ArticleNature ecology & evolution2017
Contentious relationships in phylogenomic studies can be driven by a handful of genes.
Article in Nature ecology & evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 170 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
170 citing papers in PubMed.
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- Phylogenomic conflict in Moraceae: Evidence for pervasive introgression and incomplete lineage sorting.Plant diversity · 2026Article
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- CAnDI: A New Tool to Investigate Conflict in Homologous Gene Trees and Explain Convergent Trait Evolution.Systematic biology · 2026Article
- Article
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- Comparative genomics reveals evolutionary signatures of genes associated with jumping in beetles.Zoological research · 2026Article
- Biological causes and impacts of rugged tree landscapes in phylodynamic inference.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Dissecting discordance of mitochondrial and nuclear phylogenetic trees in insects.Crop health · 2025Article
- Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants.Systematic biology · 2025Article
- A co-speciation dilemma and a lifestyle transition with genomic consequences in Wolbachia of Neotropical Drosophila.BMC genomics · 2025Article
- Phylogenomic and Population Genomic Analyses of Ultraconserved Elements Reveal Deep Coalescence and Introgression Shaped Diversification Patterns in Lamprologine Cichlids of the Congo River.Systematic biology · 2025Article
- Contamination of fungal genomes of Onygenaceae (Phylum Ascomycota) in public databases: incidence, detection, and impact.BMC genomics · 2025Article
- Early Biogeography of Otophysi Points to the Neotropics as the Cradle of Characiphysan Fishes.Ecology and evolution · 2025Article
- Ortho2Web: a workflow for disentangling the roles of hybridization and allopolyploidization in reticulation within Campanulaceae.BMC biology · 2025Article
- MyESL: A Software for Evolutionary Sparse Learning in Molecular Phylogenetics and Genomics.Molecular biology and evolution · 2025Article
110 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
Phylogenomic studies have resolved countless branches of the tree of life, but remain strongly contradictory on certain, contentious relationships. Here, we use a maximum likelihood framework to quantify the distribution of phylogenetic signal among genes and sites for 17 contentious branches and 6 well-established control branches in plant, animal and fungal phylogenomic data matrices. We find that resolution in some of these 17 branches rests on a single gene or a few sites, and that removal of a single gene in concatenation analyses or a single site from every gene in coalescence-based analyses diminishes support and can alter the inferred topology. These results suggest that tiny subsets of very large data matrices drive the resolution of specific internodes, providing a dissection of the distribution of support and observed incongruence in phylogenomic analyses. We submit that quantifying the distribution of phylogenetic signal in phylogenomic data is essential for evaluating whether branches, especially contentious ones, are truly resolved. Finally, we offer one detailed example of such an evaluation for the controversy regarding the earliest-branching metazoan phylum, for which examination of the distributions of gene-wise and site-wise phylogenetic signal across eight data matrices consistently supports ctenophores as the sister group to all other metazoans.
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