Two-domain System

The two-domain system is a biological classification by which all organisms in the tree of life are classified into two big domains, Bacteria and Archaea. It emerged from development in the knowledge of archaea diversity and challenge over the widely accepted three-domain system that defines life into Bacteria, Archaea, and Eukarya. It was predicted by the eocyte hypothesis of James A. Lake in the 1980s, which was largely superseded by the three-domain system due to better compelling evidences at the time. Better understanding of archaea, especially in their roles in the origin of eukaryotes by symbiogenesis with bacteria, led to the revival of the eocyte hypothesis in the 2000s. The two-domain system became widely appreciated after the discovery of a large group ( superphylum) of archaea called Asgard in 2017, evidences of which suggest to be the evolutionary root of eukaryotes – implying that eukaryotes are members of the domain Archaea.

While the features of Asgard archaea do not directly rule out the three-domain system, the notion that eukaryotes originated from archaea and thus belong to Archaea has been strengthened by genetic and proteomic studies. Under the three-domain system, Eukarya is mainly distinguished by the presence of "eukaryotic signature proteins" that are not found in archaea and bacteria. However, Asgards are found to contain genes that codes for several of such unique proteins, indicating that the proteins originated in archaea.

Background

Classification of life into two main divisions is not new and the first was by a French biologist Édouard Chatton. In 1938, Chatton gave a broad distinction of organisms:

# Procaryotes (that include bacteria)
# Eucaryotes (that include protozoans)

These were later named empires, and Chatton's classification as the two-empire system. Chatton used the name Eucaryotes only for protozoans, excluded other eukaryotes, and published in limited circulation so that his work was not recognised. His classification was rediscovered by Canadian bacteriologist Roger Yates Stanier of the University of California in Berkeley in 1961 while staying at the Pasteur Institute in Paris. The next year, Stanier and his colleague Cornelis Bernardus van Niel published in ''Archiv für Mikrobiologie'' (now '' Archives of Microbiology'') Chatton's classification with Eucaryotes eloborated to include higher algae, protozoans, fungi, plants and animals. It became a popular system of classification, as John O. Corliss wrote in 1986: " heChatton-Stanier concept of a kingdom (better, superkingdom) Prokaryota for bacteria (in the broadest sense) and a second superkingdom Eukaryota for all other organisms has been widely accepted with enthusiasm."

In 1977, Carl Woese and George E. Fox classified prokaryotes into two groups (kingdoms), Archaebacteria (for methanogens, the first known archaea) and Eubacteria, based on their 16S ribosomal RNA (16S rRNA) genes. In 1984, James A. Lake, Michael W. Clark, Eric Henderson, and Melanie Oakes of the University of California, Los Angeles described what was known as "a group of sulfur-dependent bacteria" as new group of organisms called eocytes (for "dawn cells") and created a new kingdom Eocyta. With it they proposed the existence of four kingdoms, based on the structure and composition of the ribosomal subunits, namely Archaebacteria, Eubacteria, Eukaryote and Eocyta Lake further analyses the rRNA sequences of the four groups and noted that eukaryotes originated from eocytes and not archaebacteria, as was generally assumed. This was the basis of the eocyte hypothesis. In 1988, he proposed the division of all life forms into two taxonomic groups:

# Karyotes (that include eukaryotes and proto-eukaryotic organisms such as eocytes)
# Parkaryotes (that consist of eubacteria and archaea such as halobacteria and methanogens)

In 1990, Woese, Otto Kandler and Mark Wheelis showed that archaea are distinct group of organisms and that eocytes (which was renamed Crenarchaeota as a phylum of Archaea but corrected as Thermoproteota in 2021) are one of them. They introduced the major division of life as domains and introduced the three-domain system that comprises domain Eucarya, domain Bacteria and domain Archaea. With a number of revisions in the details and discoveries of several new archaea, Woese's classification gradually gained acceptance as "arguably the best-developed and most widely-accepted scientific hypotheses ith the five-kingdom classificationregarding the evolutionary history of life."

But the three-domain concept did not resolve the issues with the relationship between archaea and eukaryotes. As Ford Doolittle, then at the Dalhousie University, put it in 2020: " hethree-domain tree wrongly represents evolutionary relationships, presenting a misleading view about how eukaryotes evolved from prokaryotes. The three-domain tree ''does'' recognize a specific archaeal–eukaryotic affinity, but it would have the latter arising independently, not from within, the former."

Concept

The two-domain systems relies mainly on two key concepts that define eukaryotes as members of the domain Archaea and not as a separate domain: eukaryotes originated within Archaea, and Asgards represent the origin of eukaryotes.

Eukaryotes evolved from archaea

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. As more new archaea were discovered in the early 2000s, this distinction became doubtful as eukaryotes became deeper linked to archaea. The origin of eukaryotes from archaea, meaning the two are of the same group, came to be supported by studies based on ribosome protein sequencing and phylogenetic analyses in 2004. Phylogenomic analysis of about 6000 gene sets from 185 bacterial, archaeal and eukaryotic genomes in 2007 also suggested origin of eukaryotes from Euryarchaeota (specifically the Thermoplasmatales).

In 2008, researchers from Natural History Museum, London and Newcastle University reported a comprehensive analysis of 53 genes from archaea, bacteria and eukaryotes that included essential componen