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Increased taxon sampling greatly reduces phylogenetic error.

Derrick J Zwickl1, David M Hillis

  • 1Section of Integrative Biology and Center for Computational Biology and Bioinformatics, University of Texas, Austin, Texas 78712, USA. zwickl@mail.utexas.edu

Systematic Biology
|September 14, 2002
PubMed
Summary

Extensive taxon sampling significantly improves phylogenetic accuracy by reducing errors. This study highlights the importance of considering phylogenetic scope, search thoroughness, and evolutionary models when evaluating taxon sampling strategies for more reliable evolutionary trees.

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Area of Science:

  • Evolutionary Biology
  • Computational Biology
  • Systematics

Background:

  • Conflicting views exist on the impact of taxon sampling on phylogenetic accuracy.
  • Some researchers advocate for extensive sampling, while others propose using fewer exemplar taxa to reduce computational complexity.

Purpose of the Study:

  • To investigate factors influencing the perceived benefits of extensive taxon sampling in phylogenetic analyses.
  • To reconcile differing perspectives on taxon sampling strategies by examining study design elements.

Main Methods:

  • Evaluated phylogenetic error across varying taxon sample sizes, considering random tree selection error.
  • Assessed the influence of phylogenetic scope and tree search thoroughness on accuracy.
  • Examined the impact of simulation model complexity and different phylogenetic optimality criteria.

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Main Results:

  • Phylogenetic error decreases with increased taxon sampling, especially when considering random tree selection error and phylogenetic scope.
  • More thorough tree searches reduce phylogenetic error, particularly with larger taxon sample sizes.
  • Complex evolutionary models and increased taxon sampling yield greater improvements in accuracy.

Conclusions:

  • Extensive taxon sampling is crucial for enhancing overall phylogenetic accuracy.
  • Study design elements such as scope, search methods, and models significantly affect the perceived benefits of taxon sampling.