Fig 3. Relative occurrence of a taxonomic group as the sister group of each clade in the unrooted trees.

For each taxonomic group in a cluster the sister was determined and counted. Multiple occurrences of different groups in the sister were accounted for by their relative occurrence. If the taxonomic group was paraphyletic, each monophyletic subgroup was determined and the sister of these were noted. The values of these subgroups were added up by multiplying the individual values of the sister by the fraction of the subgroup of the whole taxonomic group. To compare, the final values of each taxonomic group were normalized by dividing by the highest count a possible sister has gotten. It is apparent that Gammaproteobacteria are always overrepresented. It is not clear if the observed effects are due to overrepresentation of certain taxa in the data set or due to relative abundance of LGT.