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Bayesian Analysis Using a Simple Likelihood Model Outperforms Parsimony for Estimation of Phylogeny from Discrete Morphological Data

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  • April M Wright
  • David M Hillis

Abstract

Despite the introduction of likelihood-based methods for estimating phylogenetic trees from phenotypic data, parsimony remains the most widely-used optimality criterion for building trees from discrete morphological data. However, it has been known for decades that there are regions of solution space in which parsimony is a poor estimator of tree topology. Numerous software implementations of likelihood-based models for the estimation of phylogeny from discrete morphological data exist, especially for the Mk model of discrete character evolution. Here we explore the efficacy of Bayesian estimation of phylogeny, using the Mk model, under conditions that are commonly encountered in paleontological studies. Using simulated data, we describe the relative performances of parsimony and the Mk model under a range of realistic conditions that include common scenarios of missing data and rate heterogeneity.

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  • April M Wright & David M Hillis, 2014. "Bayesian Analysis Using a Simple Likelihood Model Outperforms Parsimony for Estimation of Phylogeny from Discrete Morphological Data," PLOS ONE, Public Library of Science, vol. 9(10), pages 1-6, October.
    • Handle: RePEc:plo:pone00:0109210
    DOI: 10.1371/journal.pone.0109210
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    References listed on IDEAS

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    1. Bryan Kolaczkowski & Joseph W. Thornton, 2004. "Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous," Nature, Nature, vol. 431(7011), pages 980-984, October.
    2. Xing Xu & Hailu You & Kai Du & Fenglu Han, 2011. "An Archaeopteryx-like theropod from China and the origin of Avialae," Nature, Nature, vol. 475(7357), pages 465-470, July.
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    Cited by:

    1. Neil Brocklehurst & Robert R Reisz & Vincent Fernandez & Jörg Fröbisch, 2016. "A Re-Description of ‘Mycterosaurus’ smithae, an Early Permian Eothyridid, and Its Impact on the Phylogeny of Pelycosaurian-Grade Synapsids," PLOS ONE, Public Library of Science, vol. 11(6), pages 1-27, June.
    2. Spade David A., 2020. "An extended model for phylogenetic maximum likelihood based on discrete morphological characters," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 19(1), pages 1-11, February.
    3. Tiago R Simões & Oksana Vernygora & Ilaria Paparella & Paulina Jimenez-Huidobro & Michael W Caldwell, 2017. "Mosasauroid phylogeny under multiple phylogenetic methods provides new insights on the evolution of aquatic adaptations in the group," PLOS ONE, Public Library of Science, vol. 12(5), pages 1-20, May.

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