A long discussed and unresolved question in ecology and evolution is to determine the mechanisms that originate and set an upper limit to diversity in ecosystems. Ecological and evolutionary views have focused on themechanisms that enable or constraint species coexistence, genetic variation and the genetics of speciation respectively, but a unified theory of biodiversity linking those approaches in the same framework is still missing. Classic and current models of diversity have recently opened and reinvigorated the search for evolutionary and ecological patterns in a unified framework. At NCEAS, I intend to work towards a unified theory of biodiversity by modeling multiple biological levels and spatial scales using novel computational and analytic approaches. I will also test these models with the huge amount of data on multiple levels and scales, collected and meticulously catalogued, that is becoming available for scientific analysis. In particular, I will integrate neutral theories of molecular and species diversity by linking ecological interactions to explicit mechanisms of speciation by implementing models of evolving graphs at molecular and ecological levels. This will allow me to study how interacting graphs at multiple biological levels generate and alter diversity and better understand the evolution of diversity at different biological levels under neutral or natural selection. Finally, these models will allow the linking of the origin, evolution and coexistence of diversity to molecular, sexual and trophic behavior at ecological and evolutionary scales.