Abstract
The eocyte hypothesis, in which Eukarya emerged from within Archaea, has been boosted by the description of a new candidate archaeal phylum, “Lokiarchaeota”, from metagenomic data. Eukarya branch within Lokiarchaeota in a tree reconstructed from the concatenation of 36 universal proteins. However, individual phylogenies revealed that lokiarchaeal proteins sequences have different evolutionary histories. The individual markers phylogenies revealed at least two subsets of proteins, either supporting the Woese or the Eocyte tree of life. Strikingly, removal of a single protein, the elongation factor EF2, is sufficient to break the Eukaryotes-Lokiarchaea affiliation. Our analysis suggests that the three lokiarchaeal EF2 proteins have a chimeric organization that could be due to contamination and/or homologous recombination with patches of eukaryotic sequences. A robust phylogenetic analysis of RNA polymerases with a new dataset indicates that Lokiarchaeota and related phyla of the Asgard superphylum are sister group to Euryarchaeota, not to Eukarya, and supports the monophyly of Archaea with their rooting in the branch leading to Thaumarchaeota.
Highlights
The topology of the tree of Life (ToL), especially the evolutionary relationships between Archaea and Eukarya, is a major debated question in Biology that deeply impacts our understanding of the history of life on Earth [1,2,3,4,5,6]
We investigated the position of the archaeal phylum ‘Thorachaeota’, shown to be sister group to Lokiarchaeota in a phylogenetic tree based on the concatenated alignment of 16 ribosomal proteins [30], and of more recently described related phyla
We performed individual phylogenetic analyses of the 36 universal proteins used by Spang and co-workers, using the same methodology (Maximum likelihood, maximum likelihood (ML))
Summary
The topology of the tree of Life (ToL), especially the evolutionary relationships between Archaea and Eukarya, is a major debated question in Biology that deeply impacts our understanding of the history of life on Earth [1,2,3,4,5,6]. The genomes of the three Lokiarchaea encode many eukaryote-specific proteins (ESPs) never before detected in Archaea, such as multiple G-proteins and novel components of the ESCRT-III vesicular transport system, supporting the idea that Eukarya originated from an ancestral Lokiarchaeon [14]. This result has been widely reported with Lokiarchaeota being presented as the “missing link” that bridges the gap between prokaryotes (simple life) and eukaryotes (complex life) and as an almost definitive argument supporting the eocyte hypothesis [6,13,19]. These authors showed that the imbalanced number of species in the dataset studied by
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