Fig 1. Model of an introgression sweep after a secondary contact.

Species trees: phylogenetic relationships between the recipient, donor and outgroup species. Note that the time scale is not respected (T_d and T_sp are very large) and that all species are assumed to have the same size. Coloured background: frequency of the selected allele in the different species. A single favourable haplotype is introduced into the recipient species through a rare hybridization event with the donor (red arrow) where it eventually reaches fixation. Superimposed coalescent tree: coalescent tree of a sample of n lineages, taken from the recipient population at a neutral site located at a distance d from the focus of selection. k lineages escape the selective sweep (see Eq (2)) and their polymorphism is a subsample of the neutral site frequency spectrum (see Eq (6)). The other n − k lineages trace back as a single lineage into the donor species.