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A generalized Robinson-Foulds distance for labeled trees.

Samuel Briand1, Christophe Dessimoz2,3,4,5,6, Nadia El-Mabrouk7

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We introduce an extended Robinson-Foulds (RF) distance to compare phylogenetic trees with labeled nodes, accounting for different evolutionary events. This new metric offers improved biological relevance for gene evolution studies.

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Area of Science:

  • Phylogenetics
  • Computational Biology
  • Evolutionary Biology

Background:

  • The Robinson-Foulds (RF) distance is a standard metric for comparing phylogenetic trees.
  • However, the traditional RF distance does not account for the biological meaning of internal nodes, such as speciation or duplication events.
  • This limitation hinders its application in gene evolution studies where branching event types are crucial.

Purpose of the Study:

  • To extend the Robinson-Foulds (RF) distance to incorporate labeled internal nodes in phylogenetic trees.
  • To develop a more biologically relevant measure for comparing gene trees by considering the types of evolutionary events.

Main Methods:

  • Introduced a node flip operation in addition to edge contractions and extensions to extend the RF distance.
  • Explored the properties of this extended RF distance, particularly for binary labeled trees.
  • Developed a 2-approximation algorithm for computing the extended RF distance.

Main Results:

  • The extended RF distance accounts for labeled internal nodes, offering greater biological insight.
  • An optimal edit path for labeled trees may necessitate contracting shared edges, unlike in the unlabeled case.
  • The proposed 2-approximation algorithm demonstrates strong empirical performance.

Conclusions:

  • The extended Robinson-Foulds distance provides a more biologically meaningful way to compare phylogenetic trees with labeled nodes.
  • This advancement opens new algorithmic avenues for analyzing evolutionary relationships, particularly in the context of gene family evolution.
  • An implementation and simulation data are publicly available for reproducibility and further research.