A new view of the tree of life
Open accessAbstract
The tree of life is one of the most important organizing principles in biology 1 . Gene surveys suggest the existence of an enormous number of branches 2 , but even an approximation of the full scale of the tree has remained elusive. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships 3–5 or on the known, well-classified diversity of life with an emphasis on eukaryotes 6 . These approaches overlook the dramatic change in our understanding of life's diversity resulting from genomic sampling of previously unexamined environments. New methods to generate genome sequences illuminate the identity of organisms and their metabolic capacities, placing them in community and ecosystem contexts 7,8 . Here, we use new genomic data from over 1,000 uncultivated and little known organisms, together with published sequences, to infer a dramatically expanded version of the tree of life, with Bacteria, Archaea and Eukarya included. The depiction is both a global overview and a snapshot of the diversity within each major lineage. The results reveal the dominance of bacterial diversification and underline the importance of organisms lacking isolated representatives, with substantial evolution concentrated in a major radiation of such organisms. This tree highlights major lineages currently underrepresented in biogeochemical models and identifies radiations that are probably important for future evolutionary analyses.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Numerous studies support possibility 3 (neither domain arose from the other, such that LUCA was the common ancestor of bacteria and archaea sampled here).
“numerous studies support possibility 3 [47, 147, 148]”
From Evidence for corrin biosynthesis in the last universal common ancestor (2025) · cites this paper as [147]
The bacterial candidate phyla radiation (CPR) and the DPANN archaea diversify near the base of the Bacteria and Archaea respectively.
“Trees visualized at https://itol.embl.de/itol.cgiusing Netwick files from Hug et al. (2016) concatenated ribosomal proteins in place of 16S rRNA genes (Fig. 3B) indicate that a large radiation of predominantly uncultured mesophilic taxa, which are comprised of potentially symbiotic organisms with small cells and genomes and are referred to as the bacterial candidate phyla radiation (CPR) and the”
From The Emergence of Life (2019) · cites this paper as Hug et al. 2016
Cites
Complex archaea that bridge the gap between prokaryotes and eukaryotes
Spang, A., Saw, J. H., Jørgensen, S. L., Zaremba-Niedzwiedzka, K., Martijn, J., Lind, A. E., van Eijk, R., Schleper, C., Guy, L., & Ettema, T. J. G. (2015) · Nature · doi:10.1038/nature14447 · Cited by 1,324 · see citing works
Unusual biology across a group comprising more than 15% of domain Bacteria
Brown, C. T., Hug, L. A., Thomas, B. C., Sharon, I., Castelle, C. J., Singh, A., Wilkins, M. J., Wrighton, K. C., Williams, K. H., & Banfield, J. F. (2015) · Nature · doi:10.1038/nature14486 · Cited by 1,216 · see citing works
Self-citationArchaea and fungi of the human gut microbiome: correlations with diet and bacterial residents
Hoffmann, C., Dollive, S., Grunberg, S., Chen, J., Li, H., Wu, G. D., Lewis, J. D., & Bushman, F. D. (2013) · PLoS ONE · doi:10.1371/journal.pone.0066019 · Cited by 808 · see citing works
Castelle, C. J., Wrighton, K. C., Thomas, B. C., Hug, L. A., Brown, C. T., Wilkins, M. J., Frischkorn, K. R., Tringe, S. G., Singh, A., Markillie, L. M., et al. (2015) · Current Biology · doi:10.1016/j.cub.2015.01.014 · Cited by 536 · see citing works
Self-citationMapping the Tree of Life: Progress and Prospects
Pace, N. R. (2009) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00033-09 · Cited by 286 · see citing works
Pace, N. R. (2006) · Nature · doi:10.1038/441289a · Cited by 276 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
A communal catalogue reveals Earth's multiscale microbial diversity
Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G., et al. (2017) · Nature · doi:10.1038/nature24621 · Cited by 2,684 · see citing works
Shotgun metagenomics, from sampling to analysis
Quince, C., Walker, A. W., Simpson, J. T., Loman, N. J., & Segata, N. (2017) · Nature Biotechnology · doi:10.1038/nbt.3935 · Cited by 2,202 · see citing works
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Parks, D. H., Rinke, C., Chuvochina, M., Chaumeil, P.-A., Woodcroft, B. J., Evans, P. N., Hugenholtz, P., & Tyson, G. W. (2017) · Nature Microbiology · doi:10.1038/s41564-017-0012-7 · Cited by 1,882 · see citing works
Scaling laws predict global microbial diversity
Locey, K. J., & Lennon, J. T. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1521291113 · Cited by 1,184 · see citing works
The Origin and Diversification of Mitochondria
Roger, A. J., Muñoz-Gómez, S. A., & Kamikawa, R. (2017) · Current Biology · doi:10.1016/j.cub.2017.09.015 · Cited by 1,142 · see citing works
Fusobacterium nucleatum — symbiont, opportunist and oncobacterium
Brennan, C. A., & Garrett, W. S. (2019) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0129-6 · Cited by 1,205 · see citing works
Stress and stability: applying the Anna Karenina principle to animal microbiomes
Zaneveld, J. R., McMinds, R., & Vega Thurber, R. (2017) · Nature Microbiology · doi:10.1038/nmicrobiol.2017.121 · Cited by 977 · see citing works
Asnicar, F., Thomas, A. M., Beghini, F., Mengoni, C., Manara, S., Manghi, P., Zhu, Q., Bolzan, M., Cumbo, F., May, U., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16366-7 · Cited by 869 · see citing works
GToTree: A user-friendly workflow for phylogenomics
Lee, M. D. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz188 · Cited by 552 · see citing works
The Transporter Classification Database (TCDB): 2021 update
Saier, M. H., Reddy, V. S., Moreno-Hagelsieb, G., Hendargo, K. J., Zhang, Y., Iddamsetty, V., Lam, K. J. K., Tian, N., Russum, S., Wang, J., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1004 · Cited by 467 · see citing works
Accurate and complete genomes from metagenomes
Chen, L.-X., Anantharaman, K., Shaiber, A., Eren, A. M., & Banfield, J. F. (2020) · Genome Research · doi:10.1101/gr.258640.119 · Cited by 401 · see citing works
Self-citationZhao, Y., Jaber, V., & Lukiw, W. J. (2017) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2017.00318 · Cited by 379 · see citing works
Challenges in evidencing the earliest traces of life
Javaux, E. J. (2019) · Nature · doi:10.1038/s41586-019-1436-4 · Cited by 297 · see citing works
Cyanobacteria and biogeochemical cycles through Earth history
Sánchez-Baracaldo, P., Bianchini, G., Wilson, J. D., & Knoll, A. H. (2022) · Trends in Microbiology · doi:10.1016/j.tim.2021.05.008 · Cited by 279 · see citing works
A rooted phylogeny resolves early bacterial evolution
Coleman, G. A., Davín, A. A., Mahendrarajah, T. A., Szánthó, L. L., Spang, A., Hugenholtz, P., Szöllősi, G. J., & Williams, T. A. (2021) · Science · doi:10.1126/science.abe0511 · Cited by 285 · see citing works
Phylogenomics provides robust support for a two-domains tree of life
Williams, T. A., Cox, C. J., Foster, P. G., Szöllősi, G. J., & Embley, T. M. (2019) · Nature Ecology & Evolution · doi:10.1038/s41559-019-1040-x · Cited by 274 · see citing works
Integrative modeling of gene and genome evolution roots the archaeal tree of life
Williams, T. A., Szöllősi, G. J., Spang, A., Foster, P. G., Heaps, S. E., Boussau, B., Ettema, T. J. G., & Embley, T. M. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1618463114 · Cited by 233 · see citing works
Genomic diversity, lifestyles and evolutionary origins of DPANN archaea
Dombrowski, N., Lee, J.-H., Williams, T. A., Offre, P., & Spang, A. (2019) · FEMS Microbiology Letters · doi:10.1093/femsle/fnz008 · Cited by 230 · see citing works
Spang, A., Stairs, C. W., Dombrowski, N., Eme, L., Lombard, J., Caceres, E. F., Greening, C., Baker, B. J., & Ettema, T. J. G. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0406-9 · Cited by 200 · see citing works
Self-citationRoot of the Tree: The Significance, Evolution, and Origins of the Ribosome
Bowman, J. C., Petrov, A. S., Frenkel-Pinter, M., Penev, P. I., & Williams, L. D. (2020) · Chemical Reviews · doi:10.1021/acs.chemrev.9b00742 · Cited by 197 · see citing works
The microbiome in posttraumatic stress disorder and trauma-exposed controls: an exploratory study
Hemmings, S. M. J., Malan-Müller, S., van den Heuvel, L. L., Demmitt, B. A., Stanislawski, M. A., Smith, D. G., Bohr, A. D., Stamper, C. E., Hyde, E. R., Morton, J. T., et al. (2017) · Psychosomatic Medicine · doi:10.1097/psy.0000000000000512 · Cited by 208 · see citing works
Resilience of the oral microbiome
Wade, W. G. (2021) · Periodontology 2000 · doi:10.1111/prd.12365 · Cited by 205 · see citing works
The last universal common ancestor between ancient Earth chemistry and the onset of genetics
Weiss, M. C., Preiner, M., Xavier, J. C., Zimorski, V., & Martin, W. F. (2018) · PLOS Genetics · doi:10.1371/journal.pgen.1007518 · Cited by 186 · see citing works
Zhou, X., Shen, X.-X., Hittinger, C. T., & Rokas, A. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msx302 · Cited by 164 · see citing works
Horizontal gene transfer constrains the timing of methanogen evolution
Wolfe, J. M., & Fournier, G. P. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0513-7 · Cited by 160 · see citing works
Time to test antibacterial therapy in Alzheimer’s disease
Panza, F., Lozupone, M., Solfrizzi, V., Watling, M., & Imbimbo, B. P. (2019) · Brain · doi:10.1093/brain/awz244 · Cited by 161 · see citing works
Symbiosis in eukaryotic evolution
López-García, P., Eme, L., & Moreira, D. (2017) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2017.02.031 · Cited by 154 · see citing works
Koonin, E. V. (2016) · F1000Research · doi:10.12688/f1000research.8737.1 · Cited by 152 · see citing works
Domagal-Goldman, S. D., Wright, K. E., Domagal-Goldman, S. D., Wright, K. E., Adamala, K., Arina de la Rubia, L., Bond, J., Dartnell, L. R., Goldman, A. D., Lynch, K., et al. (2016) · Astrobiology · doi:10.1089/ast.2015.1460 · Cited by 136 · see citing works
“…following: sequence diversity of genes other than 16S rRNA, those related to the reproductive and energy-generation processes believed to be common to all cells (Fournier and Gogarten, 2010), suites of genes (Parfrey et al., 2010), or even entire genomes (Ciccarelli et al., 2006; Hug et al., 2016).”
Evolution of resilience in protein interactomes across the tree of life
Zitnik, M., Sosič, R., Feldman, M. W., & Leskovec, J. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1818013116 · Cited by 130 · see citing works
An estimate of the deepest branches of the tree of life from ancient vertically evolving genes
Moody, E. R., Mahendrarajah, T. A., Dombrowski, N., Clark, J. W., Petitjean, C., Offre, P., Szöllősi, G. J., Spang, A., & Williams, T. A. (2022) · eLife · doi:10.7554/elife.66695 · Cited by 95 · see citing works
Cultured microbes represent a substantial fraction of the human and mouse gut microbiota
Lagkouvardos, I., Overmann, J., & Clavel, T. (2017) · Gut Microbes · doi:10.1080/19490976.2017.1320468 · Cited by 104 · see citing works
Phylogenetic Signal, Congruence, and Uncertainty across Bacteria and Archaea
Martinez-Gutierrez, C. A., & Aylward, F. O. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab254 · Cited by 95 · see citing works
ATP synthase evolution on a cross-braced dated tree of life
Mahendrarajah, T. A., Moody, E. R. R., Schrempf, D., Szánthó, L. L., Dombrowski, N., Davín, A. A., Pisani, D., Donoghue, P. C. J., Szöllősi, G. J., Williams, T. A., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-42924-w · Cited by 86 · see citing works
“…the Diaphero-trites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeaota, and Nanohaloarchaeota) 16 – 18 , that were originally interpreted as early divergingbranchesoneachsideoftherootofthetreeoflife 2 ,mightbe important for our understanding of the deep split separating Archaea and Bacteria 19 .”
BackgroundMethodParsons, C., Stüeken, E. E., Rosen, C. J., Mateos, K., & Anderson, R. E. (2021) · Geobiology · doi:10.1111/gbi.12419 · Cited by 91 · see citing works
Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition
Taib, N., Megrian, D., Witwinowski, J., Adam, P., Poppleton, D., Borrel, G., Beloin, C., & Gribaldo, S. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-01299-7 · Cited by 82 · see citing works
Camprubí, E., de Leeuw, J. W., House, C. H., Raulin, F., Russell, M. J., Spang, A., Tirumalai, M. R., & Westall, F. (2019) · Space Science Reviews · doi:10.1007/s11214-019-0624-8 · Cited by 84 · see citing works
“…symbiotic organisms with small cells and genomes and are referred to as the bacterial candidate phyla radiation (CPR) and the DPANN archaea, diversify near the base of the Bacteria and Archaea respectively (Brown et al. 2015; Castelle et al. 2015; Hug et al. 2016; Castelle and Banfield 2018).”
BackgroundScientific novelty beyond the experiment
Hallsworth, J. E., Udaondo, Z., Pedrós‐Alió, C., Höfer, J., Benison, K. C., Lloyd, K. G., Cordero, R. J. B., de Campos, C. B. L., Yakimov, M. M., & Amils, R. (2023) · Microbial Biotechnology · doi:10.1111/1751-7915.14222 · Cited by 62 · see citing works
Berkemer, S. J., & McGlynn, S. E. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa089 · Cited by 52 · see citing works
ESX/Type VII Secretion Systems—An Important Way Out for Mycobacterial Proteins
Vaziri, F., & Brosch, R. (2019) · Microbiology Spectrum · doi:10.1128/microbiolspec.psib-0029-2019 · Cited by 50 · see citing works
The evolution and spread of sulfur cycling enzymes reflect the redox state of the early Earth
Mateos, K., Chappell, G., Klos, A., Le, B., Boden, J., Stüeken, E., & Anderson, R. (2023) · Science Advances · doi:10.1126/sciadv.ade4847 · Cited by 43 · see citing works
Hidden Concepts in the History and Philosophy of Origins-of-Life Studies: A Workshop Report
Mariscal, C., Barahona, A., Aubert-Kato, N., Aydinoglu, A. U., Bartlett, S., Cárdenas, M. L., Chandru, K., Cleland, C., Cocanougher, B. T., Comfort, N., et al. (2019) · Origins of Life and Evolution of Biospheres · doi:10.1007/s11084-019-09580-x · Cited by 36 · see citing works
Evidence for corrin biosynthesis in the last universal common ancestor
Modjewski, L. D., Karavaeva, V., Mrnjavac, N., Knopp, M., Martin, W. F., & Sousa, F. L. (2025) · The FEBS Journal · doi:10.1111/febs.17367 · Cited by 15 · see citing works
“Though debates exist about LUCA’s organizational state [145,146], very few studies directly address the physiology of LUCA [47] and numerous studies support possibility 3 [47,147,148], which, given the homologies (Fig.”
Inskeep, W. P., Jay, Z. J., McKay, L. J., & Dlakić, M. (2025) · Nature Communications · doi:10.1038/s41467-024-55079-z · Cited by 9 · see citing works
“…processes of early-evolved thermophiles in sulfidic and low-oxygen filamentous microbial communities Reviewer #1 (Remarks to the Author): This manuscript presents an interesting set of molecular data from microbial communities living in two (similar but also contrasting) hot springs in the YNP.”
Arnoux, J. (2026) · Thèse de doctorat, Université Paris-Saclay / PPanGGOLiN · doi:10.70675/eee354d9zf63dz48ebz9444zd1809f8fb74d
- Authors
- 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., Suzuki, Y., Dudek, N., Relman, D. A., Finstad, K. M., Amundson, R., Thomas, B. C., & Banfield, J. F.
- Affiliations
- University of California, Berkeley (US)
- University of Texas at Austin Marine Science Institute (US)
- Japan Atomic Energy Agency (JP)
- The University of Tokyo (JP)
- University of California, Santa Cruz (US)
- VA Palo Alto Health Care System (US)
- Corresponding author
- Banfield, Jillian F.
- ORCID
- Venue
- Nature Microbiology
- Published
- 2016-04-11
- Volume
- 1
- Issue
- 5
- Pages
- 16048-16048
- ISSN
- 2058-5276 (ISSN-L)
- OpenAlex
- W2315521535
- Cited by
- 2,039
- References
- 6
- Citations by year
- 2026: 122 · 2025: 154 · 2024: 190 · 2023: 176 · 2022: 182 · 2021: 249 · 2020: 279 · 2019: 233 · 2018: 206 · 2017: 183 · 2016: 65
- FWCI
- 119.05
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Nature Microbiology (publishedVersion, cc-by)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (publishedVersion)
- eScholarship (California Digital Library) (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Universitätsbibliographie, Universität Duisburg-Essen (submittedVersion)
- Funders
- National Science Foundation (DEAC02-05CH11231, 1406956)
- U.S. Department of Energy (-AC02-05CH11231, 05CH11231, DE AC02 05CH11231, DOE‐SC10010566, SC10010566, DE-AC02-)
- National Aeronautics and Space Administration (DE-AC02-05CH11231)
- Joint Genome Institute (AC02-05CH11231, DE–AC02–05CH11231)
- Ministry of Economy, Trade and Industry
- Office of Science (DOE-SC10010566, DEAC02–05CH11231, AC02-05CH11231, DE-AC02, 05CH11231)
- U.S. Navy
- Agency for Natural Resources and Energy
- Office of Naval Research (DE-AC02-05CH11231, N00014)
- Division of Environmental Biology
- Biological and Environmental Research (05CH11231, DOE-SC10010566, DE-AC02 − 05CH11231, AC02-05CH11231)
- Lawrence Berkeley National Laboratory (AC02‐05CH11231, DE-AC02-05CH11231, 05CH11231)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protist diversity and phylogeny
- Keywords
- tree of life, microbial diversity, bacterial diversification, archaea, eukaryotes, biogeochemical modeling, metabolic diversity
- MeSH terms
- Archaea, Bacteria, Phylogeny, Ecosystem, Evolution, Molecular, Biodiversity, Eukaryota
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
