Cited by 699Genomics and Phylogenetic StudiesPlant Diversity and EvolutionProtist diversity and phylogeny

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Phylogenomics: the beginning of incongruence?

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JEFFROY, O, BRINKMANN, H, DELSUC, F, PHILIPPE, H·2006·Trends in Genetics

DOI 10.1016/j.tig.2006.02.003

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Abstract

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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Authors: JEFFROY, O., BRINKMANN, H., DELSUC, F., & PHILIPPE, H.
Affiliations: Canadian Institute for Advanced Research (CA)
Corresponding author: PHILIPPE, H
ORCID: BRINKMANN, H
DELSUC, F
PHILIPPE, H
Venue: Trends in Genetics
Publisher: Elsevier BV
Published: 2006-04
Volume: 22
Issue: 4
Pages: 225-231
ISSN: 0168-9525 (ISSN-L)
DOI: 10.1016/j.tig.2006.02.003
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: other-oa
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
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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Phylogenomics: the beginning of incongruence?

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