An archaeal origin of eukaryotes supports only two primary domains of life

Abstract

The discovery of the Archaea and the proposal of the three-domains 'universal' tree, based on ribosomal RNA and core genes mainly involved in protein translation, catalysed new ideas for cellular evolution and eukaryotic origins. However, accumulating evidence suggests that the three-domains tree may be incorrect: evolutionary trees made using newer methods place eukaryotic core genes within the Archaea, supporting hypotheses in which an archaeon participated in eukaryotic origins by founding the host lineage for the mitochondrial endosymbiont. These results provide support for only two primary domains of life-Archaea and Bacteria-because eukaryotes arose through partnership between them.S ince their discovery by Carl Woese and his co-workers in 1977, the Archaea have figured prominently in hypotheses for eukaryotic origins 1,2 . Although similar to Bacteria in terms of cell structure, molecular phylogenies for ribosomal RNA and a small core of genes, that mainly have essential roles in protein translation 3 , suggested that the Archaea were more closely related to the eukaryotic nuclear lineage; that is, to the host cell that acquired the mitochondrion 4 . The idea that Archaea and eukaryotes are more closely related to each other than either is to Bacteria depends on analyses suggesting that the root of the tree should be placed on the bacterial stem, or within the Bacteria 5-12 , implying that the prokaryotes-cells that lack a nucleus-are a paraphyletic group 13 . The main question now debated is whether core components of the eukaryotic nuclear lineage descend from a common ancestor shared with Archaea, as in the three-domains tree 14 (Fig. 1), which is also often called the 'universal tree' or 'tree of life' 15-17 , or from within the Archaea, as proposed by archaeal-host hypotheses for eukaryotic origins 2 . The archaeal-host scenario with the greatest phylogenetic support is the eocyte hypothesis 18 , which proposes a sister-group relationship between eukaryotes and the eocytes (or Crenarchaeota 14 ), one of the major archaeal divisions (Fig. 1). However, the three-domains-eocyte debate remains controversial because different phylogenetic methods have delivered different results, often from the same data 19 . This disagreement is due, at least in part, to the difficulties associated with resolving ancient divergences in phylogenetic trees. Challenges of reconstructing ancient relationshipsA major issue in reconstructing ancient relationships is the strength and quality of historical signal remaining after the millions of years since the divergence of Archaea and eukaryotes. The earliest fossils identified as eukaryotic appeared by about 1.8 billion years ago 20 ; over this enormous span of time, the accumulation of multiple substitutions in DNA and protein sequences might have erased any signal that would allow the relationship between archaeal and eukaryotic core genes to be established 21 . However, more recent simulations and empirical studies suggest that there are reasons to be cautiously optimistic ...

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

“…These include elucidation of several phyla previously lacking genomic representatives [27][28][29] , including the Patescibacteria superphylum 4 , which has subsequently been referred to as the 'Candidate Phyla Radiation' (CPR) as it may consist of upwards of 35 candidate phyla 10,30 . Notable evolutionary and metabolic insights include the discovery of eukaryotic-like cytoskeleton genes in the archaeon Lokiarchaeota 31,32 and the identification of putative methane-metabolizing genes in the Bathyarchaeota and Verstraetearchaeota phyla 33,34 . These initial studies demonstrate the need for additional genomic representatives across the tree of life in order to more fully appreciate microbial evolution and metabolism.…”

Evolution of viruses and cells: do we need a fourth domain of life to explain the origin of eukaryotes?

“…It paved the way for the subsequent discovery that most likely only two primary domains (both prokaryotic, archaea and bacteria) exist [81,82]. The unforeseen discovery of a third domain of life (the archaea) also gave credibility to the possibility that other domains might have gone unnoted too.…”

Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis

“…Initially, phylogenetic analyses suggested that the eocyte was most likely the sister group of the Crenarchaeota [3]. However, the most recent and sophisticated studies carried out to address this problem point towards the Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota group [23] as the most likely closest relative of the eocyte [8,9,24]. Under this well-supported scenario, the emergence of the first eukaryote must have post-dated the origins and initial radiations of both the a-Proteobacteria and the Archaebacteria.…”

“…Under this well-supported scenario, the emergence of the first eukaryote must have post-dated the origins and initial radiations of both the a-Proteobacteria and the Archaebacteria. As a consequence, and despite the radically different cellular organization and subsequent ecological success of the eukaryotes, Eukaryota is younger than Archaebacteria and Eubacteria, and thus it cannot have been one of the primary lineages of life [8,14].…”