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Summary
This summary is machine-generated.

Reconstructing gene family evolution with horizontal gene transfer requires time-consistent reconciliations. This study provides a mathematical framework and a fast algorithm to determine if such biologically feasible evolutionary histories exist.

Keywords:
History of gene familiesHorizontal gene transferReconciliation mapTime-consistencyTree reconciliation

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Area of Science:

  • Computational Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Reconstructing gene family history is possible without horizontal gene transfer using event-labeled gene trees.
  • Reconciliation of gene trees with species trees is simplified by knowing event labels.
  • Unlabeled reconciliations may violate time-consistency, rendering them biologically infeasible.

Purpose of the Study:

  • Investigate the mathematical structure of event-labeled reconciliation problems incorporating horizontal gene transfer.
  • Address the issue of time-consistency in event-labeled gene tree reconciliation.
  • Develop a method to determine the existence of time-consistent reconciliation maps.

Main Methods:

  • Developed a convenient axiomatic framework for time-consistent reconciliations.
  • Derived a complete characterization of time-consistent reconciliations based on weak conditions.
  • Designed an [Formula: see text]-time algorithm relying on acyclicity checks of an auxiliary graph.

Main Results:

  • Provided a complete characterization of time-consistent reconciliations for gene trees with horizontal transfer.
  • Developed an efficient algorithm to decide the existence of time-consistent reconciliation maps.
  • The algorithm avoids explicit timing map construction, relying on graph acyclicity.

Conclusions:

  • The combinatorial characterization of time consistency is crucial for inferring gene family histories with horizontal transfer from orthology data.
  • The fast algorithm for time consistency checking is a valuable component for tree reconciliation tools.
  • This work advances the inference of evolutionary histories, particularly in the presence of horizontal gene transfer.