Examples of cases where phylogenetic incongruence and the local rearrangement of the core structure are linked to each other. (A) The core genome alignment of Bacillaceae around the histidine and tryptophan biosynthetic operons. The names of the genes showing significant phylogenetic incongruence are shown in red. (B) The ML trees of the genes in these operons. The genes that were not detected as incongruent by the SH test are enclosed in parentheses. The names of the organisms in which the core arrangement around the operon are conserved are shown in red. Note that these trees are unrooted because outgroup rooting is not possible here due to the possible existence of horizontal transfers.