Inferring ancient divergences requires genes with strong phylogenetic signals
Abstract
To tackle incongruence, the topological conflict between different gene trees, phylogenomic studies couple concatenation with practices such as rogue taxon removal or the use of slowly evolving genes. Phylogenomic analysis of 1,070 orthologues from 23 yeast genomes identified 1,070 distinct gene trees, which were all incongruent with the phylogeny inferred from concatenation. Incongruence severity increased for shorter internodes located deeper in the phylogeny. Notably, whereas most practices had little or negative impact on the yeast phylogeny, the use of genes or internodes with high average internode support significantly improved the robustness of inference. We obtained similar results in analyses of vertebrate and metazoan phylogenomic data sets. These results question the exclusive reliance on concatenation and associated practices, and argue that selecting genes with strong phylogenetic signals and demonstrating the absence of significant incongruence are essential for accurately reconstructing ancient divergences.
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In an analysis of 1030 gene trees of one-to-one orthologs from 23 fungi species, all 1030 gene trees were topologically distinct from each other and from the species tree.
“For example, in an analysis of 1030 gene trees of one-to-one orthologs from 23 fungi species, all 1030 gene trees were topologically distinct from each other and from the species tree [40].”
From OrthoFinder: phylogenetic orthology inference for comparative genomics (2019) · cites this paper as [40]
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- Authors
- Salichos, L., & Rokas, A.
- Affiliations
- Vanderbilt University (US)
- Corresponding author
- Rokas, Antonis
- Venue
- Nature
- Published
- 2013-05
- Volume
- 497
- Issue
- 7449
- Pages
- 327-331
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2012220164
- Cited by
- 616
- References
- 9
- Citations by year
- 2026: 29 · 2025: 29 · 2024: 37 · 2023: 29 · 2022: 28 · 2021: 43 · 2020: 48 · 2019: 52 · 2018: 53 · 2017: 68 · 2016: 58 · 2015: 65 · 2014: 56 · 2013: 21
- FWCI
- 25.36
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protist diversity and phylogeny
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Keywords
- gene tree discordance, phylogenetic signal strength, gene tree reconciliation, yeast phylogeny, orthologs, phylogenetic robustness
- MeSH terms
- Candida, Genes, Fungal, Models, Genetic, Phylogeny, Saccharomyces, Time Factors, Sequence Alignment, Genome, Fungal, Evolution, Molecular, Databases, Genetic
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