Cited by 474Genomics and Phylogenetic StudiesRNA and protein synthesis mechanismsEvolution and Paleontology Studies

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Modeling Compositional Heterogeneity

Foster, Peter G·2004·Systematic Biology

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Abstract

Compositional heterogeneity among lineages can compromise phylogenetic analyses, because models in common use assume compositionally homogeneous data. Models that can accommodate compositional heterogeneity with few extra parameters are described here, and used in two examples where the true tree is known with confidence. It is shown using likelihood ratio tests that adequate modeling of compositional heterogeneity can be achieved with few composition parameters, that the data may not need to be modelled with separate composition parameters for each branch in the tree. Tree searching and placement of composition vectors on the tree are done in a Bayesian framework using Markov chain Monte Carlo (MCMC) methods. Assessment of fit of the model to the data is made in both maximum likelihood (ML) and Bayesian frameworks. In an ML framework, overall model fit is assessed using the Goldman-Cox test, and the fit of the composition implied by a (possibly heterogeneous) model to the composition of the data is assessed using a novel tree-and model-based composition fit test. In a Bayesian framework, overall model fit and composition fit are assessed using posterior predictive simulation. It is shown that when composition is not accommodated, then the model does not fit, and incorrect trees are found; but when composition is accommodated, the model then fits, and the known correct phylogenies are obtained.

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Authors: Foster, P. G.
Affiliations: Natural History Museum (GB)
Corresponding author: Foster, Peter G
ORCID: Foster, Peter G
Venue: Systematic Biology
Publisher: Oxford University Press (OUP)
Published: 2004-06-01
Volume: 53
Issue: 3
Pages: 485-495
ISSN: 1063-5157 (ISSN-L)
1076-836X
DOI: 10.1080/10635150490445779
OpenAlex: W2168573791
Cited by: 474
References: 44
Citations by year: 2026: 9 · 2025: 15 · 2024: 12 · 2023: 18 · 2022: 25 · 2021: 22 · 2020: 30 · 2019: 29 · 2018: 24 · 2017: 24 · 2016: 11 · 2015: 37 · 2014: 48 · 2013: 22 · 2012: 19
FWCI: 4.47
Type: journal article
Language: en
Open access: closed
Licence: academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor, 4601 d)
Locations: Systematic Biology (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
Keywords: compositional heterogeneity, phylogenetic models, likelihood ratio test, model fit assessment, posterior predictive simulation, Bayesian phylogenetics, Markov chain Monte Carlo, tree search, model misspecification
MeSH terms: Base Composition, Bayes Theorem, Classification, Computer Simulation, Markov Chains, Models, Genetic, Monte Carlo Method, Phylogeny, Likelihood Functions

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