Table 3. Log-likelihood values (lnL), parameter estimates and likelihood ratio tests for Clade model analyses of the melanopsin and rhodopsin data set.
| Clade model |
Site class 0 |
Site class 1 |
Site class 2 |
lnLa | npb | 2ΔlnLc | d.f. | P-value | |||
|---|---|---|---|---|---|---|---|---|---|---|---|
| ω0 | p0 | ω1 | p1 | ω2, ω3 | p2 | ||||||
| Melanopsin (opn4m2) | |||||||||||
| CmC_Pa | 0.180 | 0.375 | 1 | 0.019 | ω2=0.014 ω3(Pa)= 1.370 | 0.606 | −5706.616 | 21 | 21.721 | 1 | 3.154E−06 |
| CmC_Gb | 0.017 | 0.614 | 1 | 0.019 | ω2=0.184 ω3(Gb)= 0.484 | 0.367 | −5717.026 | 21 | 0.8999 | 1 | 0.343 |
| M2a_rel | 0.017 | 0.617 | 1 | 0.019 | ω2= ω3=0.187 | 0.365 | −5717.476 | 20 | |||
| Rhodopsin (rho) | |||||||||||
| CmC Pa | 0.147 | 0.329 | 1 | 0.028 | ω2= 0.0013 ω3(Pa)= 0.059 | 0.643 | −4279.794 | 21 | 3.420 | 1 | 0.064 |
| CmC Gb | 0.154 | 0.314 | 1 | 0.027 | ω2=0.0031 ω3(Gb)= 0.0 | 0.659 | −4281.461 | 21 | 0.086 | 1 | 0.770 |
| M2a_rel | 0.152 | 0.317 | 1 | 0.028 | ω2= ω3=0.0028 | 0.655 | −4281.504 | 20 | |||
a
ln(likelihood) value.
b
Number of parameters.
c
Twice the difference of ln(likelihood) between the two models compared.