ArticleSystematic biology2021
Six-State Amino Acid Recoding is not an Effective Strategy to Offset Compositional Heterogeneity and Saturation in Phylogenetic Analyses.
Article in Systematic biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 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
- 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
- Modeling compositional heterogeneity resolves deep phylogeny of flowering plants.Plant diversity · 2025Article
- The Last Universal Common Ancestor of Ribosome-Encoding Organisms: Portrait of LUCA.Journal of molecular evolution · 2024Review
- Phylogenomic diversity of archigregarine apicomplexans.Open biology · 2024Article
- Acoelomorph flatworm monophyly is a long-branch attraction artefact obscuring a clade of Acoela and Xenoturbellida.Proceedings. Biological sciences · 2024Article
- Ocean to Tree: Leveraging Single-Molecule RNA-Seq to Repair Genome Gene Models and Improve Phylogenomic Analysis of Gene and Species Evolution.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Bases-dependent Rapid Phylogenetic Clustering (Bd-RPC) enables precise and efficient phylogenetic estimation in viruses.Virus evolution · 2024Article
- Incongruence in the phylogenomics era.Nature reviews. Genetics · 2023Review
- Early Divergence and Gene Exchange Highways in the Evolutionary History of Mesoaciditogales.Genome biology and evolution · 2023Article
- Major Revisions in Pancrustacean Phylogeny and Evidence of Sensitivity to Taxon Sampling.Molecular biology and evolution · 2023Review
- 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
- 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
- Article
- A Practical Guide to Design and Assess a Phylogenomic Study.Genome biology and evolution · 2022Article
- BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data.Genetics · 2022Article
- Polyzoa is back: The effect of complete gene sets on the placement of Ectoprocta and Entoprocta.Science advances · 2022Article
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2 authors.
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Abstract
Six-state amino acid recoding strategies are commonly applied to combat the effects of compositional heterogeneity and substitution saturation in phylogenetic analyses. While these methods have been endorsed from a theoretical perspective, their performance has never been extensively tested. Here, we test the effectiveness of six-state recoding approaches by comparing the performance of analyses on recoded and non-recoded data sets that have been simulated under gradients of compositional heterogeneity or saturation. In our simulation analyses, non-recoding approaches consistently outperform six-state recoding approaches. Our results suggest that six-state recoding strategies are not effective in the face of high saturation. Furthermore, while recoding strategies do buffer the effects of compositional heterogeneity, the loss of information that accompanies six-state recoding outweighs its benefits. In addition, we evaluate recoding schemes with 9, 12, 15, and 18 states and show that these consistently outperform six-state recoding. Our analyses of other recoding schemes suggest that under conditions of very high compositional heterogeneity, it may be advantageous to apply recoding using more than six states, but we caution that applying any recoding should include sufficient justification. Our results have important implications for the more than 90 published papers that have incorporated six-state recoding, many of which have significant bearing on relationships across the tree of life. [Compositional heterogeneity; Dayhoff 6-state recoding; S&R 6-state recoding; six-state amino acid recoding; substitution saturation.].
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