Collaborative Research: phyloregion, computational infrastructure for biogeographic regionalization and macroecology in the R computing environment

在共享生物群的基础上建立地理比较，对于研究生物地理学和在地球气候迅速变暖的情况下管理生物多样性至关重要。然而，用于分析和处理大规模物种生物地理数据的计算工具还没有完全开发出来。在历史上，生物地理区域的分类是基于对区域的生态、分类组成或植被特征的描述。最近的方法提供了更多的量化和客观的分类，但概括地概括了早期的努力，并忽视了物种共同的系统发育关系所捕捉的进化影响。由于生物地理学领域传统上是作为观察科学而不是实验科学发展起来的，因此开发可复制的分析工具将生物地理学转化为可复制的工作流程是至关重要的。为生物地理区划和宏观生态学而设计的R软件包PhyloRegion可以克服这些计算挑战。它包含了生物地理区划、宏观生态学、保护和可视化的工具，在进化论、微生物多样性、系统学、生态学、系统发育学等多个学科中具有潜在的应用前景。在这个项目中，研究团队计划大幅提高系统区域功能的计算效率，增加新的功能，并创建一个用户引导的生物地理学软件开发模型。该项目将在系统区域开发和实施用于生物组进化和生物地理调查的新工具。建立新的隶属度模型，将采样单位表示为多个组的部分隶属度，用于分析大型生物地理数据集。它将用新的工具来扩展系统区域，以可视化生物地理、宏观生态和进化的模式。系统区域将得到增强，以便在R和RevBayes(贝叶斯系统地理的C++工具)之间传递对象，以通过R进行系统地理可视化。最后，它将引入新的保护工具，反映系统发育多样性的关键维度，包括丰富度、差异性和规律性。PhyloRegion已经被广泛使用，并代表了R中为数不多的为巨型进化和大生态数据集量身定做的生物地理资源之一。这项研究将创建新的、开源的、免费分布的软件工具，有可能在生物地理学和其他领域产生革命性的影响。将利用讲习班和会议进行传播，并介绍中间R编码和生物地理工具的实施。研讨会将针对教师、博士后，特别是研究生和本科生，他们将接受关于在他们的研究中使用和应用系统区域的培训，并帮助开发他们自己的新的生物地理功能，以组装成R包。研究团队将与德克萨斯农工大学科珀斯克里斯蒂分校和东南大学现有的多样性项目合作，招募不同的本科生参与者，并为他们提供了解研究生院的资源。该项目的所有产品将通过计算机代码、出版物、会议、讲习班和小插曲免费传播和开放源码。将使用PhyloRegion Vignettes为本科生和早期研究生创建一门高级课程。这笔拨款将用于指导一名博士后研究员、一名研究生和许多本科生。将特别鼓励妇女和传统上任职人数不足的群体申请博士后研究职位以及参加讲习班。该生态区域项目可以在https://CRAN.R-project.org/package=phyloregionThis上访问，该奖项反映了国家科学基金会的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Establishing geographical comparisons based on shared biota is crucial to the study of biogeography and for managing biological diversity in the face of rapid warming of the Earth’s climate. However, the computational tools to analyze and manipulate the massive-scale species biogeography data has not been fully developed. Historically, classifications of biogeographic regions were based on descriptions of the ecology, taxonomic composition or vegetation features of regions. Recent approaches provided more quantitative, and objective classifications, but broadly recapitulated earlier efforts and overlooked the evolutionary implications captured by the shared phylogenetic relationships of species. Because the field of biogeography has traditionally developed as an observational science rather than an experimental one, developing replicable analytical tools for biogeography into reproducible workflows is critical. The R software package phyloregion – designed for biogeographic regionalization and macroecology – can overcome these computational challenges. It contains tools for biogeographical regionalization, macroecology, conservation, and visualization, and has potential application in various disciplines including evolution, microbial diversity, systematics, ecology, phylogenetics, and many others. In this project, the research team plans to substantially increase computational efficiency of functions in phyloregion, to add new functionality, and create a model for user-guided software development in biogeography.The project will develop and implement new tools in phyloregion for biome evolution and biogeographical investigations. Novel Grade of Membership model that represents sampling units as partial memberships in multiple groups will be established to analyze large biogeographic datasets. It will extend phyloregion with new tools to visualize patterns of biogeography, macroecology and evolution. Phyloregion will be enhanced to pass objects between R and RevBayes (a C++ tool for Bayesian phylogeography) for phylogeographic visualization through R. Finally, it will introduce new tools for conservation that reflect the key dimensions of phylogenetic diversity including richness, divergence and regularity. Phyloregion is already widely used and represents one of only a few biogeographical resources in R tailored for megaphylogenies and macroecological datasets. This research will create new, open-source, and freely distributed software tools with potential for transformative impact in biogeography and beyond. Workshops and conferences will be used for dissemination, and to provide introduction to intermediate R coding and implementation of biogeographical tools. Workshops will target a mix of faculty, postdocs, and especially graduate and undergraduate students, who will be trained on the use and application of phyloregion in their research, and to help develop their own novel biogeographic functions to assemble into an R package. The research team will work with existing diversity programs at Texas A&M University-Corpus Christi and Southeastern to recruit diverse undergraduate participants, and provide resources for them to learn about graduate school. All products from this project will be disseminated free and open-sourced through computer codes, publications, conferences, workshops and vignettes. Phyloregion vignettes will be used to create an upper-division course for undergraduate and early graduate students. The grant will support the mentoring of one postdoctoral researcher and a graduate student and many undergraduates. Women and traditionally underrepresented groups will be specifically encouraged to apply for the postdoctoral research position, as well as for the workshops. The phyloregion project can be accessed at https://CRAN.R-project.org/package=phyloregionThis award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.