Data and code for "Species interactions affect dispersal: a meta-analysis"

README Elvire Bestion 2024-05-28 1. General Information 1.1. Title of Dataset Data and code for: Species interactions affect dispersal: a meta-analysis, Bestion et al 2024, Philosophical Transactions B, doi: 10.5281/zenodo.10940162 1.2. Author information First author information • Name: Elvire Bestion • Orcid: 0000-0001-5622-7907 • Institution: Station d’Ecologie Théorique et Expérimentale, CNRS, UAR 2029 • Address: 2 route du CNRS, 09200 Moulis, France • Email: elvire.bestion@sete.cnrs.fr Last author information • Name: Julien Cote • Orcid: 0000-0002-4453-5969 • Institution: Centre de Recherche sur la Biodiversité et l’Environnement (CRBE), UMR 5300 CNRS-IRD-TINP-UT3 • Address: Université Toulouse III – Paul Sabatier, Bât 4R1, 118 route de Narbonne, 31062 Toulouse, France • Email: julien.cote@univ-tlse3.fr 1.3. Abstract Context-dependent dispersal allows organisms to seek and settle in habitats improving their fitness. Despite the importance of species interactions in determining fitness, a quantitative synthesis on how they affect dispersal is lacking. We present a meta-analysis asking (1) whether the interaction experienced and/or perceived by a focal species (detrimental interaction with predators, competitors, parasites, or beneficial interaction with resources, hosts, mutualists) affects its dispersal, (2) how the species’ ecological and biological background affects the direction and strength of this interaction-dependent dispersal. After a systematic search focusing on actively dispersing species, we extracted 397 effect sizes from 118 empirical studies encompassing 221 species pairs; arthropods were best represented, followed by vertebrates, protists and others. Detrimental species interactions increased the focal species’ dispersal (adjusted effect: 0.33 [0.06,0.60]), while beneficial interactions decreased it (-0.55 [-0.92,-0.17]). The effect depended on the dispersal phase, with detrimental interactors having opposite impacts on emigration and transience. Interaction-dependent dispersal was negatively related to species’ interaction strength, and depended on the global community composition, with cues of presence having stronger effects than presence of the interactor, and the ecological complexity of the community. Our work demonstrates the importance of interspecific interactions on dispersal plasticity with consequences for metacommunity dynamics. 1.4. Keywords context-dependent dispersal, metacommunity dynamics, predator-prey interactions, competition, host-parasite interactions, biotic interactions 1.5. Date of data collection A search on Web of Science was conducted on the 20th of October 2021, yielding 21499 results, which were subsequently filtered to 118 studies and 397 effect sizes. 1.6. Taxon or species from which data was collected The search was done across species, with the only species criterion being that focal species should be active dispersers. The final dataset contains data for 144 focal taxa and 165 interacting taxa. 2. Sharing and access information 2.1. Licenses and restrictions placed on the data The data is usable under Creative Commons Attribution 4.0 International licence but we would appreciate if we were contacted prior to meaningful use, and this dataset and the matching paper cited if appropriate. 2.2. Links to publications that cite or use the data This dataset corresponds to the data used in: Bestion E, Legrand D, Baines CB, Bonte D, Coulon A, Dahirel M, Delgado M, Deshpande JN, Duncan AB, Fronhofer EA, Gounand I, Jacob S, Kaltz O, Massol F, Matthysen E, Parmentier T, Saade C, Schtickzelle N, Zilio G, Cote J. 2024. Species interactions affect dispersal: a meta-analysis. Philosophical Transactions B, 379:20230127, doi: 10.1098/rstb.2023.0127 2.3. Links to other publicly accessible locations of the data The data can be found on zenodo at doi: 10.5281/zenodo.10940162 2.4. Was data derived from another source? Yes. The data used in this meta-analysis was sourced from 118 primary research papers, see output/Table_bibliography.docx for a list of the primary research articles. 2.5. Recommended citation for this dataset Bestion et al, 2024. Data and code for: Species interactions affect dispersal: a meta-analysis, Philosophical Transactions B, Zenodo, doi: 10.5281/zenodo.10940162 3. Data and file overview 3.1. Directory structure .|- data | |- Database_Bestion.csv | |- Phylogeny_focal.csv | |- Phylogeny_interactor.csv | |- catalogue_life_taxonomy.csv |- interm| |- R_session_info_2024-04-02.txt | |- dredge_mod.rds | |- dredge_mod_detrimental.rds | |- dredge_mod_beneficial.rds | |- list_best_mod.rds | |- list_best_mod_detrimental.rds | |- list_best_mod_beneficial.rds | |- av_mod.rds | |- av_mod_detrimental.rds| |- av_mod_beneficial.rds | |- FigureXX | |- Plot_relationship_variance_sample_size.png|- output | |- Figure_2_type_and_nature_interactor.png | |- Figure_3_dispersal_phase.png | |- Figure_4_biotic_context.png | |- Figure_5_generalism.png | |- Figure_6_interaction_strength.png | |- Figure_S1_prisma_plot.png | |- Figure_S2_focal_phylogenetic_tree.png | |- Figure_S3_Sankey_plots_by_phylum_class.png | |- Figure_S4_Sankey_general_plot.png | |- Figure_S5_Funnel_full_mod.png | |- Figure_S6_Funnel_detrimental_beneficial.png | |- Figure_S7_duration_generation_type_study.png | |- Tables_main_text_and_supplementary.docx | |- Tables_information_in_the_main_text_and_supplementary.docx | |- Table_bibliography.docx |- raw_data| |- Raw_database_Bestion.csv | |- Phylogeny_focal.csv | |- Phylogeny_interactor.csv |- 00_Analysis.Rproj |- 0_functions.R |- 1_data_preparation.R |- 2_analysis.R |- README.docx |- README.html |- README.md|- README.Rmd |- renv.lock 3.2. Description of directories Name Description data Directory for cleaned datasets used in this study after the cleaning step interm Directory for saving intermediate calculation steps from R script output Directory for saving figures and tables resulting from the analysis found in the main article and supplementary data raw_data Directory for the raw datasets used in this study 3.3. Description of primary data files The raw data files are in the /raw_data folder and the cleaned data files in the /data folder Data in the /raw_data folder Name Description Raw_database_Bestion.csv the database for the 119 papers selected for the meta-analysis, with information to calculate effect sizes. This dataset will be cleaned, effect sizes will be calculated, and it will be transformed to data/Database_Bestion.csv through the 0_data_preparation.R script. Note that this dataset contains more rows than the Database_Bestion finally used in the meta-analysis, as 6 rows with very high variance of the effect size were excluded for model stability, leading to exclude one study Phylogeny_focal.csv a dataset containing the names of each focal taxa as well as their taxonomic identity derived from the taxize R package with all of the species in the raw database Phylogeny_interactor.csv a dataset containing the names of each interactor taxa as well as their taxonomic identity derived from the taxize R package with all of the species in the raw database Data in the /data folder Name Description Database_Bestion.csv the database for the 118 papers finally used in the meta-analysis with the calculated effect sizes and the cleaned variables needed for the meta-analysis Phylogeny_focal.csv a dataset containing the names of each focal taxa as well as their taxonomic identity derived from the taxize R package, filtered to contain taxonomic info for the 118 studies instead of 119 Phylogeny_interactor.csv a dataset containing the names of each interactor taxa as well as their taxonomic identity derived from the taxize R package, filtered to contain taxonomic info for the 118 studies instead of 119 catalogue_life_taxonomy.csv a dataset containing information about the number of species for taxons at different levels of resolution gathered from the catalogue of life 3.4. Description of files in the interm and output folders derived using R The project leads to the creation of intermediate calculation steps from the R script that are stored in the /interm folder and of figures and tables resulting from the analysis found in the main article and supplementary data that are stored in the /output folder. Objects in the /interm folder Name Description R_session_info_2024-04-02.txt the session information about the R version and R packages used when running the R code dredge_mod.rds the R object resulting from the dredge of the main model. Note that the dredge is very time intensive, thus we save the R object to the intern folders. Running the code will overwrite this object dredge_mod_detrimental.rds the R object resulting from the dredge of the main model for the detrimental interaction subset dredge_mod_beneficial.rds the R object resulting from the dredge of the main model for the beneficial interaction subset list_best_mod.rds the R object resulting from the list of best models (with deltaic<2) from the dredge of the main model list_best_mod_detrimental.rds the R object resulting from the list of best models (with deltaic<2) from the dredge of the main model for the detrimental interaction subset list_best_mod_beneficial.rds the R object resulting from the list of best models (with deltaic<2) from the dredge of the main model for the beneficial interaction subset av_mod.rds the R object resulting from the model averaging of the best models (with deltaic<2) from the dredge of the main model av_mod_detrimental.rds the R object resulting from the model averaging of the best models (wit

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