Introgression scans of chromosome 7 from the Mus musculus domesticus data set.

Results in panels (a) through (c) are based on posterior decoding (Eq. 2). Panel (a) gives the probability that PhyloNet-HMM is in one of the introgressed () states. Panel (b) shows the probability that PhyloNet-HMM is in an introgressed () state corresponding to a particular gene genealogy, where each gene genealogy is displayed in a separate row and pixel intensity varies from white to blue to represent probabilities from to . Panel (c) is identical to panel (b) except that non-introgressed () states are shown. Results in panels (d) through (f) are based upon a Viterbi-optimal trajectory. In panel (d), genomic regions are classified as having introgressed origin or not based on the hidden state that the Viterbi-optimal trajectory is in (either an or state, respectively). Panel (e) show the rooted gene genealogy inferred for each locus classified as introgressed in panel (d). Each distinct rooted gene genealogy is represented using a distinct color and row. Panel (f) shows the rooted gene genealogy inferred for the remaining loci (which were not classified as introgressed). Panel (g) shows loci sampled by the Mouse Diversity Array [36], which we used to genotype our samples. The dashed vertical line indicates the location of the Vkorc1 gene, which was shown by [2] to be a driver gene in an introgression event between ( M. m. domesticus and Mus spretus) and leading to the spread of rodenticide resistance in the wild. The grey bars indicate regions with missing data that were approximately 100 kb or longer.