ArticleNature2013
Inferring ancient divergences requires genes with strong phylogenetic signals.
Article in Nature, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 265 papers.
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Who cites it
265 citing papers in PubMed.
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- CAnDI: A New Tool to Investigate Conflict in Homologous Gene Trees and Explain Convergent Trait Evolution.Systematic biology · 2026Article
- phyloPipeR: An R Package for End-to-End Phylogenetic Reconstruction and Tree Comparison.Current issues in molecular biology · 2026Article
- The sequence alignment problem: boundary conditions as the unifying principle.Briefings in bioinformatics · 2026Review
- Persistent conflict in palaeognath phylogeny revealed by quartet-based and ML analyses.Frontiers in zoology · 2026Article
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- Practical Guide and Review of Fossil Tip-Dating in Phylogenetics.Systematic biology · 2026Review
- Dissecting mitogenomic conflict to illuminate angiosperm deep phylogeny: Sequence and architectural evidence.Plant diversity · 2026Article
- Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants.Systematic biology · 2025Article
- PickMe: Sample Selection for Species Tree Reconstruction using Coalescent Weighted Quartets.Systematic biology · 2025Article
- Impact of incomplete lineage sorting and natural selection on the phylogenetic and taxonomic uncertainties of Aspidistra in Taiwan.Botanical studies · 2025Article
- Phylogenetic Insights from a NovelPlants (Basel, Switzerland) · 2025Article
- Paleobiome dynamics shaped a large Gondwanan plant radiation.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Concatenation fails to describe the anomalous radiation of giant cockroaches (Blattodea: Blaberidae) despite moderate to low discordance.BMC ecology and evolution · 2025Article
- Deep origins, distinct adaptations, and species-level status indicated for a glacial relict seal.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Ancient Host-Virus Gene Transfer Hints at a Diverse Pre-LECA Virosphere.Journal of molecular evolution · 2025Article
205 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.