Section: Evolutionary Biology
Topic: Evolution, Computer sciences

Rehabilitating the benefits of gene tree correction in the presence of incomplete lineage sorting

Lafond, Manuel1orcid    ; Scornavacca, Celine2orcid   
1Université de Sherbrooke, Sherbrooke, Canada
2Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier, CNRS, IRD, EPHE), Montpellier, France

Corresponding author(s): Lafond, Manuel (manuel.lafond@USherbrooke.ca); Scornavacca, Celine (celine.scornavacca@umontpellier.fr)

10.24072/pcjournal.674 - Peer Community Journal, Volume 6 (2026), article no. e7

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Gene trees play an important role in various areas of phylogenomics. However, their reconstruction often relies on limited-length sequences and may not account for complex evolutionary events, such as gene duplications, losses, or incomplete lineage sorting (ILS), which are not modeled by standard phylogenetic methods. To address these challenges, it is common to first infer gene trees using fast algorithms for conventional models, then refine them through species tree-aware correction methods. Recently, it has been argued that such corrections can lead to overfitting and force gene trees to resemble the species tree, thereby obscuring genuine gene-level variation caused by ILS. In this paper, we challenge and refute this hypothesis, and we demonstrate that, when applied carefully, correction methods can offer significant benefits, even in the presence of ILS.

Published online:
DOI: 10.24072/pcjournal.674
Type: Research article
Keywords: Gene trees, species trees, phylogenomics, incomplete lineage sorting, Gene trees, species trees, phylogenomics, incomplete lineage sorting

Lafond, Manuel  1 ; Scornavacca, Celine  2

1 Université de Sherbrooke, Sherbrooke, Canada
2 Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier, CNRS, IRD, EPHE), Montpellier, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights
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Lafond, M.; Scornavacca, C. Rehabilitating the benefits of gene tree correction in the presence of incomplete lineage sorting. Peer Community Journal, Volume 6 (2026), article  no. e7. https://doi.org/10.24072/pcjournal.674

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.evolbiol.100872

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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