The powers and pitfalls of parsimony

@article{Stewart1993ThePA,
  title={The powers and pitfalls of parsimony},
  author={C B Stewart},
  journal={Nature},
  year={1993},
  volume={361},
  pages={603-607}
}
Parsimony analysis is a powerful tool for the study of biological evolution. It is used to construct phylogenetic trees, to evaluate alternative hypotheses objectively, and to study evolutionary pattern and process. Yet, as comparative data sets expand, the pitfalls of parsimony analysis are catching experts and novices alike. 
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206 Citations
Background Citations
32
Methods Citations
12

206 Citations

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Citation Type

Is parsimony a justified criterion in the assessment of possible phylogenetic reconstructions
TLDR
It can be concluded that parsimony analysis cannot be used in evolutionary studies with any confidence and that, if it is renounced, as it appears necessary, current methods of cladistic analysis become unmanageable.
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  • R. Page
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    Current protocols in bioinformatics
  • 2003
This unit provides a general introduction to phylogeny. It defines common terms and discusses the issue of rooting trees, in addition to comparing gene and species trees. Methods for inferring…
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  • Biology
    Philosophical transactions of the Royal Society of London. Series B, Biological sciences
  • 1995
TLDR
The composite tree is derived by applying a parsimony algorithm to over a hundred previous estimates, and is well resolved, containing 160 nodes, and will be a useful framework for comparative biologists.
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An alignment-free approach which considers the mutual occurrences of l-mers with at most k mismatches between a pair of DNA sequences in order to define a distance the species, which leads to reliable phylogenetic trees.
A frequency-dependent significance test for parsimony.
TLDR
A recently described frequency-dependent significance test is extended to handle any number of taxa and a modification of the Kishino-Hasegawa sites test is described, useful for detecting historical signals beyond those patterns which arise purely from irregular base compositions between the compared sequences.
Phylogenetic analysis and comparative genomics
Progress and pitfalls in systematics: cladistics, DNA and morphology
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Molecular approaches separate phylogenetic reconstruction from biological evaluation and will never replace morphological analysis in Systematics, but molecular methods also facilitate the direct investigation of morphological evolution by revealing the genetic basis of morphogenesis in model systems or by permitting the genetic analysis of diagnostic character changes by genetic mapping.
The Origin and Early Development of the Method of Minimum Evolution for the Reconstruction of Phylogenetic Trees
TLDR
The method of minimum evolution was introduced by Edwards and Cavalli-Sforza (1963) and its relationship to the subsequently developed parsimony methods and the logical basis of the methods are discussed, with special reference to probability models.
TOPIARY PRUNING AND WEIGHTING REINFORCE AN AFRICAN ORIGIN FOR THE HUMAN MITOCHONDRIAL DNA TREE
  • C. Wills
  • Computer Science
    Evolution; international journal of organic evolution
  • 1996
TLDR
The ability of topiary pruning to “unscramble” artificial data sets that have high levels of homoplasy is demonstrated, and is shown to be similar in its effects to the weighting method of Kluge and Farris (1969), although with the additional advantage of reducing the number of taxa to the point where bootstrapping is feasible.
Phylogenetic place of guinea pigs: no support of the rodent-polyphyly hypothesis from maximum-likelihood analyses of multiple protein sequences.
TLDR
The overall evidence does not support Graur et al.'s hypothesis, which radically contradicts the traditional view of rodent monophyly, and demonstrates that one must be careful in choosing a proper method for phylogenetic inference and that an argument based on a small data set (with respect to the length of the sequence and especially the number of species) may be unstable.
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