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DISTANCE DATA REVISITED.

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SKEWNESS AND PERMUTATION.

Mari Källersjö1,2, James S Farris1,3, Arnold G Kluge4

  • 1Naturhistoriska riksmuseet, Molekylärsystematiska laboratoriet, Box 50007, S-104 05 Stockholm, Sweden.

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|December 21, 2021
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Summary

The skewness criterion for phylogenetic structure can be misleading due to sensitivity to character frequencies. A more reliable method uses permutation tests and support measures across multiple phylogenetic trees.

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Area of Science:

  • Phylogenetics
  • Computational Biology
  • Systematics

Background:

  • The skewness criterion is a common method for assessing phylogenetic structure.
  • However, it is sensitive to character state frequencies and the number of characters, potentially yielding misleading results.
  • Existing methods like permutation tests can be computationally intensive or imply structure in ambiguous data.

Purpose of the Study:

  • To evaluate the limitations of the skewness criterion in phylogenetic analysis.
  • To identify more robust statistical methods for inferring phylogenetic structure.
  • To propose an improved approach using support measures across multiple trees.

Main Methods:

  • Critically analyzed the skewness criterion's sensitivity to data properties.
  • Evaluated permutation tests using approximate parsimony calculations.
  • Developed and tested a support measure that considers multiple phylogenetic trees.

Main Results:

  • The skewness criterion is unreliable due to its sensitivity to character frequencies and insufficient consideration of character number.
  • Minimal tree length tests can suggest strong phylogenetic structure even with ambiguous data.
  • A support measure incorporating multiple trees provides a more satisfactory assessment of phylogenetic structure.

Conclusions:

  • The skewness criterion should be used with caution in phylogenetic analyses.
  • Permutation tests offer an alternative but can be problematic with ambiguous data.
  • Support measures considering multiple trees represent a more robust approach for evaluating phylogenetic structure.