ArticleGenome biology and evolution2019
The Prevalence and Impact of Model Violations in Phylogenetic Analysis.
Article in Genome biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed.
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- Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants.Systematic biology · 2025Article
- Towards molecular evolutionary epigenomics with an expanded nucleotide code involving methylated bases.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
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- Dating the Origin and Spread of Plastids and Chromatophores.International journal of molecular sciences · 2025Article
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- Evolutionary sparse learning reveals the shared genetic basis of convergent traits.Nature communications · 2025Article
- Robustness of Ancestral Sequence Reconstruction to Among-site and Among-lineage Evolutionary Heterogeneity.Molecular biology and evolution · 2025Article
- Unraveling myriapod evolution: sealion, a novel quartet-based approach for evaluating phylogenetic uncertainty.NAR genomics and bioinformatics · 2025Article
- nT4X and nT4M: Novel Time Non-reversible Mixture Amino Acid Substitution Models.Journal of molecular evolution · 2025Article
- A shared developmental genetic basis for sexually antagonistic male and female adaptations in the toothed water strider.Evolution letters · 2025Article
- Dating the origin of a viral domestication event in parasitoid wasps attacking Diptera.Proceedings. Biological sciences · 2025Article
- A quartet-based approach for inferring phylogenetically informative features from genomic and phenomic data.Computational and structural biotechnology journal · 2025Article
- The Characterization of Ancient Methanococcales Malate Dehydrogenases Reveals That Strong Thermal Stability Prevents Unfolding Under Intense γ-Irradiation.Molecular biology and evolution · 2024Article
- NeMu: a comprehensive pipeline for accurate reconstruction of neutral mutation spectra from evolutionary data.Nucleic acids research · 2024Article
- Identification, distribution, and hosts ofJournal of nematology · 2024Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In phylogenetic inference, we commonly use models of substitution which assume that sequence evolution is stationary, reversible, and homogeneous (SRH). Although the use of such models is often criticized, the extent of SRH violations and their effects on phylogenetic inference of tree topologies and edge lengths are not well understood. Here, we introduce and apply the maximal matched-pairs tests of homogeneity to assess the scale and impact of SRH model violations on 3,572 partitions from 35 published phylogenetic data sets. We show that roughly one-quarter of all the partitions we analyzed (23.5%) reject the SRH assumptions, and that for 25% of data sets, tree topologies inferred from all partitions differ significantly from topologies inferred using the subset of partitions that do not reject the SRH assumptions. This proportion increases when comparing trees inferred using the subset of partitions that rejects the SRH assumptions, to those inferred from partitions that do not reject the SRH assumptions. These results suggest that the extent and effects of model violation in phylogenetics may be substantial. They highlight the importance of testing for model violations and possibly excluding partitions that violate models prior to tree reconstruction. Our results also suggest that further effort in developing models that do not require SRH assumptions could lead to large improvements in the accuracy of phylogenomic inference. The scripts necessary to perform the analysis are available in https://github.com/roblanf/SRHtests, and the new tests we describe are available as a new option in IQ-TREE (http://www.iqtree.org).
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