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.