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Testing adequacy for DNA substitution models
BACKGROUND: Testing model adequacy is important before a DNA substitution model is chosen for phylogenetic inference. Using a mis-specified model can negatively impact phylogenetic inference, for example, the maximum likelihood method can be inconsistent when the DNA sequences are generated under a...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6585133/ https://www.ncbi.nlm.nih.gov/pubmed/31221105 http://dx.doi.org/10.1186/s12859-019-2905-3 |
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author | Chen, Wei Kenney, Toby Bielawski, Joseph Gu, Hong |
author_facet | Chen, Wei Kenney, Toby Bielawski, Joseph Gu, Hong |
author_sort | Chen, Wei |
collection | PubMed |
description | BACKGROUND: Testing model adequacy is important before a DNA substitution model is chosen for phylogenetic inference. Using a mis-specified model can negatively impact phylogenetic inference, for example, the maximum likelihood method can be inconsistent when the DNA sequences are generated under a tree topology which is in the Felsentein Zone and analyzed with a mis-specified or inadequate model. However, model adequacy testing in phylogenetics is underdeveloped. RESULTS: Here we develop a simple, general, powerful and robust model test based on Pearson’s goodness-of-fit test and binning of site patterns. We demonstrate through simulation that this test is robust in its high power to reject the inadequate models for a large range of different ways of binning site patterns while the Type I error is controlled well. In the real data analysis we discovered many cases where models chosen by another method can be rejected by this new test, in particular, our proposed test rejects the most complex DNA model (GTR+I+ Γ) while the Goldman-Cox test fails to reject the commonly used simple models. CONCLUSIONS: Model adequacy testing and bootstrap should be used together to assess reliability of conclusions after model selection and model fitting have already been applied to choose the model and fit it. The new goodness-of-fit test proposed in this paper is a simple and powerful model adequacy testing method serving such a regular model checking purpose. We caution against deriving strong conclusions from analyses based on inadequate models. At a minimum, those results derived from inadequate models can now be readly flagged using the new test, and reported as such. |
format | Online Article Text |
id | pubmed-6585133 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-65851332019-06-27 Testing adequacy for DNA substitution models Chen, Wei Kenney, Toby Bielawski, Joseph Gu, Hong BMC Bioinformatics Methodology Article BACKGROUND: Testing model adequacy is important before a DNA substitution model is chosen for phylogenetic inference. Using a mis-specified model can negatively impact phylogenetic inference, for example, the maximum likelihood method can be inconsistent when the DNA sequences are generated under a tree topology which is in the Felsentein Zone and analyzed with a mis-specified or inadequate model. However, model adequacy testing in phylogenetics is underdeveloped. RESULTS: Here we develop a simple, general, powerful and robust model test based on Pearson’s goodness-of-fit test and binning of site patterns. We demonstrate through simulation that this test is robust in its high power to reject the inadequate models for a large range of different ways of binning site patterns while the Type I error is controlled well. In the real data analysis we discovered many cases where models chosen by another method can be rejected by this new test, in particular, our proposed test rejects the most complex DNA model (GTR+I+ Γ) while the Goldman-Cox test fails to reject the commonly used simple models. CONCLUSIONS: Model adequacy testing and bootstrap should be used together to assess reliability of conclusions after model selection and model fitting have already been applied to choose the model and fit it. The new goodness-of-fit test proposed in this paper is a simple and powerful model adequacy testing method serving such a regular model checking purpose. We caution against deriving strong conclusions from analyses based on inadequate models. At a minimum, those results derived from inadequate models can now be readly flagged using the new test, and reported as such. BioMed Central 2019-06-20 /pmc/articles/PMC6585133/ /pubmed/31221105 http://dx.doi.org/10.1186/s12859-019-2905-3 Text en © The Author(s) 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License(http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Methodology Article Chen, Wei Kenney, Toby Bielawski, Joseph Gu, Hong Testing adequacy for DNA substitution models |
title | Testing adequacy for DNA substitution models |
title_full | Testing adequacy for DNA substitution models |
title_fullStr | Testing adequacy for DNA substitution models |
title_full_unstemmed | Testing adequacy for DNA substitution models |
title_short | Testing adequacy for DNA substitution models |
title_sort | testing adequacy for dna substitution models |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6585133/ https://www.ncbi.nlm.nih.gov/pubmed/31221105 http://dx.doi.org/10.1186/s12859-019-2905-3 |
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