Skip to main content

Advertisement

SpringerLink
Log in

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

  • Article
  • Published:

From Nature Ecology & Evolution

View current issue Submit your manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

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.

Similar content being viewed by others

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.

References

  1. Embley, T. M. & Martin, W. Eukaryotic evolution, changes and challenges. Nature 440, 623–630 (2006).

    CAS  PubMed  Google Scholar 

  2. Martin, W. F., Garg, S. & Zimorski, V. Endosymbiotic theories for eukaryote origin. Phil. Trans. R. Soc. Lond. B 370, 20140330 (2015).

    Google Scholar 

  3. Roger, A. J., Muñoz-Gómez, S. A. & Kamikawa, R. The origin and diversification of mitochondria. Curr. Biol. 27, R1177–R1192 (2017).

    CAS  PubMed  Google Scholar 

  4. Martijn, J. & Ettema, T. J. G. From archaeon to eukaryote: the evolutionary dark ages of the eukaryotic cell. Biochem. Soc. Trans. 41, 451–457 (2013).

    CAS  PubMed  Google Scholar 

  5. Williams, T., Foster, P. G., Cox, C. J. & Embley, T. M. An archaeal origin of eukaryotes supports only two primary domains of life. Nature 504, 231–236 (2013).

    CAS  PubMed  Google Scholar 

  6. Woese, C. R. & Fox, G. E. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl Acad. Sci. USA 74, 5088–5090 (1977).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Kurland, C. G., Collins, L. J. & Penny, D. Genomics and the irreducible nature of eukaryote cells. Science 312, 1011–1014 (2006).

    CAS  PubMed  Google Scholar 

  8. Woese, C. R., Kandler, O. & Wheelis, M. L. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl Acad. Sci. USA 87, 4576–4579 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Tourasse, N. J. & Gouy, M. Accounting for evolutionary rate variation among sequence sites consistently changes universal phylogenies deduced from rRNA and protein-coding genes. Mol. Phylogenet. Evol. 13, 159–168 (1999).

    CAS  PubMed  Google Scholar 

  10. Cox, C. J., Foster, P. G., Hirt, R. P., Harris, S. R. & Embley, T. M. The archaebacterial origin of eukaryotes. Proc. Natl Acad. Sci. USA 105, 20356–20361 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Foster, P. G., Cox, C. J. & Embley, T. M. The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods. Phil. Trans. R. Soc. Lond. B 364, 2197–2207 (2009).

    Google Scholar 

  12. Raymann, K., Brochier-Armanet, C. & Gribaldo, S. The two-domain tree of life is linked to a new root for the Archaea. Proc. Natl Acad. Sci. USA 112, 6670–6675 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Guy, L. & Ettema, T. J. G. The archaeal ‘TACK’ superphylum and the origin of eukaryotes. Trends Microbiol. 19, 580–587 (2011).

    CAS  PubMed  Google Scholar 

  14. Williams, T., Foster, P. G., Nye, T. M. W., Cox, C. J. & Embley, T. M. A congruent phylogenomic signal places eukaryotes within the Archaea. Proc. Biol. Sci. 279, 4870–4879 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Hug, L. A. et al. A new view of the tree of life. Nat. Microbiol. 1, 16048 (2016).

    CAS  PubMed  Google Scholar 

  16. Lake, J., Henderson, E., Oakes, M. & Clark, M. W. Eocytes: a new ribosome structure indicates a kingdom with a close relationship to eukaryotes. Proc. Natl Acad. Sci. USA 81, 3786–3790 (1984).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Eme, L., Spang, A., Lombard, J., Stairs, C. W. & Ettema, T. J. G. Archaea and the origin of eukaryotes. Nat. Rev. Microbiol. 15, 711–723 (2017).

    CAS  PubMed  Google Scholar 

  18. Williams, T. A., Embley, T. M., Williams, T. A. & Embley, T. M. Changing ideas about eukaryotic origins. Phil. Trans. R. Soc. Lond. B 370, 20140318 (2015).

    Google Scholar 

  19. Spang, A. et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521, 173–179 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017).

    CAS  PubMed  Google Scholar 

  21. Hartman, H. & Fedorov, A. The origin of the eukaryotic cell: a genomic investigation. Proc. Natl Acad. Sci. USA 99, 1420–1425 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Da Cunha, V., Gaia, M., Gadelle, D., Nasir, A. & Forterre, P. Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes. PLoS Genet. 13, e1006810 (2017).

    PubMed  PubMed Central  Google Scholar 

  23. Gaia, M., Da Cunha, V. & Forterre, P. in Molecular Mechanisms of Microbial Evolution (ed. Rampelotto, P. H.) 55–99 (Springer, 2018).

  24. Da Cunha, V., Gaia, M., Nasir, A. & Forterre, P. Asgard archaea do not close the debate about the universal tree of life topology. PLoS Genet. 14, e1007215 (2018).

    PubMed  PubMed Central  Google Scholar 

  25. Spang, A. et al. Asgard archaea are the closest prokaryotic relatives of eukaryotes. PLoS Genet. 14, e1007080 (2018).

    PubMed  PubMed Central  Google Scholar 

  26. Hirt, R. P. et al. Microsporidia are related to fungi: evidence from the largest subunit of RNA polymerase II and other proteins. Proc. Natl Acad. Sci. USA 96, 580–585 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Lartillot, N., Brinkmann, H. & Philippe, H. Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol. Biol. 7 (Suppl. 1), S4 (2007).

  28. Bergsten, J. A review of long-branch attraction. Cladistics 21, 163–193 (2005).

    PubMed  Google Scholar 

  29. Nasir, A., Kim, K. M., Da Cunha, V. & Caetano-Anollés, G. Arguments reinforcing the three-domain view of diversified cellular life. Archaea 2016, 1851865 (2016).

    PubMed  PubMed Central  Google Scholar 

  30. Penny, D., McComish, B. J., Charleston, M. A. & Hendy, M. D. Mathematical elegance with biochemical realism: the covarion model of molecular evolution. J. Mol. Evol. 53, 711–723 (2001).

    CAS  PubMed  Google Scholar 

  31. Harish, A. & Kurland, C. G. Empirical genome evolution models root the tree of life. Biochimie 138, 137–155 (2017).

    CAS  PubMed  Google Scholar 

  32. Philippe, H. & Forterre, P. The rooting of the universal tree of life is not reliable. J. Mol. Evol. 49, 509–523 (1999).

    CAS  PubMed  Google Scholar 

  33. Harish, A. & Kurland, C. G. Akaryotes and Eukaryotes are independent descendants of a universal common ancestor. Biochimie 138, 168–183 (2017).

    CAS  PubMed  Google Scholar 

  34. Yang, S., Doolittle, R. F. & Bourne, P. E. Phylogeny determined by protein domain content. Proc. Natl Acad. Sci. USA 102, 373–378 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Caetano-Anolles, G. An evolutionarily structured universe of protein architecture. Genome Res. 13, 1563–1571 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Mayr, E. Two empires or three? Proc. Natl Acad. Sci. USA 95, 9720–9723 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Narrowe, A. B. et al. Complex evolutionary history of translation Elongation Factor 2 and diphthamide biosynthesis in Archaea and parabasalids. Genome Biol. Evol. 10, 2380–2393 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Brochier, C., Forterre, P. & Gribaldo, S. Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox. Genome Biol. 5, R17 (2004).

    PubMed  PubMed Central  Google Scholar 

  39. Brochier, C., Gribaldo, S., Zivanovic, Y., Confalonieri, F. & Forterre, P. Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales? Genome Biol. 6, R42 (2005).

    PubMed  PubMed Central  Google Scholar 

  40. Le, S. Q. & Gascuel, O. An improved general amino acid replacement matrix. Mol. Biol. Evol. 25, 1307–1320 (2008).

    CAS  PubMed  Google Scholar 

  41. Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307–321 (2010).

    CAS  PubMed  Google Scholar 

  42. Nguyen, L. T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).

    CAS  PubMed  Google Scholar 

  43. Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Lartillot, N. & Philippe, H. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol. Biol. Evol. 21, 1095–1109 (2004).

    CAS  PubMed  Google Scholar 

  45. Foster, P. Modeling compositional heterogeneity. Syst. Biol. 53, 485–495 (2004).

    PubMed  Google Scholar 

  46. Zhou, Y., Brinkmann, H., Rodrigue, N., Lartillot, N. & Philippe, H. A dirichlet process covarion mixture model and its assessments using posterior predictive discrepancy tests. Mol. Biol. Evol. 27, 371–384 (2010).

    CAS  PubMed  Google Scholar 

  47. Lartillot, N. L., Odrigue, N. I. R., Tubbs, D. A. S. & Icher, J. A. R. PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst. Biol. 62, 611–615 (2013).

    CAS  PubMed  Google Scholar 

  48. Bollback, J. P. Bayesian model adequacy and choice in phylogenetics. Mol. Biol. Evol. 19, 1171–1180 (2002).

    CAS  PubMed  Google Scholar 

  49. Susko, E. & Roger, A. J. On reduced amino acid alphabets for phylogenetic inference. Mol. Biol. Evol. 24, 2139–2150 (2007).

    CAS  PubMed  Google Scholar 

  50. Hrdy, I. et al. Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I. Nature 432, 618–622 (2004).

    CAS  PubMed  Google Scholar 

  51. Whelan, S. Spatial and temporal heterogeneity in nucleotide sequence evolution. Mol. Biol. Evol. 25, 1683–1694 (2008).

    CAS  PubMed  Google Scholar 

  52. Gouy, R., Baurain, D. & Philippe, H. Rooting the tree of life: the phylogenetic jury is still out. Phil. Trans. R. Soc. Lond. B 370, 20140329 (2015).

    Google Scholar 

  53. Crotty, S. M. et al. GHOST: recovering historical signal from heterotachously-evolved sequence alignments. Syst. Biol. https://doi.org/10.1093/sysbio/syz051 (2019).

  54. Graybeal, A. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol. 47, 9–17 (1998).

    CAS  PubMed  Google Scholar 

  55. Hedtke, S. M., Townsend, T. M. & Hillis, D. M. Resolution of phylogenetic conflict in large data sets by increased taxon sampling. Syst. Biol. 55, 522–529 (2006).

    PubMed  Google Scholar 

  56. Castelle, C. J. & Banfield, J. F. Major new microbial groups expand diversity and alter our understanding of the tree of life. Cell 172, 1181–1197 (2018).

    CAS  PubMed  Google Scholar 

  57. Parks, D. H. et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat. Microbiol. 2, 1533–1542 (2017).

    CAS  PubMed  Google Scholar 

  58. Roth, A. C. J., Gonnet, G. H. & Dessimoz, C. Algorithm of OMA for large-scale orthology inference. BMC Bioinform. 9, 518 (2008).

    Google Scholar 

  59. Altenhoff, A. M. et al. Standardized benchmarking in the quest for orthologs. Nat. Methods 13, 425–430 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. Williams, T. A. & Embley, T. M. Archaeal ‘dark matter’ and the origin of eukaryotes. Genome Biol. Evol. 6, 474–481 (2014).

    PubMed  PubMed Central  Google Scholar 

  61. Betts, H. C. et al. Integrated genomic and fossil evidence illuminates life’s early evolution and eukaryote origin. Nat. Ecol. Evol. 2, 1556–1562 (2018).

    PubMed  PubMed Central  Google Scholar 

  62. Roch, S. & Steel, M. Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent. Theor. Popul. Biol. 100C, 56–62 (2015).

    PubMed  Google Scholar 

  63. Roch, S., Nute, M. & Warnow, T. Long-branch attraction in species tree estimation: inconsistency of partitioned likelihood and topology-based summary methods. Syst. Biol. 68, 281–297 (2019).

    PubMed  Google Scholar 

  64. Steel, M. & Rodrigo, A. Maximum-likelihood supertrees. Syst. Biol. 57, 243–250 (2008).

    PubMed  Google Scholar 

  65. Akanni, W. A., Wilkinson, M., Creevey, C. J., Foster, P. G. & Pisani, D. Implementing and testing Bayesian and maximum-likelihood supertree methods in phylogenetics. R. Soc. Open Sci. 2, 140436 (2015).

    PubMed  PubMed Central  Google Scholar 

  66. Zhang, C., Sayyari, E. & Mirarab, S. in Comparative Genomics. RECOMB-CG 2017. Lecture Notes in Computer Science Vol . 10562 (eds Meidanis, J. & Nakhleh, L.) 53–75 (Springer, 2017).

  67. Iwabe, N., Kuma, K., Hasegawa, M., Osawa, S. & Miyata, T. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl Acad. Sci. USA 86, 9355–9359 (1989).

    CAS  PubMed  PubMed Central  Google Scholar 

  68. Gogarten, J. P. et al. Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes. Proc. Natl Acad. Sci. USA 86, 6661–6665 (1989).

    CAS  PubMed  PubMed Central  Google Scholar 

  69. Fournier, G. P. & Gogarten, J. P. Rooting the ribosomal tree of life. Mol. Biol. Evol. 27, 1792–1801 (2010).

    CAS  PubMed  Google Scholar 

  70. Lake, J., Skophammer, R. G., Herbold, C. W. & Servin, J. Genome beginnings: rooting the tree of life. Phil. Trans. R. Soc. Lond. B 364, 2177–2185 (2009).

    CAS  Google Scholar 

  71. Cavalier-Smith, T. Rooting the tree of life by transition analyses. Biol. Direct 1, 19 (2006).

    PubMed  PubMed Central  Google Scholar 

  72. Williams, T. A. et al. New substitution models for rooting phylogenetic trees. Phil. Trans. R. Soc. Lond. B 370, 20140336 (2015).

    Google Scholar 

  73. Klopfstein, S., Vilhelmsen, L. & Ronquist, F. A nonstationary Markov model detects directional evolution in hymenopteran morphology. Syst. Biol. 64, 1089–1103 (2015).

    PubMed  PubMed Central  Google Scholar 

  74. Cherlin, S. et al. The effect of non-reversibility on inferring rooted phylogenies. Mol. Biol. Evol. 35, 984–1002 (2018).

    CAS  PubMed  Google Scholar 

  75. Tria, F. D. K., Landan, G. & Dagan, T. Phylogenetic rooting using minimal ancestor deviation. Nat. Ecol. Evol. 1, 0193 (2017).

    Google Scholar 

  76. Szöllõsi, G. J., Rosikiewicz, W., Boussau, B., Tannier, E. & Daubin, V. Efficient exploration of the space of reconciled gene trees. Syst. Biol. 62, 901–912 (2013).

    PubMed  PubMed Central  Google Scholar 

  77. Timmis, J. N., Ayliffe, Ma, Huang, C. Y. & Martin, W. Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat. Rev. Genet. 5, 123–135 (2004).

    CAS  PubMed  Google Scholar 

  78. McInerney, J. O., O’Connell, M. J. & Pisani, D. The hybrid nature of the Eukaryota and a consilient view of life on Earth. Nat. Rev. Microbiol. 12, 449–455 (2014).

    CAS  PubMed  Google Scholar 

  79. Gray, M. W. & Doolittle, W. F. Has the endosymbiont hypothesis been proven? Microbiol. Rev. 46, 1–42 (1982).

    CAS  PubMed  PubMed Central  Google Scholar 

  80. Brown, J. R. & Doolittle, W. F. Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc. Natl Acad. Sci. USA 92, 2441–2445 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  81. Zhaxybayeva, O., Lapierre, P. & Gogarten, J. P. Ancient gene duplications and the root(s) of the tree of life. Protoplasma 227, 53–64 (2005).

    PubMed  Google Scholar 

  82. Knoll, A. H. Paleobiological perspectives on early eukaryotic evolution. Cold Spring Harb. Perspect. Biol. 6, a016121 (2014).

    PubMed  PubMed Central  Google Scholar 

  83. Butterfield, N. J. Early evolution of the Eukaryota. Palaeontology 58, 5–17 (2015).

    Google Scholar 

  84. Parfrey, L. W., Lahr, D. J. G., Knoll, A. H. & Katz, L. A. Estimating the timing of early eukaryotic diversification with multigene molecular clocks. Proc. Natl Acad. Sci. USA 108, 13624–13629 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  85. Spang, A. et al. Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism. Nat. Microbiol. 4, 1138–1148 (2019).

    CAS  PubMed  Google Scholar 

  86. Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  87. Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  88. Criscuolo, A. & Gribaldo, S. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol. Biol. 10, 210 (2010).

    PubMed  PubMed Central  Google Scholar 

  89. Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q. & Vinh, L. S. UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 35, 518–522 (2018).

    CAS  PubMed  Google Scholar 

  90. Williams, T. et al. Data from ‘Phylogenomics provides robust support for a two-domains tree of life’ (Figshare, 2019); https://doi.org/10.6084/m9.figshare.8950859.v2

  91. Williams, T. A. et al. Integrative modeling of gene and genome evolution roots the archaeal tree of life. Proc. Natl Acad. Sci. USA 114, E4602–E4611 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

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.

Author information

Authors and Affiliations

  1. School of Biological Sciences, University of Bristol, Bristol, UK

    Tom A. Williams

  2. Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal

    Cymon J. Cox

  3. Department of Life Sciences, Natural History Museum, London, UK

    Peter G. Foster

  4. MTA-ELTE “Lendület” Evolutionary Genomics Research Group, Budapest, Hungary

    Gergely J. Szöllősi

  5. Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary

    Gergely J. Szöllősi

  6. Evolutionary Systems Research Group, Centre for Ecological Research, Hungarian Academy of Sciences, Tihany, Hungary

    Gergely J. Szöllősi

  7. Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, UK

    T. Martin Embley

Authors
  1. Tom A. Williams
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Cymon J. Cox
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Peter G. Foster
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Gergely J. Szöllősi
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. T. Martin Embley
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

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.

Corresponding authors

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

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Figs. 1–17, Tables 1–15 and Discussion.

Reporting Summary

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41559-019-1040-x

  • Springer Nature Limited

This article is cited by

Search

Navigation