DOI: 10.5061/dryad.j3tx95xps
title: Bees travelling south: climate-induced range shifts and suitable habitat losses in south-eastern neotropics

description: 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.
description: 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.
description: # Bees travelling south: climate-induced range shifts and suitable habitat
 losses in south-eastern neotropics
 [https://doi.org/10.5061/dryad.j3tx95xps](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](https://github.com/marlonecobos/kuenm) to understand how the kuenm package works and the directory structure needed.* We used QGIS ([https://qgis.org/en/site/](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](https://moure.cria.org.br/)) * *Tribe*: Bee tribe corresponding for each species (following [Moure's Bee Catalogue](https://moure.cria.org.br/)) * *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/](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: * [https://doi.org/10.15468/dl.pxha7z](https://doi.org/10.15468/dl.pxha7z)