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A Venturi Effect Can Help Cure Our Trees
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Co-divergence and tree topology.

T Calamoneri1, A Monti1, B Sinaimeri2,3,4

  • 1Computer Science Department, Sapienza University of Rome, Rome, Italy.

Journal of Mathematical Biology
|June 17, 2019
PubMed
Summary
This summary is machine-generated.

Phylogenetic tree reconciliation, a method for evolutionary history, faces challenges with the NP-hard maximum co-divergence problem. This study reveals that common heuristics perform poorly on caterpillar trees, but an equivalence to subsequence problems allows efficient optimal reconciliation.

Keywords:
CaterpillarsCo-phylogenyReconciliations

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Area of Science:

  • Computational Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Phylogenetic tree reconciliation is key to understanding host-parasite co-evolutionary histories.
  • The maximum co-divergence problem, aiming to maximize co-speciations, is NP-hard for general trees.
  • Current heuristics for this problem lack guaranteed performance.

Purpose of the Study:

  • To analyze the impact of tree topology on the maximum co-divergence problem.
  • To evaluate the performance of existing heuristics on specific tree structures like caterpillars.
  • To develop an efficient method for computing optimal reconciliations.

Main Methods:

  • Investigated the maximum co-divergence problem on caterpillar host and parasite trees.
  • Demonstrated the inadequacy of common heuristics for caterpillar tree topologies.
  • Established an equivalence between maximum co-divergence and a subsequence problem on permutations.

Main Results:

  • Heuristics for maximum co-divergence can yield arbitrarily suboptimal results for caterpillar trees.
  • The problem's complexity is linked to finding the longest subsequence with specific properties.
  • An efficient polynomial-time algorithm for optimal time-feasible reconciliation was developed.

Conclusions:

  • Tree topology significantly influences the difficulty and solution quality of maximum co-divergence.
  • The established permutation-based equivalence provides a pathway for efficient computation of optimal reconciliations.
  • This work offers insights into the computational complexity and algorithmic solutions for evolutionary history reconstruction.