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Table 2 Results of LRT for positive selection analysis in GGT-family members of selected clades

From: “Phylogenetic and evolutionary analysis of functional divergence among Gamma glutamyl transpeptidase (GGT) subfamilies”

Foreground Branch

Model

Parameter estimated (frequency ‘f’, omega ‘ω’)

Ln L

2∆LnL for LRT Pairs M2/M2a

 

Model, M0

ω01=0.44

 

-23188.93

 

0 = ω1)

Bacteria 1

Site class

0

1

2a

2b

 

68.53

 

Branch site

f

0.20

0.23

0.26

0.30

-22809.80

Model, M2

ω0

0.25

1.00

0.25

1.00

(0<ω<1)

ω1

0.25

1.00

1.00

1.00

 

Site class

0

1

2a

2b

 

Branch site

f

0.28

0.32

0.19

0.21

-22775.54

Model, M2a

ω0

0.25

1.00

0.25

1.000

(0<ω<1)

ω1

0.25

1.00

999.00

999.00

Model, M0

ω01=0.44

    

-23188.93

0 = ω1)

Bacteria 3

Site class

0

1

2a

2b

 

69.99

 

Branch site

f

0.21

0.25

0.25

0.29

-22805.67

Model, M2`

ω0

0.25

1.00

0.25

1.00

(0<ω<1)

ω1

0.25

1.00

1.00

1.00

 

Site class

0

1

2a

2b

 

Branch site

f

0.20

0.24

0.26

0.30

-22770.68

Model, M2a

ω0

0.25

1.00

0.25

1.00

(0<ω<1)

ω1

0.25

1.00

999.00

999.00

Model, M0

ω01=0.44

    

-23188.93

0 = ω1)

Bact4ext

Site class

0

1

2a

2b

 

69.90

 

Branch site

f

0.21362

0.24819

0.24895

0.28924

-22805.67

Model, M2

ω0

0.24612

1.00000

0.24612

1.00000

(0<ω<1)

ω1

0.24612

1.00000

1.00000

1.00000

 

Site class

0

1

2a

2b

 

Branch site

f

0.21

0.24

0.25

0.29

-22770.72

Model, M2a

ω0

0.25

1.00

0.25

1.00

(0<ω<1)

ω1

0.25

1.00

999.00

999.00

Model, M0

ω01=0.44

    

-23188.93

0 = ω1)

Eukaryotes

Site class

0

1

2a

2b

 

111.79

 

Branch site

f

0.16

0.19

0.30

0.35

-22807.60

Model, M2

ω0

0.25

1.00

0.25

1.00

(0<ω<1)

ω1

0.25

1.00

1.00

1.00

 

Site class

0

1

2a

2b

 

Branch site

f

0.09

0.10

0.37

0.43

-22751.71

Model, M2a

ω0

0.26

1.00

0.26

1.00

(0<ω<1)

ω1

0.26

1.00

999.00

999.00

  1. Positive selection analyses (M0, M2 and M2a) are performed by using ‘Codeml’ implemented in PAML. LnL: log likelihood. LRT: likelihood ratio test. 2∆lnL: twice the log-likelihood difference of two compared models. Model M2 and M2a are tested for null hypothesis and alternate hypothesis respectively. The significant tests are performed at level of significance cut-off value of 1 % using BEB statically methods. Null hypothesis was tested by fixing omega equal to 1. 2∆LnL = 2(LnLM2- LnLM2a)