The origin and early evolution of eukaryotes in the light of phylogenomics
Open accessAbstract
Phylogenomics of eukaryote supergroups suggest a highly complex last common ancestor of eukaryotes and a key role of mitochondrial endosymbiosis in the origin of eukaryotes.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
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?
A major event in the evolution of eukaryotes was when organisms capable of engulfing other organisms acquired mitochondria and chloroplasts.
“Complexity can also occur within cells; a major event in the evolution of eukaryotes was when organisms capable of engulfing other organisms acquired mitochondria (permitting aerobic respiration for energy) and chloroplasts (permitting oxygenic photosynthesis) (Koonin, 2010).”
From The Astrobiology Primer v2.0 (2016) · cites this paper as Koonin, 2010
The Eukaryotes and The archaeal and bacterial roots of eukaryotes sections describe mitochondria as widespread in eukaryotes and plastids as an additional organelle in particular lineages. But Eukaryogenesis: where did the eukaryotes come from? rejects the argument that phagocytosis was necessary for mitochondrial acquisition, while The supergroups of eukaryotes and the root of the eukaryotic evolutionary tree places plastid acquisition on the Plantae lineage. The source therefore supports organelle acquisition, not the claim that organisms already capable of engulfing others acquired both as one major event. (LLM, conf=0.88)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302 · see citing works
Hershko, A., & Ciechanover, A. (1998) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.67.1.425 · Cited by 8,840 · see citing works
The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists
Adl, S., Simpson, A., Farmer, M. A., Andersen, R., Anderson, O., Barta, J. R., Bowser, S., Brugerolle, G., Fensome, R., Fredericq, S., et al. (2005) · Journal of Eukaryotic Microbiology · doi:10.1111/j.1550-7408.2005.00053.x · Cited by 1,749 · see citing works
Gray, M. W., Burger, G., & Lang, B. F. (1999) · Science · doi:10.1126/science.283.5407.1476 · Cited by 1,710 · see citing works
A kingdom-level phylogeny of eukaryotes based on combined protein data.
Baldauf, S., Roger, A., Wenk-Siefert, I., & Doolittle, W. (2000) · Science · doi:10.1126/science.290.5493.972 · Cited by 1,243 · see citing works
Phylogenomics and the reconstruction of the tree of life
Delsuc, F., Brinkmann, H., & Philippe, H. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1603 · Cited by 1,228 · see citing works
Protein Tyrosine Kinase Structure and Function
Hubbard, S. R., & Till, J. H. (2000) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.69.1.373 · Cited by 1,176 · see citing works
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
Koonin, E. V., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Krylov, D. M., Makarova, K. S., Mazumder, R., Mekhedov, S., Nikolskaya, A. N., Rao, B. S., et al. (2004) · Genome biology · doi:10.1186/gb-2004-5-2-r7 · Cited by 1,092 · see citing works
Self-citationThe Age of Crosstalk: Phosphorylation, Ubiquitination, and Beyond
Hunter, T. R. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.11.019 · Cited by 946 · 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
Ubiquitin-binding domains — from structures to functions
Đikić, I., Wakatsuki, S., & Walters, K. J. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2767 · Cited by 859 · see citing works
Ubiquitin-mediated proteolysis: biological regulation via destruction
Ciechanover, A. J., Orian, A., & Schwartz, A. L. (2000) · BioEssays · doi:10.1002/(sici)1521-1878(200005)22:5 · Cited by 845 · see citing works
Specificity in Signal Transduction
Pawson, T. J. (2004) · Cell · doi:10.1016/s0092-8674(03)01077-8 · Cited by 816 · see citing works
Origin and function of ubiquitin-like proteins
Hochstrasser, M. (2009) · Nature · doi:10.1038/nature07958 · Cited by 784 · see citing works
Baldauf, S. L. (2003) · Science · doi:10.1126/science.1085544 · Cited by 782 · see citing works
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world
Koonin, E., & Wolf, Y. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn668 · Cited by 722 · see citing works
Self-citationSpecialization and evolution of endogenous small RNA pathways
Chapman, E. J., & Carrington, J. C. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2179 · Cited by 688 · see citing works
Rare genomic changes as a tool for phylogenetics
Rokas, A., & Holland, P. W. H. (2000) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(00)01967-4 · Cited by 688 · see citing works
The evolution of spliceosomal introns: patterns, puzzles and progress
Roy, S. W., & Gilbert, W. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1807 · Cited by 642 · see citing works
The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological DiversityPreprint
Galagan, J. E., Nusbaum, C., Roy, A., Endrizzi, M. G., Macdonald, P., FitzHugh, W., Calvo, S., Engels, R., Smirnov, S., Atnoor, D., et al. (2002) · Genome Research · doi:10.1101/gr.223902 · Cited by 625 · see citing works
The Eukaryotic Genome as an RNA Machine
Amaral, P., Dinger, M. E., Mercer, T. R., & Mattick, J. S. (2008) · Science · doi:10.1126/science.1155472 · Cited by 621 · see citing works
Doolittle, W. F. (1998) · Trends in Genetics · doi:10.1016/s0168-9525(98)01494-2 · Cited by 600 · see citing works
Keeling, P. J., Burger, G., Durnford, D. G., Lang, B. F., Lee, R. W., Pearlman, R. E., Roger, A. J., & Gray, M. W. (2005) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2005.09.005 · Cited by 579 · see citing works
Conserved domains in DNA repair proteins and evolution of repair systems
Aravind, L. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.5.1223 · Cited by 561 · see citing works
Origins and evolution of eukaryotic RNA interference
Shabalina, S. A., & Koonin, E. V. (2008) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2008.06.005 · Cited by 559 · see citing works
Self-citationThe ring of life provides evidence for a genome fusion origin of eukaryotes
Rivera, M. C., & Lake, J. A. (2004) · Nature · doi:10.1038/nature02848 · Cited by 546 · see citing works
Comparative genomics and evolution of proteins involved in RNA metabolism
Anantharaman, V. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.7.1427 · Cited by 541 · see citing works
Introns and the origin of nucleus–cytosol compartmentalization
Martin, W. F., & Koonin, E. V. (2006) · Nature · doi:10.1038/nature04531 · Cited by 497 · see citing works
Self-citationHampl, V., Hug, L. A., Leigh, J., Dacks, J. B., Lang, B. F., Simpson, A. G. B., & Roger, A. J. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0807880106 · Cited by 484 · see citing works
The Closest BLAST Hit Is Often Not the Nearest Neighbor
Koski, L. B., & Golding, G. B. (2001) · Journal of Molecular Evolution · doi:10.1007/s002390010184 · Cited by 466 · see citing works
The origin and early evolution of mitochondria.
Gray, M. W., Burger, G., & Lang, B. F. (2001) · Genome biology · doi:10.1186/gb-2001-2-6-reviews1018 · Cited by 460 · see citing works
The Genome of Naegleria gruberi Illuminates Early Eukaryotic Versatility
Fritz‐Laylin, L. K., Prochnik, S. E., Ginger, M. L., Dacks, J. B., Carpenter, M. L., Field, M. C., Kuo, A., Paredez, A. R., Chapman, J., Pham, J. K., et al. (2010) · Cell · doi:10.1016/j.cell.2010.01.032 · Cited by 460 · see citing works
The Puzzle of Plastid Evolution
Archibald, J. M. (2009) · Current Biology · doi:10.1016/j.cub.2008.11.067 · Cited by 451 · see citing works
Myosin domain evolution and the primary divergence of eukaryotes
Richards, T. A., & Cavalier‐Smith, T. (2005) · Nature · doi:10.1038/nature03949 · Cited by 432 · see citing works
The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs
Jacquier, A. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2683 · Cited by 421 · see citing works
Kinomics: methods for deciphering the kinome
Johnson, S. A., & Hunter, T. R. (2004) · Nature Methods · doi:10.1038/nmeth731 · Cited by 420 · see citing works
Phylogenomics Reshuffles the Eukaryotic Supergroups
Burki, F., Shalchian‐Tabrizi, K., Minge, M. A., Skjæveland, Å., Nikolaev, S. I., Jakobsen, K. S., & Pawlowski, J. W. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000790 · Cited by 410 · see citing works
Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution
Dagan, T., Artzy-Randrup, Y., & Martin, W. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0800679105 · Cited by 409 · see citing works
The archaebacterial origin of eukaryotes
Cox, C. J., Foster, P. G., Hirt, R. P., Harris, S. R., & Embley, T. M. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0810647105 · Cited by 381 · see citing works
Animal Evolution and the Molecular Signature of Radiations Compressed in Time
Rokas, A., Krüger, D., & Carroll, S. B. (2005) · Science · doi:10.1126/science.1116759 · Cited by 371 · see citing works
Estimating the size of the bacterial pan-genome
Lapierre, P., & Gogarten, J. P. (2009) · Trends in Genetics · doi:10.1016/j.tig.2008.12.004 · Cited by 354 · see citing works
Mealybug β-proteobacterial endosymbionts contain γ-proteobacterial symbionts
von Dohlen, C. D., Kohler, S., Alsop, S. T., & McManus, W. R. (2001) · Nature · doi:10.1038/35086563 · Cited by 353 · see citing works
A unique cell division machinery in the Archaea
Lindås, A., Karlsson, E. A., Lindgren, M. T., Ettema, T. J. G., & Bernander, R. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0809467105 · Cited by 345 · see citing works
The origin of the eukaryotic cell: A genomic investigation
Hartman, H., & Fedorov, A. N. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.032658599 · Cited by 336 · see citing works
Rooting the Eukaryote Tree by Using a Derived Gene Fusion
Stechmann, A., & Cavalier‐Smith, T. (2002) · Science · doi:10.1126/science.1071196 · Cited by 335 · see citing works
Esser, C. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh160 · Cited by 324 · see citing works
Rokas, A., & Carroll, S. B. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040352 · Cited by 315 · see citing works
Ufd2, a Novel Autoantigen in Scleroderma, Regulates Sister Chromatid Separation
Spinette, S., Christoph Lengauer, C., Mahoney, J. A., Jallepalli, P. V., Wang, Z., Casciola-Rosen, L., & Rosen, A. (2004) · Cell Cycle · doi:10.4161/cc.3.12.1345 · Cited by 309 · see citing works
Makarova, K. S., Wolf, Y. I., John van der, O. O. S. T., & Koonin, E. V. (2009) · Biology Direct · doi:10.1186/1745-6150-4-29 · Cited by 305 · see citing works
Self-citationComparative Genomics, Evolution and Origins of the Nuclear Envelope and Nuclear Pore Complex
Mans, B., Anantharaman, V., Aravind, L., & Koonin, E. V. (2004) · Cell Cycle · doi:10.4161/cc.3.12.1316 · Cited by 304 · see citing works
Self-citationA korarchaeal genome reveals insights into the evolution of the Archaea
Elkins, J. G., Podar, M., Graham, D. E., Makarova, K. S., Wolf, Y., Randau, L., Hedlund, B. P., Brochier-Armanet, C., Kunin, V., Anderson, I., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0801980105 · Cited by 296 · see citing works
Self-citationReconstructing Early Events in Eukaryotic Evolution
Roger, A. J. (1999) · The American Naturalist · doi:10.1086/303290 · Cited by 283 · see citing works
Koonin, E. V. (2006) · Biology Direct · doi:10.1186/1745-6150-1-22 · Cited by 281 · see citing works
Self-citationPhosphoesterase domains associated with DNA polymerases of diverse origins
Aravind, L., & Koonin, E. V. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.16.3746 · Cited by 266 · see citing works
Self-citationIyer, L. M., Anantharaman, V., Wolf, M. Y., & Aravind, L. (2007) · International Journal for Parasitology · doi:10.1016/j.ijpara.2007.07.018 · Cited by 266 · see citing works
Phylogenomics reveals a new ‘megagroup’ including most photosynthetic eukaryotes
Burki, F., Shalchian‐Tabrizi, K., & Pawlowski, J. W. (2008) · Biology Letters · doi:10.1098/rsbl.2008.0224 · Cited by 256 · see citing works
Koonin, E. V., Wolf, Y. I., & Aravind, L. (2001) · Genome Research · doi:10.1101/gr.162001 · Cited by 248 · see citing works
Self-citationThe origins of phagocytosis and eukaryogenesis
Yutin, N., Wolf, M. Y., Wolf, Y. I., & Koonin, E. V. (2009) · Biology Direct · doi:10.1186/1745-6150-4-9 · Cited by 247 · see citing works
Self-citationFilée, J., Forterre, P., Sen-Lin, T., & Laurent, J. (2002) · Journal of Molecular Evolution · doi:10.1007/s00239-001-0078-x · Cited by 247 · see citing works
Complex Spliceosomal Organization Ancestral to Extant Eukaryotes
Collins, L., & Penny, D. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi091 · Cited by 240 · see citing works
Hackett, J. D., Yoon, H. S., Li, S., Reyes‐Prieto, A., Rümmele, S. E., & Bhattacharya, D. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm089 · Cited by 233 · see citing works
Genomics and the Irreducible Nature of Eukaryote Cells
Kurland, C. G., Collins, L. J., & Penny, D. (2006) · Science · doi:10.1126/science.1121674 · Cited by 220 · see citing works
Evolutionary origins of metabolic compartmentalization in eukaryotes
Martin, W. F. (2010) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2009.0252 · Cited by 204 · see citing works
Vaughan, S., Wickstead, B., Gull, K., & Addinall, S. G. (2004) · Journal of Molecular Evolution · doi:10.1007/s00239-003-2523-5 · Cited by 202 · see citing works
Moreira, D., von der Heyden, S., Bass, D., López‐García, P., Chao, E. E. Y., & Cavalier‐Smith, T. (2006) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2006.11.001 · Cited by 201 · see citing works
On the origin of intracellular compartmentation and organized metabolic systems
Ovádi, J., & Saks, V. A. (2003) · Molecular and Cellular Biochemistry · doi:10.1023/b:mcbi.0000009855.14648.2c · Cited by 194 · see citing works
Biochemical principles of small RNA pathways.
Liu, Q., & Paroo, Z. (2010) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.052208.151733 · Cited by 191 · see citing works
Supertrees Disentangle the Chimerical Origin of Eukaryotic Genomes
Pisani, D., Cotton, J. A., & McInerney, J. O. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm095 · Cited by 187 · see citing works
Ubiquitin-like small archaeal modifier proteins (SAMPs) in Haloferax volcanii
Humbard, M. A., Miranda, H. V., Lim, J., Krause, D. J., Pritz, J. R., Zhou, G., Chen, S., Wells, L., & Maupin-furlow, J. A. (2010) · Nature · doi:10.1038/nature08659 · Cited by 185 · see citing works
The Deep Archaeal Roots of Eukaryotes
Yutin, N., Makarova, K. S., Mekhedov, S., Wolf, Y. I., & Koonin, E. V. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn108 · Cited by 181 · see citing works
Self-citationAncestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell
Makarova, K. S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki775 · Cited by 181 · see citing works
Roger, A. J., & Hug, L. A. (2006) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2006.1845 · Cited by 180 · see citing works
Three distinct modes of intron dynamics in the evolution of eukaryotesPreprint
Carmel, L., Wolf, Y. I., Rogozin, I. B., & Koonin, E. V. (2007) · Genome Research · doi:10.1101/gr.6438607 · Cited by 178 · see citing works
Self-citationvan der Giezen, M., & Tovar, J. (2005) · EMBO Reports · doi:10.1038/sj.embor.7400440 · Cited by 177 · see citing works
The root of the eukaryote tree pinpointed
Stechmann, A., & Cavalier‐Smith, T. (2003) · Current Biology · doi:10.1016/s0960-9822(03)00602-x · Cited by 176 · see citing works
Hydrogenosomes and Mitosomes: Conservation and Evolution of Functions 1
van der Giezen, M. (2009) · Journal of Eukaryotic Microbiology · doi:10.1111/j.1550-7408.2009.00407.x · Cited by 165 · see citing works
Evaluating Support for the Current Classification of Eukaryotic Diversity
Parfrey, L. W., Barbero, E., Lasser, E. C., Dunthorn, M., Bhattacharya, D., Patterson, D. J., & Katz, L. A. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020220 · Cited by 165 · see citing works
Aravind, L., Iyer, L. M., & Anantharaman, V. (2003) · Genome biology · doi:10.1186/gb-2003-4-10-r64 · Cited by 164 · see citing works
Diversity and reductive evolution of mitochondria among microbial eukaryotes
Hjort, K., Goldberg, A., Tsaousis, A. D., Hirt, R. P., & Embley, T. (2010) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2009.0224 · Cited by 163 · see citing works
Broadly sampled multigene trees of eukaryotes
Yoon, H. S., Grant, J. R., Tekle, Y. I., Wu, M., Chaon, B., Cole, J. C., Logsdon, J. M., Jr., Patterson, D. J., Bhattacharya, D., & Katz, L. A. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-14 · Cited by 159 · see citing works
Thao, M. L., Gullan, P. J., & Baumann, P. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.7.3190-3197.2002 · Cited by 144 · see citing works
Evolution of cytomotive filaments: The cytoskeleton from prokaryotes to eukaryotes
Löwe, J., & Amos, L. (2008) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2008.08.010 · Cited by 135 · see citing works
Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure
Korkhin, Y., Ünligil, U. M., Littlefield, O., Nelson, P. J., Stuart, D. I., Sigler, P. B., Bell, S. D., & Abrescia, N. G. A. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000102 · Cited by 134 · see citing works
Csürös, M., & Miklos, I. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp123 · Cited by 133 · see citing works
Keeling, P. J., & McFadden, G. I. (1998) · Trends in Microbiology · doi:10.1016/s0966-842x(97)01185-2 · Cited by 127 · see citing works
Field, M. C., & Dacks, J. B. (2009) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2008.12.004 · Cited by 122 · see citing works
The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods
Foster, P. G., Cox, C. J., & Embley, T. M. (2009) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2009.0034 · Cited by 120 · see citing works
Guigas, G., Kalla, C., & Weiß, M. (2007) · FEBS Letters · doi:10.1016/j.febslet.2007.09.054 · Cited by 118 · see citing works
Reconstructing/Deconstructing the Earliest Eukaryotes
Dacks, J. B., & Doolittle, W. F. (2001) · Cell · doi:10.1016/s0092-8674(01)00584-0 · Cited by 118 · see citing works
Structure and function of the GINS complex, a key component of the eukaryotic replisome
MacNeill, S. A. (2010) · Biochemical Journal · doi:10.1042/bj20091531 · Cited by 117 · see citing works
Shifting Players and Paradigms in Cell-Specific Transcription
D’Alessio, J. A., Wright, K. J., & Tjian, R. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.12.011 · Cited by 115 · see citing works
The Biological Big Bang model for the major transitions in evolution
Koonin, E. V. (2007) · Biology Direct · doi:10.1186/1745-6150-2-21 · Cited by 115 · see citing works
Self-citationThe new phylogeny of eukaryotes
Philippe, H., Germot, A., & Moreira, D. (2000) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(00)00137-4 · Cited by 113 · see citing works
Tahirov, T. H., Makarova, K. S., Rogozin, I. B., Pavlov, Y. I., & Koonin, E. V. (2009) · Biology Direct · doi:10.1186/1745-6150-4-11 · Cited by 110 · see citing works
Self-citationCritical Analysis of Eukaryotic Phylogeny: A Case Study Based on the HSP70 Family
Germot, A., & Philippe, H. (1999) · Journal of Eukaryotic Microbiology · doi:10.1111/j.1550-7408.1999.tb04594.x · Cited by 105 · see citing works
Predation between prokaryotes and the origin of eukaryotes
Davidov, Y., & Jurkevitch, É. (2009) · BioEssays · doi:10.1002/bies.200900018 · Cited by 99 · see citing works
Poole, A. M., & Penny, D. (2007) · Nature · doi:10.1038/447913a · Cited by 95 · see citing works
The origin of mitochondria in light of a fluid prokaryotic chromosome model
Esser, C., Martin, W., & Dagan, T. (2007) · Biology Letters · doi:10.1098/rsbl.2006.0582 · Cited by 92 · see citing works
Evolutionary position of breviate amoebae and the primary eukaryote divergence
Minge, M. A., Silberman, J. D., Orr, R. J. S., Cavalier‐Smith, T., Shalchian‐Tabrizi, K., Burki, F., Skjæveland, Å., & Jakobsen, K. S. (2008) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2008.1358 · Cited by 91 · see citing works
Transcription and Translation are Coupled in Archaea
French, S. L., Santangelo, T. J., Beyer, A. L., & Reeve, J. N. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm007 · Cited by 91 · see citing works
Comparative genomics and structural biology of the molecular innovations of eukaryotes
Aravind, L., Iyer, L. M., & Koonin, E. V. (2006) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2006.04.006 · Cited by 90 · see citing works
Self-citationBapteste, E., Charlebois, R. L., MacLeod, D., & Brochier, C. (2005) · Genome Biology · doi:10.1186/gb-2005-6-10-r85 · Cited by 89 · see citing works
Rogozin, I. B., Basu, M. K., Csürös, M., & Koonin, E. V. (2009) · Genome Biology and Evolution · doi:10.1093/gbe/evp011 · Cited by 88 · see citing works
Self-citationKinome signaling through regulated protein–protein interactions in normal and cancer cells
Pawson, T. J., & Kofler, M. (2009) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2009.02.005 · Cited by 87 · see citing works
Evolution of specificity in the eukaryotic endomembrane system
Dacks, J. B., Peden, A. A., & Field, M. C. (2008) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2008.08.041 · Cited by 86 · see citing works
The Incredible Expanding Ancestor of Eukaryotes
Koonin, E. V. (2010) · Cell · doi:10.1016/j.cell.2010.02.022 · Cited by 83 · see citing works
Self-citationGenomes as documents of evolutionary history
Boussau, B., & Daubin, V. (2009) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2009.09.007 · Cited by 81 · see citing works
Organization of Mammalian Cytoplasm
Hudder, A., Nathanson, L., & Deutscher, M. P. (2003) · Molecular and Cellular Biology · doi:10.1128/mcb.23.24.9318-9326.2003 · Cited by 77 · see citing works
Interspecific evolution: microbial symbiosis, endosymbiosis and gene transfer
Hoffmeister, M., & Martin, W. F. (2003) · Environmental Microbiology · doi:10.1046/j.1462-2920.2003.00454.x · Cited by 75 · see citing works
The Diversity Of Eukaryotes And The Root Of The Eukaryotic Tree
Brinkmann, H., & Philippe, H. (2008) · Advances in experimental medicine and biology · doi:10.1007/978-0-387-74021-8_2 · Cited by 65 · see citing works
ROY, S. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.07.002 · Cited by 62 · see citing works
Ancient ESCRTs and the evolution of binary fission
Samson, R. Y., & Bell, S. D. (2009) · Trends in Microbiology · doi:10.1016/j.tim.2009.08.003 · Cited by 60 · see citing works
Cell division and the ESCRT complex
Ettema, T. J. G., & Bernander, R. (2009) · Communicative & Integrative Biology · doi:10.4161/cib.7523 · Cited by 58 · see citing works
Horizontal gene transfer: the path to maturity
Koonin, E. V. (2003) · Molecular Microbiology · doi:10.1046/j.1365-2958.2003.03808.x · Cited by 57 · see citing works
Self-citationProteasomes in the archaea from structure to function
Maupin-furlow, J. A. (2000) · Frontiers in bioscience · doi:10.2741/furlow · Cited by 54 · see citing works
Csürös, M., Rogozin, I. B., & Koonin, E. V. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn039 · Cited by 53 · see citing works
Self-citationThe oligomerization and ligand‐binding properties of Sm‐like archaeal proteins (SmAPs)
Mura, C., Kozhukhovsky, A., Gingery, M., Phillips, M., & Eisenberg, D. S. (2003) · Protein Science · doi:10.1110/ps.0224703 · Cited by 53 · see citing works
Early evolution comes full circle
Martin, W. F., & Embley, T. M. (2004) · Nature · doi:10.1038/431134a · Cited by 52 · see citing works
Archaeal histones: structures, stability and DNA binding
Reeve, J. N., Bailey, K. A., Li, W.-T., Marc, F., Sandman, K., & Soares, D. J. (2004) · Biochemical Society Transactions · doi:10.1042/bst0320227 · Cited by 52 · see citing works
Evolution of transcriptional control in mammals
Wilson, M. D., & Odom, D. T. (2009) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2009.10.003 · Cited by 51 · see citing works
Vishwanath, P., Favaretto, P., Hartman, H., Mohr, S. C., & Smith, T. F. (2004) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2004.07.003 · Cited by 49 · see citing works
Sizing up the genomic footprint of endosymbiosis
Eliáš, M., & Archibald, J. M. (2009) · BioEssays · doi:10.1002/bies.200900117 · Cited by 48 · see citing works
A positive definition of prokaryotes
Martin, W. F., & Koonin, E. V. (2006) · Nature · doi:10.1038/442868c · Cited by 48 · see citing works
Self-citationAncestral relationships of the major eukaryotic lineages.
Sogin, M. L., Morrison, H. G., Hinkle, G., & Silberman, J. D. (1996) · PubMed · Cited by 48 · see citing works
Origin of Eukaryotic Endomembranes: A Critical Evaluation of Different Model Scenarios
Jékely, G. (2008) · Advances in experimental medicine and biology · doi:10.1007/978-0-387-74021-8_3 · Cited by 47 · see citing works
The archaebacterial origin of eukaryotes
Embley, T. M. (2009) · Comparative Biochemistry and Physiology Part A Molecular & Integrative Physiology · doi:10.1016/j.cbpa.2009.04.498 · Cited by 47 · see citing works
Koonin, E. V., Makarova, K. S., & Elkins, J. G. (2007) · Biology Direct · doi:10.1186/1745-6150-2-38 · Cited by 41 · see citing works
Self-citationBlombach, F., Makarova, K. S., Marrero, J., Siebers, B., Koonin, E. V., & John van der, O. O. S. T. (2009) · Biology Direct · doi:10.1186/1745-6150-4-39 · Cited by 36 · see citing works
Self-citationDeep Questions in the Tree of Life
Keeling, P. J. (2007) · Science · doi:10.1126/science.1149593 · Cited by 33 · see citing works
Venâncio, T. M., Balaji, S., Iyer, L. M., & Aravind, L. (2009) · Genome biology · doi:10.1186/gb-2009-10-3-r33 · Cited by 33 · see citing works
Podar, M., Wall, M. A., Makarova, K. S., & Koonin, E. V. (2008) · Biology Direct · doi:10.1186/1745-6150-3-2 · Cited by 28 · see citing works
Self-citationMartin, W. F., Dagan, T., Koonin, E. V., DiPippo, J. L., Gogarten, J. P., & Lake, J. A. (2007) · Science · doi:10.1126/science.316.5824.542c · Cited by 26 · see citing works
Self-citationDaniels, J., Kelly, S. L., Wickstead, B., & Keith Gull, B. (2009) · Biology Direct · doi:10.1186/1745-6150-4-24 · Cited by 23 · see citing works
Lessons from structural and biochemical studies on the archaeal exosome
Hartung, S., & Hopfner, K. (2009) · Biochemical Society Transactions · doi:10.1042/bst0370083 · Cited by 20 · see citing works
Evaluating Support for the Current Classification of Eukaryotic Diversity
Parfrey, L. W., Barbero, E., Lasser, E. C., Dunthorn, M. S., Bhattacharya, D., Patterson, D. J., & Katz, L. A. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0020220.eor · Cited by 19 · see citing works
Comprehensive analysis of the origin of eukaryotic genomes
Saruhashi, S., Hamada, K., Miyata, D., Horiike, T., & Shinozawa, T. (2008) · Genes & Genetic Systems · doi:10.1266/ggs.83.285 · Cited by 17 · see citing works
Approaches to defining the ancestral eukaryotic protein complexome
Ceulemans, H., Beke, L., & Bollen, M. (2006) · BioEssays · doi:10.1002/bies.20373 · Cited by 10 · see citing works
Flagged first, then by citations
4 of the 141 references couldn’t be matched to a known paper.
Research works printed but not linked: 1
- Entrez Genome http://www.ncbi.nlm.nih.gov/sites/genome
Cited by
Sorted by citations
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
Biochemistry and Evolution of Anaerobic Energy Metabolism in Eukaryotes
Müller, M., Mentel, M., van Hellemond, J. J., Henze, K., Woehle, C., Gould, S. B., Yu, R.-Y., van der Giezen, M., Tielens, A. G. M., & Martin, W. F. (2012) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.05024-11 · Cited by 838 · 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
Gray, M. W. (2012) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a011403 · Cited by 639 · see citing works
Archaea and the origin of eukaryotes
Eme, L., Spang, A., Lombard, J., Stairs, C. W., & Ettema, T. J. G. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.133 · Cited by 549 · see citing works
The dynamic roles of intracellular lipid droplets: from archaea to mammals
Murphy, D. J. (2011) · PROTOPLASMA · doi:10.1007/s00709-011-0329-7 · Cited by 392 · see citing works
Evolution and functional cross‐talk of protein post‐translational modifications
Beltrão, P., Bork, P., Krogan, N. J., & van Noort, V. (2013) · Molecular Systems Biology · doi:10.1002/msb.201304521 · Cited by 379 · see citing works
The archaeal ‘TACK’ superphylum and the origin of eukaryotes
Guy, L., & Ettema, T. J. G. (2011) · Trends in Microbiology · doi:10.1016/j.tim.2011.09.002 · Cited by 344 · see citing works
The evolution of the cytoskeleton
Wickstead, B., & Keith Gull, B. (2011) · The Journal of Cell Biology · doi:10.1083/jcb.201102065 · Cited by 318 · see citing works
Genome reduction as the dominant mode of evolution
Wolf, Y. I., & Koonin, E. V. (2013) · BioEssays · doi:10.1002/bies.201300037 · Cited by 312 · see citing works
Self-citationSex is a ubiquitous, ancient, and inherent attribute of eukaryotic life
Speijer, D., Lukeš, J., & Eliáš, M. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1501725112 · Cited by 301 · see citing works
On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks
Eme, L., Sharpe, S. C., Brown, M. W., & Roger, A. J. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a016139 · Cited by 287 · see citing works
Ball, S. G., Colleoni, C., Cenci, U., Raj, J. N., & Tirtiaux, C. (2011) · Journal of Experimental Botany · doi:10.1093/jxb/erq411 · Cited by 273 · see citing works
“Megavirales”, a proposed new order for eukaryotic nucleocytoplasmic large DNA viruses
Colson, P., de Lamballerie, X. N., Yutin, N., Sassan Asgari, B., Bigot, Y., Bideshi, D. K., Cheng, X.-W., Federici, B. A., Etten, J. L. V., Koonin, E. V., et al. (2013) · Archives of Virology · doi:10.1007/s00705-013-1768-6 · Cited by 265 · see citing works
Self-citationLate acquisition of mitochondria by a host with chimaeric prokaryotic ancestry
Pittis, A. A., & Gabaldón, T. (2016) · Nature · doi:10.1038/nature16941 · Cited by 259 · see citing works
Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements
Koonin, E. V., & Dolja, V. V. (2014) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00049-13 · Cited by 242 · see citing works
Self-citationProbing the evolution, ecology and physiology of marine protists using transcriptomics
Caron, D., Alexander, H., Allen, A., Archibald, J., Armbrust, E., Bachy, C., Bell, C., Bharti, A., Dyhrman, S., Guida, S. M., et al. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2016.160 · Cited by 189 · see citing works
Early evolution of the Eukaryota
Butterfield, N. J. F. (2014) · Palaeontology · doi:10.1111/pala.12139 · Cited by 219 · see citing works
Dolja, V. V., & Koonin, E. V. (2017) · Virus Research · doi:10.1016/j.virusres.2017.10.020 · Cited by 219 · see citing works
Self-citationUntangling the evolution of Rab G proteins: implications of a comprehensive genomic analysis
Kloepper, T. H., Kienle, N., Fasshauer, D., & Munro, S. (2012) · BMC Biology · doi:10.1186/1741-7007-10-71 · Cited by 193 · see citing works
Lindquist, S., & Kelly, J. W. (2011) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a004507 · Cited by 188 · see citing works
Bacterial proteins pinpoint a single eukaryotic root
Derelle, R., Torruella, G., Klimeš, V., Brinkmann, H., Kim, E., Vlček, Č., Lang, B. F., & Eliáš, M. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1420657112 · Cited by 187 · see citing works
From complete genome sequence to ‘complete’ understanding?
Galperin, M. Y., & Koonin, E. V. (2010) · Trends in biotechnology · doi:10.1016/j.tibtech.2010.05.006 · Cited by 173 · see citing works
Self-citationHorizontal gene transfer in eukaryotes: The weak‐link model
Huang, J. (2013) · BioEssays · doi:10.1002/bies.201300007 · Cited by 166 · see citing works
Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade
Thrash, J. C., Boyd, A., Huggett, M. J., Grote, J., Carini, P., Yoder, R. J., Robbertse, B., Spatafora, J. W., Rappé, M. S., & Giovannoni, S. J. (2011) · Scientific Reports · doi:10.1038/srep00013 · Cited by 166 · see citing works
Csürös, M., Rogozin, I. B., & Koonin, E. V. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002150 · Cited by 163 · see citing works
Self-citationEvolutionary Diversity of the Mitochondrial Calcium Uniporter
Bick, A. G., Calvo, S. E., & Mootha, V. K. (2012) · Science · doi:10.1126/science.1214977 · Cited by 158 · see citing works
Malina, C., Larsson, C., & Nielsen, J. (2018) · FEMS Yeast Research · doi:10.1093/femsyr/foy040 · Cited by 155 · see citing works
The Physiology of Phagocytosis in the Context of Mitochondrial Origin
Martin, W. F., Tielens, A. G. M., Mentel, M., Garg, S. G., & Gould, S. B. (2017) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00008-17 · Cited by 152 · see citing works
Wolbachia Associations with Insects: Winning or Losing Against a Master Manipulator
Correa, C. C., & Ballard, J. W. O. (2016) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2015.00153 · Cited by 150 · see citing works
Lasda, E. L., & Blumenthal, T. (2011) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.71 · Cited by 146 · see citing works
The Repatterning of Eukaryotic Genomes by Random Genetic Drift
Lynch, M., Bobay, L., Catania, F., Goût, J.-F., & Rho, M. (2011) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-082410-101412 · Cited by 144 · see citing works
Energetics and genetics across the prokaryote-eukaryote divide
Lane, N. J. (2011) · Biology Direct · doi:10.1186/1745-6150-6-35 · Cited by 142 · 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
“Complexity can also occur within cells; a major event in the evolution of eukaryotes was when organisms capable of engulfing other organisms acquired mitochondria (permitting aerobic respiration for energy) and chloroplasts (permitting oxygenic photosynthesis) (Koonin, 2010).”
Rooting the Eukaryotic Tree with Mitochondrial and Bacterial Proteins
Derelle, R., & Lang, B. F. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr295 · Cited by 134 · see citing works
Bioenergetic Constraints on the Evolution of Complex LifePreprint
Lane, N. J. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a015982 · Cited by 133 · see citing works
Origin and Evolution of Plastids and Photosynthesis in EukaryotesPreprint
McFadden, G. I. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a016105 · Cited by 129 · 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
Three-Dimensional Reconstruction of Bacteria with a Complex Endomembrane System
Santarella‐Mellwig, R., Pruggnaller, S., Roos, N., Mattaj, I. W., & Devos, D. P. (2013) · PLoS Biology · doi:10.1371/journal.pbio.1001565 · Cited by 127 · see citing works
From archaeon to eukaryote: the evolutionary dark ages of the eukaryotic cell
Martijn, J., & Ettema, T. J. G. (2013) · Biochemical Society Transactions · doi:10.1042/bst20120292 · Cited by 123 · see citing works
Basu, S., Patil, S., Mapleson, D., Russo, M. T., Vitale, L. A., Fevola, C., Maumus, F., Casotti, R., Möck, T., Cáccamo, M., et al. (2017) · New Phytologist · doi:10.1111/nph.14557 · Cited by 122 · see citing works
The Quest for a Universal Theory of Life
Cleland, C. E. (2019) · Cambridge University Press eBooks · doi:10.1017/9781139046893 · Cited by 122 · see citing works
Origin and Early Evolution of the Eukaryotic Cell
Gabaldón, T. (2021) · Annual Review of Microbiology · doi:10.1146/annurev-micro-090817-062213 · Cited by 121 · see citing works
Eukaryogenesis, how special really?
Booth, A., & Doolittle, W. F. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1421376112 · Cited by 116 · see citing works
Speijer, D. (2010) · BioEssays · doi:10.1002/bies.201000097 · Cited by 115 · see citing works
Eukaryotic Origins: How and When Was the Mitochondrion Acquired?Preprint
Poole, A. M., & Gribaldo, S. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a015990 · Cited by 113 · see citing works
The Common Ancestor of Archaea and Eukarya Was Not an Archaeon
Forterre, P. (2013) · Archaea · doi:10.1155/2013/372396 · Cited by 112 · see citing works
Baumgarten, S., Bayer, T., Aranda, M., Liew, Y. J., Carr, A. R., Micklem, G., & Voolstra, C. R. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-704 · Cited by 111 · see citing works
Forterre, P. (2010) · Research in Microbiology · doi:10.1016/j.resmic.2010.10.005 · Cited by 110 · see citing works
Can Plant Viruses Cross the Kingdom Border and Be Pathogenic to Humans?
Balique, F., Lecoq, H., Raoult, D., & Colson, P. (2015) · Viruses · doi:10.3390/v7042074 · Cited by 109 · see citing works
Mosaic origin of the eukaryotic kinetochore
Tromer, E. C., van Hooff, J. J. E., Kops, G. J. P. L., & Snel, . (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1821945116 · Cited by 106 · see citing works
Winding paths to simplicity: genome evolution in facultative insect symbionts
Lo, W., Huang, Y., & Kuo, C. (2016) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuw028 · Cited by 107 · see citing works
Highly Conserved Mitochondrial Genomes among Multicellular Red Algae of the Florideophyceae
Yang, E. C., Kim, K. M., Kim, S. Y., Lee, J., Boo, G. H., Lee, J., Nelson, W. A., Yi, G., Schmidt, W. E., Fredericq, S., et al. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv147 · Cited by 99 · see citing works
Origin and Diversification of Eukaryotes
Katz, L. A. (2010) · Annual Review of Microbiology · doi:10.1146/annurev-micro-090110-102808 · Cited by 94 · see citing works
Quéméner, E. D., Brochier‐Armanet, C., Forterre, P., & Gribaldo, S. (2010) · Research in Microbiology · doi:10.1016/j.resmic.2010.10.004 · Cited by 94 · see citing works
Concepts of the last eukaryotic common ancestor
O’Malley, M. A., Leger, M. M., Wideman, J. G., & Ruiz‐Trillo, I. (2019) · Nature Ecology & Evolution · doi:10.1038/s41559-019-0796-3 · Cited by 93 · see citing works
Oxygen, animals and aquatic bioturbation: An updated account
Butterfield, N. J. (2018) · Geobiology · doi:10.1111/gbi.12267 · Cited by 89 · see citing works
Planctomycetes and eukaryotes: A case of analogy not homology
McInerney, J. O., Martin, W. F., Koonin, E. V., Allen, J. F., Galperin, M. Y., Lane, N. J., Archibald, J. M., & Embley, T. M. (2011) · BioEssays · doi:10.1002/bies.201100045 · Cited by 89 · see citing works
Self-citationA meta‐analysis of the strength and nature of cytoplasmic genetic effects
Dobler, R., Rogell, B., Budar, F., & Dowling, D. K. (2014) · Journal of Evolutionary Biology · doi:10.1111/jeb.12468 · Cited by 88 · see citing works
Dissecting genome reduction and trait loss in insect endosymbionts
Latorre, A., & Manzano-Marı́n, A. (2016) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.13222 · Cited by 87 · see citing works
A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution
Grau‐Bové, X., Navarrete, C., Chiva, C., Pribasnig, T., Antó, M., Torruella, G., Galindo, L. J., Lang, B. F., Moreira, D., López‐García, P., et al. (2022) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01771-6 · Cited by 85 · see citing works
Phylogenomic Test of the Hypotheses for the Evolutionary Origin of Eukaryotes
Rochette, N. C., Brochier‐Armanet, C., & Gouy, M. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/mst272 · Cited by 82 · see citing works
Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes
Saw, J. H. W., Spang, A., Zaremba-Niedźwiedzka, K., Juzokaite, L., Dodsworth, J. A., Murugapiran, S. K., Colman, D. R., Takacs‐Vesbach, C. D., Hedlund, B. P., Guy, L., et al. (2015) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2014.0328 · Cited by 80 · see citing works
Cyanobacterial nitrogenases: phylogenetic diversity, regulation and functional predictions
Esteves-Ferreira, A. A., Cavalcanti, J. H. F., Vaz, M. G. M. V., de Alvarenga, L. V., Nunes‐Nesi, A., & Araújo, W. L. (2017) · Genetics and Molecular Biology · doi:10.1590/1678-4685-gmb-2016-0050 · Cited by 80 · see citing works
The Pre-Endosymbiont Hypothesis: A New Perspective on the Origin and Evolution of MitochondriaPreprint
Gray, M. W. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a016097 · Cited by 80 · see citing works
A Briefly Argued Case That Asgard Archaea Are Part of the Eukaryote Tree
Fournier, G. P., & Poole, A. M. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.01896 · Cited by 79 · see citing works
Evolutionary defined role of the mitochondrial DNA in fertility, disease and ageing
Otten, A. B. C., & Smeets, H. J. M. (2015) · Human Reproduction Update · doi:10.1093/humupd/dmv024 · Cited by 77 · see citing works
Phylogenomic Reconstruction Indicates Mitochondrial Ancestor Was an Energy Parasite
Wang, Z., & Wu, M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0110685 · Cited by 75 · see citing works
From the scala naturae to the symbiogenetic and dynamic tree of life
Kutschera, U. (2011) · Biology Direct · doi:10.1186/1745-6150-6-33 · Cited by 74 · see citing works
Global Patterns of Protein Domain Gain and Loss in Superkingdoms
Nasir, A., Kim, K. M., & Caetano‐Anollés, G. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003452 · Cited by 74 · see citing works
Deciphering the Evolutionary History of Open and Closed Mitosis
Sazer, S., Lynch, M., & Needleman, D. J. (2014) · Current Biology · doi:10.1016/j.cub.2014.10.011 · Cited by 74 · see citing works
A Novel Protein Kinase-Like Domain in a Selenoprotein, Widespread in the Tree of Life
Dudkiewicz, M., Szczepińska, T., Grynberg, M., & Pawłowski, K. (2012) · PLoS ONE · doi:10.1371/journal.pone.0032138 · Cited by 73 · see citing works
Evolution of intrinsic disorder in eukaryotic proteins
Ahrens, J. B., Nunez-Castilla, J., & Siltberg-Liberles, J. (2017) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-017-2559-0 · Cited by 72 · see citing works
Chernikova, D., Motamedi, S., Csürös, M., Koonin, E. V., & Rogozin, I. B. (2011) · Biology Direct · doi:10.1186/1745-6150-6-26 · Cited by 72 · see citing works
Self-citationCommon origins and host-dependent diversity of plant and animal viromes
Dolja, V. V., & Koonin, E. V. (2011) · Current Opinion in Virology · doi:10.1016/j.coviro.2011.09.007 · Cited by 71 · see citing works
Self-citationThe Evolution of the Hallmarks of Aging
Lemoine, M. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.693071 · Cited by 69 · see citing works
Losing Complexity: The Role of Simplification in Macroevolution
O’Malley, M. A., Wideman, J. G., & Ruiz‐Trillo, I. (2016) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2016.04.004 · Cited by 69 · see citing works
Serial endosymbiosis or singular event at the origin of eukaryotes?
Lane, N. J. (2017) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2017.04.031 · Cited by 69 · see citing works
Early evolution without a tree of life
Martin, W. F. (2011) · Biology Direct · doi:10.1186/1745-6150-6-36 · Cited by 68 · see citing works
Erives, A. J. (2017) · Epigenetics & Chromatin · doi:10.1186/s13072-017-0162-0 · Cited by 66 · see citing works
The Archaeal Legacy of Eukaryotes: A Phylogenomic Perspective
Guy, L., Saw, J. H., & Ettema, T. J. G. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a016022 · Cited by 65 · see citing works
Tiengwe, C., Marcello, L., Farr, H., Gadelha, C., Burchmore, R., Barry, J. D., Bell, S. D., & McCulloch, R. (2012) · PLoS ONE · doi:10.1371/journal.pone.0032674 · Cited by 64 · see citing works
Ginger, M. L., Fritz‐Laylin, L. K., Fulton, C., Cande, W. Z., & Dawson, S. C. (2010) · Protist · doi:10.1016/j.protis.2010.09.001 · Cited by 63 · see citing works
Endosymbiosis and its implications for evolutionary theory
O’Malley, M. A. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1421389112 · Cited by 63 · see citing works
Andersen, R. A. (2013) · Handbook of Microalgal Culture · doi:10.1002/9781118567166.ch1 · Cited by 62 · see citing works
Keys to eukaryality: Planctomycetes and ancestral evolution of cellular complexity
Fuerst, J. A. (2012) · Frontiers in Microbiology · doi:10.3389/fmicb.2012.00167 · Cited by 61 · see citing works
Jiang, C., Wang, G., Xiong, J., Yang, W., Sun, Z., Feng, J.-M., Warren, A., & Miao, W. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.11.018 · Cited by 61 · see citing works
When integration fails: Prokaryote phylogeny and the tree of life
O’Malley, M. A. (2012) · Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences · doi:10.1016/j.shpsc.2012.10.003 · Cited by 59 · see citing works
Breath-giving cooperation: critical review of origin of mitochondria hypotheses
Zachar, I., & Szathmáry, E. (2017) · Biology Direct · doi:10.1186/s13062-017-0190-5 · Cited by 59 · see citing works
Imhof, S., Zhang, J., Wang, H., Bui, K. H., Nguyen, H. T., Atanasov, I. C., Hui, W. H., Yang, S. K., Zhou, Z. H., & Hill, K. L. (2019) · eLife · doi:10.7554/elife.52058 · Cited by 58 · see citing works
Introduction: Semiotic Scaffolding
Hoffmeyer, J. (2015) · Biosemiotics · doi:10.1007/s12304-015-9236-1 · Cited by 58 · see citing works
Prokaryotic Ubiquitin-Like Protein Modification
Maupin-furlow, J. A. (2014) · Annual Review of Microbiology · doi:10.1146/annurev-micro-091313-103447 · Cited by 57 · see citing works
The Evolution of Algae by Secondary and Tertiary Endosymbiosis
Archibald, J. M. (2012) · Advances in botanical research · doi:10.1016/b978-0-12-391499-6.00003-7 · Cited by 57 · see citing works
Keeling, P. J. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a016196 · Cited by 57 · see citing works
Sequence Features of Mitochondrial Transporter Protein Families
Gyimesi, G., & Hediger, M. A. (2020) · Biomolecules · doi:10.3390/biom10121611 · Cited by 56 · see citing works
Bittman, E. L. (2015) · Journal of Biological Rhythms · doi:10.1177/0748730415618297 · Cited by 55 · see citing works
Intracellular Rickettsiales: Insights into manipulators of eukaryotic cells
Renvoisé, A., Merhej, V., Georgiades, K., & Raoult, D. (2011) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2011.05.009 · Cited by 53 · see citing works
The D 1‐ D 2 region of the large subunit ribosomal DNA as barcode for ciliates
Stoeck, T., Przyboś, E., & Dunthorn, M. (2013) · Molecular Ecology Resources · doi:10.1111/1755-0998.12195 · Cited by 53 · see citing works
Relative timing of mitochondrial endosymbiosis and the “pre‐mitochondrial symbioses” hypothesis
Gabaldón, T. (2018) · IUBMB Life · doi:10.1002/iub.1950 · Cited by 54 · see citing works
The evolution of eukaryotic cells from the perspective of peroxisomes
Bolte, K., Rensing, S. A., & Maier, U. (2014) · BioEssays · doi:10.1002/bies.201400151 · Cited by 52 · see citing works
- Authors
- Koonin, E. V.
- Affiliations
- National Institutes of Health (US)
- Corresponding author
- Koonin, Eugene V
- ORCID
- Koonin, Eugene V
- Venue
- Genome Biology
- Published
- 2010
- Volume
- 11
- Issue
- 5
- Pages
- 209
- ISSN
- 1465-6906 (ISSN-L)
- PMC
- PMC2898073
- OpenAlex
- W2144889160
- Cited by
- 345
- References
- 141
- Citations by year
- 2026: 10 · 2025: 8 · 2024: 15 · 2023: 7 · 2022: 7 · 2021: 21 · 2020: 13 · 2019: 27 · 2018: 20 · 2017: 26 · 2016: 31 · 2015: 32 · 2014: 35 · 2013: 28 · 2012: 28
- FWCI
- 12.12
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- U.S. Department of Health and Human Services
- National Institutes of Health
- U.S. National Library of Medicine
- 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
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- eukaryotic origin, eukaryotic evolution, last common ancestor, mitochondrial endosymbiosis, phylogenomics, eukaryotic phylogeny
- MeSH terms
- Archaea, Bacteria, Phylogeny, Genomics, 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