Data from: From hot to cold spots: Climate change will change diversity patterns of small mammals in a biodiversity hotspot
Data files
Jun 26, 2025 version files 244.21 MB
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binary_maps_species.zip
2.97 MB
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rasters_pres_abs_species.zip
23.32 MB
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raw_data_and_scripts.zip
182.42 KB
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README.md
6.54 KB
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response_curves.zip
217.73 MB
Abstract
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 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