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: 2113425
• 负责人: April Wright
• 金额: $ 19.37万
• 依托单位: Southeastern Louisiana University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-06-01 至 2024-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2113425&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.

在共享生物群的基础上建立地理比较对于生物地理学的研究和在面对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。历史上，生物地理区域的分类是基于对区域生态、分类学组成或植被特征的描述。最近的方法提供了更多的定量和客观的分类，但笼统地概括了早期的努力，忽视了物种共享的系统发育关系所带来的进化意义。由于生物地理学领域传统上是作为一门观察科学而不是实验科学发展起来的，因此将生物地理学的可复制分析工具开发成可复制的工作流程至关重要。为生物地理区划和宏观生态学设计的R软件包phyloregion可以克服这些计算挑战。它包含用于生物地理区划、宏观生态学、保护和可视化的工具，并在包括进化、微生物多样性、系统分类学、生态学、系统发育学和许多其他学科中具有潜在的应用。在本项目中，研究小组计划大幅提高系统区域功能的计算效率，增加新的功能，并为生物地理学的用户导向软件开发创建一个模型。该项目将开发和实施新的系统区域工具，用于生物群落进化和生物地理调查。建立了一种新的隶属度模型，该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。它将扩展系统区域与新的工具，以可视化模式的生物地理学，宏观生态学和进化。系统区域将在R和RevBayes（一种用于贝叶斯系统地理的c++工具）之间传递对象，从而通过R实现系统地理可视化。最后，它将引入新的保护工具，以反映系统发育多样性的关键维度，包括丰富度、分化度和规则性。Phyloregion已经被广泛使用，是R中为数不多的为巨葡萄发生和宏观生态数据集量身定制的生物地理资源之一。这项研究将创造新的、开源的、免费分发的软件工具，在生物地理学和其他领域具有变革性影响的潜力。讲习班和会议将用于传播，并介绍中级R编码和生物地理工具的实施。研修班的目标是教师、博士后，特别是研究生和本科生，他们将接受在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生物地理功能，以整合到R包中。该研究团队将与德州农工大学科珀斯克里斯蒂分校和东南大学现有的多元化项目合作，招募多元化的本科生参与者，并为他们提供学习研究生院的资源。该项目的所有产品将通过计算机代码、出版物、会议、讲习班和小插图免费和开源传播。系统区域的小插曲将被用来为本科生和早期研究生创建一个高年级课程。这笔资金将用于指导一名博士后研究员、一名研究生和多名本科生。将特别鼓励妇女和传统上代表性不足的群体申请博士后研究职位，以及参加研讨会。系统区项目可以在https://CRAN.R-project.org/package=phyloregionThis上访问，该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

Handling Logical Character Dependency in Phylogenetic Inference: Extensive Performance Testing of Assumptions and Solutions Using Simulated and Empirical Data

处理系统发育推断中的逻辑字符依赖性：使用模拟和经验数据对假设和解决方案进行广泛的性能测试

• DOI: 10.1093/sysbio/syad006
• 发表时间: 2023
• 期刊: Systematic Biology
• 影响因子: 6.5
• 作者: Simões, Tiago R;Vernygora, Oksana V;de Medeiros, Bruno A;Wright, April M
• 通讯作者: Wright, April M

Lessons learned from organizing and teaching virtual phylogenetics workshops

从组织和教授虚拟系统发育学研讨会中汲取的经验教训

• DOI: 10.18061/bssb.v1i2.8425
• 发表时间: 2022
• 期刊: Bulletin of the Society of Systematic Biologists
• 作者: Barido-Sottani, Joëlle;Justison, Joshua A.;Borges, Rui;Brown, Jeremy M.;Dismukes, Wade;Do Rosario Petrucci, Bruno;Guimarães Fabreti, Luiza;Höhna, Sebastian;Landis, Michael J.;Lewis, Paul O.
• 通讯作者: Lewis, Paul O.

Revticulate: An R framework for interaction with RevBayes

Revticulate：与 RevBayes 交互的 R 框架

• DOI: 10.1111/2041-210x.13852
• 发表时间: 2022
• 期刊: Methods in Ecology and Evolution
• 影响因子: 6.6
• 作者: Charpentier, Caleb P.;Wright, April M.
• 通讯作者: Wright, April M.