Figure 3

Illustration of how a shared polymorphism among the sampled sequences becomes counted as a "singleton" as one works backwards in time. In (a), the A/G bases for a shared polymorphism are shown for four sampled sequences. The three coalescent time intervals of this asymmetrical genealogy (T _j , with j = 4, 3, or 2 sampled and/or ancestral sequences) are labeled on the left. The solid bar marks the G to A mutation in the common ancestor of the two leftmost sampled sequences (open dot), which results in the A/G shared polymorphism. The first event is the coalescence of the two leftmost sampled sequences in T₄ (a). This coalescence reduces the number of alleles to three as the two leftmost sampled sequences in T₄ are replaced by their common ancestor in T₃ (b). In the process, their shared polymorphism is replaced by the "singleton" of their common ancestor. This replacement is the basis of the expanded definition for a "singleton" (Table 1).