Gene tree species tree reconciliation with gene conversion

Gene tree/species tree reconciliation is a recent decisive progress in phylogenetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by gene-scale events such as duplication, loss, transfer, which translates mathematically into a mapping between gene tree nodes and species tree nodes or branches. Gene conversion is a frequent and important biological event, which results in the replacement of a gene by a copy of another from the same species and in the same gene tree. Including this event in reconciliations has never been attempted because this changes as well the solutions as the methods to construct reconciliations. Standard algorithms based on dynamic programming become ineffective. We propose here a novel mathematical framework including gene conversion as an evolutionary event in gene tree/species tree reconciliation. We describe a randomized algorithm giving in polynomial running time a reconciliation minimizing the number of duplications, losses and conversions. We show that the space of reconciliations includes an analog of the Last Common Ancestor reconciliation, but is not limited to it. Our algorithm outputs any optimal reconciliation with non null probability. We argue that this study opens a research avenue on including gene conversion in reconciliation, which can be important for biology. This work is funded by the Agence Nationale pour la Recherche, Ancestrome project ANR10-BINF-01-01. Damir Hasić Department of Mathematics, Faculty of Science, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina E-mail: [email protected], [email protected] Eric Tannier Inria Grenoble Rhône-Alpes, F-38334 Montbonnot, France Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France 2 Damir Hasić, Eric Tannier