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Table 2 Likelihood ratio test statistics for models of variable selective pressure among sites in G6PC2

From: Susceptibility to type 2 diabetes may be modulated by haplotypes in G6PC2, a target of positive selection

Codon frequency model

LRT Models

Degrees of freedom

−2ΔLnLd

p value

% of sites (average dN/dS)

Positively selected sites

F3x4

 

M1a vs M2aa

2

18.33

1.05x10−4

0.99% (2.72)

 
 

M7 vs M8b

2

46.36

8.58x10−11

4.67% (1.49)

G137 (BEB, REL, FEL), A297 (BEB), L298 (BEB, REL, FEL), E316 (BEB), G351 (BEB, REL)

 

M8ac vs M8

1

11.79

5.96x10−4

 

F61

 

M1a vs M2a

2

9.15

1.03x10−2

0.75% (2.40)

 
 

M7 vs M8

2

39.46

2.69x10−9

4.93% (1.32)

 
 

M8a vs M8

1

6.68

9.77x10−3

  
  1. aM1a is a nearly neutral model that assumes one ω class between 0 and 1 and one class with ω = 1; M2a (positive selection model) is the same as M1a plus an extra class of ω > 1
  2. bM7 is a null model that assumes that 0 < ω < 1 is beta distributed among sites; M8 (positive selection model) is the same as M7 but also includes an extra category of sites with ω > 1
  3. cM8a is the same as M8, except that the 11th category cannot allow positive selection, but only neutral evolution
  4. d2ΔlnL: twice the difference of the natural logs of the maximum likelihood of the models being compared
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BMC Ecology and Evolution

ISSN: 2730-7182

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