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Table 3 Branch- and branch-site detection of positive selection (PAML)

From: Molecular evolution of a gene cluster of serine proteases expressed in the Anopheles gambiae female reproductive tract

Model

ω (back)

ω (fore)

lnL

χ2

p

Model

ω (back)

ω(fore)

lnL

χ2

p

AGAP005194 - branch test (foreground ω> background ω)

AGAP005196 - branch test (foreground ω> background ω)

Test for A. merus

Test for A. melas + A. merus

H0

0.46

0.46

-1779.96

  

H0

0.34

0.34

-1331.85

  

H1

0.45

infinite

-1780.10

n.a.

n.a.

H1

0.31

2.22

-1329.46

4.77

0.03

H2

0.36

1.09

-1776.10

7.72

0.01

H2

0.27

0.66

-1329.97

3.76

0.05

AGAP005194 - branch test (foreground ω> 1)

  

AGAP005196 - branch test (foreground ω> 1)

  

H0 (ω = 1)

0.36

1.00

-1776.13

  

H0 (ω = 1)

0.31

1.00

-1329.79

  

H2

0.36

1.09

-1776.10

0.05

0.82

H1

0.31

2.22

-1329.46

0.66

0.42

AGAP005195 - branch test (foreground ω> background ω)

AGAP005196 § - branch test (foreground ω> background ω)

Test for A. merus

     

Test for A. melas

     

H0

0.62

0.62

-1859.32

  

H0

0.38

0.38

-1067.31

  

H1

0.59

0.97

-1858.97

n.a.

n.a.

H1

0.35

infinite

-1065.96

2.70

1.00

H2

0.55

1.38

-1858.00

2.65

0.10

H2

0.33

1.59

-1066.02

2.58

0.11

Test for A. melas

     

Test for A. melas + A. merus

   

H0

0.62

0.62

-1859.32

  

H0

0.38

0.38

-1067.31

  

H1

0.65

0.21

-1858.65

1.34

0.25

H1

0.32

2.14

-1065.25

4.12

0.04

H2

0.64

0.15

-1858.59

1.46

0.23

H2

0.29

0.69

-1065.96

2.70

0.10

Test for A. melas + A. merus

   

AGAP005196 § - branch test (foreground ω> 1)

 

H0

0.62

0.62

-1859.32

  

H0 (ω = 1)

0.32

1.00

-1065.54

  

H1

0.61

0.72

-1859.28

0.08

0.78

H1

0.32

2.14

-1065.25

0.59

0.44

H2

0.60

0.71

-1859.24

0.15

0.69

      

AGAP005195 - branch-site test for A. melas + A. merus

AGAP005196 - branch-site test for A. melas

Model A1 (ω = 1)

-

-

-1809.83

  

Model A1 (ω = 1)

-

-

-1053.14

  

Model A (ω variable)

-

-

-1803.44

12.78

3.51 × 10 -4 *

Model A (ω variable)

-

-

-1057.53

8.77

0.00*

Sites with d N /d S > 1

71

    

Sites with d N /d S > 1

-

    
  1. ω > 1 and p values < 0.05 are in bold. Only sites identified by BEB as statistically significant for d N /d S >1 are reported
  2. * significant after Bonferroni's correction [p < 0.016 (0.05/3)]; § computed on a reduced dataset (without A. arabiensis and A. quadriannulatus samples)