Thesis (Ph.D.)--Boston University / PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you. / Neotropical montane forests of the Ecuadorian Andes harbor a disproportionate amount of global biodiversity, yet the ecological and evolutionary processes that generate and sustain this diversity are poorly known. Determining the relative roles of historical vicariance, natural selection and genetic drift in generating diversity are active areas of investigation, but no clear pattern has emerged. My research focuses on a direct developing cloud forest frog ( Pristimantis w-nigrum ) found along the Eastern and Western versants of the Ecuadorian Andes. By integrating morphological data, multi-locus sequence data and geographic and environmental data, I demonstrate that: (1) Pristimantis w-nigrum harbors substantial genetic diversity, despite morphological stasis, and may comprise a species complex; (2) Genetic differentiation of mitochondrial DNA identifies eight divergent lineages and highly structured populations along both eastern and western slopes of the Ecuadorian Andes; (3) Multiple nuclear markers show lesser but still substantial population structure; (4) Isolation by distance best explains the pattern of genetic variation, but temperature and precipitation also contribute to genetic and morphological variation; (5) The timing of genetic divergence among mtDNA lineages coincides with sequential paleogeological bouts of Andean orogenesis during the late Miocene and early Pliocene, with terminal lineages diverging during the Pleistocene; (6) Populations have experienced little or no gene flow. (7) Those on the Western slope have maintained large effective population sizes, while populations on the Eastern slope appear to have suffered severe bottlenecks. Taken together, these results suggest a long sequential history of vicariance following the orogeny of the Northern Andes and that allopatric speciation may be a common mode of divergence in montane ectothermic vertebrates with low vagility. In addition, estimation of the species phylogeny and historical and contemporary demographic parameters using multiple loci highlight the utility of a multi-locus approach, particularly in cases where diversification may have occurred relatively recently. The identification of cryptic diversity in the P. w-nigrum suggests that evolutionary processes of isolation and divergence are occurring in the Andes and that the Andes may be an important generator of new species as well as a repository of high biodiversity. / 2031-01-01