An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers

Jean-Philippe Doyon 1 Celine Scornavacca 2 Yu Gorbunov 3 Gergely Szöllősi 4 Vincent Ranwez 5 Vincent Berry 6, *
* Corresponding author
1 LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
2 Center for Bioinformatics (ZBIT)
3 IITP - Institute for Information Transmission Problems
4 BPGE - Bioinformatique, phylogénie et génomique évolutive
PEGASE - Département PEGASE [LBBE]
5 UMR ISEM - Institut des Sciences de l'Evolution de Montpellier
6 MAB - Méthodes et Algorithmes pour la Bioinformatique
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
Abstract : Tree reconciliation methods aim at estimating the evolutionary events that cause discrepancy between gene trees and species trees. We provide a discrete computational model that considers duplications, transfers and losses of genes. The model yields a fast and exact algorithm to infer time consistent and most parsimonious reconciliations. Then we study the conditions under which parsimony is able to accurately infer such events. Overall, it performs well even under realistic rates, transfers being in general less accurately recovered than duplications. An implementation is freely available at http://www.atgc-montpellier.fr/MPR.
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Jean-Philippe Doyon, Celine Scornavacca, Yu Gorbunov, Gergely Szöllősi, Vincent Ranwez, et al.. An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers. RECOMB-CG: Comparative Genomics, Oct 2010, Ottawa, Canada. pp.93-108, ⟨10.1007/978-3-642-16181-0_9⟩. ⟨lirmm-00818889⟩

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