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Related Concept Videos

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Related Experiment Video

Updated: Dec 10, 2025

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
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Reconstruction of time-consistent species trees.

Manuel Lafond1, Marc Hellmuth2

  • 1Department of Computer Science, Université de Sherbrooke, 2500 Boul. de l'Université, Sherbrooke, J1K 2R1 Canada.

Algorithms for Molecular Biology : AMB
|August 27, 2020
PubMed
Summary

Reconstructing gene family evolution requires finding a biologically feasible species tree. This study presents a polynomial-time algorithm to construct a time-consistent species tree, even with horizontal gene transfer (HGT).

Keywords:
Gene evolutionHorizontal gene transferPolynomial-time algorithmSpecies evolutionTime-consistencyTree reconciliation

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Area of Science:

  • Computational Biology
  • Evolutionary Genetics
  • Phylogenetics

Background:

  • Gene family history is reconstructed from evolutionary event relations of genes (orthologs, paralogs, xenologs).
  • Assessing biological feasibility of gene trees requires reconciliation with a time-consistent species tree.

Purpose of the Study:

  • To determine if a time-consistent species tree exists for a given event-labeled gene tree, even with horizontal gene transfer (HGT).
  • To develop an efficient algorithm for constructing such species trees when they exist.

Main Methods:

  • Consideration of event-labeled gene trees including speciations, duplications, and HGT.
  • Development of a cubic-time algorithm for species tree reconciliation.

Main Results:

  • Despite NP-hardness in related problems, finding a time-consistent species tree for a given gene tree is solvable in polynomial time.
  • A cubic-time algorithm successfully decides the existence of and constructs a time-consistent species tree.

Conclusions:

  • The reconciliation of event-labeled gene trees with unknown species trees, including HGT, is computationally tractable.
  • The developed algorithm provides an efficient method for inferring evolutionary history and species relationships.