|
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 |
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, 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 |
|||||