Table 1 

Likelihood ratio test statistics for models of variable selective pressure among sites (F61 model of codon frequency). 

Region/selection model(number of codons) 
d.f. 
2ΔLnL 
P value 
% of sites(average dN/dS) 
Selected sites 


Loop1 (269) 

M7 versus M8 
2 
10.04 
0.0066 
1.3% (1.37) 
182 (0.99, n.s.) 
M8a versus M8 
1 
4.87 
0.027 
 
 
Loop 2 Nterm (251) 

M7 versus M8 
2 
25.86 
<0.0001 
1.3% (1.78) 
416 (0.99, 0.99),417 (0.98, 1), 421 (0.91, 0.99) 
M8a versus M8 
1 
10.98 
0.0009 
 

Loop 2 Cterm (81) 

M7 versus M8 
2 
<0.01 
>0.99 
 
 
M8a versus M8 
1 
1.96 
0.16 
 

SSD (164) 

M7 versus M8 
2 
5.70 
0.058 
 
 
M8a versus M8 
1 
0.02 
>0.88 
 
 
Loop 3 (248) 

M7 versus M8 
2 
0.004 
>0.99 
 
 
M8a versus M8 
1 
1.52 
0.21 
 
 


M7 is a null model that assumes that 0<ω<1 is beta distributed among sites; M8a assumes 0<ω≤1; these two models are compared to M8, which includes an extra category of sites with ω>1 (positive selection). d.f., degree of freedom; 2ΔLnL, twice the difference of the natural logs of the maximum likelihood of the models being compared; P value, P value of rejecting the neutral models (M7 or M8a) in favor of the positive selection model (M8); % of sites (average dN/dS), estimated percentage of sites evolving under positive selection by M8 (dN/dS for these codons); selected sites, the position refers to the entire NPC1 human sequence, P values obtained from BEB and REL analyses are shown. BEB, Bayes empirical Bayes; REL, random effects likelihood; SSD, sterol sensing domain. 

AlDaghri et al. BMC Medicine 2012 10:140 doi:10.1186/1741701510140 