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The accuracy of methods for coding and sampling higher-level taxa for phylogenetic analysis: a simulation study.

J J Wiens1

  • 1Section of Amphibians and Reptiles, Carnegie Museum of Natural History, Pittsburgh, Pennsylvania 15213-4080, USA. wiensj@clpgh.org

Systematic Biology
|June 18, 2002
PubMed
Summary

Phylogenetic analyses using higher taxa perform poorly. The majority coding method is most accurate for higher taxa, suggesting "common equals primitive" in many cases.

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Systematic biology·2002

Area of Science:

  • Phylogenetics
  • Systematics
  • Evolutionary Biology

Background:

  • Phylogenetic analyses often use higher taxa (genera, families) as terminal taxa.
  • This approach necessitates managing interspecific variation within these higher taxa.
  • Morphological studies frequently employ higher taxa in phylogenetic reconstruction.

Purpose of the Study:

  • To review and compare parsimony methods for coding and sampling higher taxa.
  • To evaluate the relative accuracies of different methods using computer simulations.
  • To identify optimal strategies for incorporating variation within higher taxa into phylogenetic analyses.

Main Methods:

  • Computer simulations were used to compare various parsimony methods for coding and sampling higher taxa.

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  • Methods evaluated included majority (modal) coding, missing data, polymorphic coding, and fixed-only coding.
  • Species-level data were used as a benchmark for comparison against higher-taxon methods.

    • Main Results:

    • Methods coding higher taxa as terminals generally performed worse than using species as terminals.
    • Majority (modal) coding of higher taxa was more accurate than other higher-taxon coding methods (e.g., missing, polymorphic).
    • The fixed-only method (excluding variable characters) showed very poor performance, supported by squamate reptile data.

    Conclusions:

    • Using species as terminals is generally more accurate for phylogenetic analyses than using higher taxa.
    • Majority coding is the most accurate method when higher taxa must be used, implying "common equals primitive" can be a useful heuristic.
    • Incorporating variation within taxa and using detailed state distribution information are crucial for accurate phylogenetics.