The DOI matches its Crossref record; 21 of the 21 references it cites were found in a registry or an index.
Phylogenomics and the reconstruction of the tree of life
Open accessOverview
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
Verification
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.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
Woese, C. R. (1987) · Microbiological Reviews · doi:10.1128/mr.51.2.221-271.1987 · Cited by 5,042 · cited 1×
“As the size of the sequences increases,the magnitude ofthe stochastic error decreases.”
BackgroundLateral gene transfer and the nature of bacterial innovation
Ochman, H., Lawrence, J. G., & Groisman, E. A. (2000) · Nature · doi:10.1038/35012500 · Cited by 3,816
Nothing in Biology Makes Sense except in the Light of Evolution
Dobzhansky, T. (1973) · The American Biology Teacher · doi:10.2307/4444260 · Cited by 3,219
Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies
Strimmer, K., & von Haeseler, A. (1996) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025664 · Cited by 2,531
Evidence for a clade of nematodes, arthropods and other moulting animals
Aguinaldo, A. M. A., Turbeville, J. M., Linford, L. S., Rivera, M. C., Garey, J. R., Raff, R. A., & Lake, J. A. (1997) · Nature · doi:10.1038/387489a0 · Cited by 1,609
Genome-scale approaches to resolving incongruence in molecular phylogenies.
Rokas, A., Williams, B. L., King, N., & Carroll, S. B. (2003) · Nature · doi:10.1038/nature02053 · Cited by 1,512
The new animal phylogeny: Reliability and implications
Adoutte, A., Balavoine, G., Lartillot, N., Lespinet, O., Prud'homme, B., & de Rosa, R. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.9.4453 · Cited by 512 · cited 1×
“For example,the misplacement of microsporidia at the base of the eukaryotic tree, instead of as a sister-group of fungi,was revealed by the comparison of several single-gene phylogenies 123 .”
BackgroundThe New View of Animal Phylogeny
Halanych, K. M. (2004) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev.ecolsys.35.112202.130124 · Cited by 489
Cited by
Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices
Chernomor, O., von Haeseler, A., & Minh, B. Q. (2016) · Systematic Biology · doi:10.1093/sysbio/syw037 · Cited by 2,252
A phylogenomic study of birds reveals their evolutionary history
Hackett, S. J., Kimball, R. T., Reddy, S., Bowie, R. C. K., Braun, E. L., Braun, M. J., Chojnowski, J. L., Cox, W. A., Han, K.-L., Harshman, J., et al. (2008) · Science · doi:10.1126/science.1157704 · Cited by 2,125
Toward Automatic Reconstruction of a Highly Resolved Tree of Life
Ciccarelli, F. D., Doerks, T., von Mering, C., Creevey, C. J., Snel, B., & Bork, P. (2006) · Science · doi:10.1126/science.1123061 · Cited by 1,663
Tunicates and not cephalochordates are the closest living relatives of vertebrates
Delsuc, F., Brinkmann, H., Chourrout, D., & Philippe, H. (2006) · Nature · doi:10.1038/nature04336 · Cited by 1,651
Self-citationAsgard 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
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
Self-citationLartillot, N., Brinkmann, H., & Philippe, H. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-s1-s4 · Cited by 705
Self-citationPhylogenomics: The beginning of incongruence?
JEFFROY, O., BRINKMANN, H., DELSUC, F., & PHILIPPE, H. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.02.003 · Cited by 698
Self-citationInsights into bilaterian evolution from three spiralian genomes
Simakov, O., Marletaz, F., Cho, S.-J., Edsinger-Gonzales, E., Havlak, P., Hellsten, U., Kuo, D.-H., Larsson, T., Lv, J., Arendt, D., et al. (2013) · Nature · doi:10.1038/nature11696 · Cited by 656
eggNOG v4.0: nested orthology inference across 3686 organisms
Powell, S., Forslund, K., Szklarczyk, D., Trachana, K., Roth, A., Huerta-Cepas, J., Gabaldón, T., Rattei, T., Creevey, C., Kuhn, M., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1253 · Cited by 652
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
Taxon sampling and the accuracy of phylogenetic analyses
(2008) · Journal of Systematics and Evolution · doi:10.3724/sp.j.1002.2008.08016 · Cited by 553
Pattern pluralism and the Tree of Life hypothesis
Doolittle, W. F., & Bapteste, E. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0610699104 · Cited by 546
Phylogenetic tree building in the genomic age
Kapli, P., Yang, Z., & Telford, M. J. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0233-0 · Cited by 533
TreeFam: a curated database of phylogenetic trees of animal gene families
Li, H. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj118 · Cited by 523
Contentious relationships in phylogenomic studies can be driven by a handful of genes
Shen, X.-X., Hittinger, C. T., & Rokas, A. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0126 · Cited by 520
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis.
(2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-99 · Cited by 475
Wang, H.-C., Minh, B. Q., Susko, E., & Roger, A. J. (2018) · Systematic Biology · doi:10.1093/sysbio/syx068 · Cited by 466
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
Impact of missing data on phylogenies inferred from empirical phylogenomic data sets
Roure, B., Baurain, D., & Philippe, H. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mss208 · Cited by 365
Self-citationThe origin and early evolution of eukaryotes in the light of phylogenomics
Koonin, E. V. (2010) · Genome Biology · doi:10.1186/gb-2010-11-5-209 · Cited by 345
Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies
Rodríguez-Ezpeleta, N., Brinkmann, H., Roure, B., Lartillot, N., Lang, B. F., & Philippe, H. (2007) · Systematic Biology · doi:10.1080/10635150701397643 · Cited by 323
Self-citationPhilippe, H., Delsuc, F., Brinkmann, H., & Lartillot, N. (2005) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev.ecolsys.35.112202.130205 · Cited by 306
Self-citationResolution of Phylogenetic Conflict in Large Data Sets by Increased Taxon Sampling
Hedtke, S. M., Townsend, T. M., & Hillis, D. M. (2006) · Systematic Biology · doi:10.1080/10635150600697358 · Cited by 303
Burki, F., Kaplan, M., Tikhonenkov, D. V., Zlatogursky, V., Minh, B. Q., Radaykina, L. V., Smirnov, A., Mylnikov, A. P., & Keeling, P. J. (2016) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2015.2802 · Cited by 301
A Post-Synaptic Scaffold at the Origin of the Animal Kingdom
Sakarya, O., Armstrong, K. A., Adamska, M., Adamski, M., Wang, I.-F., Tidor, B., Degnan, B. M., Oakley, T. H., & Kosik, K. S. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000506 · Cited by 291
“[3], is that sponges and Cnidarians form part of a monophyletic”
BackgroundHaMStR: Profile hidden markov model based search for orthologs in ESTs
Ebersberger, I., Strauss, S., & von Haeseler, A. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-157 · Cited by 288
Phylogenomic evidence for multiple losses of flight in ratite birds
Harshman, J., Braun, E. L., Braun, M. J., Huddleston, C. J., Bowie, R. C. K., Chojnowski, J. L., Hackett, S. J., Han, K.-L., Kimball, R. T., Marks, B. D., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0803242105 · Cited by 239
The Tree and Net Components of Prokaryote Evolution
Puigbò, P., Wolf, Y. I., & Koonin, E. V. (2010) · Genome Biology and Evolution · doi:10.1093/gbe/evq062 · Cited by 181
Torruella, G., Derelle, R., Paps, J., Lang, B. F., Roger, A. J., Shalchian-Tabrizi, K., & Ruiz-Trillo, I. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/msr185 · Cited by 169
Huerta-Cepas, J., Dopazo, H., Dopazo, J., & Gabaldón, T. (2007) · Genome Biology · doi:10.1186/gb-2007-8-6-r109 · Cited by 176
Pitfalls in supermatrix phylogenomics
Philippe, H., Vienne, D. M. D., Ranwez, V., Roure, B., Baurain, D., & Delsuc, F. (2017) · European Journal of Taxonomy · doi:10.5852/ejt.2017.283 · Cited by 173
Self-citationRyan, J. F., Pang, K., Program, N. C. S., Mullikin, J. C., Martindale, M. Q., & Baxevanis, A. D. (2010) · EvoDevo · doi:10.1186/2041-9139-1-9 · Cited by 160
“Methods based on whole-genome content rather than large concatenated data matrices can provide an independent assessment of current phylogenetic hypotheses and, due to the rarity of events measured, may arguably be more appropriate in this context [14,16].”
BackgroundThe impact of fossils and taxon sampling on ancient molecular dating analyses
Hug, L. A., & Roger, A. J. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm115 · Cited by 144
Lateral gene transfer as a support for the tree of life
Abby, S. S., Tannier, E., Gouy, M., & Daubin, V. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1116871109 · Cited by 133
Cloutier, A., Sackton, T. B., Grayson, P., Clamp, M., Baker, A. J., & Edwards, S. V. (2019) · Systematic Biology · doi:10.1093/sysbio/syz019 · Cited by 124
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
Phylogenetic Signal, Congruence, and Uncertainty across Bacteria and Archaea
Martinez-Gutierrez, C. A., & Aylward, F. O. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab254 · Cited by 95
PETERSON, K. J., SUMMONS, R. E., & DONOGHUE, P. C. J. (2007) · Palaeontology · doi:10.1111/j.1475-4983.2007.00692.x · Cited by 93
Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition
Taib, N., Megrian, D., Witwinowski, J., Adam, P., Poppleton, D., Borrel, G., Beloin, C., & Gribaldo, S. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-01299-7 · Cited by 82
Genome structures resolve the early diversification of teleost fishes
Parey, E., Louis, A., Montfort, J., Bouchez, O., Roques, C., Iampietro, C., Lluch, J., Castinel, A., Donnadieu, C., Desvignes, T., et al. (2023) · Science · doi:10.1126/science.abq4257 · Cited by 87
Marcet-Houben, M., & Gabaldón, T. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004357 · Cited by 83
Comparative bioacoustics: a roadmap for quantifying and comparing animal sounds across diverse taxa
Odom, K. J., Araya‐Salas, M., Morano, J. L., Ligon, R. A., Leighton, G. M., Taff, C. C., Dalziell, A. H., Billings, A. C., Germain, R. R., Pardo, M., et al. (2021) · Biological Reviews · doi:10.1111/brv.12695 · Cited by 81
Novel scenarios of early animal evolution--is it time to rewrite textbooks?
Dohrmann, M., & Worheide, G. (2013) · Integrative and Comparative Biology · doi:10.1093/icb/ict008 · Cited by 71
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
Roure, B., & Philippe, H. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-17 · Cited by 64
Self-citationAgent of whirling disease meets orphan worm: phylogenomic analyses firmly place Myxozoa in Cnidaria
Nesnidal, M. P., Helmkampf, M., Bruchhaus, I., El-Matbouli, M., & Hausdorf, B. (2013) · PLoS ONE · doi:10.1371/journal.pone.0054576 · Cited by 64
Chen, D., Hosner, P. A., Dittmann, D. L., O’Neill, J. P., Birks, S. M., Braun, E. L., & Kimball, R. T. (2021) · BMC Ecology and Evolution · doi:10.1186/s12862-021-01935-1 · Cited by 52
Markov, G. V., Paris, M., Bertrand, S., & Laudet, V. (2008) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2008.06.011 · Cited by 48
Yang, C., Lin, F., Li, Q., Li, T., & Zhao, J. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00394 · Cited by 44
The mouth, the anus, and the blastopore—open questions about questionable openings
Hejnol, A., & Martindale, M. Q. (2009) · Animal Evolution · doi:10.1093/acprof:oso/9780199549429.003.0004 · Cited by 37
Koonin, E. V. (2014) · Antonie van Leeuwenhoek · doi:10.1007/s10482-014-0169-5 · Cited by 34
Dai, W., Zou, M., Yang, L., Du, K., Chen, W., Shen, Y., Mayden, R. L., & He, S. (2018) · Scientific Reports · doi:10.1038/s41598-017-18432-5 · Cited by 26
Genomic, phylogenetic, and cell biological insights into metazoan origins
Nichols, S. A., Dayel, M. J., & King, N. (2009) · Animal Evolution · doi:10.1093/acprof:oso/9780199549429.003.0003 · Cited by 24
Arnoldt, H., Strogatz, S. H., & Timme, M. (2015) · Physical Review E · doi:10.1103/physreve.92.052909 · Cited by 17
Metadata
- Authors
- Delsuc, F., Brinkmann, H., & Philippe, H.
- Venue
- Nature Reviews Genetics
- Published
- 2005-05
- Volume
- 6
- Issue
- 5
- Pages
- 361-375
- ISSN
- 1471-0056 (ISSN-L)
- 1471-0064
- OpenAlex
- W2056568233
- Cited by
- 1,236
- References
- 21
- FWCI
- 3.99
- Type
- journal article
- Language
- en
- Open access
- green
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
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
