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 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

-

-


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.

Al-Daghri et al. BMC Medicine 2012 10:140   doi:10.1186/1741-7015-10-140

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