Two-domain system in the context of "Symbiogenesis"

The eukaryotes (/juːˈkærioʊts, -əts/) are the domain of Eukaryota or Eukarya, organisms whose cells have a membrane-bound nucleus. All animals, plants, fungi, seaweeds, and many unicellular organisms are eukaryotes. They constitute a major group of life forms alongside the two groups of prokaryotes: the Bacteria and the Archaea. Eukaryotes represent a small minority of the number of organisms, but given their generally much larger size, their collective global biomass is much larger than that of prokaryotes.

The eukaryotes emerged within the archaeal phylum Promethearchaeota. Ignoring mitochondrial DNA (which is bacterial rather than archaeal), this would imply only two domains of life, Bacteria and Archaea, with eukaryotes incorporated among the Archaea. Eukaryotes first emerged during the Paleoproterozoic, likely as flagellated cells. The leading evolutionary theory is they were created by symbiogenesis between an anaerobic Promethearchaeota archaeon and an aerobic proteobacterium, which formed the mitochondria. A second episode of symbiogenesis with a cyanobacterium created the plants, with chloroplasts.

The three-domain system is a taxonomic classification system that groups all cellular life into three domains, namely Archaea, Bacteria and Eukarya, introduced by Carl Woese, Otto Kandler and Mark Wheelis in 1990. The key difference from earlier classifications such as the two-empire system and the five-kingdom classification is the splitting of Archaea (previously named "archaebacteria") from Bacteria as completely different organisms.

The three domain hypothesis is considered obsolete by some who believe that eukaryotes do not form a separate domain of life, but arose from a fusion between an Archaea species and a Bacteria species. (see Two-domain system)

The two-empire system (two-superkingdom system) was the top-level biological classification system in general use from the early 20th century until the establishment of the three-domain system (which itself is currently being challenged by the two-domain system). It classified cellular life into Prokaryota and Eukaryota as either "empires" or "superkingdoms". When the three-domain system was introduced, some biologists preferred the two-superkingdom system, claiming that the three-domain system overemphasized the division between Archaea and Bacteria. However, given the current state of knowledge and the rapid progress in biological scientific advancement, especially due to genetic analyses, that view has all but vanished.

Some prominent scientists, such as the late Thomas Cavalier-Smith, still hold and held to the two-empire system. The late Ernst Mayr, one of the 20th century's leading evolutionary biologists, wrote dismissively of the three-domain system, "I cannot see any merit at all in a three empire cladification." Additionally, the scientist Radhey Gupta argues for a return to the two-empire system, claiming that the primary division within prokaryotes should be among those surrounded by a single membrane (monoderm), including gram-positive bacteria and archaebacteria, and those with an inner and outer cell membrane (diderm), including gram-negative bacteria.

In biological taxonomy, a domain (/dəˈmeɪn/ or /doʊˈmeɪn/) (Latin: regio or dominium), also dominion, superkingdom, realm, or empire, is the highest taxonomic rank of all organisms taken together. It was introduced in the three-domain system of taxonomy devised by Carl Woese, Otto Kandler and Mark Wheelis in 1990.

According to the domain system, the tree of life consists of either three domains, Archaea, Bacteria, and Eukarya, or two domains, Archaea and Bacteria, with Eukarya included in Archaea. In the three-domain model, the first two are prokaryotes, single-celled microorganisms without a membrane-bound nucleus. All organisms that have a cell nucleus and other membrane-bound organelles are included in Eukarya and called eukaryotes.

Asgard archaea (previously known as superphylum "Asgard" or phylum "Asgardarchaeota") are a kingdom belonging to the domain Archaea that contain eukaryotic signature proteins.

After including the kingdom category into ICNP, the only validly published names of this group are kingdom Promethearchaeati and phylum Promethearchaeota. All formerly proposed "phyla" would be de-ranked to classes in this framework. It appears that the eukaryotes, the domain that contains the animals, plants, fungi and protists, emerged within the Promethearchaeati, in a branch containing the "Heimdallarchaeia" [de; es]. This supports the two-domain system of classification over the three-domain system.