DOI: 10.6084/m9.figshare.25974817
title: Global Biodiversity Patterns in Climate Space

description: <b>Exploring Biodiversity Patterns in Climate Space</b><b>Summary of Dataset Contents</b>This dataset supports the manuscript "Biodiversity patterns redefined in environmental space," which explores biodiversity patterns in environmental space. The data encompasses various metrics and measurements that map species occurrences and richness in both climate and geographical spaces, offering a novel perspective on the mechanisms driving broad-scale biodiversity patterns. The dataset includes processed data in the form of tables across multiple tabs in an XLS file named “Full_Data_Set_Perspective_Piece.xlsx”, accompanied by R scripts for pattern exploration named “Script_Perspective_Piece.R”.<b>Description of the Data and File Structure</b>The data is organized into several tabs within an XLS file named “Full_Data_Set_Perspective_Piece.xlsx”, each corresponding to different aspects of the study. Below is a detailed description of each tab and its columns:<b>Tab: Fig1_G_space_mapping</b>This table maps species occurrences and richness in both climate and geographical spaces.ID: The ID of each geographical cell.ge_p_nc: The geographical occurrences of <i>Panthera onca</i>.g_p_jgr: The geographical occurrences of <i>Panthera pardus</i>.clm_p_n: The climatic occurrences of <i>Panthera onca</i>.clm_p_j: The climatic occurrence overlap among the two species.e_mmml_: The richness of mammal species in environmental space.Dlty_vr: Variable used to create a color code for duality plotting.Dlty_pl: Variable used to create a color code for duality plotting.geometry: Spatial information in Well-Known Text (WKT) format.<b>Tabs: Fig2_Temperature_Space_20, Fig2_Temperature_Space_40, Fig2_Temperature_Space_60</b>These tables define one-dimensional climate spaces at different resolutions, containing bird richness data.MinX: Minimum temperature of the bin.MaxX: Maximum temperature of the bin.Climate_Area: Geographical area occupied by that climate bin (scaled in km²).Richness: Number of bird species in the bin.<b>Tabs: Fig_2D_E_Space_20_20, Fig_2D_E_Space_40_40, Fig_2D_E_Space_60_60</b>These tables define two-dimensional climate spaces at different resolutions, containing bird richness data.x: X coordinate of a two-dimensional climate space.y: Y coordinate of a two-dimensional climate space.MinX: Minimum value of PC2 scores for the bin.MinY: Minimum value of PC2 scores for the bin.MaxX: Maximum value of PC1 scores for the bin.MaxY: Maximum value of PC1 scores for the bin.Richness: Number of bird species in the bin.<b>Tab: Fig3_Area_and_Isolation</b>This table explores patterns of area and isolation in climate space at a resolution of 20 equal intervals.x: X coordinate of a two-dimensional climate space.y: Y coordinate of a two-dimensional climate space.MinX: Minimum value of PC2 scores for the bin.MinY: Minimum value of PC2 scores for the bin.MaxX: Maximum value of PC1 scores for the bin.MaxY: Maximum value of PC1 scores for the bin.Climate_Area: Geographical extent covered by the bin (km²).AverageDistAmongFrags: Distance among fragments of a climate.<b>Tabs: Fig4_amphibians_RSFD, Fig4_birds_RSFD</b>These tables contain range size frequency distribution data for amphibians and birds.spp: Species identity.rs.g: Range size in geographical space.rs.e: Range size in environmental space.std.rs.g: Standardized geographical range size (Z standardization).std.rs.e: Standardized environmental range size (Z standardization).<b>Tabs: Fig4_amphibian_RSFD_Density, Fig4_birds_RSFD_Density</b>These tables contain range size frequency distribution density data for amphibians and birds.Space: Space where the range size was measured (G-Space or E-Space).Range_Size: Range size in geographical and environmental space.<b>Tab: Fig5_Amphibian_Phylo_Measures</b>This table contains phylogenetic measures for amphibians in climate space.x: X coordinate of a two-dimensional climate space.y: Y coordinate of a two-dimensional climate space.MinX: Minimum value of PC2 scores for the bin.MinY: Minimum value of PC2 scores for the bin.MaxX: Minimum value of PC1 scores for the bin.MaxY: Maximum value of PC1 scores for the bin.Richness: Number of amphibian species in the bin.PD: Faith's Phylogenetic Diversity (PD) of the bin.STD.PD: Standardized PD controlling for species richness.Data was Derived from the Following Sources:Climate data: CHELSA (https://chelsa-climate.org/bioclim/) and CGIAR (https://cgiarcsi.community)Vector range maps of amphibians and mammals: International Union for Conservation of Nature (https://iucn.org)Bird range maps: BirdLife (version 2020.1, http://datazone.birdlife.org)<b>Code/Software</b>The dataset includes R scripts used for processing and analyzing the data, and generating the figures presented in the study. The scripts facilitate reproducibility and comprehension of the workflow:Required Libraries and Versions:ggplot2: For plotting (version 3.3.5)sf: For handling spatial data frames (version 1.0-3)dplyr: For data manipulation (version 1.0.7)wesanderson: For color palettes (version 0.3.6)MetBrewer: For additional color palettes (version 0.2.0)Main Script:Script_Perspective_Piece.R: This script includes functions to read data, process it, and explore all patterns described in the manuscript. Each section of the script corresponds to a different figure or analysis, with comments and documentation to guide the user through the process.<br>