56, (p1 = 0.017), ω = 1.14	−28494.39	M7/M8	2	4.12
Fr: free ratios	66	(see Figure 2)	−29068.70	M0/Fr	65	271.98**
Ta: two ratios	2	ω0 = 0.24, ωa = 0.17	−29186.20	M0/Ta	1	26.98**
Tb: two ratios	2	ω0 = 0.22, ωb = 0.16	−29198.04	M0/Tb	1	13.30**
Tc: two ratios	2	ω0 = 0.21, ωc = 0.40	−29202.33	M0/Tc	1	4.72*
Td: two ratios	2	ω0 = 0.21, ω d  = 1.25	−29196.13	M0/Td	1	17.12**
Te: two ratios	2	ω0 = 0.21, ωe = 0.27	−29202.86	M0/Te	1	3.66
Tf: two ratios	2	ω0 = 0.21, ωf = 0.56	−29197.39	M0/Tf	1	14.60**
A	4	p0 = 0.70, p1 = 0.23, (p2a = 0.05, p2b = 0.02), ω0 = 0.17,(ω1 = 1.00), b: ω2a = 0.17, ω2b = 1.00, f: ω 2a  = 12.83, ω 2b  = 12.83	−28827.71
A1	3	p0 = 0.52, p1 = 0.17, (p2a = 0.23, p2b = 0.08), ω0 = 0.17,(ω1 = 1.00), b: ω2a = 0.17, ω2b = 1.00, f: ω2a = 1.00, ω2b = 1.00	−28830.08	A/A1	1	4.74*

Selection analysis by three kinds of models was performed using codeml implemented in PAML. np: number of free parameters. lnL: log likelihood. LRT: likelihood ratio test. df: degrees of freedom. 2ΔlnL: twice the log-likelihood difference of the models compared. The significant tests at 5% cutoff are labeled with * and at 1% cutoff are labeled with **.