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

合作研究：R计算环境中的系统发育区、生物地理区域化和宏观生态学的计算基础设施

• 批准号: 2416314
• 负责人: Barnabas Daru
• 金额: $ 58.51万
• 依托单位: Stanford University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-10-01 至 2025-05-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2416314&HistoricalAwards=false
• 关键词: Collaborative; Research; phyloregion; computational; infrastructure

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.

建立基于Shared的地理比较对于对生物地理学的研究和管理多样性的迅速变暖，以分析和操纵大规模的物种生物地理学数据拥有拥有拥有的大规模物种拥有拥有的计算工具至关重要已经有充分的发展。传统上，生物地理学领域是一种观察科学，而不是生物地理学工作流程的实验性onee分析工具。微生物多样性，系统学，生态学以及其他许多人计划实质上提高功能的计算效率在生物群岛进化和生物地理学模型中，将单位作为多组的部分成员的生物地理数据集中的髋关节模型。通过系统发育多样性，差异和规律性的可视化。生物地理学及以后的生物地理工具的编码和启动。克里斯蒂（To）和东南部的totheastern toecruit didergrad uate参与者，并为他们提供有关研究生院的资源一名博士后研究员和安德格拉杜阿（Andergradua TES）将特别鼓励妇女获得的妇女和妇女的指定。 SF'SFFLY的使命，并通过使用Toundation的知识分子优点和更广泛的影响审查标准进行评估而被认为值得支持。