Illustration of the lineage sorting process. (A) Effects on the genealogy. The process starts with a random distribution of lineages when the ancestral population splits. The lineage in black is an outgroup to lineages in blue, so that the blue lineages show a closer relationship between populations than to the black lineage (incomplete lineage sorting). When the blue lineages in the top population reach fixation (through a selective sweep for instance), any lineage from the other populations will constitute an outgroup, thereby completing the sorting of lineages. (B) Two types of genealogies illustrating the possible relationships between an archaic lineage and modern human lineages. (C) Local effects in the genome at different time points. The curves represent the progression of lineage sorting for two independent regions, evolving under neutrality (black curve) and positive selection (blue curve), respectively. Longer fixation times are associated with more recombination so that neutrality produces smaller external regions.
