Fig. 4.

Hidden paralogs example and witness of non-orthology gene quartet. (A) Example of labeled gene tree containing hidden paralogs due to asymmetric gene losses between human and mouse. This can occur when an ancestral duplication is first followed by a speciation then by asymmetric genes losses. The resulting paralogs are wrongly inferred as orthologs because they are the mutually closest pairs between two genomes (Human₁, Mouse₂ sequences). OMA attempts to identify such cases through the use of a third species (here a monkey) that has retained both copies, which can act as witnesses of non-orthology.(B) The four extant genes form a quartet with branches labeled a–e