Table 2.
Results of LRT for positive selection analysis in GGT-family members of selected clades
| Foreground Branch | Model | Parameter estimated (frequency ‘f’, omega ‘ω’) | Ln L | 2∆LnL for LRT Pairs M2/M2a | ||||
|---|---|---|---|---|---|---|---|---|
| Model, M0 | ω0 =ω1=0.44 | -23188.93 | ||||||
| (ω0 = 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 | ω0 =ω1=0.44 | -23188.93 | ||||||
| (ω0 = 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 | ω0 =ω1=0.44 | -23188.93 | ||||||
| (ω0 = 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 | ω0 =ω1=0.44 | -23188.93 | ||||||
| (ω0 = 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 | |||
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)