TABLE 1.

Rhodopsin positive selection results based on a CodeML random‐site model comparison (M1a vs. M2a and M7 vs. M8a) and the maximum‐likelihood gene tree. The pairs of models were tested using a Likelihood Ratio Test (LRT) following a χ² distribution. Values of each site class ω₀ , ω₁ and ω₂ are specified for models M1a and M2a. The shape parameters p and q are specified for models M7 and M8. The value ω_p corresponds to the positively selected site class for M8. The proportion of each site class is given in parentheses

				Parameter
Model	np	lnL	κ	ω0 /p	ω1 /q	ω2 /ωp	Null	LRT	df	p
M1a	3	−5266	2.144	0.001 (91.7%)	1 (8.3%)
M2a	5	−4999	2.702	0.017 (89.9%)	1 (83%)	9.797 (1.7%)	M1a	534	2	<.0001
M7	3	−5314	2.377	0.007	0.018
M8	5	−5005	2.807	0.028	0.205	9.548 (2%)	M7	618	2	<.0001

Abbreviations: np, number of parameters; lnL, ln likelihood; κ, transition/transversion ratio; Null, null model; df, degrees of freedom.