Table 2 dN/dS (ω) rates for null (M₀) and branch models (M₂) for UV, Blue, Long wavelength (LW), and RH7 opsins using species and gene trees and different number of taxa. Increasing the number of taxa shows significant differences between rates across nocturnal (ω₁) and diurnal species (ω₂) for color opsins but not for RH7 opsin, which served as a control.

Opsin	ω₀	ω₁	ω₂	n	LnL₀	LnL₂	d.f.	2LnL	p-value
M₂ vs. M₀ gene trees
UV	0.0328	0.0482	0.01643	24	−13222.396	−13196.06	48	52.54	<0.001*
Blue	0.03251	0.0403	0.02945	23	−11310.806	−11308.083	46	5.449	0.0196
LW	0.03264	0.0521	0.01173	24	−11232.972	−11174.84	48	116.27	<0.001*
RH7	0.0653	0.0594	0.06719	33	−22578.67	−22577.68	66	1.978	0.15
UV	0.03058	0.0445	0.02324	14	−6892.501	−6887.289	28	9.6	<0.001*
Blue	0.0354	0.0343	0.03602	17	−9822.971	−9822.9126	34	0.115	0.735
LW	0.03893	0.0434	0.03445	17	−6690.525	−6689.4261	34	2.197	0.138
M₂ vs. M₀ species trees
UV	0.03206	0.0411	0.02609	24	−13265.664	−13260.007	49	11.314	<0.001*
Blue	0.03361	0.0465	0.02922	23	−11333.887	−11328.244	47	11.287	<0.001*
LW	0.03309	0.0495	0.02589	24	−11247.362	−11233.584	49	28.779	<0.001*

Using species tree shows differences for all three opsins. ω_0: rates for null model, ω_1: rates for diurnal species, ω₂ for nocturnal species, n: number of taxa, LnL_0/2: log likelihood scores for M₀/M_2, d.f.: degrees of freedom for M₂. 2LnL: twice the LnL₂–LnL₀, * highly significant p-value (<0.001), with rates from corresponding models in bold.

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