Hybridization plays an important role in the evolution of certain groups of organisms, adaptation to their environments, and diversification of their genomes. The evolutionary histories of such groups are reticulate, and methods for reconstructing them are still in their infancy and have limited applicability. We present a maximum likelihood method for inferring reticulate evolutionary histories while accounting simultaneously for incomplete lineage sorting. Additionally, we propose methods for assessing confidence in the amount of reticulation and the topology of the inferred evolutionary history. Our method obtains accurate estimates of reticulate evolutionary histories on simulated datasets. Furthermore, our method provides support for a hypothesis of a reticulate evolutionary history inferred from a set of house mouse (Mus musculus) genomes. As evidence of hybridization in eukaryotic groups accumulates, it is essential to have methods that infer reticulate evolutionary histories. The work we present here allows for such inference and provides a significant step toward putting phylogenetic networks on par with phylogenetic trees as a model of capturing evolutionary relationships.
