Bayesian analysis using a simple likelihood model outperforms parsimony for estimation of phylogeny from discrete morphological data

PLoS One. 2014 Oct 3;9(10):e109210. doi: 10.1371/journal.pone.0109210. eCollection 2014.

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.

Publication types

  • Evaluation Study
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Bayes Theorem*
  • Biological Evolution
  • Computer Simulation
  • Likelihood Functions
  • Models, Biological
  • Phylogeny*

Grant support

AMW received financial support for material purchases related to this project from the National Science Foundation's Doctoral Dissertation Improvement Grant (number 201203267-001; http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5234). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.