Parallel reduction in expression, but no loss of functional constraint, in two opsin paralogs within cave populations of Gammarus minus (Crustacea: Amphipoda)

Table 2 Parameter estimate, likehoods, and likehood ration test (LRT) results for three models of coding sequence evolution of the Ops1 and Ops2 genes

Gene	Model	ω₀	ω₁	ω₂	L	2*ΔL	P
Ops1	One-Ratio, H_0: ω₀₌ω₁₌ω₂	0.1681	0.1681	0.1681	−1851.5071
	Two-Ratio, H_1: ω₀₌ω_1≠ω₂	0.1807	0.1807	0.1506	−1851.4025	0.2093	0.6473
	Three-Ratio, H_2: ω_0≠ω_1≠ω₂	0.0195	0.2756	0.1507	−1845.6865	11.4325	0.0007
Ops2	One-Ratio, H_0: ω₀₌ω₁₌ω₂	0.3034	0.3034	0.3034	−1958.1442
	Two-Ratio, H_1: ω₀₌ω_1≠ω₂	0.1589	0.1589	0.5334	−1952.6264	11.0356	0.0009
	Three-Ratio, H_2: ω_0≠ω_1≠ω₂	0.0426	0.2208	0.5335	−1950.0496	5.1536	0.0232

See Figure 3 for the topology and branch-specific non-synonymous to synonymous rate ratios (ω). The one-ratio model assumes a single ω on all branches, the two-ratio model allows for a background rate and a cave-specific rate, and the three-ratio model allows for a background rate, a derived surface rate, and a derived cave-specific rate.

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