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The Path-Label Reconciliation (PLR) Dissimilarity Measure for Gene Trees

Authors Alitzel López Sánchez , José Antonio Ramírez-Rafael , Alejandro Flores-Lamas , Maribel Hernández-Rosales , Manuel Lafond

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Author Details

Alitzel López Sánchez
  • Computer Science Department, Université de Sherbrooke, Canada
José Antonio Ramírez-Rafael
  • Center for Research and Advanced Studies of the National Polytechnic Institute, Irapuato, Gto., Mexico
  • Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Germany
  • Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
Alejandro Flores-Lamas
  • Center for Research and Advanced Studies of the National Polytechnic Institute, Irapuato, Gto., Mexico
Maribel Hernández-Rosales
  • Center for Research and Advanced Studies of the National Polytechnic Institute, Irapuato, Gto., Mexico
Manuel Lafond
  • Computer Science Department, Université de Sherbrooke, Canada

Funding

  • López Sánchez, Alitzel: Bourse d'excellence de la Faculté de Sciences, Université de Sherbrooke.
  • Ramírez-Rafael, José Antonio: CONAHCYT scholarship, Mexico.
  • Lafond, Manuel: NSERC Discovery program

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Alitzel López Sánchez, José Antonio Ramírez-Rafael, Alejandro Flores-Lamas, Maribel Hernández-Rosales, and Manuel Lafond. The Path-Label Reconciliation (PLR) Dissimilarity Measure for Gene Trees. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 20:1-20:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
https://doi.org/10.4230/LIPIcs.WABI.2024.20

Abstract

In this study, we investigate the problem of comparing gene trees reconciled with the same species tree using a novel semi-metric, called the Path-Label Reconciliation (PLR) dissimilarity measure. This approach not only quantifies differences in the topology of reconciled gene trees, but also considers discrepancies in predicted ancestral gene-species maps and speciation/duplication events, offering a refinement of existing metrics such as Robinson-Foulds (RF) and their labeled extensions LRF and ELRF. A tunable parameter α also allows users to adjust the balance between its species map and event labeling components. We show that PLR can be computed in linear time and that it is a semi-metric. We also discuss the diameters of reconciled gene tree measures, which are important in practice for normalization, and provide initial bounds on PLR, LRF, and ELRF. To validate PLR, we simulate reconciliations and perform comparisons with LRF and ELRF. The results show that PLR provides a more evenly distributed range of distances, making it less susceptible to overestimating differences in the presence of small topological changes, while at the same time being computationally efficient. Our findings suggest that the theoretical diameter is rarely reached in practice. The PLR measure advances phylogenetic reconciliation by combining theoretical rigor with practical applicability. Future research will refine its mathematical properties, explore its performance on different tree types, and integrate it with existing bioinformatics tools for large-scale evolutionary analyses. The open source code is available at: https://pypi.org/project/parle/.

Subject Classification

ACM Subject Classification
  • Applied computing → Molecular evolution
Keywords
  • Reconciliation
  • gene trees
  • species trees
  • evolutionary scenarios

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