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Phylogenomics provides robust support for a two-domains tree of life
Open accessAbstract
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 (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]
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu033 · Cited by 32,291
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msu300 · Cited by 26,046
Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010) · Systematic Biology · doi:10.1093/sysbio/syq010 · Cited by 18,376
UFBoot2: Improving the Ultrafast Bootstrap Approximation
Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q., & Vinh, L. S. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msx281 · Cited by 10,881
Accelerated Profile HMM Searches
Eddy, S. R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002195 · Cited by 6,975
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
Woese, C. R., Kandler, O., & Wheelis, M. L. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.12.4576 · Cited by 6,128
Phylogenetic structure of the prokaryotic domain: The primary kingdoms
Woese, C. R., & Fox, G. E. (1977) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.74.11.5088 · Cited by 4,131
An Improved General Amino Acid Replacement Matrix
Le, S. Q., & Gascuel, O. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn067 · Cited by 3,127
A new view of the tree of life
Hug, L. A., Baker, B. J., Anantharaman, K., Brown, C. T., Probst, A. J., Castelle, C. J., Butterfield, C. N., Hernsdorf, A. W., Amano, Y., Ise, K., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.48 · Cited by 2,039
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Lewis, W. H., Tahon, G., Geesink, P., Sousa, D. Z., & Ettema, T. J. G. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-020-00458-8 · Cited by 639
Expanded diversity of Asgard archaea and their relationships with eukaryotes
Liu, Y., Makarova, K. S., Huang, W.-C., Wolf, Y. I., Nikolskaya, A. N., Zhang, X., Cai, M., Zhang, C., Xu, W., Luo, Z.-H., et al. (2021) · Nature · doi:10.1038/s41586-021-03494-3 · Cited by 338
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Cai, C., Tihelka, E., Giacomelli, M., Lawrence, J. F., Ślipiński, A., Kundrata, R., Yamamoto, S., Thayer, M. K., Newton, A. F., Leschen, R. A. B., et al. (2022) · Royal Society Open Science · doi:10.1098/rsos.211771 · Cited by 289
Incongruence in the phylogenomics era
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Metadata
- 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)
- PMC
- PMC6942926
- 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
- Update notices
- correction (2020-10-19)
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- 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 › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › 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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