Spatial patterns of genetic variation are shaped by a variety of population genetic processes, and can therefore be a rich source of information about population history. The work presented here focuses on two drivers of spatial variation: recent secondary contact after isolation, and responses to spatially varying selection. The first chapter describes expected genome-wide patterns of coancestry resulting from secondary contact between two differentiated populations, with the continuous movement of individuals by diffusive local migration. Using analytic expressions derived for expected linkage disequilibrium (LD), an inference framework was developed to estimate the timing of secondary contact and gene flow. This was applied to genomic data from spatially distributed admixed human populations, providing an alternative to commonly used admixture models. The following chapters examine patterns of spatial variation that are influenced by selection. While continued gene flow acts to homogenize allele frequencies between different populations, differential selection across space can maintain consistent patterns of geographic variation. These patterns are historically well studied, especially in the context of local adaptation. Here, genome-wide patterns of geographic variation in D. simulans is described, in order to better understand the process of local adaptation in this species, and in Drosophlia in general. Chapter two compares and contrasts patterns of differentiation between pairs of northern and southern populations of D. simulans in Australia and North America, with a focus on patterns of convergence and parallelism. There is evidence for parallel differentiation between the two continents in regions of the genome associated with regulation of gene expression. Contrary to patterns observed in the closely related Drosophila melanogaster, the spatial distribution of genetic variation in D. simulans does not support temperate adaptation outside of the species ancestral range. The results of this study suggest that populations on the two continents may have experienced independent, and different, adaptive trajectories, and that there may be limited power to detect parallel differentiation from comparing pairs of populations. Following the results of chapter two, chapter three presents a more detailed examination of genetic variation in D. simulans collected along the North American east coast and Central America. By analyzing patterns of genetic variation in 8 North American and one Panamanian population, this study identifies genetic variants that are associated with environmental gradients along the sampled transect. This study finds some evidence for the potential role of gene regulation in local adaptation, and significant overlap with D. melanogaster of genes containing latitudinally associated alleles. This study also reveals geographically inconsistent patterns of genetic variation along the cline, highlighting the need for further sampling, both temporally and geographically, in order to obtain a better understanding of population dynamics and adaptation in this species. (Gene lists and Gene Ontology enrichments for chapter 3 are available online as Supplemental file 1 and Supplemental file 2).