DOI: 10.5061/dryad.jdfn2z3m0
title: Data from: From hot to cold spots: Climate change will change diversity patterns of small mammals in a biodiversity hotspot

description: Climate change represents one of the main current threats to biodiversity.
 Changes in temperature and precipitation regimes are expected to induce
 species range shifts and alter diversity and distribution patterns in the
 Atlantic forest. In this paper, we evaluate if protected areas and forest
 remnants will ensure the richness and the phylogenetic diversity of small
 mammals under scenarios of future climate change. Species distribution
 models were used to assess the potential distribution of small mammals
 using baseline and future (2050 and 2070) in the optimistic and
 pessimistic scenarios of greenhouse gas emissions. Our results showed that
 climate changes will lead to a strong reduction in the suitable climatic
 areas for small mammals in the AF. The shrinkage in the potential
 distribution will lead to high loss of TD and PD. The southeastern region
 of the Atlantic Forest is likely to experience the most pronounced decline
 in PD, while some small areas in the southern and northeastern regions are
 projected to increase PD in the future. We predict a strong decline in TD
 and in PD from biodiversity hotspots regions in the AF under climate
 change scenarios. Since small mammals have low dispersal ability, and
 because most of the AF is highly fragmented, it is unlikely that this
 biome will sustain small mammal biodiversity in the future
description: # From hot to cold spots: Climate change will change diversity patterns of
 small mammals in a biodiversity hotspot. ### Description of the Data and
 File Structure Within the folder **"raw_data_and_scripts.zip"**,
 there are two spreadsheets containing occurrence data for each species
 used to build the models and a phylogenetic tree. All missing data
 represented as NA. The first spreadsheet is named:
 **"00_occ_cleaned_dryad.csv"** * **species**: Scientific name of
 the species * **longitude**: Decimal values indicating the longitude of
 the species' occurrence * **latitude**: Decimal values indicating the
 latitude of the species' occurrence * **Year**: Year when the data
 was collected * **Source**: Source from which the data was obtained *
 **coordinate_precision**: Indicates whether the precision of the
 coordinates was reduced to protect threatened species. We reduced the
 precision of the coordinate data to threatened species (e.g., *Callistomys
 pictus, Chaetomys subspinosus, Drymoreomys albimaculatus, Hylaeamys
 oniscus, Phaenomys ferrugineus, Phyllomys lundi, Phyllomys
 mantiqueirensis, Rhagomys rufescens, Thylamys velutinus, Trinomys eliasi,
 Trinomys moojeni, Wilfredomys oenax*). The following columns are filled
 with "yes" or "no", indicating whether each type of
 filtering was applied: * **date_filter**: Keeps only coordinates collected
 in a specific year * **precision_filter**: Keeps only coordinates with
 precise latitude and longitude * **precision_filter_date**: Keeps only
 coordinates with precise date information * **america_filter**: Keeps only
 coordinates located within the American continent * **bias_filter**:
 Indicates whether the data was filtered to reduce spatial bias The second
 spreadsheet is named: **"species_list.csv"** * **species**:
 Scientific name of the species The phylogenetic tree is
 named **"Tree_bootstrap_500.txt"** and contains a phylogenetic
 tree for species of small mammals used in this study. The folder
 **"binary_maps_species.zip"** contains binary presence-absence
 maps for each species, for the present and for future scenarios under both
 optimistic and pessimistic climate emission scenarios. The files are in
 JPG format. The binary maps are compatible with the CC0 license waiver and
 were not derived from any external sources. The folder
 **"rasters_pres_abs_species.zip"** contains the presence-absence
 raster files for each species, for the present and for future scenarios
 under both optimistic and pessimistic emission scenarios. The files are in
 TIFF format. The rasters are compatible with the CC0 license waiver and
 were not derived from any external sources. The folder
 **"response_curves.zip"** contains the response curves for each
 species, for each climatic variable, and modeling algorithm. The files are
 in JPG format. The response curves are compatible with the CC0 license
 waiver and were not derived from any external sources. ### Code / Software
 The folder **"raw_data_and_scripts.zip"** includes the R scripts
 used to perform the analyses and to generate the figures presented in the
 manuscript. All scripts were written in R (version 4.4.1) and include
 annotations throughout. Abaixo fornecemos o nome de cada script, uma breve
 descricao e quais dados sao necessarios.
 **01_01_01_script_occurrence_download_spocc_specieslink**: script to
 download occurrences. Imput data: "species_list.csv" in the
 folder "raw_data_and_scripts.zip"
 **01_01_02_script_occurrence_download_sibbr**: script to download
 occurrences. Imput data: "species_list.csv"  in the
 folder "raw_data_and_scripts.zip"
 **01_01_03_script_occurrence_download_portal_biodiversidade**: script to
 download occurrences. Imput data: "species_list.csv"  in the
 folder "raw_data_and_scripts.zip"
 **01_01_04_script_occurrence_download_data_papers:**  script to download
 occurrences. Imput data: "species_list.csv"  in the
 folder "raw_data_and_scripts.zip"
 **01_02_script_occurrence_integrated**: script to create a combined table
 with all occurrences. Input data: table generated in the scripts:
 01_01_01_script_occurrence_download_spocc_specieslink, 01_01_02_script_occurrence_download_sibbr, 01_01_03_script_occurrence_download_portal_biodiversidade, 01_01_04_script_occurrence_download_data_papers. **01_03_script_occurrence_cleaning**: script to clean the occurrence records. Input data: table generated in the script 01_02_script_occurrence_integrated. **02_01_script_download_covariate**: script to download bioclimatic variables. Input data: not needed. **02_02_script_prepare_covariate**: script to prepare the bioclimatic variables. Input data: data downloaded in the script 02_01_script_download_covariate. **03_sdm_flexsdm_boyce_mhv**: script to fit the Species distribution models. Input data: cleaned records generated in script 01_03_script_occurrence_cleaning and bioclimatic variables prepared in script 02_02_script_prepare_covariate.  **04_01_phylo_div_calc**: script to calculate the phylogenetic diversity and taxonomic diversity of the species. Input data: phylogenetic tree "Tree_bootstrap_500.txt" and rasters generated in the script 03_sdm_flexsdm_boyce_mhv. **04_01_phylo_div_SES_calc:** script to calculate the standardized effect size for phylogenetic diversity. Input data: phylogenetic tree "Tree_bootstrap_500.txt"  in the folder "raw_data_and_scripts.zip" and rasters generated in the script 03_sdm_flexsdm_boyce_mhv. **04_sdm_extract_doing_maps_each_species**: script to generate individual maps for each species in each scenario. Input data: rasters generated in the script 03_sdm_flexsdm_boyce_mhv. **05_01_figures**: script used to generate the figures of the manuscript. Input data: rasters generated in the script 04_01_phylo_div_calc and 04_01_phylo_div_SES_calc. **05_02_PA_and_reman_calc_mhv**: script used to calculate the percentage of diversity in forest remnants and protected areas. Input data: rasters generated in the script 04_01_phylo_div_calc. **05_03_area**: script used to calculate the area for each species. Input data: rasters generated in the script 03_sdm_flexsdm_boyce_mhv. **05_04_plot_tree**: script used to produce a figure with the phylogenetic tree. Input data: phylogenetic tree "Tree_bootstrap_500.txt"  in the folder "raw_data_and_scripts.zip". **Methods** Methods used to construct the data here deposited can be visualized in detail in the manuscript: [https://onlinelibrary.wiley.com/doi/epdf/10.1111/ddi.70026](https://onlinelibrary.wiley.com/doi/epdf/10.1111/ddi.70026)