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Understanding why we find different types and numbers of species in different places has been a long-standing question for biologists. Ecological communities provide a conceptual and literal framework for unraveling generalizations about the composition, distribution, and dynamics of biodiversity. Communities assemble via ecological and evolutionary mechanisms that lead to the accumulation of species and the development of species interactions. Insights into the dynamics of community assembly have relied extensively on theoretical work or studies with limited spatiotemporal scale. Directly studying community structure through time using long-term time-series data offers an exciting opportunity to link evolutionary relatedness across multiple taxa and the ecological attributes of the communities in which they occur, within a dynamic framework. Oceanic archipelagos provide a chance to sample communities from discrete time points during community assembly. Present-day communities face threats, such as climate change and invasive species, demanding more holistic approaches that consider all species in an ecosystem and the interactions between them. Advancements in molecular techniques, bioinformatics, and data science have led to the possibility of a more comprehensive understanding of the structural properties of communities and of biodiversity overall. The research presented here explores the interplay of ecological and evolutionary processes on biodiversity dynamics over deep time. I employ multiple research approaches including field collections, laboratory work with environmental DNA and museum specimens, macroecological theory, and network thinking to create a novel synthesis of information for understanding the evolution of ecological communities. First, I highlight the singular importance of insular systems for studying fundamental questions in ecology and evolutionary biology. By recording patterns of species accumulation and genetic distances in multiple arthropod lineages, I explore patterns of community assembly over time and how they differ between lineages. Additionally, I investigate systematic deviations in observed species abundance distributions from predictions of theory for understanding community steady state. Last, I demonstrate the implications of shifting network architecture metrics for understanding ecosystem change. My work makes critical advances in understanding biodiversity, community assembly, and the consequences of environmental perturbations on ecological communities.