title: The Role of microRNAs in the Repeated Parallel Diversification of Lineages of Midas Cichlid Fish from Nicaragua.
abstract: 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 of miRNA regulation in the diversification of six cichlid species of 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 miRNA target sites on 8,232 Midas 3'-UTRs. Using population genomic calculations of SNP diversity, we found the miRNA genes to be more conserved than protein coding genes. In contrast to what has been observed in other cichlid fish, but similar to what has been typically found in other groups, we observed genomic signatures of purifying selection on the miRNA targets by comparing these sites with the less conserved nontarget portion of the 3'-UTRs. However, in one species pair that has putatively speciated sympatrically in crater Lake Apoyo, we recovered a different pattern of relaxed purifying selection and high genetic divergence at miRNA 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.
authors.affiliation: Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany.
authors.forename: Paolo
authors.initials: P
authors.lastname: Franchini
authors.affiliation: Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany.
authors.forename: Peiwen
authors.initials: P
authors.lastname: Xiong
authors.affiliation: Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany School of Earth Environmental & Biological Sciences, Queensland University of Technology, Brisbane, QLD, Australia.
authors.forename: Carmelo
authors.initials: C
authors.lastname: Fruciano
authors.affiliation: Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany axel.meyer@uni-konstanz.de.
authors.forename: Axel
authors.initials: A
authors.lastname: Meyer
mesh_terms: D000818:Animals; D023681:Cichlids / Q000235:genetics*; D004272:DNA, Mitochondrial; D019143:Evolution, Molecular; D049810:Genetic Speciation; D035683:MicroRNAs / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics; D009527:Nicaragua; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D004272:DNA, Mitochondrial; D035683:MicroRNAs
keywords: Neotropical cichlids; adaptation; gene regulation; miRNA; purifying selection; sympatric speciation