The Rooting of the Universal Tree of Life Is Not Reliable
Abstract
Several composite universal trees connected by an ancestral gene duplication have been used to root the universal tree of life. In all cases, this root turned out to be in the eubacterial branch. However, the validity of results obtained from comparative sequence analysis has recently been questioned, in particular, in the case of ancient phylogenies. For example, it has been shown that several eukaryotic groups are misplaced in ribosomal RNA or elongation factor trees because of unequal rates of evolution and mutational saturation. Furthermore, the addition of new sequences to data sets has often turned apparently reasonable phylogenies into confused ones. We have thus revisited all composite protein trees that have been used to root the universal tree of life up to now (elongation factors, ATPases, tRNA synthetases, carbamoyl phosphate synthetases, signal recognition particle proteins) with updated data sets. In general, the two prokaryotic domains were not monophyletic with several aberrant groupings at different levels of the tree. Furthermore, the respective phylogenies contradicted each others, so that various ad hoc scenarios (paralogy or lateral gene transfer) must be proposed in order to obtain the traditional Archaebacteria-Eukaryota sisterhood. More importantly, all of the markers are heavily saturated with respect to amino acid substitutions. As phylogenies inferred from saturated data sets are extremely sensitive to differences in evolutionary rates, present phylogenies used to root the universal tree of life could be biased by the phenomenon of long branch attraction. Since the eubacterial branch was always the longest one, the eubacterial rooting could be explained by an attraction between this branch and the long branch of the outgroup. Finally, we suggested that an eukaryotic rooting could be a more fruitful working hypothesis, as it provides, for example, a simple explanation to the high genetic similarity of Archaebacteria and Eubacteria inferred from complete genome analysis.
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The younger inferred ages of some nodes in the ATP synthase analysis may be due in part to the shorter ATP synthase alignment (433-512 AA) and lower phylogenetic resolution reducing the species tree calibrations and braces to the ATP synthase phylogeny through gene and species tree incongruence.
“In part, this may be due to the shorter alignment of ATP synthase (433-512AA, Supplementary Figs. 4–7, 10) and lower phylogenetic resolution102 reducing the species tree calibrations and braces to the ATP synthase phylogeny through gene and species tree incongruence (Supplementary Information).”
From ATP synthase evolution on a cross-braced dated tree of life (2023) · cites this paper as [102]
Cites
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Saitou, N., & Nei, M. (1987) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040454 · Cited by 59,962 · see citing works
The Neutral Theory of Molecular Evolution
Kimura, M. (1979) · Scientific American · doi:10.1038/scientificamerican1179-98 · Cited by 7,698 · see citing works
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
Woese, C. R., Kandler, O., & Wheelis, M. L. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.12.4576 · Cited by 6,128 · see citing works
Cases in which Parsimony or Compatibility Methods Will be Positively Misleading
Felsenstein, J. (1978) · Systematic Biology · doi:10.1093/sysbio/27.4.401 · Cited by 3,221 · 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
Horizontal gene transfer among genomes: The complexity hypothesis
Jain, R., Rivera, M. C., & Lake, J. A. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.7.3801 · Cited by 1,170 · see citing works
Molecular archaeology of the Escherichia coli genome
Lawrence, J. G., & Ochman, H. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.16.9413 · Cited by 939 · see citing works
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
Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes.
Gogarten, J. P., Kibak, H., Dittrich, P., Taiz, L., Bowman, E. J., Bowman, B. J., Manolson, M. F., Poole, R. J., Date, T., Oshima, T., et al. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.17.6661 · Cited by 781 · see citing works
Genome phylogeny based on gene content
Snel, ., Peer Bork, B., & Huynen, M. A. (1999) · Nature Genetics · doi:10.1038/5052 · Cited by 708 · see citing works
MOLPHY version 2.3 : programs for molecular phylogenetics based on maximum likelihood
Adachi, J. (1996) · Cited by 605 · see citing works
MUST, a computer package of Management Utilities for Sequences and Trees
Philippe, H. (1993) · Nucleic Acids Research · doi:10.1093/nar/21.22.5264 · Cited by 600 · see citing works
Self-citationDoolittle, W. F. (1998) · Trends in Genetics · doi:10.1016/s0168-9525(98)01494-2 · Cited by 600 · see citing works
The structure of cytochromec and the rates of molecular evolution
Dickerson, R. E. (1971) · Journal of Molecular Evolution · doi:10.1007/bf01659392 · Cited by 544 · see citing works
Hirt, R. P., Logsdon, J. M., Jr., Healy, B., Dorey, M. W., Doolittle, W. F., & Embley, T. M. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.2.580 · Cited by 518 · see citing works
Early evolution and the origin of eukaryotes
Sogin, M. L. (1991) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(05)80192-3 · Cited by 500 · see citing works
Archaea and the prokaryote-to-eukaryote transition
Brown, J. R., & Doolittle, W. F. (1997) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.61.4.456-502.1997 · Cited by 485 · see citing works
Determining divergence times with a protein clock: Update and reevaluation
Feng, D.-F., Cho, G. S., & Doolittle, R. F. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.24.13028 · Cited by 416 · see citing works
Models of amino acid substitution and applications to mitochondrial protein evolution
Yang, Z., Nielsen, R., & Hasegawa, M. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025888 · Cited by 414 · see citing works
Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications.
Brown, J. R., & Doolittle, W. F. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.7.2441 · Cited by 379 · see citing works
Evidence that eukaryotes and eocyte prokaryotes are immediate relatives
Rivera, M. C., & Lake, J. A. (1992) · Science · doi:10.1126/science.1621096 · Cited by 342 · see citing works
Generation Time and Genomic Evolution in Primates
Sarich, V. M., & Wilson, A. C. (1973) · Science · doi:10.1126/science.179.4078.1144 · Cited by 331 · see citing works
Evolutionary distances for protein-coding sequences: modeling site- specific residue frequencies
Halpern, A. L., & Bruno, W. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025995 · Cited by 325 · see citing works
How good are deep phylogenetic trees?
Philippe, H., & Laurent, J. (1998) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(98)80028-2 · Cited by 324 · see citing works
Self-citationMoreira, D., & López‐García, P. (1998) · Journal of Molecular Evolution · doi:10.1007/pl00006408 · Cited by 324 · see citing works
Koonin, E. V., Mushegian, A. R., Galperin, M. Y., & Walker, D. R. (1997) · Molecular Microbiology · doi:10.1046/j.1365-2958.1997.4821861.x · Cited by 310 · see citing works
Are Guinea Pigs Rodents? The Importance of Adequate Models in Molecular Phylogenetics
Sullivan, J. M., & Swofford, D. L. (1997) · Journal of Mammalian Evolution · doi:10.1023/a:1027314112438 · Cited by 283 · see citing works
Assessing the Impact of Secondary Structure and Solvent Accessibility on Protein Evolution
Goldman, N., Thorne, J. L., & Jones, D. T. (1998) · Genetics · doi:10.1093/genetics/149.1.445 · Cited by 281 · see citing works
Poole, A. M., Jeffares, D. C., & Penny, D. (1998) · Journal of Molecular Evolution · doi:10.1007/pl00006275 · Cited by 274 · see citing works
Gupta, R., & Golding, G. B. (1993) · Journal of Molecular Evolution · doi:10.1007/bf00182743 · Cited by 270 · see citing works
The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny.
Baldauf, S. L., Palmer, J. D., & Doolittle, W. F. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.15.7749 · Cited by 269 · see citing works
Brinkmann, H., & Philippe, H. (1999) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026166 · Cited by 258 · see citing works
Self-citationJeffares, D. C., Poole, A. M., & Penny, D. (1998) · Journal of Molecular Evolution · doi:10.1007/pl00006280 · Cited by 252 · see citing works
Archaeal Genomics: An Overview
Olsen, G. J., & Woese, C. R. (1997) · Cell · doi:10.1016/s0092-8674(00)80284-6 · Cited by 247 · see citing works
Where is the root of the universal tree of life?
Forterre, P., & Philippe, H. (1999) · BioEssays · doi:10.1002/(sici)1521-1878(199910)21:10 · Cited by 244 · see citing works
Self-citationGermot, A., Philippe, H., & Guyader, H. L. (1997) · Molecular and Biochemical Parasitology · doi:10.1016/s0166-6851(97)00064-9 · Cited by 238 · see citing works
Self-citationOn the maximum likelihood method in molecular phylogenetics
Hasegawa, M., Kishino, H., & Saitou, N. (1991) · Journal of Molecular Evolution · doi:10.1007/bf02101285 · Cited by 229 · see citing works
Naylor, G. J. P., & Brown, W. M. (1998) · Systematic Biology · doi:10.1080/106351598261030 · Cited by 224 · see citing works
Tempo, mode, the progenote, and the universal root.
Doolittle, W. F., & Brown, J. R. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.15.6721 · Cited by 194 · see citing works
Philippe, H., Sörhannus, U., Baroin‐Tourancheau, A., Perasso, R., Gasse, F., & Adoutte, A. (1994) · Journal of Evolutionary Biology · doi:10.1046/j.1420-9101.1994.7020247.x · Cited by 156 · see citing works
Self-citationHashimoto, T., Sánchez, L. B., Shirakura, T., Müller, M., & Hasegawa, M. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.12.6860 · Cited by 149 · see citing works
The Root of the Tree of Life in the Light of the Covarion Model
Lopez, P., Forterre, P., & Philippe, H. (1999) · Journal of Molecular Evolution · doi:10.1007/pl00006572 · Cited by 139 · see citing works
Self-citationA covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages
Lockhart, P. J., Steel, M., Barbrook, A. C., Huson, D. H., Charleston, M., & Howe, C. J. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026025 · Cited by 139 · see citing works
The molecular phylogeny of eukaryota: solid facts and uncertainties
Phillipe, H. (1998) · Parasitology International · doi:10.1016/s1383-5769(98)80093-7 · Cited by 126 · see citing works
Gribaldo, S., & Cammarano, P. (1998) · Journal of Molecular Evolution · doi:10.1007/pl00006407 · Cited by 123 · see citing works
The nature of the last universal ancestor and the root of the tree of life, still open questions
Forterre, P., Benachenhou, N., Confalonieri, F., Duguet, M., Elie, C., & Labedan, B. (1992) · Biosystems · doi:10.1016/0303-2647(92)90004-i · Cited by 107 · see citing works
Self-citationCao, Y., Waddell, P. J., Okada, N., & Hasegawa, M. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025891 · Cited by 92 · see citing works
Lawson, F. S., Charlebois, R. L., & Dillon, J. A. (1996) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025665 · Cited by 90 · see citing works
Rodent monophyly: pitfalls of molecular phylogenies.
Philippe, H. (1997) · PubMed · Cited by 88 · see citing works
Self-citationEvidence for the early divergence of tryptophanyl- and tyrosyl-tRNA synthetases
Brown, J. R., Robb, F. T., Weiss, R. B., & Doolittle, W. F. (1997) · Journal of Molecular Evolution · doi:10.1007/pl00006206 · Cited by 69 · see citing works
A bacterial antibiotic resistance gene with eukaryotic origins
Brown, J. R., Zhang, J., & Hodgson, J. E. (1998) · Current Biology · doi:10.1016/s0960-9822(98)70238-6 · Cited by 58 · see citing works
de Pouplana, L. R., Frugier, M., Quinn, C. L., & SCHIMMEL, P. R. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.1.166 · Cited by 52 · see citing works
Voelker, G., & Edwards, S. V. (1998) · Systematic Biology · doi:10.1080/106351598260608 · Cited by 44 · see citing works
Gene duplications and horizontal gene transfer during early evolution
Gogarten, J. P., Hilario, E., & Olendzenski, L. (1996) · Origins of Life and Evolution of Biospheres · doi:10.1007/bf02459760 · Cited by 25 · see citing works
Eukaryotic Traits in Archaebacteria
Zillig, W. (1987) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.1987.tb40599.x · Cited by 22 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
An index of substitution saturation and its application
Xia, X., Xie, Z., Salemi, M., Chen, L., & Wang, Y. (2002) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(02)00326-3 · Cited by 1,560 · see citing works
Chemical Diversity in the Sialic Acids and Related α-Keto Acids: An Evolutionary Perspective
Angata, T., & Varki, A. P. (2002) · Chemical Reviews · doi:10.1021/cr000407m · Cited by 1,232 · see citing works
A review of long-branch attraction
Bergsten, J. (2005) · Cladistics · doi:10.1111/j.1096-0031.2005.00059.x · Cited by 1,162 · see citing works
The origin and evolution of model organisms
Hedges, S. B. (2002) · Nature Reviews Genetics · doi:10.1038/nrg929 · Cited by 806 · see citing works
Mitochondrial Genome Evolution and the Origin of Eukaryotes
Lang, B. F., Gray, M. W., & Burger, G. (1999) · Annual Review of Genetics · doi:10.1146/annurev.genet.33.1.351 · Cited by 724 · 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
Using PhyloSuite for molecular phylogeny and tree‐based analyses
Xiang, C., Gao, F., Jakovlić, I., Lei, H., Hu, Y., Zhang, H., Zou, H., Wang, G., & Zhang, D. (2023) · iMeta · doi:10.1002/imt2.87 · Cited by 577 · see citing works
An archaeal origin of eukaryotes supports only two primary domains of life
Williams, T. A., Foster, P. G., Cox, C. J., & Embley, T. M. (2013) · Nature · doi:10.1038/nature12779 · Cited by 519 · see citing works
Origin of first cells at terrestrial, anoxic geothermal fields
Mulkidjanian, A. Y., Bychkov, A. Y., Dibrova, D. V., Galperin, M. Y., & Koonin, E. V. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1117774109 · Cited by 447 · see citing works
Horizontal gene transfer: A critical view
Kurland, C. G., Canbäck, B., & Berg, O. G. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1632870100 · Cited by 409 · see citing works
Phylogenomics of Eukaryotes: Impact of Missing Data on Large Alignments
Philippe, H., Snell, E. A., Bapteste, E. P., Lopez, P., Holland, P. W. H., & Casañe, D. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh182 · Cited by 398 · see citing works
Self-citationThe 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
Chen, W., Bonillo, C., & Lecointre, G. (2003) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(02)00371-8 · Cited by 356 · see citing works
Chiari, Y., Cahais, V., Galtier, N., & Delsuc, F. (2012) · BMC Biology · doi:10.1186/1741-7007-10-65 · Cited by 340 · see citing works
How good are deep phylogenetic trees?
Philippe, H., & Laurent, J. (1998) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(98)80028-2 · Cited by 324 · see citing works
Self-citationAncient Phylogenetic Relationships
Gribaldo, S., & Philippe, H. (2002) · Theoretical Population Biology · doi:10.1006/tpbi.2002.1593 · Cited by 314 · see citing works
Self-citationJoint Bayesian Estimation of Alignment and Phylogeny
Redelings, B. D., & Suchard, M. A. (2005) · Systematic Biology · doi:10.1080/10635150590947041 · Cited by 306 · see citing works
Reconstructing Early Events in Eukaryotic Evolution
Roger, A. J. (1999) · The American Naturalist · doi:10.1086/303290 · Cited by 283 · see citing works
Merging Genomes with Geochemistry in Hydrothermal Ecosystems
Reysenbach, A., & Shock, E. L. (2002) · Science · doi:10.1126/science.1072483 · Cited by 283 · 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
Glansdorff, N., Xu, Y., & Labedan, B. (2008) · Biology Direct · doi:10.1186/1745-6150-3-29 · Cited by 264 · see citing works
Brinkmann, H., & Philippe, H. (1999) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026166 · Cited by 258 · see citing works
Self-citationEstimating Species Trees from Unrooted Gene Trees
Liu, L., & Yu, L. (2011) · Systematic Biology · doi:10.1093/sysbio/syr027 · Cited by 255 · see citing works
Delsuc, F., Scally, M., Madsen, O., Stanhope, M. J., JONG, W. W. D., Catzeflis, F. M., Springer, M. S., & Douzery, E. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003989 · Cited by 251 · see citing works
Where is the root of the universal tree of life?
Forterre, P., & Philippe, H. (1999) · BioEssays · doi:10.1002/(sici)1521-1878(199910)21:10 · Cited by 244 · see citing works
Self-citationHorizontal gene transfer among microbial genomes: new insights from complete genome analysis
Eisen, J. A. (2000) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(00)00143-x · Cited by 243 · see citing works
Tristan, L., Douady, C. J., Gouy, M., Trontelj, P., Briolay, J., & Gibert, J. (2006) · Molecular Ecology · doi:10.1111/j.1365-294x.2006.02888.x · Cited by 238 · see citing works
Gene Family Evolution and Homology: Genomics Meets Phylogenetics
Thornton, J. W., & DeSalle, R. (2000) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.1.1.41 · Cited by 225 · see citing works
Rooting the tree of life by transition analyses.
Cavalier‐Smith, T. (2006) · Biology Direct · doi:10.1186/1745-6150-1-19 · Cited by 221 · see citing works
Moulin, L., Béna, G., Masson‐Boivin, C., & Stępkowski, T. (2003) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(03)00255-0 · Cited by 209 · see citing works
The universal tree of life: an update
Forterre, P. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00717 · Cited by 186 · see citing works
Self-citationArchaeal Phylogeny Based on Ribosomal Proteins
Matte-Tailliez, O., Brochier‐Armanet, C., Forterre, P., & Philippe, H. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004122 · Cited by 180 · see citing works
Self-citationFraser, C. M., Eisen, J. A., & Salzberg, S. L. (2000) · Nature · doi:10.1038/35021244 · Cited by 179 · see citing works
Borowiec, M. L., Lee, E. K., Chiu, J. C., & Plachetzki, D. C. (2015) · doi:10.1101/013946 · Cited by 172 · see citing works
Khuri, S., Bakker, F. T., & Dunwell, J. M. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003840 · Cited by 169 · 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
Strommer, J. N. (2010) · The Plant Journal · doi:10.1111/j.1365-313x.2010.04458.x · Cited by 161 · see citing works
Rooting Phylogenetic Trees with Distant Outgroups: A Case Study from the Commelinoid Monocots
Graham, S. W., Olmstead, R. G., & Barrett, S. C. H. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003999 · Cited by 158 · see citing works
Evolution of RNA editing in trypanosome mitochondria
Simpson, L., Thiemann, O. H., Savill, N. J., Alfonzo, J. D., & Maslov, D. A. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.13.6986 · Cited by 155 · see citing works
Horiike, T., Hamada, K., Kanaya, S., & Shinozawa, T. (2001) · Nature Cell Biology · doi:10.1038/35055129 · Cited by 152 · see citing works
Phylogenetic identification of lateral genetic transfer events
Beiko, R. G., & Hamilton, N. (2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-15 · Cited by 153 · see citing works
Wägele, J. W., & Mayer, C. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-147 · Cited by 152 · see citing works
Shih, P. M., & Matzke, N. J. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1305813110 · Cited by 151 · see citing works
Liu, Y., Cox, C. J., Wang, W., & Goffinet, B. (2014) · Systematic Biology · doi:10.1093/sysbio/syu049 · Cited by 149 · see citing works
Tristan, L., Douady, C. J., Malard, F., & Gibert, J. (2006) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2006.08.020 · Cited by 147 · see citing works
Evolution of arginine deiminase (ADI) pathway genes
Zúñiga, M. (2002) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(02)00277-4 · Cited by 145 · see citing works
Martin, W. F., Rotte, C., Hoffmeister, M., Theißen, U., Gelius‐Dietrich, G., Ahr, S., & Henze, K. (2003) · IUBMB Life · doi:10.1080/1521654031000141231 · Cited by 145 · see citing works
Bacterial dormancy and culturability: the role of autocrine growth factors Commentary
Kell, D. B. (2000) · Current Opinion in Microbiology · doi:10.1016/s1369-5274(00)00082-5 · Cited by 142 · see citing works
The Root of the Tree of Life in the Light of the Covarion Model
Lopez, P., Forterre, P., & Philippe, H. (1999) · Journal of Molecular Evolution · doi:10.1007/pl00006572 · Cited by 139 · see citing works
Self-citationGalewski, T., Tilak, M., Sanchez-Brosseau, S., Chevret, P., Paradis, E., & Douzery, E. (2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-80 · Cited by 136 · see citing works
The nature of the universal ancestor and the evolution of the proteome
Doolittle, W. F. (2000) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(00)00096-8 · Cited by 134 · see citing works
Molecular Evolution Within the L-Malate and L-Lactate Dehydrogenase Super-Family
Madern, D. (2002) · Journal of Molecular Evolution · doi:10.1007/s00239-001-0088-8 · Cited by 131 · see citing works
TreSpEx-detection of misleading signal in phylogenetic reconstructions based on tree information
Struck, T. H. (2014) · Evolutionary Bioinformatics · doi:10.4137/ebo.s14239 · Cited by 128 · see citing works
On the Origin of Cells and Viruses
Koonin, E. V. (2009) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.2009.04992.x · Cited by 122 · see citing works
Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato
Beukes, C. W., Palmer, M., Manyaka, P., Chan, W. Y., Avontuur, J. R., van Zyl, E., Huntemann, M., Clum, A., Pillay, M., Palaniappan, K., et al. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01154 · 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
Dunn, C. W., Pugh, P. R., & Haddock, S. H. D. (2005) · Systematic Biology · doi:10.1080/10635150500354837 · Cited by 118 · see citing works
Becerra, A., Delaye, L., Islas, S., & Lazcano, A. (2007) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev.ecolsys.38.091206.095825 · Cited by 115 · see citing works
Dumas, E., Christina Boritsch, E., Vandenbogaert, M., Rodríguez de la Vega, R. C., Thiberge, J.-M., Caro, V., Gaillard, J.-L., Heym, B., Girard-Misguich, F., Brosch, R., et al. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evw001 · Cited by 112 · see citing works
About the last common ancestor, the universal life‐tree and lateral gene transfer: a reappraisal
Glansdorff, N. (2000) · Molecular Microbiology · doi:10.1046/j.1365-2958.2000.02126.x · Cited by 115 · 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
Self-citationHorizontal Gene Transfer and Endophytes: An Implication for the Acquisition of Novel Traits
Tiwari, P., & Bae, H. (2020) · Plants · doi:10.3390/plants9030305 · Cited by 113 · see citing works
Phylogenetic Inferences from Molecular Sequences: Review and Critique
Brocchieri, L. (2001) · Theoretical Population Biology · doi:10.1006/tpbi.2000.1485 · Cited by 112 · see citing works
Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes
Hassanin, A., Veron, G., Ropiquet, A., van Vuuren, B. J., Lécu, A., Goodman, S. M., Haider, J., & Nguyen, T. T. (2021) · PLoS ONE · doi:10.1371/journal.pone.0240770 · Cited by 114 · see citing works
Rooting the tree of life: the phylogenetic jury is still out
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Self-citationThe prokaryotic tree of life: past, present…and future?
McInerney, J. O., Cotton, J. A., & Pisani, D. (2008) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2008.01.008 · Cited by 108 · see citing works
A Comprehensive View on Proteasomal Sequences: Implications for the Evolution of the Proteasome
Gille, C., Goede, A., Schlötelburg, C., Preißner, R., Kloetzel, P., Göbel, U. B., & Frömmel, C. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)01470-5 · Cited by 107 · see citing works
How stands the Tree of Life a century and a half after The Origin?
O'Malley, M. A., & Koonin, E. V. (2011) · Biology Direct · doi:10.1186/1745-6150-6-32 · Cited by 106 · see citing works
The Universal Ancestor was a Thermophile or a Hyperthermophile: Tests and Further Evidence
Giulio, M. D. (2003) · Journal of Theoretical Biology · doi:10.1006/jtbi.2003.3197 · Cited by 104 · see citing works
Decoding the genomic tree of life
Simonson, A., Servin, J. A., Skophammer, R., Herbold, C., Rivera, M. C., & Lake, J. (2005) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.0501996102 · Cited by 79 · see citing works
Cladogenesis, coalescence and the evolution of the three domains of life
Zhaxybayeva, O., & Gogarten, J. P. (2004) · Trends in Genetics · doi:10.1016/j.tig.2004.02.004 · Cited by 98 · see citing works
Cuif, J., Lecointre, G., Perrin, C., Tillier, A., & Tillier, S. (2003) · Zoologica Scripta · doi:10.1046/j.1463-6409.2003.00133.x · Cited by 100 · see citing works
Molecular evidence for the evolution of photosynthesis
Blankenship, R. E. (2001) · Trends in Plant Science · doi:10.1016/s1360-1385(00)01831-8 · Cited by 97 · see citing works
The Potential Value of Indels as Phylogenetic Markers: Position of Trichomonads as a Case Study
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Self-citationAssessing evolutionary relationships among microbes from whole-genome analysis
Eisen, J. A. (2000) · Current Opinion in Microbiology · doi:10.1016/s1369-5274(00)00125-9 · Cited by 92 · 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
Bittner, L., Payri, C. E., Couloux, A., Cruaud, C., de Reviers, B., & ROUSSEAU, F. (2008) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2008.06.018 · Cited by 89 · see citing works
The Last Common Ancestor: What's in a name?
Delaye, L., Becerra, A., & Lazcano, A. (2005) · Origins of Life and Evolution of Biospheres · doi:10.1007/s11084-005-5760-3 · Cited by 83 · see citing works
Struck, T. H., Nesnidal, M. P., Purschke, G., & Halanych, K. M. (2008) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2008.05.015 · Cited by 84 · see citing works
Veyrunes, F., Britton‐Davidian, J., Robinson, T. J., Fichet-Calvet, É., Denys, C., & Chevret, P. (2005) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2005.02.011 · Cited by 84 · see citing works
Comment on "The 1.2-Megabase Genome Sequence of Mimivirus"
Moreira, D., & López‐García, P. (2005) · Science · doi:10.1126/science.1110820 · Cited by 83 · see citing works
The Consistent Phylogenetic Signal in Genome Trees Revealed by Reducing the Impact of Noise
Dutilh, B. E., Huynen, M. A., Bruno, W., & Snel, . (2004) · Journal of Molecular Evolution · doi:10.1007/s00239-003-2575-6 · Cited by 82 · see citing works
Using Core Genome Alignments To Assign Bacterial Species
Chung, M. C., Munro, J. B., Tettelin, H., & Hotopp, J. C. D. (2018) · mSystems · doi:10.1128/msystems.00236-18 · Cited by 80 · see citing works
Coherence, correspondence, and the renaissance of morphology in phylogenetic systematics
Assis, L. C. S. (2009) · Cladistics · doi:10.1111/j.1096-0031.2009.00261.x · Cited by 74 · see citing works
Genome beginnings: rooting the tree of life
Lake, J. A., Skophammer, R. G., Herbold, C. W., & Servin, J. A. (2009) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2009.0035 · Cited by 74 · see citing works
Ancient gene duplications and the root(s) of the tree of life
Zhaxybayeva, O., Lapierre, P., & Gogarten, J. P. (2005) · PROTOPLASMA · doi:10.1007/s00709-005-0135-1 · Cited by 75 · see citing works
Defining the Core of Nontransferable Prokaryotic Genes: The Euryarchaeal Core
Nesbø, C. L., Boucher, Y., & Doolittle, W. F. (2001) · Journal of Molecular Evolution · doi:10.1007/s002390010224 · Cited by 72 · see citing works
Petitjean, C., Deschamps, P., López‐García, P., Moreira, D., & Brochier‐Armanet, C. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv015 · Cited by 73 · see citing works
The Evolution of Light-harvesting Antennas
Green, B. R. (2003) · Advances in photosynthesis and respiration · doi:10.1007/978-94-017-2087-8_4 · Cited by 73 · see citing works
Rooting the Ribosomal Tree of Life
Fournier, G. P., & Gogarten, J. P. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq057 · Cited by 72 · see citing works
Convergent Evolution of the Army Ant Syndrome and Congruence in Big-Data Phylogenetics
Borowiec, M. L. (2018) · Systematic Biology · doi:10.1093/sysbio/syy088 · Cited by 72 · see citing works
Ribosomal proteins: Toward a next generation standard for prokaryotic systematics?
Ramulu, H. G., Groussin, M., Talla, E., Planel, R., Daubin, V., & Brochier‐Armanet, C. (2014) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2014.02.013 · Cited by 70 · see citing works
Cavalier‐Smith, T., & Chao, E. E. Y. (2020) · PROTOPLASMA · doi:10.1007/s00709-019-01442-7 · Cited by 68 · see citing works
The Chalcidoidea bush of life: evolutionary history of a massive radiation of minute wasps
Cruaud, A., Rasplus, J., Zhang, J., Burks, R. A., Delvare, G., Fusu, L., GUMOVSKY, A. V., Huber, J., Janšta, P., Mitroiu, M., et al. (2023) · Cladistics · doi:10.1111/cla.12561 · Cited by 117 · see citing works
HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees
Fér, T., & Schmickl, R. (2018) · Evolutionary Bioinformatics · doi:10.1177/1176934317742613 · Cited by 67 · 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
Self-citationGayral, P., Blondin, L., Guidolin, O., Carreel, F., Hippolyte, I., Perrier, X., & Iskra‐Caruana, M. (2010) · Journal of Virology · doi:10.1128/jvi.00401-10 · Cited by 62 · see citing works
Deep Origin of Plastid/Parasite ATP/ADP Translocases
Amiri, H., Karlberg, O., & Andersson, S. G. E. (2003) · Journal of Molecular Evolution · doi:10.1007/s00239-002-2387-0 · Cited by 63 · 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
“In practice, it is difficult to trace gene duplications back to LUCA, so the number of genes that can be analysed is low, and the long basal branches in the resulting trees may be particularly sensitive to phylogenetic error [14].”
Molecular systematics of dormice (Rodentia: Gliridae) and the radiation of Graphiurus in Africa
Montgelard, C., Matthee, C. A., & Robinson, T. J. (2003) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2003.2458 · Cited by 61 · see citing works
- Authors
- Philippe, H., & Forterre, P.
- Affiliations
- Université Paris-Sud (FR)
- Venue
- Journal of Molecular Evolution
- Published
- 1999-10
- Volume
- 49
- Issue
- 4
- Pages
- 509-523
- ISSN
- 0022-2844 (ISSN-L)
- OpenAlex
- W2108093581
- Cited by
- 267
- References
- 55
- Citations by year
- 2026: 4 · 2025: 7 · 2024: 8 · 2023: 13 · 2022: 5 · 2021: 6 · 2020: 3 · 2019: 4 · 2018: 11 · 2017: 9 · 2016: 2 · 2015: 11 · 2014: 9 · 2013: 9 · 2012: 7
- FWCI
- 5.98
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Journal of Molecular Evolution (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of Allergy and Infectious Diseases
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protist diversity and phylogeny
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- universal tree of life, root placement, long-branch attraction, protein phylogeny, elongation factors, ATPase, tRNA synthetase, carbamoyl phosphate synthetase, horizontal gene transfer, paralogy
- MeSH terms
- Adenosine Triphosphatases, Animals, Archaea, Bacteria, Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing), Eubacterium, Humans, Phylogeny, Databases, Factual, Evolution, Molecular, Gene Duplication
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