The role of microRNAs in the repeated parallel diversification of lineages of midas cichlid fish from Nicaragua

Cichlid fishes are an ideal model system for studying biological diversification because they provide textbook examples of rapid speciation. To date, there has been little focus on the role of gene regulation during cichlid speciation.However, in recent years, gene regulation has been recognized as a powerful force linking diversification in gene function to speciation. Here, we investigated the potential role ofmiRNA regulation in thediversificationof six cichlid speciesof the Midas cichlid lineage (Amphilophus spp.) inhabiting the Nicaraguan crater lakes. Using several genomic resources, we inferred 236 Midas miRNA genes that were used to predict the miRNAtarget sites on 8,232Midas 30-UTRs.Using population genomic calculations ofSNPdiversity,wefoundthemiRNAgenes tobe more conserved than protein coding genes. In contrast to what has been observed in other cichlid fish, but similar towhat has been typically found in other groups,weobserved genomic signatures of purifying selection on themiRNAtargets by comparing these sites with the less conserved nontarget portion of the 30-UTRs. However, in one species pair that has putatively speciated sympatrically in crater Lake Apoyo,werecovered a different pattern of relaxed purifying selection and high genetic divergence atmiRNA targets. Our results suggest that sequence evolution at miRNA binding sites could be a critical genomic mechanism contributing to the rapid phenotypic evolution of Midas cichlids.