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PhD candidate Rafael Leite receives doctoral dissertation improvement grant funding approval from the National Science Foundation

Project Summary

The Neotropical lowlands harbor the richest fauna on Earth, and yet there is some dispute regarding the major mechanisms responsible for promoting and maintaining such high levels of biodiversity. Several hypotheses have been formulated to account for patterns of diversification in the Neotropical lowlands, and molecular-based studies supporting each of these hypotheses have traditionally been based on qualitative assessments and ad hoc explanations of phylogenetic trees. Nevertheless, over interpretations may arise because these approaches fail to incorporate the stochastic variance of genealogies into the phylogenetic procedure. More recently, inferences within a rigorous statistical framework, under the tenets of the coalescent theory, are explicitly considering the stochasticity inherent to the coalescence of gene lineages and the genetic processes shaping species structure and speciation events. In this context, the testing of alternative historical hypotheses is devised a priori to accommodate biologically more realistic models. Spiny-rats of the genus Proechimys offer an amenable and excellent focal group for exploring aspects of diversification in the Neotropical lowlands, using coalescent-based methods. This dissertation research will investigate historical relationships within Proechimys to provide well-resolved patterns of population divergence and species differentiation for these diverse and widespread Neotropical rodents. In addition, coalescent-based approaches will be applied to address the following specific aims: (1) clarify the interspecific relationships within the genus Proechimys using methods that account for genealogical discordances among gene trees and between gene trees and the species tree, thereby evaluating the monophyly of species group; (2) test genetic predictions derived from major biogeographic hypotheses for explaining patterns of diversification in the Neotropics; (3) infer a model of population divergence for P. roberti, and estimate the timing of divergence and migration rates between populations divided into major interfluves south of the mid-lower Amazon River. Mitochondrial DNA cytochrome b sequences will be obtained for all tissue samples of Proechimys (more than 1,100 available). In addition, a sub-sampling of around 400 samples will be selected for sequencing of 6–8 nuclear gene loci. Collection gaps within the distribution of P. roberti will be filled with additional fieldwork to the Xingu-Tapajós interfluve during 2011. A clear understanding of Proechimys phylogeny and biogeography, and the population dynamics of P. roberti, will provide, at unprecedented sampling scales, key insights for future studies addressing Neotropical diversification, particularly in Amazonia and adjacent regions.

Biogeography of Central American mammals

This figure will be published in a book chapter by the University of Chicago Press (Bones, Clones and Biomes: The History and Geography of Recent Neotropical Mammals) later this year.  In this figure, gray areas are between 800 and 2000 m and areas in black are >2000 m.  Compared with its total land area, Central America contains a disproportionately large amount of biodiversity owing to its complex topography and position between the Nearctic and Neotropical realms.  The geologic history of the region is correspondingly complex and our understanding is far from complete.  This figure shows the major physiogeographic features that have impacted the evolution of mammals in the region.  Both biogeographic and phylogeographic patterns for mammals are not well articulated, although some conclusions based on analysis of molecular data are emerging.  For example, the actual biodiversity for mammals, particularly for rodents, likely is much higher than currently documented.  The historical events and geographic features that have shaped Central America seem to have affected mammals and other groups in the similar fashion.  These include dispersal events both prior and subsequent to the permanent land bridge between North and South America, the northern Andes orogeny, in situ divergence both between and within the northern and southern Central American mountain ranges as well as between Atlantic and Pacific lowlands separated by these highland areas, and the barriers represented by three areas (Isthmus of Tehuantepec, Nicaraguan Depression and Central Panama) that were submerged for various times in the past.  In general, mid-and high-elevation faunas are relatively diverse and contain higher levels of endemism than do lowland areas, although radiations have occurred among both lowland and montane taxa.  Rodents exhibit more genetic structure than do bats, ungulates and primates over comparable geographic sampling.  In many cases, estimated levels of molecular divergence correspond to events that occurred in the early Pleistocene or late Pliocene. Unfortunately, continued and rapid change in land use practices throughout Central America may preclude a complete and accurate reconstruction of the historical biogeography of the region.

Ana Laura Almendra and Duke S. Rogers

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