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Table 3 Parameters and likelihood scores of TFIIAγ genes under codon and branch-site models

From: Molecular evolution of the duplicated TFIIAγgenes in Oryzeae and its relatives

Model

p

ln

2ΔL

Estimate of parameters

Positively selective site

M0: one ratio

1

-5020.93

184.74**

ω:0.055

none

Codon model

M1: nearly neutral

1

-4915.09

211.68**

p0 = 0.938, p1 = 0.062

ω0 = 0.038, ω1 = 1.0

not allowed

M2: positive selection

3

-4915.09

0

p0 = 0.938, p1 = 0.044,

p2 = 0.017

ω0 = 0.038, ω1 = 1.0,

ω2 = 1.0

none

M3: discrete

5

-4818.28

193.62**

p0 = 0.714, p1 = 0.224,

p2 = 0.063

ω0 = 0.008, ω1 = 0.124,

ω2 = 0.480

none

M7: beta

2

-4815.29

 

p = 0.200, q = 2.073

not allowed

M8: beta & ω

4

-4815.29

0

p0 = 1.0, p = 0.200,

q = 2.073

p1 = 0, ω = 2.0

none

Branch-site model

Foreground: TFIIAγ1

     

Model A

3

-4915.04

0.10

p0 = 0.910, p1 = 0.060

(p2+p3 = 0.030) ω2 = 1.0

none

Model B

5

-4840.74

-44.92

p0 = 0.806, p1 = 0.194 (p2+p3 = 0)

ω0 = 0.015,ω1 = 0.259,

ω2 = 0

none

Foreground: TFIIAγ5

     

Model A

3

-4908.26

13.66**

p0 = 0.929, p1 = 0.058

(p2+p3 = 0.013) ω2 = ∞

90T

Model B

5

-4840.74

-44.92

p0 = 0.806, p1 = 0.194 (p2+p3 = 0)

ω0 = 0.015, ω1 = 0.259,

ω2 = 0

none

  1. **Significant at P < 0.01 level; *** Significant at the P < 0.001 level.
  2. p, number of parameters.