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Model adequacy and the macroevolution of angiosperm functional traits

Matthew W. Pennell, Richard G. FitzJohn, William K. Cornwell, Luke J. Harmon
doi: https://doi.org/10.1101/004002
Matthew W. Pennell
1Department of Biological Sciences & Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, U.S.A
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Richard G. FitzJohn
2Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia;
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  • For correspondence: rich.fitzjohn@gmail.com
William K. Cornwell
3School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia;
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  • For correspondence: w.cornwell@unsw.edu.au
Luke J. Harmon
1Department of Biological Sciences & Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, U.S.A
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  • For correspondence: lukeh@uidaho.edu
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Abstract

All models are wrong and sometimes even the best of a set of models is useless. Modern phylogenetic comparative methods (PCMs) are almost exclusively model-based and therefore making robust inferences from PCMs requires using a model of trait evolution that is a good explanation for the data. To date, researchers using PCMs have evaluated the explanatory power of a model only in terms of relative, not absolute, fit. Here we develop a general statistical framework for assessing the absolute fit, or adequacy, of phylogenetic models for the evolution of quantitative traits. We use our approach to test whether commonly used models are adequate de scriptors of the macroevolutionary dynamics of real comparative data. We fit models of trait evolution to 337 comparative datasets covering three key Angiosperm functional traits and evaluated the absolute fit of the models to each dataset. Overall, the models we used are very inadequate for the evolution of these traits; this was true for many different groups and at many different scales. Furthermore, the relative support for a model had very little to do with its absolute adequacy. We argue that assessing model adequacy should be a key step in comparative analyses.

There are known knowns; there are things we know we know. We also know there are known unknowns; that is to say we know there are some things we do not know. But there are also unknown unknowns — the ones we don’t know we don’t know.

— Former U.S. Secretary of Defense, Donald Rumsfeld

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted April 07, 2014.
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Model adequacy and the macroevolution of angiosperm functional traits
Matthew W. Pennell, Richard G. FitzJohn, William K. Cornwell, Luke J. Harmon
bioRxiv 004002; doi: https://doi.org/10.1101/004002
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Model adequacy and the macroevolution of angiosperm functional traits
Matthew W. Pennell, Richard G. FitzJohn, William K. Cornwell, Luke J. Harmon
bioRxiv 004002; doi: https://doi.org/10.1101/004002

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