FIGURE 1 | Relationship between the Eukarya and the Archaea, as inferred from 'three primary domains' and 'two primary domains' scenarios.

From the following article:

The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?

Simonetta Gribaldo, Anthony M. Poole, Vincent Daubin, Patrick Forterre & Céline Brochier-Armanet

Nature Reviews Microbiology 8, 743-752 (October 2010)

doi:10.1038/nrmicro2426

The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?

a | In the 'three primary domains' (3D) scenario, the Eukarya, Archaea and Bacteria form three primary domains, each with a specific most recent common ancestor (1, 2 and 3), and the Eukarya and Archaea are two distinct sister lineages, implying that they share an ancestor (4), the nature of which remains undetermined. The blue bar represents the emergence of specific eukaryotic features. Branch lengths and number of lineages within each domain are arbitrary. For simplicity, the root of the universal tree of life has been placed in the bacterial branch, but note that alternative rootings in the lineage leading to the Eukarya102, 103, 104 or within the Bacteria58, 105 have been proposed. This scenario implies that such an ancestor was very likely to be 'prokaryotic' in nature and to harbour all homologous features shared between the Archaea and the Bacteria (for example, it did not have a nucleus). However, this does not mean that this ancestor must have been archaeal in nature (for example, it did not have the typical lipids that define the Archaea today and that probably appeared along the stem leading to this domain). Invoking an archaeal ancestor for eukaryotes would ignore the possibility of evolution along the branch leading to the present-day Archaea. Furthermore, eukaryotic features may have been present in this ancestor and then lost in the branch leading to the Archaea, as some evidence suggests76, 106, 107. b | In the 'two primary domains' (2D) scenario, the Archaea and the Bacteria are the two primary domains, whereas the Eukarya is a secondary domain that arose from the merging of an archaeon and a bacterium (for simplicity, only the relationship between the Archaea and the Eukarya is shown here). In this scenario, the most recent ancestor of the Eukarya (1) derives directly from within the Archaea. Therefore, the most recent ancestor of the Archaea is also the most recent ancestor of the Archaea and the Eukarya (2,4). Note that, similarly to in the 3D scenario, in the 2D scenario there is also a stem along which the characters defining the modern Eukarya (blue bar) would have arisen, similarly to the 3D scenario.

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