Eocyte hypothesis
Lake hypothesised the tree of life as having only two primary branches: prokaryotes, which include Bacteria and Archaea, and karyotes, that comprise Eukaryotes and eocytes.
Parts of this early hypothesis were revived in a newer two-domain system of biological classification which named the primary domains as Archaea and Bacteria.
In 1990, Carl Woese and his colleagues proposed that cellular life consists of three domains – Eucarya, Bacteria, and Archaea – based on the ribosomal RNA sequences.
The three-domain concept was widely accepted in genetics, and became the presumptive classification system for high-level taxonomy, and was promulgated in many textbooks.
Based on the structure and composition of their ribosomal subunits, they found that these organisms were different from other prokaryotes, bacteria and archaea, known at the time.
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.
[20][21] Introduced in 1977 by Carl Woese and George E. Fox[22] in classification, the technique indicated that archaea (with only methanogens known at the time) and bacteria were distinct groups of organisms.
[22] Based on further studies, Woese, Otto Kandler and Mark Wheelis introduced the concept of "domain" in 1990 as the highest level of biological classification, and proposed the three-domain system consisting of Eucarya, Bacteria and Archaea.
It is seen that eukaryotes share a large number of proteins with members of the TACK superphylum and that these complex archaea may have had rudimentary phagocytosis abilities to engulf bacteria.
[24] As a result of metagenomic analysis of material found nearby hydrothermal vents, another superphylum — Asgard — has been named and proposed to be more closely related to the original eukaryote and a sister group to TACK more recently.
Due to the similarities found between eukaryotes and both archaea and bacteria, it is thought that a major source of the genetic variation is through horizontal gene transfer.
[40] The eocyte hypothesis also has troubles due to the endosymbiotic theory, with the archaea being able to phagocytize bacteria for the formation of membrane-bound organelles.
As more archaeal genomes were sequenced, numerous genes coding for eukaryotic traits have been discovered in various archaean phyla, seemingly providing support for the eocyte hypothesis.
Proteomics based research has also found supporting data with the use of elongation factor 1-α (eEF-1), a common housekeeping protein, to compare structural homology between eukaryotic and archaean lineages.
[48] The so-called "eukaryotic signature proteins" actin (cytoskeletal microfilament involved in cell motility), tubulin (component of the large cytoskeleton, microtubule), and the ubiquitin system (protein degradation and recycling),[6][49] which are thought to be unique to eukaryotes, were found in TACK (comprising the phyla Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota) archaea but not in other archaea.
