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PHYLOGENOMICS

Evolutionary relationships between Archaea and eukaryotes

Nature Ecology & Evolution volume 4, pages 20–21 (2020)Cite this article

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A phylogenomic re-analysis of sequence data strongly supports the emergence of eukaryotes from within the archaeal radiation and underlines the importance of using the most accurate approaches to reconstruct ancient divergences in the tree of life.

Addressing very ancient evolutionary transitions is particularly challenging. On one hand, there is an incomplete availability of sequence data that could provide information on a particular area of the ToL. On the other hand, sequences accumulate changes over time, and this leads to a progressive erosion of the historical information they contain, all the more important the farther we aim to go back in time. Furthermore, evolutionary models and approaches to reconstruct deep phylogenies have limits in handling such ancient phylogenetic signals, leading to uncertainties or artefactual inferences. In particular, it has been observed that site homogeneous models (that is, assuming the same evolutionary process across sequence sites) are outperformed by the more realistic site and branch heterogeneous models (that is, allowing each site and branch to evolve under its own substitution pattern) in resolving ancient divergences4. Particularly when dealing with the entire ToL, the very long branches leading to Bacteria and eukaryotes with respect to that of Archaea (Fig. 1) make it particularly difficult to resolve the relationships among the three domains, and the choice of the best fitting model of sequence evolution is of primordial importance. Recent advances in the exploration of archaeal diversity5, combined with the use of more reliable approaches to reconstruct ancient phylogenies, have helped to alleviate these problems and provided strong support for the 2D scenario6,7,8,9,10, which was strengthened by the availability of the first genomic data from Asgard archaea, revealed to be the closest known relatives of eukaryotes2,11,12, as well as the isolation of the first member of this clade13.

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Fig. 1: Unrooted trees of life showing two alternative scenarios on the evolutionary relationships between eukaryotes and archaea.

Gareth Monger, under a Creative Commons licence CC BY 3.0.

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Authors and Affiliations

  1. Department of Microbiology, Unit “Evolutionary Biology of the Microbial Cell”, Institut Pasteur, Paris, France

    Simonetta Gribaldo

  2. Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France

    Céline Brochier-Armanet

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  1. Simonetta Gribaldo
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  2. Céline Brochier-Armanet
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Correspondence to Simonetta Gribaldo.

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Gribaldo, S., Brochier-Armanet, C. Evolutionary relationships between Archaea and eukaryotes. Nat Ecol Evol 4, 20–21 (2020). https://doi.org/10.1038/s41559-019-1073-1

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