Table 1 Maximum likelihood estimates of parameters and sites inferred to be under positive selection in the CAP18/LL-37 family

From: Positive selection in cathelicidin host defense peptides: adaptation to exogenous pathogens or endogenous receptors?

Model

S

p

l

κ

Estimates of parameters

PSSs

M0 (one-ratio)

16.74

1

−2119.85

2.86

ω=1.09

None

M1a (Nearly Neutral)

17.37

2

−2105.98

2.70

p0=0.27 (p1=0.73)

Not allowed

M2a (Positive Selection)

18.54

4

−2080.56

2.91

ω0=0.35 (ω1=1)

p0=0.07 (p1=0.80)

1L**, 4D*, 32V**, 35T**, 37S**

     

p2=0.13

 
     

ω0=0.14 (ω1=1)

 
     

ω2=3.98

 

M7 (beta)

17.18

2

−12105.07

2.67

p=0.79, q=0.23

Not allowed

M8 (beta&ω>1)

18.42

4

−2080.36

2.89

p=0.56, q=0.09

1L**, 4D*, 32V**, 35T**, 37S**

     

p0=0.87 (p1=0.13)

 
     

ωs=3.80

 
  1. Abbreviations: κ, transition/transversion rate ratio; l, log likelihood; p, number of parameters in the ω distribution; S represents tree length.
  2. Twice the log likelihood difference (2Δl) between null models (M1a and M7) and their alternative models (M2a and M8): M1a/M2a=50.84 (χ2 significant value: P<0.001); M7/M8=49.42 (P<0.001). PSSs identified by the Bayes Empirical Bayes (BEB) and Naive Empirical Bayes (NEB) methods under M2a and M8 with P (posterior probabilities) ⩾0.99 are indicated by **. Residues are numbered according to human LL-37. ω values in M2a and M8 as indicators of positive selection are boldfaced.
Back to article page