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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