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Table 2 Branches or group of branches tested by branch selection models

From: Evolutionary mechanisms driving the evolution of a large polydnavirus gene family coding for protein tyrosine phosphatases

Hypothesis

Test MA/MAnull

Likelihood values

χ2 value

df

LRT p-value

Clade 1

      

Clade Cα

MA

7035.70

27.77

1

1.36E-07

<0.001

 

MAnull

7049.58

    

Branch Cα

MA

7058.20

0

1

1

NS

 

MAnull

7058.20

    

Branch I

MA

7058.08

0

1

1

NS

 

MAnull

7058.08

    

Clade Z

MA

7050.24

5.25

1

0.022

<0.05

 

MAnull

7052.87

    

Branch IZ

MA

7055.64

3.58

1

0.049

<0.05

 

MAnull

7057.58

    

Clade 2

      

Clade ε

MA

2591.88

0

1

1

NS

 

MAnull

2593.91

    

Branch ε

MA

2601.60

0

1

1

NS

 

MAnull

2601.60

    

Clade RΔ

MA

2026.57

7.45

1

0.006

<0.01

 

MAnull

2030.29

    

Branch RΔ

MA

2601.78

0.03

1

0.86

NS

 

MAnull

2601.80

    

Clade 3

      

Clade S

MA

5205.54

3.15

1

0.076

NS

 

MAnull

5207.11

    

Branch H

MA

5211.87

0.05

1

0.816

NS

 

MAnull

5211.90

    

Branch HS

MA

5211.93

0

1

1

NS

 

MAnull

5211.93

    

Branch M

MA

5211.93

0

1

1

NS

 

MAnull

5211.93

    

Clade EX

MA

5193.81

13.47

1

2.42E-04

<0.001

 

MAnull

5200.55

    

Clade 4

      

Branch Q

MA

6960.59

0

1

1

NS

 

MAnull

6960.59

    

Branch K

MA

6956.33

0

1

1

NS

 

MAnull

6956.33

    

Branch P

MA

6958.79

5.14

1

0.023

<0.05

 

MAnull

6961.36

    

Clade Y

MA

6960.24

2.75

1

0.097

NS

 

MAnull

6961.61

    
  1. *Model comparisons were performed using Likelihood Ratio Test (LRT) between nested models.
  2. Model MA defines four classes of sites, where the two last classes have ω > 1 on the lineage of interest and ω < 1 for the rest of branches. This model is compared with MAnull which imposes ω=1 for the latter two classes.
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BMC Ecology and Evolution

ISSN: 2730-7182

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