Initiatives such as the human genome project and similar projects for other model genetic systems are generating vast amounts of information on the detailed genetic organization of a variety of organisms. The search for general organizing principles and new biological processes using these data requires a starting framework for a theory of genome structure. This project continues Dr. Walsh's long-term research goal of a comprehensive population-genetic theory of genome evolution, based on an understanding of how molecular forces within the cell shape the genome and, conversely, how one can make inferences on the nature of these forces from genomic sequence and structural information. Three related problems will be examined. The first is to examine how intracellular selection, drift, and gene conversion influence the within-cell substitution dynamics of organelle genes. All eukaryotes carry at least two separate genomes (the nuclear genome plus one or two organelle --- mitochondrial and chloroplast --- genomes). Organelle genomes are very widely used as genetic markers in problems as diverse as understanding human origins, tracing the genetic input from different native plants into high-yield domesticated crops, and conservation biology. The theory proposed to be developed here will provide a better understanding of how these genetic markers behave. Second, models for the conditions under which a recently duplicated gene evolves a new function (as opposed to becoming an inactive pseudogene) will be examined. There has been essentially no modeling of just how frequent (or infrequent) the evolution of new function is expected to be. Finally, models of the evolution of genome size, treating size as a quantitative- genetic character will be developed. While there is a developing theory of the behavior of an individual gene family, there is currently no general theory about how genome size as a whole evolves. //
