Table II.
Parameter estimates and likelihood scores of PLA2 for site models in PAML.
| Model | np | Estimates of parameters | lnL | LRT pairs | df | 2ΔlnL | p-value | Positively selected sites BEB (%) |
|---|---|---|---|---|---|---|---|---|
| M0:one ratio | 94 | ω=0.16513 | −41914.67 | M0/M3 | 4 | 366.4 5.04128E-78 | None | |
| M3:discrete | 98 | p0=0.18381, p1=0.61322, p2=0.20297, ω0=0.06840 ω1=0.14537,ω2=0.42278 |
−41731.47 | |||||
| M1a:neutral | 95 | p0=0.92349, p1=0.07651,ω0=0.15503, ω1=1.00000 | −41830.79 | M1a/M2a | 2 | 0 | 1.00000 | 33M (55.5), 34K (52.8) |
| M2a:selection | 97 | p0=0.92349, p1=0.03595, p2=0.04056, ω0=0.15503, ω1=1.00000, ω2=1.00000 | −41830.79 | |||||
| M7:β | 95 | p=2.25732, q=10.02539 | −45800.80 | M7/M8 | 2 | 8103.86 | 0.00000 | 28N (65.8), 34K (53.7), 50S (60.4), 54T (64.6), 58R (64.9), 75T (70.0), 88Q (77.2), 92R (50.1) |
| M8:β and ω | 97 | p0=0.99999, p=0.17653, q=1.31411, p1=0.00001, ω=2.52322 | −41748.87 | |||||
Selection analysis by site models was performed using CODEML implemented in PAML. np, number of free parameters; lnL, loglikelihood; LRT, likelihood ratio test; df, degrees of freedom; 2ΔlnL, twice the log-likelihood difference of the models compared; BEB, Bayes empirical Bayes approach. p-values with bold font indicate statistical significance.