Abstract
Reticulate species evolution, such as hybridization or introgression, is relatively common in nature. In the presence of reticulation, species relationships can be captured by a rooted phylogenetic network, and orthologous gene evolution can be modeled as bifurcating gene trees embedded in the species network. We present a Bayesian approach to jointly infer species networks and gene trees from multilocus sequence data. A novel birth-hybridization process is used as the prior for the species network. We assume a multispecies network coalescent (MSNC) prior for the embedded gene trees. We verify the ability of our method to correctly sample from the posterior distribution, and thus to infer a species network, through simulations. We reanalyze a large dataset of genes from closely related spruces, and verify the previously suggested homoploid hybridization event in this clade. Our method is available within the BEAST 2 add-on SpeciesNetwork, and thus provides a general framework for Bayesian inference of reticulate evolution.