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A Practical Guide to Phylogenetics for Nonexperts
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Transforming phylogenetic networks: Moving beyond tree space.

Katharina T Huber1, Vincent Moulton1, Taoyang Wu1

  • 1School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, UK.

Journal of Theoretical Biology
|May 26, 2016
PubMed
Summary

Researchers defined new operations for unrooted phylogenetic networks, generalizing tree operations. This allows transforming any network into another, aiding in developing search strategies for optimal phylogenetic networks.

Keywords:
Local transformationNNI operationNetwork metricNetwork spacePhylogenetic network

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Area of Science:

  • Evolutionary Biology
  • Computational Biology
  • Graph Theory

Background:

  • Phylogenetic trees model evolutionary history but struggle with reticulate evolution.
  • Reticulate evolution, common in various life forms, requires more complex models like phylogenetic networks.
  • Unrooted phylogenetic networks generalize unrooted trees for representing complex evolutionary histories.

Purpose of the Study:

  • To define novel operations on unrooted phylogenetic networks.
  • To establish a method for transforming any unrooted phylogenetic network into any other.
  • To enable new metrics and generalizations of tree space for phylogenetic networks.

Main Methods:

  • Definition of two new operations on unrooted phylogenetic networks.
  • Demonstration of network inter-transformability using these operations.
  • Exploration of connections between phylogenetic networks and cubic graphs.

Main Results:

  • Any unrooted phylogenetic network can be transformed into any other using the defined operations.
  • Generalization of the nearest-neighbor interchange (NNI) operation to phylogenetic networks.
  • Establishment of new metrics and a generalized tree space for phylogenetic networks.

Conclusions:

  • The defined operations provide a framework for manipulating and comparing unrooted phylogenetic networks.
  • These findings facilitate the development of new algorithms for searching optimal phylogenetic networks.
  • The discovered links to cubic graphs offer novel theoretical insights and practical applications in evolutionary studies.