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

该奖项是根据2009年美国复苏和再投资法案（公法111-5）资助的。研究生物多样性的一个基本问题是了解物种之间的关系。这是通过发展树来描述它们之间的关系，并促进它们在系统发育领域的研究。当这样的树从DNA序列发展出来时，它们不一定与从形态学发展出来的树相匹配，甚至也不一定与从其他DNA序列发展出来的树相匹配。从DNA发展树木的理论没有考虑到群体遗传学，也没有考虑到实际数据的混乱（例如，有限的遗传变异，缺失的数据，无法对一棵树中的所有物种进行采样，以及实际的采样努力）。这项资助的工作将通过理论发展来解决这些问题，随后用计算机模拟和从了解的研究物种收集的数据进行测试。研究人员将开发软件和指导方针，以准确估计物种树，确定这些新方法的局限性，并确定未来理论和方法发展的领域。pi将培养博士后和研究生。系统遗传学和群体遗传学交叉培训的机会将通过研讨会提供给全国的学生和教师，并在网上免费提供软件。计算机研讨会将弥合方法的理论基础和对应用这些方法感兴趣的人的背景之间的差距。因此，考虑到物种树在生物学中的核心作用，该项目将为不同领域的研究人员提供工具。这个项目开辟了一条新的研究路线，对研究生物多样性及其变化的基础科学家和应用科学家来说都是无价的。

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.