Table 7. Analyses of selection on Vertebrate rhodopsin (rh1) using PAML random sites models.
| Model | lnL | Parameters1 | Null | P [df]2 | Δ AIC§ | ||
|---|---|---|---|---|---|---|---|
| ω0/p | ω1/q | ω2/ωp | |||||
| M0 | −49624.89 | 0.08 | - | - | N/A | - | 5516.80 |
| M1a | −48355.44 | 0.05 (89%) | 1.00 (11%) | - | M0 | 0.000 [1] | 2979.91 |
| M2a | −48355.44 | 0.05 (89%) | 1.00 (3%) | 1.00 (8%) | M1a | 1 [2] | 2983.91 |
| M3 | −47104.84 | 0.01 (58%) | 0.11 (30%) | 0.44 (12%) | M0 | 0.000 [4] | 484.71 |
| M7 | −46906.24 | 0.24 | 1.19 | - | N/A | - | 81.51 |
| M8a | −46864.60 | 0.32 | 3.10 | 1.00 | N/A | - | 0.230 |
| M8 | −46863.49 | 0.32 | 2.94 | 1.14 | M7 | 0.000 [2] | 0* |
| M8a | 0.135 [1] | ||||||
1ω values of each site class are shown are shown for model M0-M3 (ω0– ω2) with the proportion of each site class in parentheses. For M7 and M8, the shape parameters, p and q, which describe the beta distribution are listed instead. In addition, the ω value for the positively selected site class (ωp, with the proportion of sites in parentheses) is shown for M8.
2Significant p-values (α ≤0.05) are bolded. Degrees of freedom are given in square brackets after the p-values.
3#Model fits were assessed by Akaike information criterion differences to the best fitting model (asterisk).
Abbreviations—lnL, ln Likelihood; p, p-value; N/A, not applicable.