Agroforestry, a farming system where crops and trees co-exist, continues to rewrite rural landscapes as governmental and nongovernmental policies have globally endorsed it as a panacea to protect biodiversity while maintaining agricultural production. But we know little about its biogeographical outcomes. My study utilizes a quasi-experimental design to describe and measure the relationship between agroforestry farming practices and biodiversity outcomes at species and genetic levels by examining a coffee agroforestry program run by an NGO in Junin, Peru. The main research question is: how do changes to agroforestry practices through participation with the NGO change biodiversity? In this study, I (1) describe how the NGO's agroforestry program alters farming practices and resource access; (2) measure biodiversity (plant species and genetic diversity of Inga oerstediana Benth.) on farms utilizing biogeographic methods paired with landscape genetic techniques; and (3) quantitatively test the impact of farming practices on biodiversity outcomes. I show that different agroforestry regimes between NGO participants and non-participants create divergent biotic landscapes, as seen by plant species and genetic diversity on farms. Interviews and vegetation data show that NGO has mixed results when examining resource distribution, species diversity, and genetic diversity. I find that NGO technicians are working within the constraints of supervisors' decisions and distribute resources, including plants, seeds, and knowledge, differently across participating communities and farmers. Differences in biotic compositions can be seen in the plant species found on farms and are related to specific farmers and their participation with the NGO, when considering the presence of plant taxonomic families and the Inga genus. The NGO has also changed the diversity and population structure of I. oerstediana on the farms that most recently received plants, indicating that individuals genetically different from the rest in the region were introduced. This dissertation represents the beginning of understanding the link between an organization's work and biodiversity changes in an agroforestry system. Using the linkage framework detailed in this dissertation, we can continue to explore the relationships between policies, organizations, and biodiversity. In a world undergoing continued land cover change and climate change, building such an understanding should be a global priority.
