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Phylogenomics provides robust support for a two-domains tree of life

An Author Correction to this article was published on 19 October 2020

This article has been updated

Abstract

Hypotheses about the origin of eukaryotic cells are classically framed within the context of a universal ‘tree of life’ based on conserved core genes. Vigorous ongoing debate about eukaryote origins is based on assertions that the topology of the tree of life depends on the taxa included and the choice and quality of genomic data analysed. Here we have reanalysed the evidence underpinning those claims and apply more data to the question by using supertree and coalescent methods to interrogate >3,000 gene families in archaea and eukaryotes. We find that eukaryotes consistently originate from within the archaea in a two-domains tree when due consideration is given to the fit between model and data. Our analyses support a close relationship between eukaryotes and Asgard archaea and identify the Heimdallarchaeota as the current best candidate for the closest archaeal relatives of the eukaryotic nuclear lineage.

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Fig. 1: The 35-gene matrix of Da Cunha et al.22 favours a 2D tree using the best-fitting models in both maximum-likelihood and Bayesian analyses.
Fig. 2: Evidence that the 3D tree is an artefact of long-branch attraction.
Fig. 3: An expanded sampling of microbial diversity supports a 2D tree.

Data availability

The data associated with our analyses are available in the FigShare repository90 at https://doi.org/10.6084/m9.figshare.8950859.v2.

Change history

  • 19 October 2020

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Acknowledgements

T.A.W. is supported by a Royal Society University Research Fellowship and the NERC (grant no. NE/P00251X/1). G.J.S. received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 714774 and grant no. GINOP-2.3.2.−15-2016-00057). P.G.F. received funding from the NERC (grant no. NE/M015831/1). C.J.C. received Portuguese national funds from the Foundation for Science and Technology (project no. UID/Multi/04326/2019) and the Portuguese node of ELIXIR, specifically BIODATA.PT ALG-01-0145-FEDER-022231. We thank G. Coleman for assistance with Fig. 2.

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All authors contributed to the conception and design of the project and to the interpretation of results. T.A.W., C.J.C., P.G.F. and G.J.S. performed analyses. T.A.W. and T.M.E. wrote the manuscript, with input from all authors.

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Correspondence to Tom A. Williams or T. Martin Embley.

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Williams, T.A., Cox, C.J., Foster, P.G. et al. Phylogenomics provides robust support for a two-domains tree of life. Nat Ecol Evol 4, 138–147 (2020). https://doi.org/10.1038/s41559-019-1040-x

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