The role of microRNAs in the diversification of Midas cichlids from Nicaragua

• Applicant: Paolo Franchini, Ph.D.
• Subject Area: Evolution, Anthropology ; Bioinformatics and Theoretical Biology
• Term: from 2014 to 2018
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 253390846

Cichlid fishes are one of the best-known model systems for the study of biological diversification, and are a text book example for extremely rapid phenotypic diversification and speciation. Each of the East African great lakes harbours hundreds of endemic species and we have begun to investigate it with molecular genetic tools. However, the complexity of this system makes it difficult to link genetic differences to phenotypic traits in these large species flocks. The Mesoamerican Midas cichlid species complex (the Amphilophus citrinellus species group) is particularly variable in ecologically relevant traits, such as body shape and pharyngeal jaw morphology, and shows a characteristic striking colour polymorphism where most individuals have dark body coloration while others are bright gold or rarely also white in their coloration. Compared to African cichlids, a limited number of species comprise this system, and most of them are only a few thousand years old. Hence, most of the genetic differences are likely to be of functional relevance, and all these young species can be hybridized which allows us to do genetic experiments. I will focus here on eight cichlid species occurring only in the large and old Lakes Nicaragua and Managua, and in the small crater lakes Apoyo and Xiloá, from Nicaragua. The endemic crater lake cichlids exhibit particular adaptations repeatedly and independently in these two crater lakes, this makes it possible to ask if particular genomic variation is causally related to repeated phenotypic innovations. Most of the research on the molecular basis of speciation and species differences has so far been limited to protein coding regions of the genome. However, in recent years, the role of gene regulation was recognized as an alternative (and possibly the main) force in driving the diversification of species. Among all gene regulatory systems, microRNAs (miRNA), small ribonucleic molecules, are being recognized as a strong regulator of gene expression at the post-transcriptional level. Yet, virtually nothing is known so far about this mechanism in cichlid fish. The advent of high throughput second generation DNA-sequencing technology now provides us with extraordinarily powerful methods to characterise the miRNA diversity in the entire genome of several species of cichlids. Thereby we can now investigate the potential role of these newly discovered regulatory mechanisms in driving the extraordinarily fast rates of speciation in cichlid fishes. Specifically, I will ask if differential expression of miRNAs during development might account for phenotypic differences between species. This has never been done before and together with research on protein coding regions of the genome, this new approach will aid to link genotype and phenotype and might provide fundamentally new insights into the processes of phenotypic differentiation and speciation.

• DFG Programme: Research Grants