Skip to main content

Table 2 Maximum Likelihood Parameter Estimates for Group-II 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...

-11770.60

0.686

= ω0

  

   M0: one ratio-2

-4303.29

0.694

= ω0

  

   PD-PS..............

-4300.30

 

ω PD = 1.41, ωPS = 0.63

P = 0.014

 

   Free ratios.......

-11580.19

 

see Figure 1

P << 0.001

 

   Free ratios-2....

-11591.23

1

ω 0 constrained to 1

P << 0.01

 

Site-specific

     

   M1: neutral.......

-11547.79

0.876

p0 = 0.124, ω0 = 0

  
   

p1 = 0.876, ω2 = 1

  

   M2: selection...

-11266.10

1.64

p0 = 0.124, ω0 = 0

P << 0.001

30 (PP ≥ 0.99)

   

p1 = 0.605, ω2 = 1

 

2 (0.95 ≤ PP < 0.99)

   

p2 = 0.271, ω 2 = 3.81

 

9 (PP < 0.95)

   M3: discrete.....

-11096.30

0.971

p0 = 0.346, ω0 = 0.078

P << 0.001

21 (PP ≥ 0.99)

   

p1 = 0.42, ω2 = 0.83

 

5 (0.95 ≤ PP < 0.99)

   

p2 = 0.234, ω 2 = 2.55

 

8 (PP < 0.95)

   M7: beta...........

-11179.33

0.532

p = 0.332, q = 0.293

  

   M8: beta&ω......

-11073.18

0.899

p0 = 0.81, p = 0.352, q = 0.348

P << 0.001

15 (PP ≥ 0.99)

   

p1 = 0.19, ω = 2.58

 

7 (0.95 ≤ PP < 0.99)

     

6 (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