title: Inferring explicit weighted consensus networks to represent alternative evolutionary histories.
abstract: BACKGROUND
  The advent of molecular biology techniques and constant increase in availability of genetic material have triggered the development of many phylogenetic tree inference methods. However, several reticulate evolution processes, such as horizontal gene transfer and hybridization, have been shown to blur the species evolutionary history by causing discordance among phylogenies inferred from different genes.
  
  
  METHODS
  To tackle this problem, we hereby describe a new method for inferring and representing alternative (reticulate) evolutionary histories of species as an explicit weighted consensus network which can be constructed from a collection of gene trees with or without prior knowledge of the species phylogeny.
  
  
  RESULTS
  We provide a way of building a weighted phylogenetic network for each of the following reticulation mechanisms: diploid hybridization, intragenic recombination and complete or partial horizontal gene transfer. We successfully tested our method on some synthetic and real datasets to infer the above-mentioned evolutionary events which may have influenced the evolution of many species.
  
  
  CONCLUSIONS
  Our weighted consensus network inference method allows one to infer, visualize and validate statistically major conflicting signals induced by the mechanisms of reticulate evolution. The results provided by the new method can be used to represent the inferred conflicting signals by means of explicit and easy-to-interpret phylogenetic networks.
authors.forename: Mehdi
authors.initials: M
authors.lastname: Layeghifard
authors.forename: Pedro R
authors.initials: PR
authors.lastname: Peres-Neto
authors.affiliation: Département d'Informatique, Université du Québec à Montréal (UQÀM), CP 8888, Succ, Centre Ville, Montréal, QC H3C 3P8, Canada. makarenkov.vladimir@uqam.ca.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Makarenkov
mesh_terms: D000465:Algorithms; D005075:Biological Evolution; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D006824:Hybridization, Genetic; D010802:Phylogeny