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The three domain system of biological classification was introduced by Carl Woese to reflect his discovery that the prokaryotes comprise two very different groups of organisms. In it, all living things are grouped into three domains. Two of these, the Bacteria and Archaea (originally Eubacteria and Archaebacteria), include prokaryotes. The third, the Eukarya or Eukaryota, includes all eukaryotes, including the older kingdoms Animalia, Plantae, Fungi, and Protista.
These domains are typically divided into kingdomss. Other ranks higher than kingdom had been used earlier, for instance empires, to group together the eukaryotes, but in these schemes the prokaryotes were retained as a single group, understood to be paraphyletic. Some have argued that such systems are actually preferable and that the differences between Bacteria and Archaea are not sufficient to warrant such a level of separate treatment.