Cited by 274Protist diversity and phylogenyGenomics and Phylogenetic StudiesOrigins and Evolution of Life

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

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Williams, Tom A., Cox, Cymon J., Foster, Peter G., Szöllősi, Gergely J., Embley, T. Martin·2019·Nature Ecology & Evolution

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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  • CAT/CATGTR offers improved resilience to long-branch attraction artefacts and is almost always better fitting than standard site-homogeneous amino acid substitution models.

    “CAT/CATGTR offers improved resilience to long-branch attraction artefacts (LBA)22 and is almost always better fitting than standard site-homogeneous amino acid substitution models (e.g. WAG)8–10,23–29.”

    From Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (2021) · cites this paper as [28]

    The Results and Discussion (page unavailable) say CAT+GTR+G4 better accounts for convergent substitutions on long branches and fits the studied alignment better than the site-homogeneous LG+G4+F model. That supports the comparison for this dataset, but the paper does not establish that CAT/CATGTR is almost always better fitting across datasets or standard models generally. (LLM, conf=0.87)

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Authors
Williams, T. A., Cox, C. J., Foster, P. G., Szöllősi, G. J., & Embley, T. M.
Affiliations
  • University of Bristol (GB)
  • University of Algarve (PT)
  • Natural History Museum (GB)
  • Eötvös Loránd University (HU)
  • Newcastle University (GB)
Corresponding author
  • Williams, Tom A.
  • Embley, T. Martin
Venue
Nature Ecology & Evolution
Published
2019-12-09
Volume
4
Issue
1
Pages
138-147
ISSN
2397-334X (ISSN-L)
OpenAlex
W2993939447
Cited by
274
References
93
Citations by year
2026: 20 · 2025: 36 · 2024: 38 · 2023: 31 · 2022: 57 · 2021: 48 · 2020: 41 · 2019: 3
FWCI
12.32
Type
journal article
Language
en
Open access
Locations
  • Nature Ecology & Evolution (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • Bristol Research (University of Bristol) (submittedVersion, other-oa)
  • Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT) (submittedVersion)
  • Newcastle University ePrints (Newcastle Univesity)
Funders
Natural Environment Research Council (NE/P00251X/1, NE/M015831/1)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protist diversity and phylogeny
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Physical Sciences › Physics and Astronomy › Astronomy and Astrophysics › Origins and Evolution of Life
Keywords
eukaryotic origin, archaea, eukaryotes, Asgard archaea, coalescent methods, gene family phylogeny
MeSH terms
Archaea, Eukaryotic Cells, Phylogeny, Genomics, Eukaryota

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