Dataset and analyses of global reptile bioregions

Dataset and scripts used to run the analyses of global reptile bioregions and the comparison among regionalisations of different vertebrate grooups. <br> The dataset contains the following files: <br> - "Reptile distribution &amp; phylogeny.Rdata": Rdata file containing four objects. 1) "comm": matrix of reptile species presence in 200 x 200 km cells across the globe; 2) "coo": coordinate of centroids of the 200 x 200 km cells; 3) "tree": phylogeny for the 9016 reptile species included in this study; 4) "coastline": global coastline used to refine the output of analyses of raster data. Species ranges were retreived from an updated version (1.5) of the "Global Assessment of Reptile Distributions" [Roll, U. et al. The global distribution of tetrapods reveals a need for targeted reptile conservation. Nat. Ecol. Evol. 1, 1677–1682 (2017)]. Phylogenetic data were retrieved from an inference-based phylogenetic tree [Tonini, J. F. R., Beard, K. H., Ferreira, R. B., Jetz, W. &amp; Pyron, R. A. Fully-sampled phylogenies of squamates reveal evolutionary patterns in threat status. Biol. Conserv. 204, 23–31 (2016)]. <br> - "Defining global reptile bioregions.R": script used to define global reptile bioregions. It includes a modified version of the "phylo.beta.pair()" function (R package "betapart"), that avoids the need of huge amount of RAM and allows a more efficient calculation of philogenetic beta diversity by identifying duplicate communities and running calculations in parallel. To run, this script needs "Reptile distribution &amp; phylogeny.Rdata". <br> - "Bioregions.zip": Bioregions of the different vertebrate groups compared in the current work (reptile, amphibians, birds, mammals) in shapefile format. For each group, we provide two shapefiles, showing realms and regions. <br> - "Random regions example.R": Script of example to test the significance of V-measure values through null-models. The example is performed on shallow regions, but the same script can be applied to any regionalisation. To run, this script needs "Bioregions.zip" to be extracted in the working directory.

本数据集及配套脚本用于开展全球爬行动物生物区系分析，以及不同脊椎动物类群生物区划方案间的对比研究。
本数据集包含以下文件：
- "Reptile distribution & phylogeny.Rdata"：Rdata格式文件，内含4个对象：①`comm`：全球200×200km网格单元内爬行动物物种存在性矩阵；②`coo`：各200×200km网格单元的质心坐标；③`tree`：本研究涉及的9016种爬行动物的系统发育树；④`coastline`：用于优化栅格数据分析结果的全球海岸线数据。物种分布范围源自《全球爬行动物分布评估》（Global Assessment of Reptile Distributions）更新至1.5版的数据[Roll, U. 等. 四足动物的全球分布揭示爬行动物保护需靶向施策. 自然·生态与进化, 1, 1677–1682 (2017)]。系统发育数据源自基于推断构建的系统发育树[Tonini, J. F. R., Beard, K. H., Ferreira, R. B., Jetz, W. & Pyron, R. A. 鳞龙类的全采样系统发育揭示濒危状态的演化模式. 生物保护, 204, 23–31 (2016)]。
- "Defining global reptile bioregions.R"：用于定义全球爬行动物生物区系的R脚本。该脚本包含了对`betapart`R包中`phylo.beta.pair()`函数的修改版本，可避免占用大量随机存取内存（RAM），并通过识别重复群落并并行运行计算，更高效地估算系统发育β多样性。运行本脚本需依赖"Reptile distribution & phylogeny.Rdata"文件。
- "Bioregions.zip"：本研究中对比的各脊椎动物类群（爬行动物、两栖动物、鸟类、哺乳类）的生物区系数据，格式为形状文件（shapefile）。针对每个类群，均提供了反映生物群区（realms）和区域（regions）的两份形状文件。
- "Random regions example.R"：用于通过零模型检验V测度值（V-measure）显著性的示例脚本。本示例以浅海区域为测试对象，但该脚本同样可应用于任何生物区划方案。运行本脚本需提前将"Bioregions.zip"解压至工作目录中。