| Multi-scale studies of genetic variation within and among species, provide insights about patterns fundamental to the origins and maintenance of biodiversity. In this dissertation I use advanced molecular and analytical approaches to assess the diversity of Eleutherodactylus frogs and Bolitoglossa salamanders in the mega-diverse rainforests of the upper Amazon of Ecuador. Across multiple spatial, temporal and taxonomic scales I found high genetic diversity within these amphibians, in various instances within both salamanders and frogs, to levels suggestive of cryptic species.; Most broadly, I use Bayesian analysis to infer a phylogeny of the upper Amazonian frogs of the Eleutherodactylus unistrigatus species group. With multiple exemplars of 15 putative species (three mtDNA fragments; 1573 base pairs), I resolve a monophyletic tree with high clade credibility values. Concurrently, I compare the performance of gene partition and evolutionary models in Bayesian analysis, both qualitatively and using Bayes factors, and conclude that the most appropriate model for these data is not the most complex model tested.; Within a single unistrigatus species, Eleutherodactylus ockendeni, my phylogeographic survey reveals three deeply divergent phylogeographic lineages---upland, lowland, and south-eastern---that are each sufficiently divergent to be distinct species. Phylogenetic and coalescent methods suggest divergence among these three clades occurred in the Miocene. Mismatch analysis indicates a recent Pleistocene population expansion.; I characterise inter-individual gene flow of lowland lineage E. ockendeni at a single locality (Napo, Ecuador) using population genetics methods without a priori population delineation (e.g. multivariate spatial autocorrelation, kinship coefficients and relatedness coefficients). The population genetic structure is best characterised as continuous isolation by distance, with very large populations sizes, high genetic diversity, and significant spatial-genetic structuring across the landscape.; For a comparative perspective across taxa, I also develop a Bayesian phylogeny (cytochrome b, n = 53) of the salamander group Bolitoglossa (Eladinea) adspersa. I found strong phylogeographic structure in B. peruviana and very high genetic diversities within B. peruviana and B. equatoriana. This study casts uncertainly on the currently recognized species' classifications of B. peruviana, B. altamazonica and B. equatoriana. |
