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Distinguishing between convergent evolution and violation of the molecular clock for three taxa

Citation

Mitchell, JD and Sumner, JG and Holland, BR, Distinguishing between convergent evolution and violation of the molecular clock for three taxa, Systematic Biology, 67, (5) pp. 905-915. ISSN 1063-5157 (2018) [Refereed Article]

Copyright Statement

Copyright 2018 The Authors

DOI: doi:10.1093/sysbio/syy038

Abstract

We give a non-technical introduction to convergence–divergence models, a new modeling approach for phylogenetic data that allows for the usual divergence of lineages after lineage-splitting but also allows for taxa to converge, i.e. become more similar over time. By examining the 3-taxon case in some detail, we illustrate that phylogeneticists have been "spoiled" in the sense of not having to think about the structural parameters in their models by virtue of the strong assumption that evolution is tree-like. We show that there are not always good statistical reasons to prefer the usual class of tree-like models over more general convergence–divergence models. Specifically, we show many 3-taxon data sets can be equally well explained by supposing violation of the molecular clock due to change in the rate of evolution along different edges, or by keeping the assumption of a constant rate of evolution but instead assuming that evolution is not a purely divergent process. Given the abundance of evidence that evolution is not strictly tree-like, our discussion is an illustration that as phylogeneticists we need to think clearly about the structural form of the models we use. For cases with four taxa, we show that there will be far greater ability to distinguish models with convergence from non-clock-like tree models.

Item Details

Item Type:Refereed Article
Keywords:akaike information criterion, convergence–divergence models, distinguishability, identifiability, likelihood, molecular clock, phylogeny
Research Division:Mathematical Sciences
Research Group:Applied Mathematics
Research Field:Biological Mathematics
Objective Division:Expanding Knowledge
Objective Group:Expanding Knowledge
Objective Field:Expanding Knowledge in the Mathematical Sciences
UTAS Author:Mitchell, JD (Mr Jonathan Mitchell)
UTAS Author:Sumner, JG (Dr Jeremy Sumner)
UTAS Author:Holland, BR (Associate Professor Barbara Holland)
ID Code:126933
Year Published:2018
Funding Support:Australian Research Council (DP150100088)
Web of Science® Times Cited:15
Deposited By:Mathematics and Physics
Deposited On:2018-07-03
Last Modified:2019-02-27
Downloads:0

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