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Comparison of mode estimation methods and application in molecular clock analysis.

S Blair Hedges1, Prachi Shah

  • 1NASA Astrobiology Institute and Department of Biology, Pennsylvania State University, 208 Mueller Laboratory, University Park, PA 16802-5301, U,S,A. sbh1@psu.edu

BMC Bioinformatics
|August 2, 2003
PubMed
Summary

Estimating divergence times in molecular clock studies can be challenging with skewed data. The bootstrapped half-range mode offers a reliable method for estimating the mode, outperforming other techniques.

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Area of Science:

  • Evolutionary biology
  • Computational biology
  • Phylogenetics

Background:

  • Molecular clock studies often yield skewed time estimates or outliers.
  • The mode is a more robust estimator than the mean or median for skewed divergence time data.
  • Various methods exist for mode estimation, each with unique strengths and weaknesses.

Purpose of the Study:

  • To compare different mode estimation methods through simulations.
  • To evaluate the performance of these methods on real molecular clock data.
  • To identify the most reliable method for estimating divergence times.

Main Methods:

  • Simulations were conducted to assess bias and variance of mode estimators.
  • The half-range mode and robust parametric mode were specifically evaluated.

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  • Bootstrapping was employed to reduce variance in mode estimation.
  • Methods were applied to real molecular clock data sets.

    • Main Results:

    • The half-range mode and robust parametric mode exhibited lower bias across various conditions.
    • The half-range mode had higher variance, while the robust parametric mode was sensitive to outliers.
    • Bootstrapping effectively reduced the variance of both estimators.
    • Simulations results were consistent with analyses of real data.

    Conclusions:

    • The bootstrapped half-range mode is recommended as a general-purpose mode estimator due to its simplicity, speed, and low bias.
    • A bootstrap method for calculating the standard error and 95% confidence interval of the mode is also suggested.