Speciation has been a subject of great interest and study since the founding of evolutionary biology by Darwin in 1859. In my thesis, I examine speciation from multiple perspectives in plethodontid salamanders. Molecular phylogenies based on combined mitochondrial and nuclear DNA are commonly used to infer patterns of speciation. Yet, we know little about how mitochondrial and nuclear DNA interact to produce a combined-data tree. How much do trees from mitochondrial and nuclear DNA differ? How are topological conflicts between these data types typically resolved in the combined-data tree? I compare mitochondrial, nuclear, and combined-data trees for 14 vertebrate clades (including new nuclear data and analyses for the salamander genus Plethodon) in order to address these and other related questions. I find that while there is a large amount of conflict between mitochondrial and nuclear trees, these conflicts are often weakly supported and are often resolved in favor of nuclear data (despite typically having fewer variable characters), with the important exception of Plethodon. The climatic niche is an important trait which has been implicated in speciation in a wide variety of organisms. However, the relationship between rate of climatic-niche evolution and climatic-niche breadth has not been explicitly tested. Using a 250 species phylogeny of Plethodontidae, and accompanying climatic niche data, I test this relationship. Generally, I find no relationship between rate of climatic-niche evolution and climatic-niche breadth. However, I did find a strong, positive relationship between rate and breadth for single climatic variables (e.g., annual precipitation). Finally, it is widely accepted that species can arise in allopatry and then later become sympatrically or parapatrically distributed. Patterns in the opposite direction are also possible, but have rarely been shown. In a multi-faceted analysis of Plethodon cinereus on Long Island, I show that two generally sympatric color morphs appear to have become parapatrically distributed. Additionally, the pure-lead populations on Long Island are divergent from other populations, suggesting incipient speciation. The distribution seems to be related to the different ecological preferences of the two morphs. These results suggest that spatial segregation of sympatric ecotypes might play an important part in parapatric speciation.