The objective my dissertation was to assess the effects of habitat loss and fragmentation on genetic diversity and landscape connectivity. I focused on Vallisneria americana Michx. (Hydrocharitaceae), a submersed aquatic plant species found in the Chesapeake Bay. Vallisneria americana has undergone dramatic changes in abundance and distribution throughout its range and has been targeted for restoration, which makes it ideal for examining the effects habitat loss and fragmentation.

I examined the naturally occurring genetic diversity across the Chesapeake Bay and its major tributaries. Sites were genetically diverse, but had a range of genotypic diversities. There were four genetic regions, corresponding with geographic regions in the Bay. Vallisneria americana has been the target of restoration, and restoration techniques could be influencing genetic diversity and potentially lowering overall success. I examined various restoration techniques across eight restoration sites, and found that technique did not greatly influence genetic diversity. However, small population size, significant inbreeding coefficients, and low overlap of allele composition among sites provide cause for concern.

Measures of functional and potential connectivity provide insights into the degree of contemporary gene flow occurring across a landscape. Pollen dispersal distance was measured using indirect paternity analysis, and is spatially restricted to only a few meters. Dispersal at this scale imposes small genetic neighborhoods within sites, evidenced by high seed relatedness within mothers. I used a graph theoretic approach to examine the distribution and potential connectivity of historic and current patches of V. americana. There was a high turnover in the distribution of patches, and connectivity varied through time, but even if all habitat were occupied, increases in overall network connectivity would not necessarily be observed.

I developed an individual based model that I used to test the ability of measures of genetic differentiation to detect changes in landscape connectivity. Genetic differentiation measures became significant after two generations, but the magnitude of change in each was small in all cases and extremely small when population sizes are greater than 100 individuals. These results suggest that genetic differentiation measures alone are inadequate to rapidly detect changes in connectivity.