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Towards a semantic approach to numerical tree inference in phylogenetics.

Lars Vogt1

  • 1Institut für Evolutionsbiologie und Ökologie, Universität Bonn, An der Immenburg 1, Bonn, D-53121, Germany.

Cladistics : the International Journal of the Willi Hennig Society
|October 14, 2021
PubMed
Summary

This study introduces a novel semantic approach for phylogenetic tree inference, replacing traditional character matrices with semantic instance anatomies. This method integrates character analysis and tree inference, enhancing reproducibility and analytical accessibility in evolutionary biology.

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Area of Science:

  • Evolutionary Biology
  • Systematics
  • Bioinformatics

Background:

  • Traditional phylogeny reconstruction separates character analysis from numerical tree inference.
  • This separation leads to methodological issues like independent homology assessment and limited reproducibility in morphological studies.
  • Current methods struggle with analytical accessibility and formalization of pre-rational stages in character analysis.

Purpose of the Study:

  • To propose a semantic approach for numerical tree inference that overcomes limitations of conventional methods.
  • To integrate character analysis and tree inference steps into a unified, analytically accessible framework.
  • To lay the groundwork for developing new algorithms for semantic phylogenetic analysis.

Main Methods:

  • Utilizes sets of semantic instance anatomies (ontology-based descriptions of specimen anatomy as semantic graphs) as the data source.
  • Replaces traditional character matrices with semantic graphs for phylogenetic analysis.
  • Combines and integrates character analysis and numerical tree inference steps.

Main Results:

  • The semantic approach avoids problems associated with independent homology assessment and character dependencies.
  • It makes both character analysis and tree inference analytically accessible and communicable.
  • Provides a rational foundation for a new paradigm in phylogenetic reconstruction.

Conclusions:

  • The semantic approach offers a more robust and reproducible method for phylogeny reconstruction.
  • It addresses key conceptual and methodological challenges in current systematic biology.
  • Further research and algorithm development are needed to fully realize the potential of this approach.