Phylogenomic view of trait evolution in the presence of incomplete lineage sorting (ILS) and introgression.

Left: The three possible genealogies of three taxa A, B, and C. Right: Phylogenetic network that models an underlying species tree (A,(B,C)) along with a reticulation from A to B, and whose associate inheritance probability is γ. The embedded solid gene tree involves ILS but no introgression, whereas the dashed gene tree involves introgression but not ILS. The states Sa, Sb, and Sc of an incongruent binary character are shown at the leaves of the phylogenetic network.