Table 3 

Results of the analysis of adaptive sequence evolution for individual branches of the invertebratetype lysozyme tree. 

Branch 
Freeratio 
2ratio 




d_{N}/d_{S} 
Bootstrap 
d_{N}/d_{S} 
2ΔL 
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, d_{N}/d_{S }rate ratios were inferred for individual branches with the freeratio 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 d_{N}/d_{S }rate ratios above 1 or below 1 was assessed with nonparametric bootstrapping using 100 replicates; d_{N}/d_{S }rate ratios larger than 1 and with bootstrap support of more than 50 are given in bold. For the second comparison, d_{N}/d_{S }rate ratios were repeatedly inferred with the 2ratio 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 d_{N}/d_{S }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 d_{N}/d_{S }rate ratios indicate those that are significantly larger than 1 according to either method. 

Schulenburg and Boehnisch BMC Evolutionary Biology 2008 8:114 doi:10.1186/147121488114 