‘treesliceR': a package for slicing phylogenies and inferring phylogenetic patterns over evolutionary time

IF 5.4 1区环境科学与生态学 Q1 BIODIVERSITY CONSERVATION

Ecography Pub Date : 2024-10-28 DOI:10.1111/ecog.07364

Matheus L. Araujo, Luiz Gabriel S. S. Ferreira, Gabriel Nakamura, Marco Túlio P. Coelho, Thiago F. Rangel

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引用次数: 0

Abstract

Phylogenetic indexes summarize the evolutionary information within a given assemblage pool based on the topology and branch lengths of a hypothesized phylogenetic tree. However, different historical contingencies experienced by these assemblages can unevenly distribute evolutionary information through time and over the phylogeny. ‘treesliceR' is an R package containing tools to flexibly cut phylogenies at different depths, and also has built‐in functions to assess spatially explicit phylogenetic patterns over time. ‘treesliceR' can slice phylogenies in any temporal orientation (‘rootwardly' or ‘tipwardly'), using different criteria (million years or phylogenetic diversity). Moreover, ‘treesliceR' contains functions to assess the rates of accumulation of any phylogenetic information (e.g. α and β diversities) through time. These functions are unique to the package and provide outputs that are ready‐to‐use in graphing functions. We demonstrated the main uses of ‘treesliceR' by investigating areas of paleo‐endemism and neo‐endemism of Passeriformes in Australia. Finally, we mapped rates of accumulation of phylogenetic β‐diversity (Cpβrate) across Australia. ‘treesliceR' is an open‐source R package under continuous progress, designed to decompose temporally any phylogenetic information.

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treesliceR"：用于切分系统进化和推断进化过程中系统进化模式的软件包

系统发育指数根据假定的系统发育树的拓扑结构和分支长度来概括特定集合库中的进化信息。然而，这些集合体所经历的不同历史偶然性会使进化信息在时间和系统发育过程中分布不均。treesliceR "是一个 R 软件包，其中包含可在不同深度灵活切割系统发生树的工具，还内置了评估随时间变化的空间显性系统发生模式的功能。treesliceR "可以使用不同的标准（百万年或系统发育多样性），以任何时间方向（"根向 "或 "端向"）切割系统发育。此外，"treesliceR "还包含评估任何系统发育信息（如 α 和 β 多样性）随时间积累率的功能。这些函数是该软件包的独有功能，可提供可在图形函数中使用的输出结果。我们通过研究澳大利亚雀形目古特有性和新特有性区域，展示了 "treesliceR "的主要用途。最后，我们绘制了澳大利亚系统发育β多样性的累积率（Cpβ率）图。treesliceR "是一个正在持续开发的开源 R 软件包，旨在对任何系统发育信息进行时间分解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Ecography 环境科学-生态学

CiteScore

11.60

自引率

3.40%

发文量

122

审稿时长

8-16 weeks

期刊介绍： ECOGRAPHY publishes exciting, novel, and important articles that significantly advance understanding of ecological or biodiversity patterns in space or time. Papers focusing on conservation or restoration are welcomed, provided they are anchored in ecological theory and convey a general message that goes beyond a single case study. We encourage papers that seek advancing the field through the development and testing of theory or methodology, or by proposing new tools for analysis or interpretation of ecological phenomena. Manuscripts are expected to address general principles in ecology, though they may do so using a specific model system if they adequately frame the problem relative to a generalized ecological question or problem. Purely descriptive papers are considered only if breaking new ground and/or describing patterns seldom explored. Studies focused on a single species or single location are generally discouraged unless they make a significant contribution to advancing general theory or understanding of biodiversity patterns and processes. Manuscripts merely confirming or marginally extending results of previous work are unlikely to be considered in Ecography. Papers are judged by virtue of their originality, appeal to general interest, and their contribution to new developments in studies of spatial and temporal ecological patterns. There are no biases with regard to taxon, biome, or biogeographical area.