Evolution of multiple phosphodiesterase isoforms in stickleback involved in cAMP signal transduction pathway

BMC Systems Biology

Table 1 Log-likelihood scores (l) and parameter estimates under several models for ω estimates in multiple PDE1Cb genes of stickleback

Models	l ^a	Average ω^b	ML-estimated parameters
Site-specific model
LRT-1
One ω ratio model (M0)	-5866.90	0.1395	P₀ = 1.0000, ω₀ = 0.1395
Discrete model (M3)	-5723.25	0.3937	P₀ = 0.7798, P₁ = 0.2063, P₂ = 0.0139, ω₀ = 0.0543, ω₁ = 0.5031, ω₂ = 17.8270
-2Δl_{[d.f. = 4]}	287.29 *
LRT-2
Neutral model (M1)	-5906.08	0.4735	P₀ = 0.5265, P₁ = 0.4735, ω₀ = 0.0000, ω₁ = 1.0000
Selection model (M2)	-5743.66	0.1743	P₀ = 0.3524, P₁ = 0.0911, P₂ = 0.5565, ω₀ = 0.0000, ω₁ = 1.0000, ω₂ = 0.1495
-2Δl_{[d.f. = 2]}	324.84 *
LRT-3
Beta model (M7)	-5763.28	0.1814	p = 0.3278, q = 1.3121, P₀ = P₁ = P₂ = 0.3333, ω₀ = 0.0030, ω₁ = 0.0866, ω₂ = 0.4548
Beta and ω model (M8)	-5763.28	0.1814	p = 0.3278, q = 1.3121, P₀ = P₁ = P₂ = 0.3333, P₃ = 0.0000, ω₀ = 0.0028, ω₁ = 0.0866, ω₂ = 0.4548, ω₃ = 0.3544
-2Δl_{[d.f. = 2]}	0.00
Branch-site model
Selection model (M2)	-5833.54	N.A.	P₀ = 0.0939, P₁ = 0.0652, P₂ = 0.8409, ω₀ = 0.0000, ω₁ = 1.0000, ω₂ = 0.0695
Discrete model (M3)	-5741.70	N.A.	P₀ = 0.3084, P₁ = 0.0562, P₂ = 0.6354, ω₀ = 0.0634, ω₁ = 0.8749, ω₂ = 0.0796

^a Log-likelihood scores.
^b Nonsynonymous–synonymous substitution ratio (ω = d_N/d_S) averaged over sites.
* p < 0.001

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