The DOI matches its Crossref record; 68 of the 71 references it cites were found in a registry or an index.
How good are deep phylogenetic trees?
Abstract
Great interest is given to species emerging early in phylogenetic reconstruction because they are often assumed to represent an ancestor. Recent studies indicate, however, that species branching deep in molecular trees are often fast-evolving ones, misplaced because of the long-branch artefact. The detection of genuinely deep-branching organisms remains an elusive task.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“the inclusion of outgroups very distant from the ingroup can cause reconstruction artifacts by attracting fast-evolving (long-branched) ingroup species toward the root (25, 27 -31)”
From Genomic data do not support comb jellies as the sister group to all other animals (2015) · cites this paper as [27]
Citations
Cites
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
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 3,261
Cases in which parsimony or compatibility methods will be positively misleading.
Felsenstein, J. (1978) · Systematic Zoology · doi:10.2307/2412923 · Cited by 2,230
Molecular evidence for an ancient duplication of the entire yeast genome
Wolfe, K. H., & Shields, D. C. (1997) · Nature · doi:10.1038/42711 · Cited by 1,785
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
Among-site rate variation and its impact on phylogenetic analyses
Yang, Z. (1996) · Trends in Ecology & Evolution · doi:10.1016/0169-5347(96)10041-0 · Cited by 1,202
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
A Framework for the Quantitative Study of Evolutionary Trees
Hendy, M. D., & Penny, D. (1989) · Systematic Zoology · doi:10.2307/2992396 · Cited by 803
Is It Better to Add Taxa or Characters to a Difficult Phylogenetic Problem?
Graybeal, A. (1998) · Systematic Biology · doi:10.1080/106351598260996 · Cited by 745
Gene translocation links insects and crustaceans
Boore, J. L., Lavrov, D. V., & Brown, W. M. (1998) · Nature · doi:10.1038/33577 · Cited by 695
Research works printed but not linked: 3
- Roger, 1998, An evaluation of Elongation Factor 1α as a phylogenetic marker for Eukaryotes, Mol Biol Evol
- Dayhoff, 1978, A model of evolutionary change in proteins, Atlas Protein Struct, 5, 345
- Lopez, 1998, A method for extracting ancient phylogenetic signal: the rooting of the universal tree of life based on elongation factors, J Mol Evol
Cited by
Sorted by citations
Items 301–324 of 324
(2020) · PeerJ · doi:10.7287/peerj.8995v0.2/reviews/2
“…tree (Sousa et al. 2019), the 108 taxon sampling is deliberately restricted to include a proportional selection of bryophytes (11 109 taxa) and tracheophytes (10) as symmetrical trees improve estimation (Huang and Knowles 110 2009) and minimise long branch attraction (Philippe and Laurent 1998).”
BackgroundL'évolution moléculaire et la révolution génomique.Preprint
Lang, B. F., Paquin, B., & Burger, G. (2017) · OSF Preprints (OSF Preprints) · doi:10.31219/osf.io/9y7ha
(2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.002.0004
(2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.002.0003
(2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.002.0007
(2009) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199549429.002.0008
Chaudhuri, A. (2022) · International Journal of Advanced Research in Biological Sciences (IJARBS) · doi:10.22192/ijarbs.2022.09.09.001
(2024) · Elsevier eBooks · doi:10.1016/b978-0-443-21719-7.10000-1
Ankel‐Simons, F. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-21719-7.00014-x
Kurihara, H., Shirai, S. M., Fujiwara, K., & Ikeda, M. (2024) · Ichthyological Research · doi:10.1007/s10228-024-00978-w
“…are constrained to be the four bases A, T, G, and C and base substitutions are reversible mutational processes, the probability of homoplasy caused by convergence or parallelism increases as the evolutionary distance between the compared taxa increases (Minaka 1997; Philippe and Laurent 1998).”
Donoso, A., Moreno-Lorenzo, M., Delgado, E., Cañada-García, J. E., Iribarren, J. A., Salicio, Y., Benito, S., Lorente‐Sorolla, C., Romero-Guerrero, J. D., Baza, M. B., et al. (2026) · Viruses · doi:10.3390/v18010101
Unique genes in plants : features, evolution and promoters
Giménez, D. S. A. (2008) · theses.fr (ABES) · doi:10.70675/45167e6ezf661z478eza6cezfa60e00dc1a9
Identification, évolution et mort cellulaire chez un groupe de protistes, les Parabasalia
Mantini, C. (2010) · theses.fr (ABES) · doi:10.70675/f770cdb7z2effz4108zbb20z40269efdeb13
Evolution et coévolution des petits ARNs régulateurs et des gènes codants chez les bactéries
Cerutti, F. (2018) · theses.fr (ABES) · doi:10.70675/2c76ef89z0680z4a91z969az00a38f354e3e
Phylogenomic study of the evolutionary history of the Archaea and their link with eukaryogenesis
Aouad, M. (2018) · theses.fr (ABES) · doi:10.70675/f9fbb237z6ebfz42f5zb132zaed46e39783a
Fossilisation expérimentale du monde à ARN
Jacquemot, P. (2020) · theses.fr (ABES) · doi:10.70675/941e8aa5zcb6cz4abaza0f7zdac9be2a29c4
Deep archaeal phylogeny and evolutionary dynamics of DPANNs
Baker, B. A. (2024) · theses.fr (ABES) · doi:10.70675/d2a702bfzb170z4a5fz9317z2d27179942d0
Assessing the Earliest Evidence for Life in the Geologic and Genomic Records
Bell, E. A., & Fournier, G. P. (2026) · Astrobiology · doi:10.1177/15311074261454242
“In addition, multiple substitutions over long evolutionary distances overprint informative sequence substi-tution events and effectively erase earlier evolutionary information (Philippe and Laurent, 1998; Duchêne et al., 2022).”
Data from: Maximum likelihood inference of small trees in the presence of long branches
Goldman, N., & Parks, S. L. (2014) · Data Archiving and Networked Services (DANS) · doi:10.5061/dryad.rp7qv.1
Metadata
- Authors
- Philippe, H., & Laurent, J.
- Affiliations
- Université Paris-Sud (FR)
- Corresponding author
- Philippe, Hervé
- ORCID
- Philippe, Hervé
- Venue
- Current Opinion in Genetics & Development
- Publisher
- Elsevier BV
- Published
- 1998-12
- Volume
- 8
- Issue
- 6
- Pages
- 616-623
- ISSN
- 0959-437X (ISSN-L)
- OpenAlex
- W2022561965
- Cited by
- 324
- References
- 71
- Citations by year
- 2026: 3 · 2025: 1 · 2024: 6 · 2023: 2 · 2022: 3 · 2021: 2 · 2020: 12 · 2019: 9 · 2018: 5 · 2017: 8 · 2015: 9 · 2014: 9 · 2013: 4 · 2012: 9
- FWCI
- 1.66
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Current Opinion in Genetics & Development (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Protist diversity and phylogeny
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Keywords
- molecular phylogeny, ancestral species, phylogenetic inference
- MeSH terms
- Animals, Humans, Phylogeny, Evolution, Molecular
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
