Distance, Consensus, and Query Algorithms for Recombinant Genealogies

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Due to recombination of DNA, the genes passed to an offspring will be a unique combination of DNA from the two grandparents. Because an organism?s DNA, or genome, is organized into chromosomes, a result of recombination is that different parts of a chromosome can have different histories going back in time. Several computer programs claim to be able to reconstruct these tangled histories of the organization of DNA, but these claims are not well validated. This project will develop a mathematical measure of similarity between reconstructions of a chromosome's history, so that researchers can test whether existing reconstruction algorithms actually work. It will also develop software to assess and display areas of agreement or disagreement among multiple reconstructions. These software tools will be incorporated into computer-based lab exercises to improve understanding of genome structure among undergraduate and graduate college biology students.This work aims to improve computational tools used in gene mapping, important in understanding traits encoded in an organism?s DNA including disease inheritance, and improving agricultural breeds of plants and animals. The tools will contribute to inferring relationships and patterns of evolution among closely related organisms, including crop species, pathogens and pests. Finally, this research will contribute to identification of genetic traits that have increased or decreased over time, such as traits involved in domestication or disease resistance. The educational materials will help prepare students to work in evolutionary biology, population genetics, and conservation science.