Three possibilities with a “ghost lineage.” A ghost lineage is an extinct or unsampled lineage (in gray), that introgressed into a sampled lineage (H2 in this case). a Ghost lineage diverged after H3 did, making it a sister lineage of (H1 + H2). In this case it is impossible to have one mutation produce an ABBA or BABA site pattern. b Ghost lineage as a sister lineage of H3. In this case it is similar to gene flow originating from H3; if a mutation occurs in the bolded branch it can produce an ABBA site pattern, which can be interpreted as evidence of gene flow between H2 and H3. c Ghost lineage diverged before H3 did. If a mutation occurs in the bold branch it can produce a BABA site pattern, which can be (incorrectly) interpreted as evidence of gene flow between H1 and H3
