The long term goal of this work is to understand the significance of the diverse levels and patterns of DNA sequence variation observed within and between species. Experimental and theoretical work has begun to reveal the ways in which natural selection and genetic linkage interact to determine levels of genomic diversity in natural populations, particularly for Drosophila. Studies have demonstrated a positive genome-wide correlation between levels of DNA variation and rates of recombination in Drosophila melanogaster and have made clear the central importance of the knowledge of the recombinational landscape for understanding genomic diversity in natural populations. Specific aims include the isolation, localization and estimation of mutation rates for microsatellite loci in D.melanogaster, D.simulans and D.pseudoobscura. These microsatellites will be used in both genetic and physical mapping studies to determine the recombinational landscapes for these species. In addition, DNA sequence and microsatellite variation will be assayed in natural populations of these species to examine the generality of the variation/recombination correlation and implications for inferences of species effective population size and species coalescent times. Tests of hypotheses to explain the correlation are proposed based on comparisons of variation on autosomes and X-chromosomes, and the analyses of the frequency distribution of DNA sequence and microsatellite variation within and between populations. Regardless of its cause, the observed correlation indicates that effective population size (Ne) is not the same for all genes across a genome, and can be dramatically reduced below the species effective population size in regions of low recombination due to selective sweeps or background selection. We will exploit this regional variation in Ne to test alternative hypotheses as to the fitness consequences of replacement, silent and noncoding sequence variants. Each of these classes of polymorphism is predicted to behave differently with regard to the relative proportion of variation within versus between species depending on whether they are weakly advantageous, strictly neutral, or slightly deleterious. These studies will provide a deeper understanding of the evolutionary forces that shape genetic change in populations over time and space and will provide a conceptual framework in which to interpret DNA polymorphism data from other organisms and humans.