The success of a species and the co-existence of communities over time ultimately depends on the stability of populations. While populations are inherently dynamic, contemporary environmental change may create population instability by altering processes such as migration, recruitment, and population growth and decline. A current goal in conservation biology and population ecology is to quantify the short- and long-term impact of anthropogenic activities, including habitat degradation and global climate change, in order to predict changes in populations, species, and communities. This knowledge is elusive, as these activities take place at multiple and often vast spatial and temporal scales, which to some degree limits the use of manipulative ecological studies to disentangle the web of human and anthropogenic influences. However, changes in population dynamics often leave genetic signatures. Biologists can use molecular ecology tools and carefully chosen study sites to investigate large-scale 'experiments in action'- natural populations already subject to specific ecological processes. I use this approach and the forest tree butternut (Juglans cinerea L.) to investigate the influence of: contemporary population decline on the distribution of genetic diversity, contrasting habitats on patterns of recruitment and colonization, and proximity to anthropogenic landscapes on rates of interspecific hybridization. Juglans cinerea represents a suite of early colonizing tree species, as well as a model conservation dilemma.My work shows the utility of a comparative, observational molecular ecology approach to investigating these processes. First, I show that the major influence on population genetic diversity is not dramatic 20th century decline due to an epidemic disease, but rather ancient range shifts following Holocene-era climatic warming. Second, I show that patterns of disturbance in upland and riparian habitats create markedly different opportunities for recruitment and spatial distribution of diversity. Third, I show that while anthropogenic landscapes facilitate extensive hybridization between J. cinerea and an introduced tree, Japanese walnut, forested landscapes greatly limit hybridization.The results of my first study suggest that the reproductive and life history characteristics of forest trees may allow them to endure extreme and rapid environmental change, even if populations are reduced in size and connectivity. However, the next two studies are a reminder that realized dispersal is quite limited in trees, particularly in the absence of suitable colonization sites. Predictions of forests' ability to track future climate change are therefore difficult to make. Together, these results emphasize that an effective conservation approach is the preservation of populations, even if small, in situ.