Bees travelling south: climate-induced range shifts and suitable habitat losses in south-eastern neotropics
Data files
Aug 06, 2024 version files 387.68 KB
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data_and_code.zip
380.37 KB
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README.md
7.32 KB
Abstract
Aim: Provide an assessment of climate change impacts on a set of wild pollinators restricted to one of the regions with the greatest diversity of bees in the world. Also, we aimed to test whether functional groups responded differently to climate projections.
Location: South-eastern South America (SES).
Taxon: Bees (Hymenoptera: Apidae sensu lato)
Methods: We selected 18 species of bees mostly restricted to the SES region, modelled their distributions and assessed the possible impacts of near future (2050) climate change in species richness and shifts in range centroids. Potential impacts related to different functional groups were evaluated through t-tests.
Results: SES species richness were projected to decrease in the northernmost regions and increase southward. Most bee species were predicted to shift their range centroids towards the south-west and south, while suitable stable areas were found in southern Brazil. We also found higher proportional losses in suitable areas for eusocial species compared to solitary ones, while generalists showed slightly lower gains than specialists.
Main conclusions: SES bees are likely to undergo changes in the near future, with projected losses of species at northern portions and southward increases. The identified stable areas in southern Brazil underscore the importance of conservation efforts in the region, particularly in natural grasslands – an endangered habitat with high bee diversity. Although our results suggest higher vulnerability for functional groups traditionally considered more resilient, it is essential to acknowledge that other factors, including habitat and mutualists availability, behavioural particularities, phenology and range size, must be determinants for the vulnerability of species to ongoing climate change.
README: Bees travelling south: climate-induced range shifts and suitable habitat losses in south-eastern neotropics
https://doi.org/10.5061/dryad.j3tx95xps
Here, we provide all the occurrence data and files to carry out all the modeling processes. Unfortunately, we cannot upload the WorldClim layers due to storage limits. However, we’ve provided all the necessary steps for bioclimatic variables preparation in the R code files.
In detail here you will find:
- All occurrences data for each bee species as separated .csv files (Data/occurrences/);
- Complete dataset with references for each record (Occurrence-data-with-references/Occurrence-data-with-references.xlsx);
- R code for data preparation and creation of subdirectories for each species, following the structure required in ‘kuenm’ package (01_data_preparation_and_folders_for_species.R);
- Folder with subdirectories for each species (kuenm_bees/), created after running 01_data_preparation_and_folders_for_species.R script;
- Folder for Augochlora iphigenia (FWP_Augochlora_iphigenia/), as an example for modeling workflow;
- R code for M selection based on dispersal simulations for Augochlora iphigenia (Augochlora_iphigenia/02_M_simulation_Augochlora_iphigenia.R), as an example - the same code structure was followed for all the other species;
- R code for the workflow for all kuenm processes (data preparation, calibration and evaluation of the candidate models, final models and post-modelling analysis) for Augochlora iphigenia (Augochlora_iphigenia/03_kuenm_Augochlora_iphigenia.R), as an example - the same code structure was followed for all the other species. Complete dataset for the species is available in occurrences.csv, cleaned and thinned records are available in thinned_occ_thin1.csv (obtained after running 01_data_preparation_and_folders_for_species.R script), while occo_train.csv refers to the subset of occurrences used for training (candidate models construction), occo_test.csv for testing models (candidate models evaluation), and occo_joint.csv for training and testing data. The first R code (01_data_preparation_and_folders_for_species.R) creates the subdirectories for each species separately with cleaned and thinned data, as well as training and testing files;
- R code (t_test/01_t-test.R) and required data (t_test/Species_area_w_traits.csv and t_test/t-tests-outputs.xlsx) used for t-tests and boxplots;
- R code (range_centroids/01_changes_in_range_centroids.R) and required data (range_centroids/centroids_585.csv) and range_centroids/dist_az_585.csv) used for evaluating changes in range centroids and circular histograms;
- R code (Figure_4_barplot_changes/01_barplot_changes.R) and required data (Figure_4_barplot_changes/barplot_changes.csv) used to make a barplot summarizing changes for each species - figure 4 in the published article
We strongly recommend to check the kuenm repository to understand how the kuenm package works and the directory structure needed.
We used QGIS (https://qgis.org/en/site/) to quantify changes in suitable areas, as well as to make map figures (Figures 1-3).
Descriptions
Species occurrences data - the .csv files in (Data/occurrences/) and in (FWP_Augochlora_iphigenia/)
- species: Currently valid scientific name
- longitude: Longitude in decimal degrees (DD)
- latitude: Latitude in decimal degrees (DD)
- these three columns above are the same in .csv files in species subdirectories (i.e., occo_joint.csv, occo_test.csv, occo_train.csv; occurrences.csv; thinned_occ_thin1.csv
Complete dataset with references (Occurrence-data-with-references/Occurrence-data-with-references.xlsx)
- Subfamily: Bee subfamily for each species (following Moure's Bee Catalogue)
- Tribe: Bee tribe corresponding for each species (following Moure's Bee Catalogue)
- Species: Currently valid scientific name
- Long: Longitude in decimal degrees (DD)
- Lat: Latitude in decimal degrees (DD)
- Ref: Reference for each occurrence record; we used public databases (GBIF and speciesLink), published literature (doi link), and unpublished data from entomological collections (collection name)
Figure 4 barplot changes (Figure_4_barplot_changes/barplot_changes.csv)
- species: currently valid species name
- parameter: gain, stable or loss of suitable areas in future scenario compared to current scenario
- percentage: value of parameter in percentage (e.g., percentage of suitable area loss)
- ssp: Shared Socioeconomic Pathway (SSP) of climate projections; we used only SSP 585
Range centroids (range_centroids/)
- species: currently valid species name
- olon: longitude of species' centroid in current scenario
- olat: latitude of species' centroid in current scenario
- tlon: longitude of species' centroid in future scenario
- tlat: latitude of species' centroid in future scenario
- dist_km: distance in km from current range centroid to projected future range centroid
- azimuth: azimuth from current range centroid to projected future range centroid, measured in degrees in the signed range -180º to +180º
t-test file (t_test/Species_area_w_traits.csv)
- Species: currently valid species name
- gain585: gain in suitable areas for SSP 585 future projection (km)
- loss585: loss in suitable areas for SSP 585 future projection (km)
- stable585: stable suitable areas for SSP 585 future projection (km)
- total585: total suitable area (in km) for SSP 585 future projection
- prop_loss585: proportional area loss in suitable areas
- prop_gain585: proportional area gain in suitable areas
- sociality: sociality life-history trait of each species (eusocial or solitary)
- nesting: nesting behavior of each species (above_ground or below_ground)
- specialization: resource specialization of each species (generalist or specialist)
t-test output (t_test/t-tests-outputs.xlsx)
- traits: bee life-history traits compared using t-tests. Sociality means that we compared eusocial versus solitary species, while nesting refers to below ground versus above ground species comparisons, and specialization refers to generalists versus specialists comparisons
- parameter: values used for t-tests comparing each group of traits. Gain is the same as gain585 loss is the same as loss585 in Species_area_w_traits.csv
- t: t-statistic for each comparison using t-tests
- p value: p-value obtained from each t-test
Code/Software
R is required to run the scripts, which were created using version 4.3.2. Annotations are provided throughout the script through 1) library loading, 2) dataset loading and cleaning, 3) analyses, and 4) figure creation. We used QGIS (https://qgis.org/en/site/) to quantify changes in suitable areas, as well as to make map figures (Figures 1-3).
Sharing/Access information
GBIF dataset with searched occurrences is available in:
Methods
We selected 18 species of bees mostly restricted to the SES region, modelled their distributions and assessed the possible impacts of near future (2050) climate change in species richness and shifts in range centroids. Potential impacts related to different functional groups were evaluated through t-tests.