Chira, A.M. and Thomas, G.H. (2016) The impact of rate heterogeneity on inference of phylogenetic models of trait evolution. Journal of Evolutionary Biology, 29 (12). pp. 2502-2518. ISSN 1010-061X
Abstract
Rates of trait evolution are known to vary across phylogenies; however, standard evolutionary models assume a homogeneous process of trait change. These simple methods are widely applied in small-scale phylogenetic studies, whereas models of rate heterogeneity are not, so the prevalence and patterns of potential rate variation in groups up to hundreds of species remain unclear. The extent to which trait evolution is modelled accurately on a given phylogeny is also largely unknown because studies typically lack absolute model fit tests. We investigated these issues by applying both rate-static and variable-rates methods on (i) body mass data for 88 avian clades of 10–318 species, and (ii) data simulated under a range of rate-heterogeneity scenarios. Our results show that rate heterogeneity is present across small-scaled avian clades, and consequently applying only standard single-process models prompts inaccurate inferences about the generating evolutionary process. Specifically, these approaches underestimate rate variation, and systematically mislabel temporal trends in trait evolution. Conversely, variable-rates approaches have superior relative fit (they are the best model) and absolute fit (they describe the data well). We show that rate changes such as single internal branch variations, rate decreases and early bursts are hard to detect, even by variable-rates models. We also use recently developed absolute adequacy tests to highlight misleading conclusions based on relative fit alone (e.g. a consistent preference for constrained evolution when isolated terminal branch rate increases are present). This work highlights the potential for robust inferences about trait evolution when fitting flexible models in conjunction with tests for absolute model fit.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2016 The Authors. Journal of Evolutionary Biology Published by John Wiley & Sons Ltd on Behalf of European Society for Evolutionary Biology. This is an open access article under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
Keywords: | absolute adequacy; body mass evolution; evolutionary models; rate-heterogeneity; relative fit; trait evolution |
Dates: |
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Institution: | The University of Sheffield |
Academic Units: | The University of Sheffield > Faculty of Science (Sheffield) > School of Biosciences (Sheffield) > Department of Animal and Plant Sciences (Sheffield) |
Depositing User: | Symplectic Sheffield |
Date Deposited: | 21 Nov 2016 14:34 |
Last Modified: | 06 Mar 2017 16:53 |
Published Version: | http://dx.doi.org/10.1111/jeb.12979 |
Status: | Published |
Publisher: | Wiley |
Refereed: | Yes |
Identification Number: | 10.1111/jeb.12979 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:107946 |
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