Figure 3.

Archaeal branch of an MLP tree combined with genomic context. The figure displays an expanded section of the maximum likelihood phylogeny tree from Figure 3. The outgroup has been omitted and the whole bacterial clade has been collapsed for clarity. Red signs indicate three deletion events suggested by the genomic context: The deletion of the hyp0940 and PPOX genes is described in the main text. The putative PPOX deletion seems to be a basal event for the Thaumarchaeota II subgroup. The large genetic rearrangement concerning the uncultured marine Crenarchaeota fosmid AD1000-56-E4 makes this sequence unique in the group of Thaumarchaeota. Next to the Thaumarchaeota, the corresponding parvulin loci with the available genomic contexts are displayed. The groups predicted from the genomic context are also well defined in the MLP tree.