This dissertation lays the foundation for a research program that highlights the important contribution that poorly-dispersing short-range endemic (SRE) organisms can have on advancing empirical and theoretical evolutionary biology. Here, SREs are represented by members of the harvestmen (Opiliones) superfamily Ischyropsalidoidea. In Chapter 1, phylogenetic analyses of an ancient rapid diversification at the base of Ischyropsalidoidea uncovers considerable incongruence across gene trees. Incongruent gene trees are not recovered in frequencies expected from a simple multispecies coalescent model, and incomplete lineage sorting is rejected as the sole contributor to gene tree conflict. In Chapter 2, an integrative taxonomy tests existing, and puts forward novel species-level taxonomic hypotheses within the Acuclavella species endemic to the inland temperate rainforest of the U.S. northern Rocky Mountains. Incongruence among taxonomic disciplines suggests rapid morphological evolution across multiple recent diversifications. Results suggest at least two undescribed species exist within inland populations of Acuclavella. Alternative combinations of incongruence across taxonomic disciplines possibly represent different stages of the speciation continuum, and suggest that different evolutionary mechanisms underlie speciation in thorn harvestmen, thus highlighting the importance of integrative species delimitation for evolutionary research. The disjunct inland temperate rainforest has become a model for recent biogeography, with a complex and recent evolutionary history suggesting that this inland forest was a refuge from Pleistocene glaciation that was compartmentalized into variously isolated pockets during the last glacial maximum (LGM). In Chapter 3, genomic-scale data are used to evaluate the evolutionary consequences of the LGM. This research finds that rivers were a major cause of refugia compartmentalization, with populations and species structured by rivers well before the LGM. Additionally, a negative correlation between elevation and heterozygosity suggests that populations were confined to lower valleys during the LGM with post-glacial colonization of higher elevations. The combined effects of rivers and glaciers paints a picture of a complex Pleistocene glacial refugia system during the LGM. This relatively high-resolution inference of past evolutionary events within an established biogeographic model system points towards the undervalued importance of using poorly dispersing short-range endemic taxa for biogeography and phylogeography.