Table 3

Results of the analysis of adaptive sequence evolution for individual branches of the invertebrate-type lysozyme tree.

Branch

Free-ratio

2-ratio



dN/dS

Bootstrap

dN/dS

L

P


A

0.089

74

3.883

2.942

0.0862

B

0.104

100

0.150

0.713

0.3985

C

0.105

100

0.097

0.004

0.9522

D

0.097

99

0.108

0.055

0.8140

E

0.076

100

0.063

0.293

0.5883

F

< 0.001

97

< 0.001

2.031

0.1541

G

0.212

79

0.229

0.642

0.4229

H

0.047

66

0.204

0.238

0.6258

I

1.454

33

0.219

0.531

0.4663

J

> 999

79

> 999

7.296

0.0069#

K

< 0.001

84

< 0.001

2.161

0.1416

L

0.041

100

0.038

2.794

0.0946

M

< 0.001

98

< 0.001

0.249

0.6180

N

3.493

87

2.572

7.653

0.0057*,#

O

0.056

100

0.044

1.831

0.1760

P

0.061

66

0.036

2.259

0.1329

Q

0.009

100

0.009

2.020

0.1552


Branch names are as depicted in Fig. 4B. For the first comparison, dN/dS rate ratios were inferred for individual branches with the free-ratio model, in which all branches were allowed to vary; the optimal model had a likelihood of ln L = -2871.29; the significance of individual branches having a dN/dS rate ratios above 1 or below 1 was assessed with non-parametric bootstrapping using 100 replicates; dN/dS rate ratios larger than 1 and with bootstrap support of more than 50 are given in bold. For the second comparison, dN/dS rate ratios were repeatedly inferred with the 2-ratio model, in which only the branch of interest was allowed to differ from the remaining branches; the significance of the individual branches to be different from the remaining branches was assessed via a likelihood ratio test comparison to the null model, in which all branches of the tree were assumed to have identical dN/dS rate ratios; the null model had a likelihood score of ln L = -2895.56; the probability P was calculated from twice the likelihood difference 2ΔL between null model and tested model; significance is indicated by * and ** for α = 0.1 and 0.05 according to the sequential Bonferroni procedure, respectively, and by # and ## for α = 0.1 and 0.05 according to the false discovery rate, respectively; bold dN/dS rate ratios indicate those that are significantly larger than 1 according to either method.

Schulenburg and Boehnisch BMC Evolutionary Biology 2008 8:114   doi:10.1186/1471-2148-8-114

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