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

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

Models l a Average ωb 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
  1. a Log-likelihood scores.
  2. b Nonsynonymous–synonymous substitution ratio (ω = dN/dS) averaged over sites.
  3. * p < 0.001
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BMC Systems Biology

ISSN: 1752-0509

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