Table 2. Log-likelihood values (lnL), parameter estimates and likelihood ratio tests for various Branch-based models testing for heterogeneous selection pressures for melanopsin and rhodopsin.

Branch model	ω0	ωPa	ωGb	lnLa	npb	H0	H1	2ΔlnLc	d.f.	P-value
Melanopsin (opn4m2)
A. One ratio: all branches have the same ω	0.08	ω0	ω0	−5800.498	17
B. One ratio: all branches have the same ω=1	1	ω0	ω0	−6407.852	16	B	A	1214.708	1	3.88E−266
C. Two ratio: (ω0), ωPa	0.077	1.189	ω0	−5794.580	18	A	C	11.836	1	0.0006
D. Two ratio: (ω0), ωPa =1	0.077	1	ω0	−5794.597	17	D	C	0.033	1	0.856
E. Two ratio: (ω0), ωGb	0.079	ω0	0.167	−5800.181	18	A	E	0.634	1	0.426
F. Free ratio (each branch has one ω)	Variable by branchd	1.127	0.137	−5777.164	31	C	F	34.832	13	0.001
Rhodopsin (rho)
A. One ratio: all branches have the same ω	0.055	ω0	ω0	−4379.978	17
B. One ratio: all branches have the same ω=1	1	ω0	ω0	−4971.150	16	B	A	1182.344	1	4.19E−259
C. Two ratio (ω0), ωPa	0.053	0.209	ω0	−4378.015	18	A	C	3.926	1	0.048
D. Two ratio: (ω0), ωPa =1	0.053	1	ω0	−4379.183	17	D	C	2.337	1	0.126
E. Two ratio: (ω0), ωGb	0.054	ω0	0.110	−4379.770	18	A	E	0.414	1	0.520
F. Free ratio (each branch has one ω)	Variable by branchd	0.199	0.072	−4365.531	31	C	F	24.968	13	0.023

Abbreviations: Gb, Garra barreimiae; H₀ and H₁, null and alternative hypothesis; Pa, Phreatichthys andruzzii.

The best-fit model is underlined.

^aln(likelihood) value.

^bNumber of parameters.

^cTwice the difference of ln(likelihood) between the two models compared.

^d(N*dN) and (S*dS) values are shown in Figures 1a and b.