Table 4

Likelihood paramater estimates under the branch-site models.

Model

Parameters

Positive Sites

Sig.


Hox1

M1a

-707.37

p0 = 0.982, p1 = 0.018; ω0 = 0.0017, ω1 = 1

Not Allowed

MA

-697.04

P0+1 = 0.935, p2 = 0.065; ω0/1 = 0.0034/1, ω2 = 999

3 (PP > 0.99)

P << 0.001

Hox2

M1a

-800.91

p0 = 0.985, p1 = 0.015; ω0 = 0.0059, ω1 = 1

Not Allowed

MA

-794.72

p0+1 = 0.981, p2 = 0.019; ω0/1 = 0.0062/1, ω2 = 17.98

1 (PP > 0.95)

P < 0.005

Hox3

M1a

-1684.44

p0 = 0.979, p1 = 0.021; ω0 = 0.0223, ω1 = 1

Not Allowed

MA

-1647.20

p0+1 = 0.833, p2 = 0.167; ω0/1 = 0.0116/1, ω2 = 170.6

12 (PP > 0.95)

P << 0.001

Hox4

M1a

-1547.08

p0 = 0.987, p1 = 0.013; ω0 = 0.0057, ω1 = 1

Not Allowed

MA

-1538.64

p0+1 = 0.987, p2 = 0.013; ω0/1 = 0.0046/1, ω2 = 3.70

1 (PP > 0.99)

P << 0.001

Hox5

M1a

-1280.06

p0 = 1.0, p1 = 0.0; ω0 = 0.0119, ω1 = 1

Not Allowed

MA-A

-1272.42

p0+1 = 0.897, p2 = 0.103; ω0/1 = 0.008/1, ω2 = 1.11

1 (PP > 0.95)

P << 0.001

MA-B

-1273.35

p0+1 = 0.925, p2 = 0.075; ω0/1 = 0.0085/1, ω2 = 477.6

None Identified

P << 0.001

MA-C

-1269.82

p0+1 = 0.903, p2 = 0.097; ω0/1 = 0.0106/1, ω2 = 76.7

4 (PP > 0.90)

P << 0.001

Hox6

M1a

-1309.19

p0 = 1.0, p1 = 0.0; ω0 = 0.0155, ω1 = 1

Not Allowed

MA

-1295.24

p0+1 = 0.754, p2 = 0.246; ω0/1 = 0.0108/1, ω2 = 999

10 (PP > 0.90)

P << 0.001

Hox7

M1a

-698.86

p0 = 1.0, p1 = 0.0; ω0 = 0.0029, ω1 = 1

Not Allowed

MA

-969.89

No Reliable Results

n.a.

Hox8

M1a

-1889.89

p0 = 0.985, p1 = 0.015; ω0 = 0.011, ω1 = 1

Not Allowed

MA

-1086.37

p0+1 = 0.949, p2 = 0.051; ω0/1 = 0.011/1, ω2 = 1.0

1 (PP > 0.95)

P < 0.05

Hox9

M1a

-1389.70

p0 = 1.0, p1 = 0.0; ω0 = 0.0101, ω1 = 1

Not Allowed

MA-A

-1386.83

p0+1 = 0.878, p2 = 0.122; ω0/1 = 0.0089/1, ω2 = 1.0

None Identified

P = 0.057

MA-B

-1380.29

No Reliable Results

n.a.

MA-C

-1269.82

p0+1 = 0.903, p2 = 0.097; ω0/1 = 0.0106/1, ω2 = 76.7

4 (PP > 0.90)

P << 0.001

MA-D

-1389.19

p0+1 = 0.9, p2 = 0.1; ω0/1 = 0.0095/1, ω2 = 1.0

1 (PP < 0.90)

n.s.

Hox10

M1a

-1747.75

p0 = 0.895, p1 = 0.105; ω0 = 0.0139, ω1 = 1

Not Allowed

MA

-1747.20

p0+1 = 0.853, p2 = 0.47 ω0/1 = 0.0123/1, ω2 = 1.0

1 (PP < 0.90)

n.s.

Hox11

M1a

-1210.27

p0 = 0.982, p1 = 0.018; ω0 = 0.0017, ω1 = 1

Not Allowed

MA

-1208.15

p0+1 = 0.973, p2 = 0.029; ω0/1 = 0.0092/1, ω2 = 1.0

None Identified

n.s.

Hox12

M1a

-1092.80

p0 = 1.0, p1 = 0.0; ω0 = 0.0229, ω1 = 1

Not Allowed

MA

1092.52

p0+1 = 0.973, p2 = 0.027; ω0/1 = 0.0226/1, ω2 = 1.0

None Identified

n.s.

Hox13

M1a

-1747.34

p0 = 1.0, p1 = 0.0; ω0 = 0.023, ω1 = 1

Not Allowed

MA

-1731.97

p0+1 = 0.918, p2 = 0.082; ω0/1 = 0.022/1, ω2 = 6.96

3 (PP > 0.90)

P << 0.001


Parameters that indicate positive selection are in bold. ℓ, likelihood of the model. Sig., significance of the model. Positive sites were identified using the Bayes empirical Bayes (BEB) method

Lynch et al. BMC Evolutionary Biology 2006 6:86   doi:10.1186/1471-2148-6-86

Open Data