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Table 3 Parameter estimates for UCP genes under different branch models, site models and branch-site models

From: Evolutionary history of the UCP gene family: gene duplication and selection

Model Parameters for branches Positively selected sites Likelihood
One-Ratio ω0 = 0.07649 None -15704.05
Branch specific    
Two-ratios (R2) ω0 = 0.0950 None -15696.32
  ω1 = 0.0660   
Three-ratios (R3) ω0 = 0.0946 None -15686.87
  ω1 = 0.0845   
  ω2 = 0.0496   
Site specific    
Neutral (M1) ω0 = 0.0657, ρ0 = 0.92529 Not allowed -15586.80
  ω1 = 1, ρ1 = 0.07471   
Selection (M2) ω0 = 0.06571, ρ0 = 0.9253   -15586.80
  ω1 = 1, ρ1 = 0.07470   
  ω2 = 1.266, ρ2 = 0.00000   
Discrete (M3) ω0 = 0.1109, ρ0 = 0.49068   -15244.05
(K = 3) ω1 = 0.10086, ρ1 = 0.38265   
  ω2 = 0.32064, ρ2 = 0.12668   
Beta (M7) ρ = 0.50769 q = 4.86274   -15243.99
Beta&ω (M8) ρ0 = 0.99, p = 0.53223 224 K (P = 0.914) -15233.43
  q = 5.57248, ρ1 = 0.00373, ω1 = 1.69524   
Branch-Site    
Model A ρ0 = 0.9155, ρ1 = 0.04732, In the foreground lineage: -15563.81
  ρ2a = 0.03529, ρ2b = 0.00182 180 H (P = 0.953), 220 L (P = 0.997), 235 M (P = 0.969)  
  ω2 = 0.06259   
Model B ρ0 = 0.49203, ρ1 = 0.43366, In foreground lineage: -15264.48
  ρ2a = 0.03950, ρ2b = 0.03481 No significant sites  
  ω0 = 0.012, ω1 = 0.12812, ω2 = 0.52 In the background lineage:  
   no significant site  
  1. The models were implemented in Codeml from PAML. Parameters in bold indicate positive selection.