Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins

Table 3 Log-likelihood analysis of possible placements of selected branches of maximum likelihood trees for the analyzed ribosomal proteins

Tree^*	Difference in log-likelihood^†	Standard error^‡	RELL-BP^§
L36 original	0.0	NA	0.7797
1→2	-45.7	11.8	0.0000
2→3	-29.1	10.9	0.0024
2→1	-42.7	10.9	0.0000
3→4	-3.1	3.6	0.2179
L31 original	0.0	NA	0.9949
1→2	-36.7	12.6	0.0007
2→1	-36.6	14.6	0.0044
S18 original	0.0	NA	0.9594
1→2	-6.7	3.9	0.0327
2→1	-20.3	8.9	0.0027
3→2	-16.7	7.1	0.0052
S18 original	0.0	NA	0.8344
4→5	-7.1	6.1	0.0838
5→4	-6.7	5.8	0.0818
L28 original	0.0	NA	0.9550
1→2	-18.9	10.5	0.0331
2→1	-19.3	9.4	0.0119

^*The numbers refer to local rearrangements of the tree as indicated on the corresponding figures. ^†Difference of the log-likelihoods relative to the best tree. ^‡ Standard error of difference in log-likelihood. ^§Bootstrap probability (BP) of the given tree calculated using the RELL method (resampling of estimated log-likelihoods) [44]). NA, standard error estimate is not applicable for the aximum likelihood tree.

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