Skip to main content

Table 1 Maximum Likelihood Parameter Estimates for Group-I PLA2 Genes.

From: Inventing an arsenal: adaptive evolution and neofunctionalization of snake venom phospholipase A2 genes

Model

â„“

ω0

Parameters

Sig.

Positive Sites

Lineage-specific

     

   M0: one ratio...

-9102.48

1.28

= ω 0

P < 0.01

 

   M0: one ratio-C

-9106.69

1

ω 0 constrained to 1

  

   M0: one ratio-2

-5153.65

1.16

= ω 0

  

   PD-PS.............

-5153.55

 

ω PD = 1.22, ω PS = 1.12

n.s.

 

   Free ratio.........

-8980.48

 

see Figure 1

P << 0.001

 

Site-specific

     

   M1: neutral.......

-8909.37

0.852

p0 = 0.148, ω0 = 0

  
   

p1 = 0.582, ω2 = 1

  

   M2: selection...

-8600.95

2.11

p0 = 0.145, ω0 = 0

P << 0.001

36 (PP ≥ 0.99)

   

p1 = 0.5, ω2 = 1

 

4 (0.95 ≤ PP < 0.99)

   

p2 = 0.355, ω 2 = 4.53

 

10 (PP < 0.95)

   M3: discrete.....

-8540.48

1.69

p0 = 0.343, ω0 = 0.115

P << 0.001

74 (PP ≥ 0.99)

   

p1 = 0.435, ω 2 = 1.43

 

7 (0.95 ≤ PP < 0.99)

   

p2 = 0.222, ω 2 = 4.63

 

4 (PP < 0.95)

   M7: beta...........

-8725.96

0.594

p = 0.266, q= 0.182

  

   M8: beta&ω......

-8544.24

1.4

p0 = 0.70, p = 0.276, q = 0.228

P << 0.001

28 (PP ≥ 0.99)

   

p1 = 0.297, ω = 3.41

 

2 (0.95 ≤ PP < 0.99)

     

9 (PP < 0.95)

  1. L is the log likelihood of the model; ω0 is the estimate of the dN/dS ratio under the model (given as a weighted average for the site-specific models); Sig. is the significance of the model when compared to it's neutral partner under the χ2-distribution; Positive sites gives the number of sites that fall within a particular Baysean posterior probability value (PP) of being in the site class ω >1. n.s., not significant.