Figure 4.
Independent mutations in perfect LD. This figure depicts a 20-lineage coalescent tree with a five-lineage subsample highlighted in bold. Light circles represent mutation pairs that appear in perfect LD only in the five-lineage sample. In contrast, dark circles represent pairs of independent mutations that occur in perfect LD in the entire 20-lineage sample. These pairs are concentrated on the longest branches of the tree that are often ancestral to many lineages, making their site frequency spectrum enriched for high frequencies.
