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The Eocyte hypothesis is a biological classification that indicates eukaryotes emerged within the prokaryotic Crenarchaeota (formerly known as eocytes), a phylum within the archaea. This hypothesis was originally proposed by James A. Lake and colleagues in 1984 based on the discovery that the shapes of ribosomes in the Crenarchaeota and eukaryotes are more similar to each other than to either bacteria or the second major kingdom of archaea, the Euryarchaeota.

The eocyte hypothesis gained considerable attention after its introduction due to the interest in determining the origin of the eukaryotic cell. This hypothesis has primarily been in contrast with the three-domain system introduced by Carl Woese in 1977. Additional evidence supporting the eocyte hypothesis was published in the 1980s, but despite fairly unequivocal evidence, support waned in favor of the three-domain system.

With advancements in genomics, the eocyte hypothesis experienced a revival beginning in the mid-2000s. 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. Furthermore, other proteins have been sequenced through proteomics with homologous structures in heat shock proteins found in both eukaryotes and archaea. The structure of these heat shock proteins were identified though X-ray crystallography to find the three dimensional structure of the proteins. These proteins however have differing purposes as the eukaryote heat shock protein is a part of the T-complex while the archaeal heat shock protein is a molecular chaperone. This creates an issue with the sequence homology that has been seen between 70 kilodalton heat shock proteins in eukaryotes and gram negative bacteria.

In addition to a Crenarchaeal origin of eukaryotes, some studies have suggested that eukaryotes may also have originated in the Thaumarchaeota. A superphylum - TACK - has been proposed that includes the Thaumarchaeota, Crenarchaeota, and other groups of archaea, so that this superphylum may be related to the origin of eukaryotes. 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.

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. The eocyte tree root may be located in the RNA World, that is the root organism may have been a Ribocyte (aka Ribocell). For cellular DNA and DNA handling an "out of virus" scenario has been proposed, i. e. string genetic information in DNA may have been an invention performed by viruses later handed over to Ribocytes twice, once transforming them into bacteria and once transforming them into archaea. Although archaeal viruses aren't as studied as bacterial phages, it is thought that dsDNA viruses lead to the incorporation of the viral genome into archaeal genomes. The transduction of genetic material through a viral vector lead to an increase in complexity in the pre-eukaryotic cells. All these findings do not change the eocyte tree as given here in principle, but zoom into a higher resolution of it.

Arguments Against
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. The horizontal gene transfer is the reason for why archaeal sequences are found in bacteria and bacterial sequences are found in archaea. This could be the reasoning for why elongation factors found in archaea and eukaryotes are so similar, the data currently out is obscured as horizontal gene transfer, vertical gene transfer, or endosymbiosis could be behind the gene sequence similarity. The Eocyte Hypothesis also has troubles due to the endosymbiotic theory and how the archaea were able to phagocytize the bacteria for the formation of membrane bound organelles. It is thought that these ancestral prokaryotes began to have ectosymbiotic relationships with other prokaryotes and slowly engulfed these symbiotes through cell membrane protrusions.

Although there has been data that attempts to confirm the relationship between eukaryotes and Chrenarcheota through the analysis of elongation factors, more recent experimentation with elongation factors provides data that disproves the eocyte hypothesis. Hasegawa et al. uses these elongation factors to help solidy that eukaryotes and archaebacteria are more closely related than archaebacteria and eubacteria that is explained in this 2 tree system.

A competing hypothesis is that prokaryotes evolved towards thriving in higher temperatures to evade viruses through the thermoreductive hypothesis, however this does not account for eukaryotes arise and only takes into consideration the prokaryotic origins. However decrease in complexity from a more complex origin is the basis of reductive evolution where a commensal relationship occurs, while this reduction explained in the thermoreduction hypothesis uses a parasitic relationship with viruses to explain the movement of complex pre-eukaryotes to a more harsh environment; that being ocean floor hydrothermal vents.