Collaborative Research: ABI Innovation: Quantifying and Exploiting the Structure of Phylogenetic Tree Space Through Network Analyses

该项目将开发一个丰富而灵活的数学框架，用于量化系统发育信号（即，关于生物体之间系谱关系的信息）包含在基因组序列的大数据集中。 为了量化这个信号，不同系统发育树之间的关系，或者这些树中的分支，将被概念化为网络。 这些网络的结构提供了有关系统发育不确定性和冲突的程度和原因的生物学意义的信息。 新开发的框架将在可作为独立应用程序和网络服务使用的公开软件中实施。 此外，开发软件的核心功能将与NSF资助的其他正在进行的重建和探索生命之树的工作（iPlant和Open Tree of Life）紧密结合，这项工作将借鉴进化生物学，计算机科学和应用数学的专业知识。 研究活动将涉及研究生和本科生研究人员和软件开发人员的直接贡献。 本科生将在师徒关系中从研究生那里学习编码。 一个本科科学通信学生将开发一个网站，说明系统发育的原则和应用系统发育研究，突出所开发的方法提供的新见解。 此外，还将举办几次面对面和远程培训讲习班，向研究人员介绍和熟悉新开发的工具。 一个针对本科生的计算生物学系列研讨会将在路易斯安那州立大学举行。 作为该项目的一部分开发的方法将提高我们理解系统发育信息的能力，这是保护，法医，农业和流行病学等各种应用不可或缺的。有关项目进展的最新情况和已开发工具的链接将在http://www.phyleauxgenetics.org/上提供。

This project will develop a rich and flexible mathematical framework for quantifying the phylogenetic signal (i.e., the information about genealogical relationships among organisms) contained within big data sets of genome sequences. To quantify this signal, the relationships among different phylogenetic trees, or the branches in those trees, will be conceptualized as networks. The structure of these networks provides biologically meaningful information about the degree and causes of phylogenetic uncertainty and conflict. The newly developed framework will be implemented in publicly available software useable as a standalone application and as a webservice. In addition, the core functionality of the developed software will be closely integrated with other ongoing NSF-funded efforts to reconstruct and explore the Tree of Life (iPlant and the Open Tree of Life).This work will draw from expertise in evolutionary biology, computer science, and applied mathematics. Research activities will involve the direct contributions of both graduate and undergraduate researchers and software developers. Undergraduates will learn to code from graduate students in mentor-apprentice relationships. An undergraduate science communications student will develop a website illustrating phylogenetic principles and applied phylogenetic research, highlighting novel insights provided by the methods developed. Additionally, several in-person and remote training workshops will be held to introduce and familiarize researchers with newly developed tools. An ongoing computational biology seminar series targeted towards undergraduates will be held at Louisiana State University. The methods developed as part of this project will improve our ability to understand phylogenetic information, which is integral to a variety of applications in conservation, forensics, agriculture, and epidemiology. Updates on project progress and links to developed tools will be available at http://www.phyleauxgenetics.org/.