Model selection may not be a mandatory step for phylogeny reconstruction

Nature Communications
Shiran AbadiItay Mayrose

Abstract

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.

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Citations

Sep 3, 2019·Natural Product Reports·Martina AdamekNadine Ziemert
Aug 23, 2019·Molecular Biology and Evolution·Diego DarribaTomas Flouri
Dec 12, 2019·Molecular Biology and Evolution·David A DuchêneSimon Y W Ho
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Jun 26, 2020·Molecular Biology and Evolution·Shiran AbadiItay Mayrose
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Software Mentioned

hLRT
BioNJ
BaseML
Treedist
PANDIT
PAML
dLRT
jModelTest
CodeML application
TreeCmp

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