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Assessing the Goodness of Fit of Phylogenetic Comparative Methods: A Meta-Analysis and Simulation Study

BACKGROUND: Phylogenetic comparative methods (PCMs) have been applied widely in analyzing data from related species but their fit to data is rarely assessed. QUESTION: Can one determine whether any particular comparative method is typically more appropriate than others by examining comparative data...

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Autor principal: Jhwueng, Dwueng-Chwuan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694968/
https://www.ncbi.nlm.nih.gov/pubmed/23826183
http://dx.doi.org/10.1371/journal.pone.0067001
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author Jhwueng, Dwueng-Chwuan
author_facet Jhwueng, Dwueng-Chwuan
author_sort Jhwueng, Dwueng-Chwuan
collection PubMed
description BACKGROUND: Phylogenetic comparative methods (PCMs) have been applied widely in analyzing data from related species but their fit to data is rarely assessed. QUESTION: Can one determine whether any particular comparative method is typically more appropriate than others by examining comparative data sets? DATA: I conducted a meta-analysis of 122 phylogenetic data sets found by searching all papers in JEB, Blackwell Synergy and JSTOR published in 2002–2005 for the purpose of assessing the fit of PCMs. The number of species in these data sets ranged from 9 to 117. ANALYSIS METHOD: I used the Akaike information criterion to compare PCMs, and then fit PCMs to bivariate data sets through REML analysis. Correlation estimates between two traits and bootstrapped confidence intervals of correlations from each model were also compared. CONCLUSIONS: For phylogenies of less than one hundred taxa, the Independent Contrast method and the independent, non-phylogenetic models provide the best fit.For bivariate analysis, correlations from different PCMs are qualitatively similar so that actual correlations from real data seem to be robust to the PCM chosen for the analysis. Therefore, researchers might apply the PCM they believe best describes the evolutionary mechanisms underlying their data.
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spelling pubmed-36949682013-07-03 Assessing the Goodness of Fit of Phylogenetic Comparative Methods: A Meta-Analysis and Simulation Study Jhwueng, Dwueng-Chwuan PLoS One Research Article BACKGROUND: Phylogenetic comparative methods (PCMs) have been applied widely in analyzing data from related species but their fit to data is rarely assessed. QUESTION: Can one determine whether any particular comparative method is typically more appropriate than others by examining comparative data sets? DATA: I conducted a meta-analysis of 122 phylogenetic data sets found by searching all papers in JEB, Blackwell Synergy and JSTOR published in 2002–2005 for the purpose of assessing the fit of PCMs. The number of species in these data sets ranged from 9 to 117. ANALYSIS METHOD: I used the Akaike information criterion to compare PCMs, and then fit PCMs to bivariate data sets through REML analysis. Correlation estimates between two traits and bootstrapped confidence intervals of correlations from each model were also compared. CONCLUSIONS: For phylogenies of less than one hundred taxa, the Independent Contrast method and the independent, non-phylogenetic models provide the best fit.For bivariate analysis, correlations from different PCMs are qualitatively similar so that actual correlations from real data seem to be robust to the PCM chosen for the analysis. Therefore, researchers might apply the PCM they believe best describes the evolutionary mechanisms underlying their data. Public Library of Science 2013-06-27 /pmc/articles/PMC3694968/ /pubmed/23826183 http://dx.doi.org/10.1371/journal.pone.0067001 Text en © 2013 Dwueng-Chwuan Jhwueng http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Jhwueng, Dwueng-Chwuan
Assessing the Goodness of Fit of Phylogenetic Comparative Methods: A Meta-Analysis and Simulation Study
title Assessing the Goodness of Fit of Phylogenetic Comparative Methods: A Meta-Analysis and Simulation Study
title_full Assessing the Goodness of Fit of Phylogenetic Comparative Methods: A Meta-Analysis and Simulation Study
title_fullStr Assessing the Goodness of Fit of Phylogenetic Comparative Methods: A Meta-Analysis and Simulation Study
title_full_unstemmed Assessing the Goodness of Fit of Phylogenetic Comparative Methods: A Meta-Analysis and Simulation Study
title_short Assessing the Goodness of Fit of Phylogenetic Comparative Methods: A Meta-Analysis and Simulation Study
title_sort assessing the goodness of fit of phylogenetic comparative methods: a meta-analysis and simulation study
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694968/
https://www.ncbi.nlm.nih.gov/pubmed/23826183
http://dx.doi.org/10.1371/journal.pone.0067001
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