Kingston, Sarah ElizabethABSTRACT Title of Dissertation: GENOME-WIDE ANALYSIS OF DIVERGENCE AND INTROGRESSION IN TOWHEE HYBRID ZONES Sarah Elizabeth Kingston, Doctor of Philosophy, 2012 Dissertation directed by: William F. Fagan, PhD, Department of Biology Michael J. Braun, PhD, Smithsonian Institution Hybrid zones offer a natural laboratory in which investigation of the evolutionary forces involved with reproductive isolation and differentiation is possible. Highly multilocus population genomics is a powerful and feasible new tool with which to address such questions of evolutionary interest. I utilize a unique spatial setting that incorporates two hybrid gradients of the towhess Pipilo maculatus and P. ocai. These species likely diverged in allopatry and are in secondary contact. I utilize genome-scale multilocus techniques to address questions regarding the architecture of differentiation and introgression across these hybrid gradients and the influence of location specific environmental factors on isolation. The multilocus analysis reveals cross-genomic variation in selective constraints on gene flow and locus-specific flexibility in the permeability of the interspecies membrane. Maintenance of historical divergence is acting in a cohesive manner, but local environmental and stochastic factors are also important driving forces. Habitat corridors for dispersal potential indicate hotspots of connectivity where the two transects meet. Both habitat connectivity and genetic differentiation between geographically disparate parental types appear to influence the dynamics of gene flow across the hybrid gradient. Environmentally-mediated gene flow in the context of secondary contact and hybridization is an important force influencing evolutionary trajectory.DissertationBiologydivergencegene-flowhybridisolation