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Updated: May 16, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Gene tree correction for reconciliation and species tree inference
Krister M Swenson1, Andrea Doroftei, Nadia El-Mabrouk
1Département d'Informatique et de Recherche Opérationnelle, Université de Montréal, CP 6128 succ Centre-Ville, Montréal, H3C 3J7, Québec, Canada. swensonk@iro.umontreal.ca.
Algorithms for Molecular Biology : AMB
|November 22, 2012
Summary
This study introduces a method to improve gene family evolution analysis by identifying and addressing problematic gene tree data. It helps infer more accurate evolutionary histories by minimizing errors from misplaced leaves.
Area of Science:
- Computational Biology
- Phylogenetics
- Evolutionary Genomics
Background:
- Gene family evolution is commonly inferred using reconciliation, embedding gene trees into species trees.
- Reconciliation's accuracy is highly sensitive to gene tree quality, with misplaced leaves causing significant errors.
- Inferring species trees from gene trees to minimize evolutionary events is an algorithmic challenge.
Purpose of the Study:
- To develop methods for preprocessing gene trees to improve reconciliation and species tree inference.
- To identify and mitigate the impact of non-apparent duplication (NAD) vertices, indicative of leaf misplacement.
- To create algorithms that minimize errors in evolutionary scenario reconstruction.
Main Methods:
- Flagging non-apparent duplication (NAD) vertices in gene trees as potential leaf misplacements.
- Developing a polynomial-time heuristic for species tree inference by removing species to eliminate NAD vertices.
- Formulating an optimization problem for reconciliation, aiming to remove minimum leaves/species to achieve NAD-free trees.
- Designing a polynomial-time algorithm for reconciliation, exact for specific gene tree classes.
Main Results:
- A heuristic for species tree inference that minimizes species removal to resolve NAD vertices.
- An exact algorithm for reconciliation on specific gene tree classes, and a general heuristic.
- Demonstrated good performance on simulated datasets for both species tree inference and reconciliation.
- Successfully identified and addressed sources of error in evolutionary scenario reconstruction.
Conclusions:
- Preprocessing gene trees by identifying NAD vertices enhances the reliability of evolutionary inference.
- The developed algorithms offer efficient solutions for improving reconciliation and species tree inference.
- This approach mitigates the impact of gene tree inaccuracies, leading to more robust evolutionary histories.
- The methods show promise for accurate reconstruction of gene family evolution.
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