The goal of this work is to extend our understanding of how evolution acts on the molecular structure of genomes. Three general areas will be investigated using theoretical population genetic models: pseudogene distributions, copy number dynamics in tandem arrays, and divergence of duplicated genes under homology-dependent conversion. Examination of pseudogene distribution provides an indicator of the relative effectiveness of selection in multigene families and may allow for discrimination, based on empirical data, of the nature of selection acting on a particular family. A more complete theory of copy number dynamics in tandem arrays is essential for understanding both satellite DNA turnover between related taxa and the behavior of runs of simple sequence DNAs (which often form restriction polymorphism markers used in genetic screening). Dynamics of divergence under homology-dependent gene conversion informs us how long individual genes remain part of a multigene family and is of considerable importance in developing theoretical models of evolution of new gene function via gene duplication. Theoretical models often suggest areas for future empirical work which are not obvious. An integral part of the proposed research is testing model predictions and assumptions from empirical data, and to strive to make testable predictions in little-examined areas of genome evolution. Thus, the proposed work examines functional, as well as evolutionary, aspects of genome organization from a rather different prospective than is normally used.
