Population genetics and species interactions: From theory to agro-ecosystems

Population genetics is the study of allele frequency distributions and changes due to evolutionary processes such as selection, adaptation, genetic drift and gene flow to understand how these processes impact populations over space and time. Population genetics theory can be utilized to understand not only population level interactions, but also interactions among closely related species. In this dissertation I have utilized population genetics in three conceptually related projects. Utilizing genome-wide gene coding markers, I have tested the impact of population size changes on the genetic diversity of coding genes in a model system (Arabidopsis lyrata subsp. petraea). This study tests population genetics theory with an empirical data set. We have also utilized genome-wide gene coding markers and divergence population genetics to determine the origin of weedy rice in California (CA). This study applies population divergence models and coalescent theory regarding probabilities of common allele ancestry back in time to determine the closest relative of weedy rice in that region. Finally, this dissertation includes a study that tests alternative models of gene flow between cultivated rice and weedy rice populations in Arkansas. The potential outcomes of the detected introgression of alleles from cultivated rice to a weedy rice biotype are discussed in the context of the phenotypic changes described in the plants that carry introgressed alleles. This study examines the rate of gene flow between groups and infers the potential evolutionary impact of this process. This dissertation covers population and species dynamics from theory to utilization of theory on both the within and between species levels. The outcomes from these studies will be useful in deciphering patterns in the larger topics of speciation and the mechanisms of adaptive divergence.