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DISTANCE DATA REVISITED.

James S Farris1

  • 1Department of Ecology and Evolution, Stole University of New York, Stony Brook NY 11794.

Cladistics : the International Journal of the Willi Hennig Society
|December 31, 2021
PubMed
Summary
This summary is machine-generated.

Branch lengths in phylogenetic trees lack physical meaning, contrary to some claims. New methods improve tree fitting, but molecular distances offer limited phylogenetic insight.

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Area of Science:

  • Phylogenetics
  • Computational Biology
  • Molecular Evolution

Background:

  • Phylogenetic trees are crucial for understanding evolutionary relationships.
  • Interpreting branch lengths in these trees, particularly those derived from distance matrices, has been a subject of debate.
  • Previous methods for constructing trees from distance data have limitations.

Purpose of the Study:

  • To address objections regarding the physical interpretation of branch lengths in phylogenetic trees.
  • To introduce and evaluate a novel method for constructing optimal or near-optimal trees from distance data.
  • To assess the utility of molecular distances in inferring phylogenetic relationships.

Main Methods:

  • Re-evaluation of arguments concerning the physical interpretation of phylogenetic tree branch lengths.
  • Development of a new algorithm for generating multiple trees with optimal or near-optimal fit to distance matrices.
  • Comparison of the performance of the new method against existing approaches.
  • Analysis of consensus trees derived from multiple near-optimal fits.

Main Results:

  • Objections to the claim that branch lengths lack physical interpretation are refuted.
  • A paradox arises from the contention that fitted lengths estimate evolutionary change.
  • The newly introduced method demonstrates superior performance in fitting trees to distance data compared to previous techniques.
  • Many previously published trees based on distance data were suboptimal.
  • Consensus trees from near-optimal fits exhibit poor resolution, indicating limited phylogenetic information in molecular distances.

Conclusions:

  • Branch lengths in distance-based phylogenetic trees do not possess a direct physical interpretation.
  • A novel method for tree construction improves upon existing techniques for distance data.
  • Molecular distance data generally provides insufficient information for robust phylogenetic inference.