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Updated: Jun 20, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Space of gene/species trees reconciliations and parsimonious models
Jean-Philippe Doyon1, Cedric Chauve, Sylvie Hamel
1DIRO, Université de Montréal, Montréal, Quebec, Canada.
Abstract:
We describe algorithms to study the space of all possible reconciliations between a gene tree and a species tree, that is counting the size of this space, uniformly generate a random reconciliation, and exploring this space in optimal time using combinatorial operators. We also extend these algorithms for optimal and sub-optimal reconciliations according to the three usual combinatorial costs (duplication, loss, and mutation). Applying these algorithms to simulated and real gene family evolutionary scenarios, we observe that the LCA (Last Common Ancestor) based reconciliation is almost always identical to the real one.
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