Examples of microRNA gene duplication histories. (a) Gene tree and most plausible reconstructed history of the mir9 cluster. The fourth member of the cluster, mir-306, evolves rapidly in flies. Its homology with mir-9/mir-79 is likely but this hairpin might also have evolved de novo. (b) The two most plausible reconstructions for the history of the mir-23 cluster. Scenario (1) postulates four paralogs in the ancestral vertebrate, where, presumably after the first duplication, one lineage either lost or gained mir-27 in the middle position of the cluster. Subsequently, in this scenario one copy of the three-membered cluster was lost in actinopterygians, while the two-membered clusters were lost in tetrapoda. Scenario (2) postulates three paralogs in the ancestral vertebrate and the independent loss of the mir-27 in two distinct clusters in the teleosts. (c) Duplication history of the mir-130 cluster reconstructed from genomic position information and the gene tree.