10.3 Incomplete lineage sorting
More rarely, the tree constructed for a specific SNP is discordant with the species tree. This is usually due to incomplete lineage sorting (ILS) – when genetic variation is present in the ancestor of two populations (e.g., the modern human–Neanderthal ancestor), then randomly fixes in a fashion that happens to conflict with the populations’ evolutionary relationships.
ILS can create discordant ABBA
or BABA
trees for a given SNP. Under ILS, we would expect to see approximately equal numbers of ABBA
and BABA
trees.