ArticleSystematic biology2015
A New Hierarchy of Phylogenetic Models Consistent with Heterogeneous Substitution Rates.
Article in Systematic biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 40 citations in OpenAlex.
- When Complex Models Fit the Wrong Mechanistic Complexity in Phylogenomic Analysis.Journal of molecular evolution · 2026Article
- piqtree: a python package for seamless phylogenetic inference with IQ-TREE.Molecular biology and evolution · 2026Article
- Random-Effects Substitution Models for Phylogenetics via Scalable Gradient Approximations.Systematic biology · 2024Article
- Reliable estimation of tree branch lengths using deep neural networks.PLoS computational biology · 2024Article
- NeMu: a comprehensive pipeline for accurate reconstruction of neutral mutation spectra from evolutionary data.Nucleic acids research · 2024Article
- A region of suppressed recombination misleads neoavian phylogenomics.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Genome report: chromosome-level draft assemblies of the snow leopard, African leopard, and tiger (Panthera uncia, Panthera pardus pardus, and Panthera tigris).G3 (Bethesda, Md.) · 2022Article
- Interrogating Phylogenetic Discordance Resolves Deep Splits in the Rapid Radiation of Old World Fruit Bats (Chiroptera: Pteropodidae).Systematic biology · 2021Article
- Root Digger: a root placement program for phylogenetic trees.BMC bioinformatics · 2021Article
- Felsenstein Phylogenetic Likelihood.Journal of molecular evolution · 2021Article
- The impracticalities of multiplicatively-closed codon models: a retreat to linear alternatives.Journal of mathematical biology · 2020Article
- IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era.Molecular biology and evolution · 2020Article
- The Prevalence and Impact of Model Violations in Phylogenetic Analysis.Genome biology and evolution · 2019Article
- Polymorphism-Aware Species Trees with Advanced Mutation Models, Bootstrap, and Rate Heterogeneity.Molecular biology and evolution · 2019Article
- Position specificity in the genusFungal systematics and evolution · 2018Article
- The Effect of Nonreversibility on Inferring Rooted Phylogenies.Molecular biology and evolution · 2018Article
- Matrix group structure and Markov invariants in the strand symmetric phylogenetic substitution model.Journal of mathematical biology · 2016Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
When the process underlying DNA substitutions varies across evolutionary history, some standard Markov models underlying phylogenetic methods are mathematically inconsistent. The most prominent example is the general time-reversible model (GTR) together with some, but not all, of its submodels. To rectify this deficiency, nonhomogeneous Lie Markov models have been identified as the class of models that are consistent in the face of a changing process of DNA substitutions regardless of taxon sampling. Some well-known models in popular use are within this class, but are either overly simplistic (e.g., the Kimura two-parameter model) or overly complex (the general Markov model). On a diverse set of biological data sets, we test a hierarchy of Lie Markov models spanning the full range of parameter richness. Compared against the benchmark of the ever-popular GTR model, we find that as a whole the Lie Markov models perform well, with the best performing models having 8-10 parameters and the ability to recognize the distinction between purines and pyrimidines.
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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.