Data for: Historical and contemporary processes drive global phylogenetic structure across geographical scales: Insights from bat communities

Aim: Patterns of evolutionary relatedness among co-occurring species are driven by scale-dependent contemporary and historical processes. Yet, we still lack a detailed understanding of how these drivers impact the phylogenetic structure of biological communities. Here, we focused on bats – one of the most speciose and vagile groups of mammals – and test the predictions of three general biogeographical hypotheses that are particularly relevant to understanding how paleoclimatic stability, local diversification rates, and geographical scales shaped their present-day phylogenetic community structure.
Location: Worldwide, across restrictive geographical extents: global, east-west hemispheres, biogeographical realms, tectonic plates, biomes, and ecoregions.
Time period: Last Glacial Maximum (~22,000 years ago) to the present.
Major taxa studied: Bats (Chiroptera)
Methods: We estimated bat phylogenetic community structure across restrictive geographical extents and modelled it as a function o...,
Details on the applications of this dataset are found within the Methods section of our study, accepted for publication in Global Ecology and Biogeography.
, Code availability
All code necessary to reproduce the analyses, figures, and BAMM setup files are available within the Open Science Framework repository (https://osf.io/amvp5/) for this study.
Software
All data manipulation and analyses were performed in R and RStudio (R Core Team, 2021; RStudio Team, 2021). Parallelized computations were done using snowfall and doSNOW (Knaus, 2015; Corporation & Weston, 2022). Geospatial manipulation was done using the sf, raster, terra, and exactextractr packages (Pebesma, 2018; Hijmans, 2021, 2022). Velocities of climate change and local spatial and long-term climatic gradients were calculated using the VoCC package (García Molinos et al., 2019). Phylogenetic manipulation and analyses were done using the packages ape, picante, PhyloMeasures and phangorn (Kembel et al., 2010; Schliep, 2011; Tsirogiannis & Sandel, 2016, 2017; Paradis & Schliep, 2019). Diversification rate estimation and posterior manipulation were done using BAMM 2.5.0 and ...

研究目的：同域共存物种间的进化亲缘关系模式由依赖于尺度的现代与历史过程所驱动。然而，目前我们仍未深入理解这些驱动因子如何影响生物群落的系统发育结构。本研究以蝙蝠——哺乳动物中物种多样性最丰富、移动性最强的类群之一——为研究对象，检验三项通用生物地理学假说的预测，这些假说对于解析古气候稳定性、局部分化速率与地理尺度如何塑造蝙蝠类群现今的群落系统发育结构具有关键意义。

研究区域：覆盖全球范围内的多种受限地理尺度：全球尺度、东西半球尺度、生物地理区尺度、构造板块尺度、生物群区尺度以及生态区尺度。

研究时段：末次冰盛期（约22000年前）至现代。

研究类群：蝙蝠（Chiroptera，翼手目）。

研究方法：我们针对多种受限地理尺度估算了蝙蝠的群落系统发育结构，并将其建模为某一函数的响应变量……本数据集的具体应用细节可见于已被《Global Ecology and Biogeography》接收待发表的研究论文的方法部分。

代码可用性：本研究用于复现分析、绘图以及BAMM配置文件的所有代码，均可在本研究的开放科学框架（Open Science Framework，OSF）仓库（https://osf.io/amvp5/）中获取。

软件使用：所有数据处理与分析均在R及RStudio环境中完成（R Core Team, 2021; RStudio Team, 2021）。并行计算使用snowfall与doSNOW工具包完成（Knaus, 2015; Corporation & Weston, 2022）。地理空间数据处理使用sf、raster、terra以及exactextractr工具包完成（Pebesma, 2018; Hijmans, 2021, 2022）。气候变化速率以及局地空间与长期气候梯度的计算使用VoCC工具包完成（García Molinos等, 2019）。系统发育数据处理与分析使用ape、picante、PhyloMeasures以及phangorn工具包完成（Kembel等, 2010; Schliep, 2011; Tsirogiannis & Sandel, 2016, 2017; Paradis & Schliep, 2019）。分化速率估算与后验分析处理使用BAMM 2.5.0及……完成。