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Table 4 The effects of codon usage bias on LRT (n = 12)

From: Tracking the connection between evolutionary and functional shifts using the fungal lipase/feruloyl esterase A family

  

Model

  

F equal

F3x4

F codon

Estimates under model A

 

p0 = 0.51693, p1 = 0.152

(p2 + p3) = 0.330

ω2 = 11.182

p0 = 0.503, p1 = 0.102

(p2 + p3) = 0.393

ω2 = 14.201

p0 = 0.477, p1 = 0.095

(p2 + p3) = 0.426

ω2 = 999

Estimates under M1a

 

p0 = 0.732, p1 = 0.267

ω0 = 0.187

p0 = 0.793, p1 = 0.206

ω0 = 0.073

p0 = 0.794, p1 = 0.205

ω0 = 0.062

Estimates under model A (ω2 = 1)

 

p0 = 0.492, p1 = 0.159

(p2 + p3) = 0.348

ω0 = 0.165

p0 = 0.537, p1 = 0.112

(p2 + p3) = 0.350

ω0 = 0.073

p0 = 0.533, p1 = 0.112

(p2 + p3) = 0.354

ω0 = 0.039

2Δl

Test 1:

22.85

33.78

35.27

 

Test 2:

10.31

6.84

6.83

  1. Note: Branch-site model A was compared to site model M1a and model A with ω2 fixed to 1 for test 1 and 2, respectively. All tests are significant at 1%; with df = 2 and df = 1 for tests 1 and 2, respectively.