Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, Tartu, 50409, Estonia.
Natural History Museum, University of Tartu, Vanemuise 46, Tartu, 51003, Estonia.
BMC Ecol Evol. 2024 Jun 11;24(1):76. doi: 10.1186/s12862-024-02256-9.
Understanding biodiversity patterns is a central topic in biogeography and ecology, and it is essential for conservation planning and policy development. Diversity estimates that consider the evolutionary relationships among species, such as phylogenetic diversity and phylogenetic endemicity indices, provide valuable insights into the functional diversity and evolutionary uniqueness of biological communities. These estimates are crucial for informed decision-making and effective global biodiversity management. However, the current methodologies used to generate these metrics encounter challenges in terms of efficiency, accuracy, and data integration.
We introduce PhyloNext, a flexible and data-intensive computational pipeline designed for phylogenetic diversity and endemicity analysis. The pipeline integrates GBIF occurrence data and OpenTree phylogenies with the Biodiverse software. PhyloNext is free, open-source, and provided as Docker and Singularity containers for effortless setup. To enhance user accessibility, a user-friendly, web-based graphical user interface has been developed, facilitating easy and efficient navigation for exploring and executing the pipeline. PhyloNext streamlines the process of conducting phylogenetic diversity analyses, improving efficiency, accuracy, and reproducibility. The automated workflow allows for periodic reanalysis using updated input data, ensuring that conservation strategies remain relevant and informed by the latest available data.
PhyloNext provides researchers, conservationists, and policymakers with a powerful tool to facilitate a broader understanding of biodiversity patterns, supporting more effective conservation planning and policy development. This new pipeline simplifies the creation of reproducible and easily updatable phylogenetic diversity analyses. Additionally, it promotes increased interoperability and integration with other biodiversity databases and analytical tools.
理解生物多样性模式是生物地理学和生态学的核心课题，对于保护规划和政策制定至关重要。考虑物种进化关系的多样性估计，如系统发育多样性和系统发育特有性指数，为生物群落的功能多样性和进化独特性提供了有价值的见解。这些估计对于明智的决策和有效的全球生物多样性管理至关重要。然而，目前用于生成这些指标的方法在效率、准确性和数据集成方面存在挑战。
我们引入了 PhyloNext，这是一个灵活且数据密集型的计算管道，专为系统发育多样性和特有性分析而设计。该管道整合了 GBIF 出现数据和 OpenTree 系统发育与 Biodiverse 软件。PhyloNext 是免费的、开源的，并提供 Docker 和 Singularity 容器，以便轻松设置。为了增强用户的可访问性，我们开发了一个用户友好的基于网络的图形用户界面，方便用户轻松高效地浏览和执行管道。PhyloNext 简化了进行系统发育多样性分析的过程，提高了效率、准确性和可重复性。自动化工作流程允许使用更新的输入数据定期重新分析，确保保护策略保持相关性，并由最新可用数据提供信息。
PhyloNext 为研究人员、保护主义者和政策制定者提供了一个强大的工具，有助于更广泛地理解生物多样性模式，支持更有效的保护规划和政策制定。这个新的管道简化了可重复和易于更新的系统发育多样性分析的创建。此外，它促进了与其他生物多样性数据库和分析工具的互操作性和集成。
