The DOI matches its Crossref record; 39 of the 39 references it cites were found in a registry or an index.
Phylogenomics: the beginning of incongruence?
Open accessAbstract
Until recently, molecular phylogenies based on a single or few orthologous genes often yielded contradictory results. Using multiple genes in a large concatenation was proposed to end these incongruences. Here we show that single-gene phylogenies often produce incongruences, albeit ones lacking statistically significant support. By contrast, the use of different tree reconstruction methods on different partitions of the concatenated supergene leads to well-resolved, but real (i.e. statistically significant) incongruences. Gathering a large amount of data is not sufficient to produce reliable trees, given the current limitation of tree reconstruction methods, especially when the quality of data is poor. We propose that selecting only data that contain minimal nonphylogenetic signals takes full advantage of phylogenomics and markedly reduces incongruence.
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“Additional sources of systematic error include poor taxon or character sampling (10,14,15), large amounts of missing data (16), and model misspecification (16,17).”
From Error, signal, and the placement of Ctenophora sister to all other animals (2015) · cites this paper as [15]
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1 retracted
RETRACTED ARTICLE: TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics
Jobb, G., von Haeseler, A., & Strimmer, K. (2004) · BMC Evolutionary Biology · doi:10.1186/1471-2148-4-18 · Cited by 1,109
RetractedMrBayes 3: Bayesian phylogenetic inference under mixed models
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A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
Guindon, S., & Gascuel, O. (2003) · Systematic Biology · doi:10.1080/10635150390235520 · Cited by 16,923
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Swofford, D. L. (2001) · Cited by 12,789
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
Castresana, J. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026334 · Cited by 10,681
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
Edgar, R. C. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-113 · Cited by 9,119
PAUP * [Phylogenetic Analysis Using Parsimony (and Other Methods)]
Cummings, M. P. (2004) · Wiley eBooks · doi:10.1002/0471650129.dob0522 · Cited by 5,252
An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis
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Cases in which Parsimony or Compatibility Methods Will be Positively Misleading
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Wooding, S. (2004) · The American Journal of Human Genetics · doi:10.1086/383584 · Cited by 3,093
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Talavera, G., & Castresana, J. (2007) · Systematic Biology · doi:10.1080/10635150701472164 · Cited by 5,599
Whole-genome analyses resolve early branches in the tree of life of modern birds
Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., Ho, S. Y. W., Faircloth, B. C., Nabholz, B., Howard, J. T., et al. (2014) · Science · doi:10.1126/science.1253451 · Cited by 1,901
Anisimova, M. O., Gil, M., Dufayard, J.-F., Dessimoz, C., & Gascuel, O. (2011) · Systematic Biology · doi:10.1093/sysbio/syr041 · Cited by 1,323
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-citationThe genome of Eucalyptus grandis
Myburg, A. A., Grattapaglia, D., Tuskan, G. A., Hellsten, U., Hayes, R. D., Grimwood, J., Jenkins, J. W., Lindquist, E., Tice, H. N., Bauer, D., et al. (2014) · Nature · doi:10.1038/nature13308 · Cited by 938
Metadata
- Authors
- JEFFROY, O., BRINKMANN, H., DELSUC, F., & PHILIPPE, H.
- Affiliations
- Canadian Institute for Advanced Research (CA)
- Corresponding author
- PHILIPPE, H
- Venue
- Trends in Genetics
- Publisher
- Elsevier BV
- Published
- 2006-04
- Volume
- 22
- Issue
- 4
- Pages
- 225-231
- ISSN
- 0168-9525 (ISSN-L)
- OpenAlex
- W2140099453
- Cited by
- 698
- References
- 39
- Citations by year
- 2026: 17 · 2025: 27 · 2024: 27 · 2023: 38 · 2022: 26 · 2021: 28 · 2020: 62 · 2019: 64 · 2018: 33 · 2017: 45 · 2016: 33 · 2015: 29 · 2014: 40 · 2013: 32 · 2012: 41
- FWCI
- 13.58
- Type
- journal article
- Language
- en
- Open access
- green
- hal.science
- Licence
- Locations
- Trends in Genetics (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- 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 › Plant Diversity and Evolution
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Protist diversity and phylogeny
- Keywords
- phylogenomics, phylogenetic incongruence, single-gene phylogeny, orthologs, data selection
- MeSH terms
- Models, Biological, Nucleotides, Phylogeny, Yeasts, Genome, Fungal, Genomics
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