Table 3

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

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 dN/dS > 1

71

Sites with dN/dS > 1

-


ω > 1 and p values < 0.05 are in bold. Only sites identified by BEB as statistically significant for dN/dS >1 are reported

* significant after Bonferroni's correction [p < 0.016 (0.05/3)]; § computed on a reduced dataset (without A. arabiensis and A. quadriannulatus samples)

Mancini et al. BMC Evolutionary Biology 2011 11:72   doi:10.1186/1471-2148-11-72

Open Data