Molecular evolution of ribosomal DNA and its transposons in Daphnia.

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A large fraction of plant and animal genomes consists of repeated sequences that impact patterns of gene expression, rates of cell division and cell size. The members of these repeated, or multigene families diverge between species, but are generally homogeneous within species, which is known as concerted evolution. This homogeneity is maintained by recombination between repeat units, the products of which are subject to genetic drift, gene flow and natural selection at the population level. The rate at which new variants spread through a gene family, and an entire species depends on rates of recombination, gene family size, the number of chromosomes on which the gene family occurs and population structure. The long-term goal of my research is to understand the mechanisms and consequences of multigene family evolution using ribosomal DNA in the waterflea, Daphnia as a model system. Ribosomal DNA (rDNA) is a multigene family whose RNA products form an integral component of ribosomes, the site of cellular protein synthesis. Ribosomes are composed of ribosomal RNA (rRNA) and protein, and the rRNA performs the catalytic functions. In plants and animals, rDNA consists of a tandem array of hundreds to thousands of repeat units on one or more chromosomes. Plants and animals have many more rDNA copies than they need to produce rRNA, and only a subset of genes is active at any one time. Even so, changes in rDNA copy number can have substantial effects on the expression of large numbers of genes, and thus has the potential to contribute to morphological and physiological variation on which natural selection can act. Despite the importance of rDNA, there is still much we do not understand about the evolution of its copy number. The proposed research will address gaps in this knowledge by testing predictions derived from current hypotheses on the evolution of rDNA. My goals over the next 5 years are to test the following predictions: (1) rates of recombination in rDNA are positively correlated with rDNA copy number, (2) rapidly-evolving regions of rRNA genes increase the rate of evolution of the ribosomal proteins with which they interact, and (3) the distribution and copy number of transposons that target a specific region of rDNA but also occur outside rDNA is a function of their relative rates of transposition, and the rate of rDNA recombination. I expect the results to be of general interest through their contribution to basic knowledge in molecular genetics and evolution.