Schematic of multidomain evolution. (a) A hypothetical multidomain family evolving by gene duplication and domain shuffling. (b)Trees representing the history for each domain in the gene family. (c)The evolutionary history of the same family showing the domains evolving in the gene tree. Reconciliation correctly infers 2 domain duplications, 1 domain transfer and 1 domain loss. The gene family (locus) tree is shown in brown; black squares represent domain duplications.