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Table 4 Likelihood paramater estimates under the branch-site models.

From: Adaptive evolution of Hox-gene homeodomains after cluster duplications

Model Parameters Positive Sites Sig.
Hox1     
   M1a -707.37 p0 = 0.982, p1 = 0.018; ω0 = 0.0017, ω1 = 1 Not Allowed  
   MA -697.04 P 0+1 = 0.935, p 2 = 0.065; ω 0/1 = 0.0034/1, ω 2 = 999 3 (PP > 0.99) P << 0.001
Hox2     
   M1a -800.91 p0 = 0.985, p1 = 0.015; ω0 = 0.0059, ω1 = 1 Not Allowed  
   MA -794.72 p 0+1 = 0.981, p 2 = 0.019; ω 0/1 = 0.0062/1, ω 2 = 17.98 1 (PP > 0.95) P < 0.005
Hox3     
   M1a -1684.44 p0 = 0.979, p1 = 0.021; ω0 = 0.0223, ω1 = 1 Not Allowed  
   MA -1647.20 p 0+1 = 0.833, p 2 = 0.167; ω 0/1 = 0.0116/1, ω 2 = 170.6 12 (PP > 0.95) P << 0.001
Hox4     
   M1a -1547.08 p0 = 0.987, p1 = 0.013; ω0 = 0.0057, ω1 = 1 Not Allowed  
   MA -1538.64 p0+1 = 0.987, p2 = 0.013; ω0/1 = 0.0046/1, ω 2 = 3.70 1 (PP > 0.99) P << 0.001
Hox5     
   M1a -1280.06 p0 = 1.0, p1 = 0.0; ω0 = 0.0119, ω1 = 1 Not Allowed  
   MA-A -1272.42 p 0+1 = 0.897, p 2 = 0.103; ω 0/1 = 0.008/1, ω 2 = 1.11 1 (PP > 0.95) P << 0.001
   MA-B -1273.35 p 0+1 = 0.925, p 2 = 0.075; ω 0/1 = 0.0085/1, ω 2 = 477.6 None Identified P << 0.001
   MA-C -1269.82 p 0+1 = 0.903, p 2 = 0.097; ω 0/1 = 0.0106/1, ω 2 = 76.7 4 (PP > 0.90) P << 0.001
Hox6     
   M1a -1309.19 p0 = 1.0, p1 = 0.0; ω0 = 0.0155, ω1 = 1 Not Allowed  
   MA -1295.24 p0+1 = 0.754, p2 = 0.246; ω0/1 = 0.0108/1, ω 2 = 999 10 (PP > 0.90) P << 0.001
Hox7     
   M1a -698.86 p0 = 1.0, p1 = 0.0; ω0 = 0.0029, ω1 = 1 Not Allowed  
   MA -969.89 No Reliable Results   n.a.
Hox8     
   M1a -1889.89 p0 = 0.985, p1 = 0.015; ω0 = 0.011, ω1 = 1 Not Allowed  
   MA -1086.37 p0+1 = 0.949, p2 = 0.051; ω0/1 = 0.011/1, ω 2 = 1.0 1 (PP > 0.95) P < 0.05
Hox9     
   M1a -1389.70 p0 = 1.0, p1 = 0.0; ω0 = 0.0101, ω1 = 1 Not Allowed  
   MA-A -1386.83 p0+1 = 0.878, p2 = 0.122; ω0/1 = 0.0089/1, ω 2 = 1.0 None Identified P = 0.057
   MA-B -1380.29 No Reliable Results   n.a.
   MA-C -1269.82 p 0+1 = 0.903, p 2 = 0.097; ω 0/1 = 0.0106/1, ω 2 = 76.7 4 (PP > 0.90) P << 0.001
   MA-D -1389.19 p0+1 = 0.9, p2 = 0.1; ω0/1 = 0.0095/1, ω 2 = 1.0 1 (PP < 0.90) n.s.
Hox10     
   M1a -1747.75 p0 = 0.895, p1 = 0.105; ω0 = 0.0139, ω1 = 1 Not Allowed  
   MA -1747.20 p0+1 = 0.853, p2 = 0.47 ω0/1 = 0.0123/1, ω 2 = 1.0 1 (PP < 0.90) n.s.
Hox11     
   M1a -1210.27 p0 = 0.982, p1 = 0.018; ω0 = 0.0017, ω1 = 1 Not Allowed  
   MA -1208.15 p0+1 = 0.973, p2 = 0.029; ω0/1 = 0.0092/1, ω 2 = 1.0 None Identified n.s.
Hox12     
   M1a -1092.80 p0 = 1.0, p1 = 0.0; ω0 = 0.0229, ω1 = 1 Not Allowed  
   MA 1092.52 p0+1 = 0.973, p2 = 0.027; ω0/1 = 0.0226/1, ω 2 = 1.0 None Identified n.s.
Hox13     
   M1a -1747.34 p0 = 1.0, p1 = 0.0; ω0 = 0.023, ω1 = 1 Not Allowed  
   MA -1731.97 p 0+1 = 0.918, p 2 = 0.082; ω 0/1 = 0.022/1, ω 2 = 6.96 3 (PP > 0.90) P << 0.001
  1. Parameters that indicate positive selection are in bold. ℓ, likelihood of the model. Sig., significance of the model. Positive sites were identified using the Bayes empirical Bayes (BEB) method