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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