An R package and online resource for macroevolutionary studies using the ray-finned fish tree of life

1. Comprehensive, time-scaled phylogenies provide a critical resource for many questions in ecology, evolution, and biodiversity. Methodological advances have increased the breadth of taxonomic coverage in phylogenetic data; however, accessing and reusing these data remain challenging.

2. We introduce the Fish Tree of Life website and associated R package fishtree to provide convenient access to sequences, phylogenies, fossil calibrations, and diversification rate estimates for the most diverse group of vertebrate organisms, the ray-finned fishes. The Fish Tree of Life website presents subsets and visual summaries of phylogenetic and comparative data, and is complemented by the R package, which provides flexible programmatic access to the same underlying data source for advanced users wishing to extend or reanalyze the data.

3. We demonstrate functionality with an overview of the website, and show three examples of advanced usage through the R package. First, we test for the presence of long branch attraction artifacts across the fish tree of life. The second example examines the effects of habitat on diversification rate in the pufferfishes. The final example demonstrates how a community phylogenetic analysis could be conducted with the package.

4. This resource makes a large comparative vertebrate dataset easily accessible via the website, while the R package enables the rapid reuse and reproducibility of research results via its ability to easily integrate with other R packages and software for molecular biology and comparative methods.

1. 全面的时间校准系统发育树（time-scaled phylogenies）为生态学、演化生物学及生物多样性领域的诸多核心问题提供了关键研究资源。尽管方法学进步已大幅拓展了系统发育数据的分类群覆盖范围，但获取与复用这些数据仍面临诸多挑战。
2. 我们推出了“鱼类生命之树”（Fish Tree of Life）网站及其配套R语言包fishtree，以便捷获取物种多样性最丰富的脊椎动物类群——辐鳍鱼类（ray-finned fishes）的序列数据、系统发育树、化石校准信息及分化速率估计值。“鱼类生命之树”网站可展示系统发育与比较数据的子集及可视化摘要，其配套的R语言包则为希望拓展分析或重新处理数据的高级用户提供了灵活的编程式数据访问接口，二者形成互补。
3. 我们通过网站功能概览展示了该资源的使用方式，并借助R语言包呈现了三个高级应用案例：其一，检验鱼类生命之树中长枝吸引（long branch attraction）假象的存在性；其二，以河豚类（pufferfishes）为研究对象，探究生境对其分化速率的影响；其三，演示如何使用该包开展群落系统发育分析。
4. 本资源可通过网站便捷获取大型脊椎动物比较数据集，而配套的R语言包可轻松与其他R语言工具包及分子生物学、比较方法相关软件集成，从而实现研究成果的快速复用与可重复性。