The evolution of ribosomal DNA in Daphnia

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It has been observed that copies of genes that are present many times within genomes (multigene families) are very similar to one another within species, even when similarity among copies in different species is very low.    This phenomenon is known as "concerted evolution". Ribosomal DNA (rDNA) is a multigene family that is present in hundreds to thousands of copies in plants and animal cells, and encodes the structural RNA molecules (rRNA) that make up ribosomes: the site of protein synthesis in all cells.  One rDNA unit consists of 3 genes that encode rRNA molecules separated by "spacers". The spacers contain sequences that control the rate of rRNA production. Some regions of the rDNA unit diverge between species very slowly while others, such as the spacers, diverge very rapidly, even among closely related species. Despite this rapid divergence, the sequences still retain their function.    I use small crustaceans (Daphnia) as a model system to study the molecular evolution of rDNA. The goal of my work is to understand the interaction between the molecular processes that cause concerted evolution, and natural selection to maintain the function of the rDNA and rRNA sequences.  I will study the impact of differences in rDNA copy number, and in the rate of molecular recombination in rDNA, on rates of concerted evolution between Daphnia species, and how these differences influence levels of variation among rDNA copies within species.  I will also determine the relative intensity with which natural selection acts on variation in different regions of the rDNA unit. The spacer sequences diverge very rapidly between species but little is known about the way they co-evolve with the proteins that must bind to them in order to control rRNA production.  I plan to identify these proteins and study the impact of genetic variation on the interaction between the proteins and the rDNA sequences to which they bind.