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The three-domain system adds a level of classification (the domains) "above" the kingdoms present in the previously used five- or six-kingdom systems.This classification system recognizes the fundamental divide between the two prokaryotic groups, insofar as Archaea appear to be more closely related to eukaryotes than they are to other prokaryotes – bacteria-like organisms with no cell nucleus.
The three-domain system presumes that eukaryotes are more closely related to archaea than to Bacteria and are sister group to Archaea, thus, it treats them as separate domain. [29] As more new archaea were discovered in the early 2000s, this distinction became doubtful as eukaryotes became deeply nested within Archaea.
It was also found that the eukaryotes are more closely related to the Archaea than they are to the Eubacteria. Although the primacy of the Eubacteria-Archaea divide has been questioned, it has been upheld by subsequent research. [22] There is no consensus on how many kingdoms exist in the classification scheme proposed by Woese.
For example, Japanese scientists reported in 1990 their study on the elongation factors Tu(EF-Tu) and G(EF-G) from various organisms that showed that eukaryotes are most closely related to archaea (methanogen and halobacteria), and not eocytes. [15] Other studies also supported the eukaroyte-archaea relationship and rejected the eocyte hypotheses.
A lineage of archaea discovered in 2015, Lokiarchaeum (of the proposed new phylum "Lokiarchaeota"), named for a hydrothermal vent called Loki's Castle in the Arctic Ocean, was found to be the most closely related to eukaryotes known at that time. It has been called a transitional organism between prokaryotes and eukaryotes.
The eukaryotes seemingly emerged within the Asgard archaea, and are closely related to the Heimdallarchaeia. [5] This implies that there are only two domains of life, Bacteria and Archaea, with eukaryotes incorporated among the Archaea.
Bacteria and Archaea are two domains of prokaryotes. The other primary type is the eukaryote cell, which has a distinct nucleus bound by a nuclear membrane and membrane-bound organelles, including mitochondria , chloroplasts , lysosomes , rough and smooth endoplasmic reticulum , and vacuoles .
They suggested and formally defined the terms Bacteria, Archaea and Eukarya for the three domains of life. [22] It was the first tree founded on molecular phylogenetics and microbial evolution as its basis. [23] [24] The model of a tree is still considered valid for eukaryotic life forms.