The role of transposable elements in generating functional diversity

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The DNA housed inside the cells of all organisms contains the genes required for building and maintaining living bodies. However, in most organisms, there are other components of the genome that are not specifically required for life and these elements may multiply within the genome in a manner similar to computer viruses multiplying on a computer hard-drive. These genetic elements are known as transposable elements and come in two forms: those which use a copy and paste mechanism (type I) and those that use a cut and paste mechanism (type II). Scientists have typically viewed the presence of these elements in genomes as parasitic and their effects on the host as either neutral or negative. However, it is increasingly recognised that these mobile elements can have a positive effect on the evolutionary potential of a species. For example, the resistance of the fruit fly Drosophila melanogaster to an organophosphate pesticide has increased as a result of the production of a novel truncated protein generated by the insertion of a transposable element in an existing longer gene. Other researchers have suggested that transposable elements may have more profound impacts on biodiversity as a whole and have suggested that the insertion of transposable elements may lead to increased evolutionary potential and may explain why some groups of organisms are particularly species rich. However, to date there has been little research that goes beyond identifying a circumstantial relationship between the abundance of transposable elements and the speciation rates of a group of organisms. In this study, we will focus on a species rich group of Neotropical catfishes that (i) have considerable differences in the transposable element content of their genomes and (ii) have lineages with different rates of speciation and (iii) show a sudden increase in speciation rate ~25 million year before present which is broadly contemporaneous with the TE expansion.We will firstly quantify the abundance of different transposable elements across the genomes of Corydoras catfishes. This will provide an accurate estimate of the TE density in different species, and by mapping these onto a phylogenetic framework, the timing of TE expansions in different species will be quantified. Subsequently, we will investigate whether TEs increase the mutation rates of promoter regions as a result of the intrinsic DNA repair mechanisms that heal TE insertion / excision sites. Next we will investigate whether catfish lineages with high speciation rates have more TEs inserted in genes and promoter regions than species with low diversification rates. Finally, we will investigate whether certain groups of genes (e.g. colour pattern genes) have been more greatly affected by TEs than other genes (e.g. housekeeping genes). The results generated in this proposal will allow a thorough investigation of the role of transposable elements in increasing the diversity of genes and their promoter regions and provide important evidence as to whether TEs underpin rapid speciation in some taxonomic groups.