title: Species Tree Estimation from Genome-Wide Data with guenomu.
abstract: The history of particular genes and that of the species that carry them can be different for a variety of reasons. In particular, gene trees and species trees can differ due to well-known evolutionary processes such as gene duplication and loss, lateral gene transfer, or incomplete lineage sorting. Species tree reconstruction methods have been developed to take this incongruence into account; these can be divided grossly into supertree and supermatrix approaches. Here we introduce a new Bayesian hierarchical model that we have recently developed and implemented in the program guenomu. The new model considers multiple sources of gene tree/species tree disagreement. Guenomu takes as input posterior distributions of unrooted gene tree topologies for multiple gene families, in order to estimate the posterior distribution of rooted species tree topologies.
authors.affiliation: Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain. leomrtns@gmail.com.|Department of Materials, Imperial College London, London, UK. leomrtns@gmail.com.
authors.forename: Leonardo
authors.initials: L
authors.lastname: de Oliveira Martins
authors.affiliation: Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.
authors.forename: David
authors.initials: D
authors.lastname: Posada
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D020440:Gene Duplication / Q000235:genetics; D022761:Gene Transfer, Horizontal / Q000235:genetics; D010802:Phylogeny
keywords: Bayesian phylogenetics; Duplications and losses; Incomplete lineage sorting; Species tree; Supermatrix; Supertree; Tree distance; Tree reconciliation