Table 3. Comparison of Codon Evolution Models in NCL Genes.

	Likelihooda
	Nearly Neutral	Positive Selection	2Δlb	P Valuec	pd	ωe
A	M1	M2	(M2 vs. M1)
	−43839.38	−43673.49	−331.78	1.33 E−72	0.093	3.05
B	M7	M8	(M7 vs. M8)
	−43806.28	−43600.42	−411.72	5.66 E−90	0.147	2.35

Part A is a comparison of model M1 versus M2. M1 allows two classes of codons (ω = 0, negative selection; ω = 1, neutral selection) and M2 an additional class under positive selection (ω > 1). Part B is a comparison of model M7 versus M8. M7 allows a continuous β-distribution of 0 < ω < 1, with an additional class (ω > 1) in M8.

^aLog likelihood values for nearly neutral (M1 and M7) or positive selection (M2 and M8) models.

^bLikelihood ratio between the two models.

^cEvaluated from χ² distribution (df = 2).

^dProportion of sites under positive selection.

^eMean ω value for sites under positive selection.