DISSERTATION RESEARCH: Phylogeographic discord in the comparative genomic history of Amazonian birds

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The production of species diversity is of fundamental interest, but the factors that cause diversification are poorly understood. Diversification is known to occur at different rates depending on the species or group of species involved, and comparative study of this variation can reveal the processes that promote diversity. Comparative phylogeography is the study of diversification at the population level within different species, and it allows us to observe differences in diversification at the point where speciation occurs. The goals of this study are to use comparative phylogeography and novel methods of generating data to detect differences in diversification across species, and to analyze the factors that promote faster diversification in some species than in others. Phylogeography will be compared across sixteen Amazonian bird species with similar distributions. A new set of genetic markers scattered across the genome will be used to generate data from 24 individuals of each species. These genetic sequences will be extracted from museum tissue samples using a new method of enriching genomic DNA for sequences of interest, and then sequenced on a next-generation sequencing instrument. New analytical tools for testing models will allow us to measure the processes that are most important in driving the diversification of a given species. The massive amount of data generated by this method will allow for analysis of more complex models than could ever be analyzed previously, giving us new insight into the processes promoting species diversity. This project provides research opportunities for undergraduate students in Louisiana and the geographic scope of the project fosters inter-institutional and international collaborations. The research provides a test of next-generation sequencing methods and a new genomic marker set, and our results will aid in the application of these methods to other study systems. New biogeographic and geographic genetic data from our work support conservation efforts in the Amazon. All specimens, audio recordings, and observational data from our fieldwork and genetic data from our lab work are deposited in publicly accessible collection and databases. We consider these resources invaluable for current and future, pure and applied research on Amazonian birds and other systems.