Benthic Foraminiferal Diversity in the Arabian Gulf: Dataset and Code Repository

Benthic Foraminiferal Diversity in the Arabian Gulf: Dataset and Code Repository Overview This repository contains all data, code, and outputs associated with our study "Benthic Foraminiferal Diversity in the Arabian Gulf: Spatial Patterns in a Basin-wide Assessment" (Amao et al., 2024). We provide a complete analytical workflow implementing stacked species distribution models (SSDMs) to map benthic foraminiferal diversity patterns and identify key environmental drivers. Dataset Description The repository includes occurrence data for 492 benthic foraminiferal species from the Arabian Gulf, representing nine orders, 39 superfamilies, 89 families, and 150 genera. This comprehensive dataset was compiled from published literature and standardized against the World Register of Marine Species (WoRMS) taxonomy. Environmental data layers include bathymetry, sea surface temperature, salinity, chlorophyll-a, dissolved oxygen, and various other oceanographic parameters derived from Bio-ORACLE and GEBCO databases. Key Findings Revealed a pronounced north-south diversity gradient that contrasts with typical latitudinal patterns in open ocean systems, demonstrating how basin-specific environmental factors override global biodiversity trends Found the northern Gulf to be a diversity hotspot due to freshwater influence from the Shatt al-Arab delta which creates habitat heterogeneity Identified an east-west diversity gradient reflecting the basin's counter-clockwise circulation pattern Demonstrated that environmental heterogeneity and stress gradients are more influential in structuring foraminiferal communities than latitude alone Established bathymetry, dissolved oxygen, iron concentration, and salinity as primary environmental controls, with thermal maxima exerting greater influence than average temperatures Repository Structure /data/: Contains raw occurrence data, processed environmental layers, and model outputs /data/raw/: Original occurrence records and environmental layers /data/processed/: Cleaned species data and standardized environmental layers /data/outputs/: Model predictions, performance metrics, and diversity maps /scripts/: All R scripts used in the analysis pipeline WORMS_Verification.Rmd: Script for taxonomic standardization Bio-ORACLE_Batch_Layer_Downloader_and_Processor.Rmd: Environmental data acquisition and processing Environmental_Layers_Composite_Image_Creator.Rmd: Visualization of environmental variables SSDM_Model.Rmd: Core species distribution modeling implementation variable_importance.Rmd: Analysis of environmental variable contributions krigged_diversity_v16_HighRes_Orthographic_.R: Spatial interpolation and diversity mapping 01_data_preparation.R through 06_run_full_analysis.R: Modular workflow scripts /figures/: High-resolution maps and visualizations /results/: Summary statistics and model evaluation metrics project_root/├── scripts/                                                                        # All R scripts for the analysis│   ├── 00_setup.R                                                             # Setup script (creates directories, loads packages)│   ├── 01_WORMS_Verification.Rmd│   ├── 02_Bio-ORACLE_Downloader.Rmd│   ├── 03_Environmental_Layers.Rmd│   ├── 04_Sampled_Locations.Rmd│   ├── 05_SSDM_Model.Rmd│   ├── 06_Variable_Importance.Rmd│   ├── 07_Krigging_Visuals.Rmd│   └── 08_Advanced_Analysis.Rmd├── R/                                                                              # Custom R functions│   ├── packages.R                                                          # Package management │   └── paths.R                                                                # Path management├── data/                                                                        # Data directories│   ├── raw/                                                                    # Original unmodified data│   │   ├── occurrence/                                                   # Species occurrence data│   │   ├── environmental/                                             # Environmental data│   │   └── shapefiles/                                                    # Boundary/shape files│   ├── processed/                                                         # Data modified by scripts│   ├── shared_data/                                                      # Data shared across multiple scripts│   └── RDS/                                                                   # R data storage├── results/                                                                    # Results and outputs│   ├── figures/                                                              # Plots and visualizations│   ├── tables/                                                               # Output tables│   ├── maps/                                                                # Generated maps│   ├── models/                                                             # Model outputs│   ├── RDS/                                                                  # R data storage│   └── advanced/                                                         # Advanced analysis outputs├── worms_results/                                                       # Outputs from WoRMS verification├── run_all.R                                                                 # Master script to run all analyses├── cleanup.R                                                               # Script to prepare for Zenodo submission └── README.md                                                           # This file Prerequisites Software Requirements R (version 4.0.0 or higher) RStudio (recommended for running R Markdown files) Reproducibility Information Our modeling approach uses an ensemble of classification tree analysis (CTA), random forests (RF), and support vector machines (SVM) algorithms implemented through the SSDM package in R. All analyses were conducted using R version 4.2.0, with full package dependency information provided in the session information at the end of each script. To reproduce our analysis, we recommend running scripts in the numbered sequence (01-06), or using the main.R script which executes the entire workflow. Usage Run the entire analysis pipeline using: r source("run_all.R")   Citation Information If you use these data or code in your research, please cite: Amao AO, Al-Ramadan K, Kaminski MA, Frontalini F (2024) Benthic Foraminiferal Diversity in the Arabian Gulf: Spatial Patterns in a Basin-wide Assessment. PLOSONE . DOI: [to be added upon publication] Additionally, please cite this dataset as: Amao AO, Al-Ramadan K, Kaminski MA, Frontalini F (2024) Data and Code for: Benthic Foraminiferal Diversity in the Arabian Gulf. Zenodo. DOI: 10.5281/zenodo.15380710 License This dataset is made available under the Creative Commons Attribution 4.0 International License (CC BY 4.0). Contact For questions regarding this dataset, please contact the corresponding author: Dr. A.O. Amao (amao@kfupm.edu.sa)