The Neotropical region is the most biologically diverse region on the planet. The region encompasses a variety of ecosystems and has long been the target of researchers interested in patterns of species diversity and distribution. More recently, molecular data have been incorporated into methods for reconstructing the historical relationships among geographical areas and their biotas. Molecular phylogenetics has provided insights into diversification patterns and the influence of Late Cenozoic events on the evolutionary history of the region. Nevertheless, considering the vast extent and complexity of the region, more studies are needed to fully appreciate the patterns of biogeography and the mechanisms that generate and maintain its biodiversity. Therefore, in Chapter 1 I employed molecular methods to reconstruct the phylogenetic relationships of the subfamily Sigmodontinae, which is the most diverse and widespread radiation of Neotropical rodents. I was able to evaluate controversial hypotheses about the paleogeographic scenarios implicated to explain the biogeography of sigmodontines. Advances in sequencing technology and analytical approaches have revolutionized the role of historical biogeography in elucidating the spatial and temporal context of diversification, and the integrative field of phylogeography was fundamental to the development of biogeography at the intraspecific level. However, the potential of phylogeography to unravel diverse historical scenarios in a tractable statistical framework has been largely unexplored for the Neotropics as a whole. In order to integrate more robust hypothesis testing to elucidate the evolutionary history of Amazonia's biota, I devoted Chapter 2 to a review of Amazonian phylogeography that I anticipate will improve the basis for interpreting the patterns and processes of diversification in Amazonia. Chapter 3 is a thorough species account of spiny rats of the genus Proechimys, which is poorly known taxonomically despite its diversity and widespread distribution in the Neotropics. This taxonomic revision will benefit researchers interested in using such information with coalescent-based methods of species delimitation aimed at an integrative and stable taxonomy. Lastly, Chapter 4 deals with the phylogeography of P. roberti. This species occurs in southeastern Amazonia and the Cerrado of central Brazil. I employed a dense taxon sampling and used coalescent-based methods to demonstrate that rivers and topography have a causal link to the geographic structure of P. roberti populations. In my dissertation, I used a combination of molecular genetics tools to provide a better understanding of the biogeography and evolution of some of the most diverse groups of Neotropical mammals. My dissertation interacts in many levels with my future research interests. These present and future efforts hold promise for unraveling the evolutionary history of the Neotropical region and its biota, and will assist in conservation decisions aiming at preserving its unparalleled biodiversity.

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<p>Because species respond individually to climate change, understanding community assembly requires examination of multiple species from a diversity of forest niches. I present the post-glacial phylogeographic history of an understory, parasitic herb (<italic>Epifagus virginiana</italic>, beechdrop) that has an obligate and host specific relationship with a common eastern North American hardwood tree (<italic>Fagus grandifolia</italic>, American beech). The migration histories of the host and parasite are compared to elucidate potential limits on the parasite's range and to understand their responses to shared climate change. Two chloroplast DNA regions were sequenced and 9 microsatellite loci genotyped from parasite specimens collected throughout the host's range. These data were compared with available cpDNA sequences from the host (McLachlan et al. 2005) and host fossil pollen records from the last 21,000 years (Williams et al. 2004). Analyses of genetic diversity reveal high population differentiation in the parasite's southern range, a possible result of long term isolation within multiple southern glacial refuges. Estimates of migration rates and divergence times using Bayesian coalescent methods show the parasite initiating its post-glacial range expansion by migrating northward into the northeast from southern areas, then westward into the midwest, a pattern consistent with the development of high density beech forests. This result is strongly confirmed through spatial linear regression models, which show host density plays a significant role in structuring parasite populations, while the initial migration routes of the host are irrelevant to parasite colonization patterns. Host density is then used as a proxy for the parasite's habitat quality in an effort to identify the geographic locations of its migration corridors. Habitat cost models are parameterized through use of the parasite's genetic data, and landscape path analyses based on the habitat map show a major migration corridor south of the Great Lakes connecting the northeast and midwest. Host density was the major determinant controlling the parasite's range expansion, suggesting a lag time between host and parasite colonization of new territory. Parasites and other highly specialized species may generally migrate slower due to their complex landscape requirements, resulting in disassociation of forest assemblages during these times. From these results, the low migration capacities of highly specialized species may be insufficient to outrun extirpation from their current ranges.</p> / Dissertation