Assignment of potential paralogs. A In an evolutionary scenario, an ancestral gene is duplicated, followed by two speciation events, followed by asymmetrical gene loss of genes x2 and y1. The paralogous genes x1 and y2 could be mistaken for orthologs, but the duplicates are retained in genome Z that can act as a witness of non-orthology. B Schematic for verifying a stable pair between x1 and y2 using genome Z. If (x1, z1) and (y2, z2) form stable pairs and are the closest relatives then x1 and y2 are paralogs and were not verified. C The only possible quartet formed when (x1, z1) and (y2, z2) are the closest related sequences is shown.