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Determining evolutionary distances from highly diverged nucleic acid sequences: operator metrics.

J A Lake1

  • 1Molecular Biology Institute, University of California, Los Angeles 90024.

Journal of Molecular Evolution
|January 1, 1987
PubMed
Summary

Operator metrics accurately measure evolutionary distances in nucleic acid sequences, even with high substitution rates. This robust method is unaffected by substitutions outside a branch, providing reliable evolutionary insights.

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Area of Science:

  • Evolutionary biology
  • Bioinformatics
  • Molecular evolution

Background:

  • Traditional methods for measuring evolutionary distances (distance matrix, parsimony) can be inaccurate with high substitution rates or extensive sequence changes.
  • These methods are susceptible to alterations in branch length measurements due to substitutions in other parts of the evolutionary tree.

Purpose of the Study:

  • To introduce and validate a novel method, operator metrics, for calculating evolutionary distances from nucleic acid sequences.
  • To demonstrate the robustness and accuracy of operator metrics, particularly under challenging evolutionary scenarios.

Main Methods:

  • Operator metrics calculate branch lengths on unrooted trees, representing transversion differences between sequences.
  • The method utilizes eigenvectors of fundamental evolutionary equations, ensuring independence from substitution rate variation among taxa.

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  • Lengths are determined per branch and are not influenced by substitutions outside that specific branch.

    • Main Results:

    • Operator metrics provide accurate evolutionary distance measurements, outperforming distance matrix and parsimony methods under conditions causing significant inaccuracies.
    • The method's validity is confirmed through examples using complex evolutionary rates and tree topologies designed to obscure true relationships.
    • Operator metrics are shown to be robust, easy to calculate, scalable to any number of taxa, and provide variance estimates.

    Conclusions:

    • Operator metrics offer a reliable and accurate approach to quantifying evolutionary distances in nucleic acid sequences.
    • The method's independence from substitution rate variation and its robustness make it suitable for analyzing complex evolutionary histories.
    • Demonstrated utility in analyzing the evolutionary origins of organelles (chloroplasts, mitochondria) and eubacteria highlights its practical application.