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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. [39] Horizontal gene transfer explains why archaeal sequences are found in bacteria and bacterial sequences are found in archaea. [39]
Metagenomic analyses recover a two-domain system with the domains Archaea and Bacteria; in this view of the tree of life, Eukaryotes are derived from Archaea. [ 58 ] [ 59 ] [ 60 ] With the later gene pool of LUCA's descendants, sharing a common framework of the AT/GC rule and the standard twenty amino acids, horizontal gene transfer would have ...
The standard hypothesis states that the ancestor of the eukaryotes diverged early from the Archaea, [97] [98] and that eukaryotes arose through symbiogenesis, the fusion of an archaean and a eubacterium, which formed the mitochondria; this hypothesis explains the genetic similarities between the groups. [93]
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.
Mitochondria and plastids contain their own ribosomes; these are more similar to those of bacteria (70S) than those of eukaryotes. [74] Proteins created by mitochondria and chloroplasts use N-formylmethionine as the initiating amino acid, as do proteins created by bacteria but not proteins created by eukaryotic nuclear genes or archaea. [75] [76]
A speculatively rooted tree for RNA genes, showing major branches Bacteria, Archaea, and Eukaryota The three-domain tree and the eocyte hypothesis (two-domain tree), 2008. [7] Phylogenetic tree showing the relationship between the eukaryotes and other forms of life, 2006. [8] Eukaryotes are colored red, archaea green, and bacteria blue.
As more new archaea were discovered in the early 2000s, this distinction became doubtful as eukaryotes became deeply nested within Archaea. The origin of eukaryotes from Archaea, meaning the two are of the same larger group, came to be supported by studies based on ribosome protein sequencing and phylogenetic analyses in 2004.
In a 2020 paper, Cavalier-Smith accepted the planctobacterial origins of Archaea and Eukaryota, noting that the evidence was not sufficient to safely distinguish between the two possibilities that eukaryotes are sisters of all archaea (as shown in the cladogram above) or that eukaryotes evolved from filarchaeotes, i.e. within Archaea (the two ...