The abundance of observed duplications and losses significantly deviate from the expected number of events at each branch (supplementary additional file 5, Supplementary Material online).
Phylogenetic analysis showed that the divergent copy was located in a long naked branch (supplementary fig. S6 z, Supplementary Material online), indicating the lack of a close relative of the copy.
However, the trees constructed for TraD and TraC, like the tree of TraG, indicate that these proteins from pTiC58 are most closely related to the orthologous proteins of pAtK84b, whereas those of pTi-SAKURA are on a separate branch (supplementary fig. S2 B and C, Supplementary Material online, and fig. 4 B).
Remarkably, none of the ω differences was significant at α = 0.05 for the five OGs with the inverse trend (higher ω in speciation branches than in duplication branches) (supplementary table S10, Supplementary Material online).
The effect of supplementary planting on branch and stem characteristics was greater in large gaps than in small ones.
The maximum age of the ORFan genes must be smaller than the age of the organism, and thus it assumed to be proportional to the relative length of their terminal branch (Supplementary Figure S1).
A similar pattern is seen with transcriptional regulators, which apparently have been lost during the evolution of M. infernorum branch (Supplementary Figures 3 and 5 [see Additional file 1]).
In particular, this explains the basal position of Methanopyrus kandleri, whose RNA polymerase exhibit a high evolutionary rate, both in previously published RNA polymerase trees and in the Figure 3 of the supplementary (where it branch together with Nanoarchaea and Korarchaeota).
Recently, Sakaki et al (2012) showed that NMD inhibition indeed leads to activation of the UPR through the IRE1α-spliced XBP1 branch (Supplementary Fig S4) as detected by a significant increase in the level of spliced XBP1 transcripts similar to the increase found following mild DTT-induced stress.
Directions of two daughter segments are determined by distributions of two angles: the 'divergence angle of branching' and the 'direction angle of branching' (supplementary material Fig. S3C).
In the alignments obtained with Random, the substitution rates were clearly overestimated with respect to the other methods, and in this case, we found significant differences in d N, d S, or d N/d S values with respect to Cons not only in the human and mouse branches but also in the horse and cow branches (supplementary file S2: tables S4 and S5, Supplementary Material online).
