Collaborative Research: ABI Innovation: A Bayesian Evolutionary Tree Analysis Database

这项合作赠款旨在开发一个原型贝叶斯进化树分析数据库（BETAbase），一个贝叶斯系统发育研究输出的交互式存储库。系统发育-物种之间的系谱关系的估计-提供了一个明确的历史观点，批判性地通知在大量和不断增长的科学学科的研究。贝叶斯统计框架越来越多地推断出不确定性，因为它允许根据更复杂和更现实的统计模型从更大和越来越复杂的数据集进行估计，并允许明确确定和适应所产生的估计中的不确定性。BETAbase的实现将大大推进贝叶斯系统发育推断领域，并通过扩展，促进依赖系统发育信息的无数生物科学领域（包括保护，医学和农业）。它将促进对已发表的系统发育研究进行更严格和一致的评价，从而提高基于这些研究的决策质量。BETAbase还将提供独特的培训机会，开发一个基于网络的教育环境，使研究人员能够获得经验和发展技能，以确定和解决贝叶斯系统发育分析过程中遇到的问题。贝叶斯系统发育研究的输出通常包括具有采样树的日志文件和系统发育模型的其他参数。过去十年积累的产出构成了一个未开发的信息来源，有可能改变贝叶斯遗传学领域和相关的生物学研究领域。BETAbase原型试图利用这种潜力：（1）促进对经验系统发育研究的更严格评估;（2）将理论研究集中在现有系统发育方法不足的领域;以及（3）实现软件工具，该软件工具使得能够请求基于经验的信息先验，该先验适当地反映了我们关于模型参数的累积知识，提供了一种替代模糊的“无信息”先验，目前用作现有贝叶斯系统发育推断软件中的默认设置。该项目将涉及两名博士后学者以及研究生和本科生的参与和培训。最后，BETAbase将保护系统社区为理解生命之树所做的大量计算投资。原型BETAbase存档和相关工具将在http://beta-base.org上分发和讨论。

This collaborative grant seeks to develop a prototype Bayesian Evolutionary Tree Analysis Database (BETAbase), an interactive repository for the output of Bayesian phylogenetic studies. Phylogenies-estimates of the genealogical relationships among species-provide an explicit historical perspective that critically informs research in a vast and growing number of scienti c disciplines. Increasingly, phylogenies are inferred in a Bayesian statistical framework, as it permits estimation under more complex and realistic statistical models from larger and increasingly complex datasets, and allows uncertainty in the resulting estimates to be clearly identified and accommodated. Implementation of BETAbase will substantially advance the field of Bayesian phylogenetic inference and, by extension, the myriad fields of biological sciences (including conservation, medicine, and agriculture) that rely on phylogenetic information. It will promote more rigorous and consistent evaluation of published phylogenetic studies thereby improving the quality of decisions based upon those studies. BETAbase will also provide unique training opportunities by developing a web-based educational environment where researchers can gain experience and develop the skills to identify and address problems encountered in the course of Bayesian phylogenetic analysis. The output of Bayesian phylogenetic studies typically includes both log files with sampled trees and the other parameters of the phylogenetic model. The output accumulated over the last decade constitutes an untapped source of information with the potential to transform the field of Bayesian phylogenetics and associated areas of biological research. The BETAbase prototype attempts to harness this potential to: (1) promote more rigorous evaluation of empirical phylogenetic studies; (2) focus theoretical e^fforts on areas where existing phylogenetic methods are de ficient; and (3) implement software tools that enable solicitation of empirically based informative priors that appropriately reflect our accumulated knowledge regarding model parameters, providing an alternative to the vague `uninformative' priors that are currently used as the default settings in existing Bayesian phylogenetic inference software. The project will involve the participation and training of two postdoctoral scholars as well as graduate and undergraduate students. Finally, BETAbase will safeguard the substantial computational investment that the systematic community has made toward understanding the Tree of Life. The prototype BETAbase archive and associated tools will be distributed and discussed at http://beta-base.org.