Evolutionary and genomic views of three genomes involving introgression.

<p>Hybridization between species B and C results in individuals of species B with genomes that are mosaics with regions of "vertical" descent from B and others of introgressive descent from C. Walking along the genomes from left to right, local genealogies are observed, and when a recombination breakpoint is crossed, the local genealogy changes. (Here, the term local genealogy refers to the local tree describing the evolutionary history of a single site in the alignment.) Switching of local genealogies of unlinked (broken by recombination) loci is known as incomplete lineage sorting (ILS). Further, the walk enters regions of introgressive descent (II and IV), where the genealogies switch due to hybridization. The complexity of the model stems from the co-occurrence of ILS and introgression, and the need to tease them apart. Within the phylogenetic network of the species (leftmost), three possible local genealogies are shown: one that agrees with how species split and diverged (red), one that is reflective of the introgression event (blue), and another that is a signature of ILS (brown).