COLLABORATIVE RESEARCH: Estimating Species Trees with Population Genetic Approaches: Working Towards a New Phylogenetic Paradigm for 21st Century Phylogenetics

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This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).A fundamental issue in studying biodiversity is understanding the relationship between species. This is approached by developing trees that describe the relationships and facilitate their study, the field of phylogenetics. When such trees are developed from DNA sequences, they do not necessarily match trees developed from morphology, or even trees developed from other DNA sequences. The theory for developing trees from DNA does not take population genetics into consideration, or the messiness of real data (e.g., limited genetic variation, missing data, inability to sample all species in a tree, and realistic sampling effort). The funded work will address these issues though theory development followed by testing with both computer simulations and data collected from well-understood study species. The investigators will develop software and guidelines for accurate species-tree estimation, identify the limits of these new methods, and identify areas for future theoretical and methodological development.The PIs will train postdocs and graduate students. Opportunities for cross-training in phylogenetics and population genetics will be provided to students and faculty nationwide through workshops and making the software freely available on the web. A computer workshop will bridge the gap between the theoretical basis of the methods and the backgrounds of those interested in applying them. Thus the project will provide tools to a diverse cross-section of researchers, given the central role of species trees in biology. This project opens a new line of research that should be invaluable to both basic and applied scientists who study biodiversity and its changes.