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Morphological phylogenetics evaluated using novel evolutionary simulations

The Author(s) 2020. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. http://creativecommons.org/licenses/by/4.0 ;ISSN: 1063-5157 ;EISSN: 1076-836X ;DOI: 10.1093/sysbio/syaa012

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  • Title:
    Morphological phylogenetics evaluated using novel evolutionary simulations
  • Author: Keating, JN ; Sansom, RS ; Sutton, MD ; Knight, CG ; Garwood, RJ
  • Subjects: 0603 Evolutionary Biology ; 0604 Genetics ; Evolutionary Biology
  • Description: Evolutionary inferences require reliable phylogenies. Morphological data has traditionally been analysed using maximum parsimony, but recent simulation studies have suggested that Bayesian analyses yield more accurate trees. This debate is ongoing, in part, because of ambiguity over modes of morphological evolution and a lack of appropriate models. Here we investigate phylogenetic methods using two novel simulation models - one in which morphological characters evolve stochastically along lineages and another in which individuals undergo selection. Both models generate character data and lineage splitting simultaneously: the resulting trees are an emergent property, rather than a fixed parameter. Standard consensus methods for Bayesian searches (Mki) yield fewer incorrect nodes and quartets than the standard consensus trees recovered using equal weighting and implied weighting parsimony searches. Distances between the pool of derived trees (most parsimonious or posterior distribution) and the true trees - measured using Robinson-Foulds (RF), subtree prune and regraft (SPR), and tree bisection reconnection (TBR) metrics - demonstrate that this is related to the search strategy and consensus method of each technique. The amount and structure of homoplasy in character data differs between models. Morphological coherence, which has previously not been considered in this context, proves to be a more important factor for phylogenetic accuracy than homoplasy. Selection-based models exhibit relatively lower homoplasy, lower morphological coherence, and higher inaccuracy in inferred trees. Selection is a dominant driver of morphological evolution, but we demonstrate that it has a confounding effect on numerous character properties which are fundamental to phylogenetic inference. We suggest that the current debate should move beyond considerations of parsimony versus Bayesian, towards identifying modes of morphological evolution and using these to build models for probabilistic search methods.
  • Publisher: Oxford University Press (OUP)
  • Creation Date: 2020-02
  • Language: English
  • Identifier: ISSN: 1063-5157
    EISSN: 1076-836X
    DOI: 10.1093/sysbio/syaa012
  • Source: Spiral
    Alma/SFX Local Collection
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