An archaeal origin of eukaryotes supports only two primary domains of life

Bacterial evolution

Woese, C. R. (1987) · Microbiological Reviews · doi:10.1128/mr.51.2.221-271.1987 · Cited by 5,042 · see citing works

The Hydrogen Hypothesis for the First Eukaryote

Martin, W., & Müller, M. (1998) · Nature · doi:10.1038/32096 · Cited by 1,282 · see citing works

Resolving difficult phylogenetic questions: Why more sequences are not enough

Philippe, H., Brinkmann, H., Lavrov, D. V., Littlewood, D. T. J., Manuel, M., Wörheide, G., & Baurain, D. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1000602 · Cited by 1,129 · see citing works

Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes.

Iwabe, N., Kuma, K., Hasegawa, M., Osawa, S., & Miyata, T. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.23.9355 · Cited by 902 · see citing works

Estimating the timing of early eukaryotic diversification with multigene molecular clocks

Parfrey, L. W., Lahr, D. J. G., Knoll, A. H., & Katz, L. A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1110633108 · Cited by 899 · see citing works

Eukaryotic evolution, changes and challenges

Embley, T. M., & Martin, W. (2006) · Nature · doi:10.1038/nature04546 · Cited by 867 · see citing works

Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model

Lartillot, N., Brinkmann, H., & Philippe, H. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-s1-s4 · Cited by 705 · see citing works

Evidence from fluid inclusions for microbial methanogenesis in the early Archaean era

Ueno, Y., Yamada, K., Yoshida, N., Maruyama, S., & Isozaki, Y. (2006) · Nature · doi:10.1038/nature04584 · Cited by 572 · see citing works

Modeling compositional heterogeneity

Foster, P. G. (2004) · Systematic Biology · doi:10.1080/10635150490445779 · Cited by 474 · see citing works

The early evolution of lipid membranes and the three domains of life

Lombard, J., López-García, P., & Moreira, D. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2815 · Cited by 320 · see citing works

Controls on development and diversity of Early Archean stromatolites

Allwood, A. C., Grotzinger, J. P., Knoll, A. H., Burch, I. W., Anderson, M. S., Coleman, M. L., & Kanik, I. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0903323106 · Cited by 305 · see citing works

Mathematical Elegance with Biochemical Realism: The Covarion Model of Molecular Evolution

Penny, D., McComish, B. J., Charleston, M. A., & Hendy, M. D. (2001) · Journal of Molecular Evolution · doi:10.1007/s002390010258 · Cited by 287 · see citing works

Mapping 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

Time for a change

Pace, N. R. (2006) · Nature · doi:10.1038/441289a · Cited by 276 · see citing works

The Rooting of the Universal Tree of Life Is Not Reliable

Philippe, H., & Forterre, P. (1999) · Journal of Molecular Evolution · doi:10.1007/pl00006573 · Cited by 267 · see citing works

Evolution of diverse cell division and vesicle formation systems in Archaea

Makarova, K. S., Yutin, N., Bell, S. D., & Koonin, E. V. (2010) · Nature Reviews Microbiology · doi:10.1038/nrmicro2406 · Cited by 228 · see citing works

Genome Networks Root the Tree of Life between Prokaryotic Domains

Dagan, T., Roettger, M., Bryant, D., & Martin, W. (2010) · Genome Biology and Evolution · doi:10.1093/gbe/evq025 · Cited by 87 · 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

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

Algae-bacteria interactions: Evolution, ecology and emerging applications

Ramanan, R., Kim, B.-H., Cho, D.-H., Oh, H.-M., & Kim, H.-S. (2016) · Biotechnology Advances · doi:10.1016/j.biotechadv.2015.12.003 · Cited by 1,301 · see citing works

Asgard archaea illuminate the origin of eukaryotic cellular complexity

Zaremba-Niedzwiedzka, K., Caceres, E. F., Saw, J. H., Bäckström, D., Juzokaite, L., Vancaester, E., Seitz, K. W., Anantharaman, K., Starnawski, P., Kjeldsen, K. U., et al. (2017) · Nature · doi:10.1038/nature21031 · Cited by 1,226 · see citing works

The physiology and habitat of the last universal common ancestor

Weiss, M. C., Sousa, F. L., Mrnjavac, N., Neukirchen, S., Roettger, M., Nelson-Sathi, S., & Martin, W. F. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.116 · Cited by 1,049 · see citing works

Endosymbiosis and Eukaryotic Cell Evolution

Archibald, J. M. (2015) · Current Biology · doi:10.1016/j.cub.2015.07.055 · Cited by 654 · see citing works

Endosymbiotic theories for eukaryote origin

Martin, W. F., Garg, S., & Zimorski, V. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2014.0330 · Cited by 583 · see citing works

Integrated genomic and fossil evidence illuminates life’s early evolution and eukaryote origin

Betts, H. C., Puttick, M. N., Clark, J. W., Williams, T. A., Donoghue, P. C. J., & Pisani, D. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0644-x · Cited by 437 · see citing works

Endosymbiotic theory for organelle origins

Zimorski, V., Ku, C., Martin, W. F., & Gould, S. B. (2014) · Current Opinion in Microbiology · doi:10.1016/j.mib.2014.09.008 · Cited by 453 · see citing works

Archaea and the Human Gut: New Beginning of an Old Story

Gaci, N., Borrel, G., Tottey, W., O’Toole, P. W., & Brugère, J.-F. (2014) · World Journal of Gastroenterology · doi:10.3748/wjg.v20.i43.16062 · Cited by 422 · see citing works

Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life

Spang, A., Caceres, E. F., & Ettema, T. J. G. (2017) · Science · doi:10.1126/science.aaf3883 · Cited by 346 · 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

Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism

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

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

Biosynthesis of polyamines and polyamine-containing molecules

Michael, A. J. (2016) · Biochemical Journal · doi:10.1042/bcj20160185 · Cited by 180 · see citing works

An origin-of-life reactor to simulate alkaline hydrothermal vents

Herschy, B., Whicher, A., Camprubi, E., Watson, C., Dartnell, L., Ward, J., Evans, J. R. G., & Lane, N. (2014) · Journal of Molecular Evolution · doi:10.1007/s00239-014-9658-4 · Cited by 194 · see citing works

Fundamental issues related to the origin of melatonin and melatonin isomers during evolution: relation to their biological functions.

Tan, D.-X., Zheng, X., Kong, J., Manchester, L., Hardeland, R., Kim, S., Xu, X., & Reiter, R. (2014) · International Journal of Molecular Sciences · doi:10.3390/ijms150915858 · Cited by 188 · see citing works

A Bioenergetic Basis for Membrane Divergence in Archaea and Bacteria

Sojo, V., Pomiankowski, A., & Lane, N. (2014) · PLoS Biology · doi:10.1371/journal.pbio.1001926 · Cited by 154 · 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

Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier?

Koonin, E. V. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2014.0333 · Cited by 145 · see citing works

Constraining the Time Interval for the Origin of Life on Earth

Pearce, B. K. D., Tupper, A. S., Pudritz, R. E., & Higgs, P. G. (2018) · Astrobiology · doi:10.1089/ast.2017.1674 · Cited by 140 · see citing works

Early Microbial Evolution: The Age of Anaerobes

Martin, W. F., & Sousa, F. L. (2016) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a018127 · Cited by 129 · see citing works

The energy expansions of evolution

Judson, O. P. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0138 · Cited by 118 · see citing works

Proton gradients at the origin of life

Lane, N. (2017) · BioEssays · doi:10.1002/bies.201600217 · Cited by 115 · see citing works

Biochemical fossils of the ancient transition from geoenergetics to bioenergetics in prokaryotic one carbon compound metabolism

Sousa, F. L., & Martin, W. F. (2014) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/j.bbabio.2014.02.001 · Cited by 100 · see citing works

Human TLR8 senses UR/URR motifs in bacterial and mitochondrial RNA

Krüger, A., Oldenburg, M., Chebrolu, C., Beisser, D., Kolter, J., Sigmund, A. M., Steinmann, J., Schäfer, S., Hochrein, H., Rahmann, S., et al. (2015) · The EMBO Reports · doi:10.15252/embr.201540861 · Cited by 99 · see citing works

The Emergence of Life

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

Evolution: Two Domains of Life or Three?

Doolittle, W. F. (2020) · Current Biology · doi:10.1016/j.cub.2020.01.010 · Cited by 75 · see citing works

New substitution models for rooting phylogenetic trees

Williams, T. A., Heaps, S. E., Cherlin, S., Nye, T. M. W., Boys, R. J., & Embley, T. M. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2014.0336 · Cited by 61 · see citing works

Scalable empirical mixture models that account for across-site compositional heterogeneity

Schrempf, D., Lartillot, N., & Szöllősi, G. (2019) · doi:10.1101/794263 · Cited by 61 · see citing works

Archaeal Histone Contributions to the Origin of Eukaryotes

Brunk, C. F., & Martin, W. F. (2019) · Trends in Microbiology · doi:10.1016/j.tim.2019.04.002 · Cited by 55 · see citing works

Late Mitochondrial Origin Is an Artifact

Martin, W. F., Roettger, M., Ku, C., Garg, S. G., Nelson-Sathi, S., & Landan, G. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx027 · Cited by 42 · see citing works

Probing the Role of Chirality in Phospholipid Membranes

Martin, H. S., Podolsky, K. A., & Devaraj, N. K. (2021) · ChemBioChem · doi:10.1002/cbic.202100232 · Cited by 36 · see citing works

Late Proterozoic Transitions in Climate, Oxygen, and Tectonics, and the Rise of Complex Life

Planavsky, N. J., Tarhan, L. G., Bellefroid, E. J., Evans, D. A. D., Reinhard, C. T., Love, G. D., & Lyons, T. W. (2015) · The Paleontological Society Papers · doi:10.1017/s1089332600002965 · Cited by 32 · see citing works

A structural phylogenetic tree of Rad52 and its annealase superfamily

Al-Fatlawi, A., Hossen, M. B., de Paula Lopes, S., Stewart, A. F., & Schroeder, M. (2025) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2024.12.012 · Cited by 3 · see citing works