The genomic and genealogical signals of introgression. (A) Schematic of the introgression process, where some modern human populations (vermilion) migrated out of Africa, came into contact with archaic humans (blue) in Eurasia followed by subsequent interbreeding events. Over many generations, archaic segments are broken down due to recombination, purged due to negative selection, and incorporated into the genomes of present-day modern humans. (B) Instantaneous Unidirectional Admixture (IUA) model for studying introgression from a donor population (P3) into a hypothesized recipient population (P2) where P1 represents a control population assumed to have no genetic contributions from P3. In this model, the ancestral relationships are traced for a single lineage per population resulting in eight unique coalescent histories with only three possible topologies, that is, branching orders among lineages. Coalescent histories where P1 and P2 coalesce first, P1 and P3 coalesce first, and P2 and P3 coalesce first are depicted in sky blue, orange, and yellow; respectively. Under the IUA model, a site pattern is defined by the configuration of ancestral (A) and derived alleles (B) at a given site for the ordered set {P1, P2, P3, O}, where O represents an outgroup population used to polarized ancestral states in practice. Each topology will result in one unique site pattern resulting from a mutation occurring on the internal branch (green stars), while all topologies can generate three additional site patterns resulting from a mutation occurring on one of the three terminal branches (pink stars). (C) In the absence of gene flow, there are four unique coalescent histories under the IUA model, one with a history of lineage sorting (LS) between P1 and P2, and three equally probable histories of incomplete lineage sorting (ILS). (D) In the presence of gene flow, there are four additional coalescent histories, where the P2 lineage traces its ancestry through P3’s side of the tree, one with a history of LS between P2 and P3, and three equally probable histories of ILS.
