The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.
Phylogenomics of Eukaryotes: Impact of Missing Data on Large Alignments
Open accessAbstract
Resolving the relationships between Metazoa and other eukaryotic groups as well as between metazoan phyla is central to the understanding of the origin and evolution of animals. The current view is based on limited data sets, either a single gene with many species (e.g., ribosomal RNA) or many genes but with only a few species. Because a reliable phylogenetic inference simultaneously requires numerous genes and numerous species, we assembled a very large data set containing 129 orthologous proteins ( approximately 30,000 aligned amino acid positions) for 36 eukaryotic species. Included in the alignments are data from the choanoflagellate Monosiga ovata, obtained through the sequencing of about 1,000 cDNAs. We provide conclusive support for choanoflagellates as the closest relative of animals and for fungi as the second closest. The monophyly of Plantae and chromalveolates was recovered but without strong statistical support. Within animals, in contrast to the monophyly of Coelomata observed in several recent large-scale analyses, we recovered a paraphyletic Coelamata, with nematodes and platyhelminths nested within. To include a diverse sample of organisms, data from EST projects were used for several species, resulting in a large amount of missing data in our alignment (about 25%). By using different approaches, we verify that the inferred phylogeny is not sensitive to these missing data. Therefore, this large data set provides a reliable phylogenetic framework for studying eukaryotic and animal evolution and will be easily extendable when large amounts of sequence information become available from a broader taxonomic range.
Overview
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
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
Estimation of primate speciation dates using local molecular clocks.
Yoder, A. D., & Yang, Z. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026389 · Cited by 494
Evolution of Key Cell Signaling and Adhesion Protein Families Predates Animal Origins
King, N., Hittinger, C. T., & Carroll, S. B. (2003) · Science · doi:10.1126/science.1083853 · Cited by 424
Fast, N. M., Kissinger, J. C., Roos, D. S., & Keeling, P. J. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003818 · Cited by 418
The Closest Unicellular Relatives of Animals
Lang, B. F., O'Kelly, C., Nerad, T., Gray, M. W., & Burger, G. (2002) · Current Biology · doi:10.1016/s0960-9822(02)01187-9 · Cited by 326
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 · cited 2×
“…phylogenies based on a single gene are generally not well resolved because of the weakness of phylogenetic signal and, more problematically , are highly sensitive to lateral gene transfers (Doolittle 1999), hidden paralogy (Page 2000), and tree reconstruction artifacts (Philippe and Laurent 1998).”
BackgroundSelf-citationThe Rooting of the Universal Tree of Life Is Not Reliable
Philippe, H., & Forterre, P. (1999) · Journal of Molecular Evolution · doi:10.1007/pl00006573 · Cited by 267
Self-citation
Cited by
Relaxed Phylogenetics and Dating with Confidence
Drummond, A. J., Ho, S. Y. W., Phillips, M. J., & Rambaut, A. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040088 · Cited by 6,463
“The metazoan alignment was a subset of a larger dataset comprising 123 genes from 36 eukaryotes [40].”
BackgroundBroad phylogenomic sampling improves resolution of the animal tree of life
Dunn, C. W., Hejnol, A., Matus, D. Q., Pang, K., Browne, W. E., Smith, S. A., Seaver, E., Rouse, G. W., Obst, M., Edgecombe, G. D., et al. (2008) · Nature · doi:10.1038/nature06614 · Cited by 1,921
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-citationThe genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans
King, N., Westbrook, M. J., Young, S. L., Kuo, A., Abedin, M., Chapman, J., Fairclough, S., Hellsten, U., Isogai, Y., Letunic, I., et al. (2008) · Nature · doi:10.1038/nature06617 · Cited by 1,139
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-citation
Metadata
- Authors
- Philippe, H., Snell, E. A., Bapteste, E., Lopez, P., Holland, P. W. H., & Casane, D.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-09
- Volume
- 21
- Issue
- 9
- Pages
- 1740-1752
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2167193190
- Cited by
- 402
- References
- 12
- FWCI
- 10.28
- Type
- journal article
- Language
- en
- Open access
- bronze
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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Phylogenomics of Eukaryotes: Impact of Missing Data on Large Alignments. https://app.cochat.ai/papers/10.1093/molbev/msh182
- The paper
- Philippe, H., Snell, E. A., Bapteste, E., Lopez, P., Holland, P. W. H., & Casane, D. (2004). Phylogenomics of Eukaryotes: Impact of Missing Data on Large Alignments. Molecular Biology and Evolution. https://doi.org/10.1093/molbev/msh182
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.
