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Table 1 Likelihood ratio test statistics for models of variable selective pressure among sites (F61 model of codon frequency).

From: Mammalian NPC1 genes may undergo positive selection and human polymorphisms associate with type 2 diabetes

Region/selection model(number of codons) d.f. -2ΔLnL Pvalue % 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 N-term (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 C-term (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 - -
  1. 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.