• cyprinodontiform
• Cyprinodontiformes
• Mammalia
• mammals

MicroRNAs (or miRNAs) are small non-coding RNA molecules that are involved in the regulation of many target genes in eukaryotic cells. This function is very important to the cells, and mature miRNA sequences are thus extremely conserved across even distantly related lineages, which makes this class of sequences an interesting subject for phylogenetic studies. In current literature, miRNAs have been classically used in phylogenetic analyses as discrete markers, while in this work the use of miRNA cluster nucleotide sequences as markers is investigated.
MiRNA clusters are constituted by multiple miRNAs that are transcribed together as a long non-coding RNA and then processed by various nucleases to produce the small mature fragments; they are thus a “mosaic” of more conserved regions (mature miRNAs) and less conserved regions (the spacers between the mature miRNAs).
The fact that there exist many different miRNA clusters is an advantage of this class of markers, because it could allow researchers to choose the ones that are more useful for their analysis. However, at present there is no way to determine, in general, which marker subset from a bigger set will be the best to use in a phylogenetic study and the choice, which is often needed (if only for economical or timing reasons), is usually made relying on already known information about the behaviour of the available markers.
Since there is no existing information about miRNA clusters as phylogenetic markers (as they have never been used in this sense), an objective method to decide which clusters to use is needed. Such a method is developed in this work, and allows the choice of the marker subset that best reconstructs either an unknown or an already known phylogeny, not only for miRNA clusters, but for any set of makers.
This method is benchmarked using both simulated data and real data from two datasets of mammalian miRNA clusters. These benchmarks, apart from providing confirmation that the method works, also give evidence that miRNA clusters can be used as phylogenetic markers.
This work also shows how this method and miRNA clusters can be used in reconstructing the phylogenetic history of a group of species, by providing a use example in which the phylogenetic relationships of fishes of the order Cyprinodontiformes (an ubiquitous order of small teleost fishes) are analysed through a set of miRNA clusters that have been chosen by our method.
The main result of this project is thus that miRNA clusters can be effectively used as phylogenetic markers, together with a method to identify the marker set that best reconstructs a phylogeny and a (small-scale) phylogenetic tree of Cyprinodontiformes.