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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)