2016
DOI: 10.1098/rsbl.2016.0081
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Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data

Abstract: Different analytical methods can yield competing interpretations of evolutionary history and, currently, there is no definitive method for phylogenetic reconstruction using morphological data. Parsimony has been the primary method for analysing morphological data, but there has been a resurgence of interest in the likelihood-based Mk-model. Here, we test the performance of the Bayesian implementation of the Mk-model relative to both equal and implied-weight implementations of parsimony. Using simulated morphol… Show more

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Cited by 183 publications
(237 citation statements)
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“…We also apply Bayesian methods to the character-taxon matrix, a novel analytical approach for hyaenodontan systematics. Bayesian methods provide powerful tools for understanding evolutionary relationships by simultaneously estimating branch lengths, phylogenetic uncertainty, and evolutionary rates while inferring phylogenetic relationships (Holder & Lewis, 2003; Wiley & Lieberman, 2011; O’Reilly et al, 2016). As part of the Bayesian analysis, we employ a recently developed expansion of Bayesian phylogenetic inference that has been called “tip-dating” (Pyron, 2011; Ronquist et al, 2012a; Beck & Lee, 2014).…”
Section: Introductionmentioning
confidence: 99%
“…We also apply Bayesian methods to the character-taxon matrix, a novel analytical approach for hyaenodontan systematics. Bayesian methods provide powerful tools for understanding evolutionary relationships by simultaneously estimating branch lengths, phylogenetic uncertainty, and evolutionary rates while inferring phylogenetic relationships (Holder & Lewis, 2003; Wiley & Lieberman, 2011; O’Reilly et al, 2016). As part of the Bayesian analysis, we employ a recently developed expansion of Bayesian phylogenetic inference that has been called “tip-dating” (Pyron, 2011; Ronquist et al, 2012a; Beck & Lee, 2014).…”
Section: Introductionmentioning
confidence: 99%
“…This was a key aspect of our study comparing the primary methods of phylogenetic reconstruction as they are commonly implemented. Our and others previous studies [1,3,4] reject parsimony in favour of a Bayesian MCMC framework in which uncertainty is incorporated, further drawing into question the veracity of Brown and colleagues' assertion that there is equivalent performance amongst methods.…”
mentioning
confidence: 99%
“…So far, all phylogenetic studies of the Rhynchocephalia have only used parsimony analysis, recovering a few distinct clades. More recently, Bayesian inference methods have been employed for phylogenetic analyses based on morphological characters (e.g., Parry et al, 2016;Wright, 2017), and recent studies suggest that Bayesian methods outperform parsimony for morphological data (O'Reilly et al, 2016;Puttick et al, 2017), recovering more accurate, but less precise results.…”
Section: Introductionmentioning
confidence: 99%