The scientific discipline of phylogenetics involves understanding the diversity of life in the context of history. Technological advances in molecular biology and computational power have created an exponential increase in the number and kind of phylogenetic studies, allowing exploration of all manner of questions concerning the evolutionary history of a group. This dissertation research is focused on phylogenetic theory and applying these methods to the plant tribe Psoraleeae (Leguminosae; Fabaceae) with an emphasis on North American (NAm) members. First, theory of phylogeny estimation is explored in a review chapter focusing on strengths and weaknesses of phylogenetic methodology. Second, methods are applied to estimating evolutionary relationships within Psoraleeae based on six chloroplast (trnD/T, trnL/F, trnS/G, trnK, matK, and rpoB-trnC) and two nuclear (ITS and waxy) DNA regions. This study explores approaches for coding insertion-deletion events (gaps) as phylogenetic characters using maximum parsimony and Bayesian Inference. Inclusion of gaps generally increased topological resolution and nodal support, attesting to their phylogenetic utility. Findings suggest inclusion of gaps to be especially useful in chloroplast-based studies as they represent a greater proportion of phylogenetic signal as compared to nuclear regions. Past Psoraleeae classification schemes were tested and taxonomic revisions suggested. Furthermore, phylogenetic comparative methods are used to investigate correlation between geography and narrow endemism in NAm Psoraleeae. Geographic variables of latitude, longitude, and elevation all correlate with range size and provide support for Rapoport's rule of species-richness following latitudinal gradients. Finally, estimated phylogenies are used to investigate divergence dates, nucleotide substitution rates, diversification rates, and the impact of climate change, past and present, on diversification of NAm Psoraleeae. Results suggest the group has undergone a recent, rapid radiation. Rates of molecular evolution are fast, relative to other Legume lineages. Topological and temporal methods confirm the existence of diversification rate shifts in NAm Psoraleeae. Quaternary climate oscillations are shown to have significantly impacted diversification in the group while current shifts from mesic to xeric climate regimes did not.