Table 3. Comparison of codon substitution models using likelihood-ratio tests and amino acid sites showing elevated non-synonymous substitution ratios (ω).

						Amino acid sites under selection
PAML Model	DF	LnL	Nested ModelComparison	Likelihood RatioTest statistic	CodonPosition	Amino AcidChange	NEB Probω >1	BEB Probω >1	ω ± SE
M0(one-ratio)	1	−4107.2882	3 vs. 0	32.310***	45	Ser-Gln	0.676	0.643	1.241±0.594
M1a (nearly-neutral)	2	−4094.4102	2 vs. 1	6.554*	66	Asp-Gly	1.000**	0.933	1.551±0.385
M2a (selection)	4	−4091.1332	8 vs. 7	13.581**	77	Arg-Gln	0.987*	0.849	1.474±0.463
M3 (discrete)	5	−4091.1332			301	Cys-Gly-Ser-Ala	0.997**	0.890	1.513±0.423
M7 (β)	2	−4097.9314			404	Ala-Val-Met	0.837	0.713	1.331±0.529
M8 (β+ω)	4	−4091.1408			472	Thr-Glu	0.795	0.709	1.321±0.549

DF degrees of freedom; LnL log-likelihood; NEB naïve empirical Bayes test; BEB Bayes empirical Bayes test; SE standard error.

Significant tests are indicated with an asterisk.