Figure 1. A schematic relationship between two samples from two species diverged T generations ago. Circles and squares represent mutations that lead to within‐sample polymorphisms and between‐sample polymorphisms, respectively. t = (t₂, t₃) where t₂ and t₃ are time lengths between successive branching events within a sample, commonly known as the coalescent time. The common ancestral sequences of the two samples do not coalesce at T generations ago because the common ancestral population was polymorphic.

Figure 2. An example of genealogy of six sequences with five mutations, three of which are of size 1 (external mutations), one of size 2 and one of size 4.