ArticleiScience2022
Resolving tricky nodes in the tree of life through amino acid recoding.
Article in iScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- The Dayhoff Exchange Score: A New Metric to Quantify Entropic Site Saturation in Amino Acid Data Sets Prior to Phylogenetic Analysis.Systematic biology · 2026Article
- Article
- Phylogenomic mixture models outperform homogeneous and partitioned models.Molecular biology and evolution · 2026Article
- Conflict in ant phylogeny results from complex interaction between multiple evolutionary signals and tree reconstruction artifacts.Molecular biology and evolution · 2026Article
- Toward a genomic understanding of the tree of life.Molecular biology and evolution · 2026Article
- Uncertainties in the phylogeny and biogeography of cave crickets.Communications biology · 2025Article
- Ant phylogeny is not resolved by the application of site heterogeneous models.Communications biology · 2025Article
- CAT-Posterior Mean Site Frequencies Improves Phylogenetic Modeling Under Maximum Likelihood and Resolves Tardigrada as the Sister of Arthropoda Plus Onychophora.Genome biology and evolution · 2025Article
- Modeling compositional heterogeneity resolves deep phylogeny of flowering plants.Plant diversity · 2025Article
- Ediacaran origin and Ediacaran-Cambrian diversification of Metazoa.Science advances · 2024Article
- Acoelomorph flatworm monophyly is a long-branch attraction artefact obscuring a clade of Acoela and Xenoturbellida.Proceedings. Biological sciences · 2024Article
- Ant backbone phylogeny resolved by modelling compositional heterogeneity among sites in genomic data.Communications biology · 2024Article
- Incongruence in the phylogenomics era.Nature reviews. Genetics · 2023Review
- Major Revisions in Pancrustacean Phylogeny and Evidence of Sensitivity to Taxon Sampling.Molecular biology and evolution · 2023Review
- The monoaminergic system is a bilaterian innovation.Nature communications · 2023Article
- Identifying and addressing methodological incongruence in phylogenomics: A review.Evolutionary applications · 2023Review
- Reply to: Available data do not rule out Ctenophora as the sister group to all other Metazoa.Nature communications · 2023Article
- Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny.Molecular biology and evolution · 2023Article
- Nitric oxide signaling in ctenophores.Frontiers in neuroscience · 2023Article
- A Practical Guide to Design and Assess a Phylogenomic Study.Genome biology and evolution · 2022Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomic data allowed a detailed resolution of the Tree of Life, but "tricky nodes" such as the root of the animals remain unresolved. Genome-scale datasets are heterogeneous as genes and species are exposed to different pressures, and this can negatively impacts phylogenetic accuracy. We use simulated genomic-scale datasets and show that recoding amino acid data improves accuracy when the model does not account for the compositional heterogeneity of the amino acid alignment. We apply our findings to three datasets addressing the root of the animal tree, where the debate centers on whether sponges (Porifera) or comb jellies (Ctenophora) represent the sister of all other animals. We show that results from empirical data follow predictions from simulations and suggest that, at the least in phylogenies inferred from amino acid sequences, a placement of the ctenophores as sister to all the other animals is best explained as a tree reconstruction artifact.
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