A summary diagram showing the branching order of different groups within archaea based upon species distribution patterns of various archaeal-specific proteins. The arrows mark the suggested evolutionary stages where proteins that are uniquely shared by the indicated groups were introduced. The details of these proteins can be found in the indicated tables (T) or Additional files (AF). The branching pattern shown here is unrooted. The dotted line for N. equitans indicates that its placement within Euryarchaeota is uncertain. The dotted line extending from the proteins found in all archaea indicates that one cannot use this to root the archaeal tree.