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.