FIGURE 2.

Effect of introgression and incomplete lineage sorting (ILS) in molecular phylogenetics. Top: The species (or population) tree is represented by the gray area. The dotted line represents a single gene genealogy. The star represents a mutation changing the ancestral allele G (black dotted line) into the derived allele T (red dotted line). Bottom: Gene genealogy inferred from molecular data. (A) Congruent gene genealogy with species/population tree; (B) ILS: ancestral polymorphism is maintained before the divergence between A and B, so that B shares the allele T with C and not with A; (C) Introgression: B receives the allele T from C by gene flow. In the case of ILS and introgression, the gene genealogy (bottom) is not consistent with the species/population tree but similar between the two. The two processes cannot be distinguished from each other when only using gene genealogy approaches.