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Model selection may not be a mandatory step for phylogeny reconstruction
Determining the most suitable model for phylogeny reconstruction constitutes a fundamental step in numerous evolutionary studies. Over the years, various criteria for model selection have been proposed, leading to debate over which criterion is preferable. However, the necessity of this procedure ha...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6389923/ https://www.ncbi.nlm.nih.gov/pubmed/30804347 http://dx.doi.org/10.1038/s41467-019-08822-w |
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author | Abadi, Shiran Azouri, Dana Pupko, Tal Mayrose, Itay |
author_facet | Abadi, Shiran Azouri, Dana Pupko, Tal Mayrose, Itay |
author_sort | Abadi, Shiran |
collection | PubMed |
description | Determining the most suitable model for phylogeny reconstruction constitutes a fundamental step in numerous evolutionary studies. Over the years, various criteria for model selection have been proposed, leading to debate over which criterion is preferable. However, the necessity of this procedure has not been questioned to date. Here, we demonstrate that although incongruency regarding the selected model is frequent over empirical and simulated data, all criteria lead to very similar inferences. When topologies and ancestral sequence reconstruction are the desired output, choosing one criterion over another is not crucial. Moreover, skipping model selection and using instead the most parameter-rich model, GTR+I+G, leads to similar inferences, thus rendering this time-consuming step nonessential, at least under current strategies of model selection. |
format | Online Article Text |
id | pubmed-6389923 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-63899232019-02-27 Model selection may not be a mandatory step for phylogeny reconstruction Abadi, Shiran Azouri, Dana Pupko, Tal Mayrose, Itay Nat Commun Article Determining the most suitable model for phylogeny reconstruction constitutes a fundamental step in numerous evolutionary studies. Over the years, various criteria for model selection have been proposed, leading to debate over which criterion is preferable. However, the necessity of this procedure has not been questioned to date. Here, we demonstrate that although incongruency regarding the selected model is frequent over empirical and simulated data, all criteria lead to very similar inferences. When topologies and ancestral sequence reconstruction are the desired output, choosing one criterion over another is not crucial. Moreover, skipping model selection and using instead the most parameter-rich model, GTR+I+G, leads to similar inferences, thus rendering this time-consuming step nonessential, at least under current strategies of model selection. Nature Publishing Group UK 2019-02-25 /pmc/articles/PMC6389923/ /pubmed/30804347 http://dx.doi.org/10.1038/s41467-019-08822-w Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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 images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Abadi, Shiran Azouri, Dana Pupko, Tal Mayrose, Itay Model selection may not be a mandatory step for phylogeny reconstruction |
title | Model selection may not be a mandatory step for phylogeny reconstruction |
title_full | Model selection may not be a mandatory step for phylogeny reconstruction |
title_fullStr | Model selection may not be a mandatory step for phylogeny reconstruction |
title_full_unstemmed | Model selection may not be a mandatory step for phylogeny reconstruction |
title_short | Model selection may not be a mandatory step for phylogeny reconstruction |
title_sort | model selection may not be a mandatory step for phylogeny reconstruction |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6389923/ https://www.ncbi.nlm.nih.gov/pubmed/30804347 http://dx.doi.org/10.1038/s41467-019-08822-w |
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