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


The origin of eukaryotes and their evolutionary relationship with the Archaea is a major biological question and the subject of intense debate. In the context of the classical view of the universal tree of life, the Archaea and the Eukarya have a common ancestor, the nature of which remains undetermined. Alternative views propose instead that the Eukarya evolved directly from a bona fide archaeal lineage. Several recent large-scale phylogenomic studies using an array of approaches are divided in supporting either one or the other scenario, despite analysing largely overlapping data sets of universal genes. We examine the reasons for such a lack of consensus and consider how alternative approaches may enable progress in answering this fascinating and as-yet-unresolved question.

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Figure 1: Relationship between the Eukarya and the Archaea, as inferred from 'three primary domains' and 'two primary domains' scenarios.
Figure 2: Comparison of the data sets used in five of the phylogenomic analyses.
Figure 3: A two-step phylogenomic approach to investigating the relationship between the Archaea and the Eukarya.


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The authors thank the Fondation des Treilles for support, along with the four anonymous referees for their valuable comments. A.M.P. is a Royal Swedish Academy of Sciences Research Fellow supported by a grant from the Knut and Alice Wallenberg Foundation. V.D. is supported by the grants 'Phylariane', 'Ecogenome' and 'Living Deep' from the French ANR (National Agency for Research). C.B.A. is supported by an Action Thématique et Incitative sur Programme (ATIP) of the French Centre National de la Recherche Scientifique (CNRS).

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Family of homologous proteins constructed by comparing predicted proteins from complete genome sequences.

Distance method

Parametric phylogenetic method that aims to find the tree that minimizes the distance among sequences in a model of sequence evolution.


One of the three main divisions of life: the Archaea, the Bacteria and the Eukarya.

Horizontal gene transfer

The integration of an exogenous gene into the genome of an organism.


The most recent ancestor of all present-day eukaryotic lineages.


The most recent ancestor of all present-day organisms.

Maximum-likelihood method

Parametric phylogenetic method that aims to maximize thelikelihood of a tree; that is, the probability of observing the studied alignment according to the tree topology and to a model of sequence evolution.

Maximum-parsimony method

A non-parametric phylogenetic method that aims to find the set of trees which minimizes the number of evolutionary changes.

Monophyletic group

A group of organisms consisting of an ancestor and its descendants.


Derived from a speciation event.


Derived from a gene duplication event.

Single-gene phylogenetic analysis

Reconstruction of a phylogenetic tree based on the comparison of homologous sequences representing a single gene.

Taxonomic sampling

Sampling of homologous sequences chosen for a phylogenetic analysis from all available sequences.

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Gribaldo, S., Poole, A., Daubin, V. et al. The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?. Nat Rev Microbiol 8, 743–752 (2010).

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