Interpretive diagrams showing the suggested evolutionary stages where genes for some of the signature proteins that are specific for the Crenarchaeota and Euryarchaeota as well as some of the Crenarchaeota subgroups, likely originated. The top diagram (A) indicates the evolutionary interpretation of the signature proteins in the absence of any other information, whereas that below (B) indicates our interpretation of this data taking into consideration other relevant information discussed in the text. The branching pattern shown here is unrooted and the proteins that are shared by all archaea were introduced in a common ancestor of all archaea. The dotted line for N. equitans in (B) indicates that its placement within Euryarchaeota lineage is uncertain. The abbreviations T and AF in these figures as well as others refer to tables and Additional files.