title: Fast algorithm for the reconciliation of gene trees and LGT networks.
abstract: In phylogenomics, reconciliations aim at explaining the discrepancies between the evolutionary histories of genes and species. Several reconciliation models are available when the evolution of the species of interest is modelled via phylogenetic trees; the most commonly used are the DL model, accounting for duplications and losses in gene evolution and yielding polynomially-solvable problems, and the DTL model, which also accounts for gene transfers and implies NP-hard problems. However, when dealing with non-tree-like evolutionary events such as hybridisations, phylogenetic networks - and not phylogenetic trees - should be used to model species evolution. Reconciliation models involving phylogenetic networks are still at their early days. In this paper, we propose a new reconciliation model in which the evolution of species is modelled by a special kind of phylogenetic networks - the LGT networks. Our model considers duplications, losses and transfers of genes, but restricts transfers to happen through some specific arcs of the network, called secondary arcs. Moreover, we provide a polynomial algorithm to compute the most parsimonious reconciliation between a gene tree and an LGT network under this model. Our method, when combined with quartet decomposition methods to detect putative "highways" of transfers, permits to refine their analyses by allowing to examine the two possible directions of a highway and even consider combinations of highways.
authors.affiliation: Institut des Sciences de l'Evolution, Université de Montpellier, CNRS, IRD, EPHE 34095 Montpellier Cedex 5, France. Electronic address: Celine.Scornavacca@umontpellier.fr.
authors.forename: Celine
authors.initials: C
authors.lastname: Scornavacca
authors.affiliation: Department of Mathematics and Computer Science, University of the Balearic Islands, E-07122 Palma, Spain. Electronic address: joancarles.pons@uib.es.
authors.forename: Joan Carles Pons
authors.initials: JCP
authors.lastname: Mayol
authors.affiliation: Department of Mathematics and Computer Science, University of the Balearic Islands, E-07122 Palma, Spain. Electronic address: gabriel.cardona@uib.es.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Cardona
mesh_terms: D000465:Algorithms; D019143:Evolution, Molecular; D053263:Gene Regulatory Networks / Q000502:physiology*; D008957:Models, Genetic; D010802:Phylogeny
keywords: Highways of transfers.; Phylogenetic network; Phylogenetic tree; Reconciliation method