World fish occurrences at ecoregion level

• Overview
• Data sources
• Workflow
• Content
• Installation
• Usage
• Citation
• Contributing
• Acknowledgments
• References

Overview

This project is dedicated to retrieve, clean and check GBIF occurrences for all fish species of the World (n = 35,035 species). Occurrences are aggregated at the ecoregion level (Spalding et al., 2007) for marine species and at the drainage basin level (Tedesco et al., 2017) for freshwater species.

Data sources

This project uses the following databases:

Database	Usage	Reference	Link
Fishbase	Get fish species accepted names	Froese R & Pauly D (2000)	link
GBIF	Get fish occurrences at World scale	GBIF.org (2024)	link
MEOW	Aggregate occurrences for marine species	Spalding et al. (2007)	link
Drainage basins	Aggregate occurrences for freshwater species	Tedesco et al. (2017)	link
Natural Earth	World maps	None	link

A comprehensive description of all these databases is available here.

Workflow

The analysis pipeline follows these steps:

1. Find GBIF accepted names & identifiers from Fishbase accepted names
2. Download GBIF occurrences
3. Clean and check GBIF occurrences
4. Intersect occurrences w/ marine ecoregions layer (marine species)
5. Intersect occurrences w/ drainage basins layer (terrestrial species)
6. Export layers in outputs/
7. Compute marine and freshwater species richness
8. Export World maps in figures/

Content

This repository is structured as follow:

• DESCRIPTION: contains project metadata (authors, description, license, dependencies, etc.).

• make.R: main R script to set up and run the entire project. Open this file to follow the workflow step by step.

• R/: contains R functions developed especially for this project.

• data/: contains raw data used in this project. See the README for further information.

• analyses/: contains R scripts to run the workflow. The order to run these scripts is explained in the make.R and the description of each script is available in the header of each file.

• outputs/: contains the outputs of the project. See the README for a complete description of the files.

• figures/: contains the figures used to validate et visualize the outputs.

Installation

To install this compendium:

• Fork this repository using the GitHub interface.
• Clone your fork using git clone fork-url (replace fork-url by the URL of your fork). Alternatively, open RStudio IDE and create a New Project from Version Control.

Usage

Launch the make.R file with:

source("make.R")

Notes

• All required packages listed in the DESCRIPTION file will be installed (if necessary)
• All required packages and R functions will be loaded
• Each script in analyses/ can be run independently
• Some steps listed in the make.R might take time (several hours)

Citation

Please use the following citation:

Casajus N & Loiseau N (2024) A database on World fish species occurrences at ecoregion and drainage basin level. URL: https://github.com/phenofish/gbif-ecoregions/.

Contributing

All types of contributions are encouraged and valued. For more information, check out our Contributor Guidelines.

Please note that this project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Acknowledgments

This project has been developed for the FRB-CESAB research group Phenofish that aims to create a global database of fish functional traits integrating physiology and ecology across World aquatic ecosystems.

References

Froese R & Pauly D (2000) FishBase 2000: Concepts, designs and data sources. ICLARM, Los Banos, Philippines. URL: https://www.fishbase.se/.

GBIF.org (2024) GBIF Home Page. Available from: https://www.gbif.org [17 February 2024].

Spalding MD et al. (2007) Marine Ecoregions of the World: A Bioregionalization of Coastal and Shelf Areas. BioScience, 57(7), 573-583. DOI: https://doi.org/10.1641/B570707.

Tedesco P et al. (2017) A global database on freshwater fish species occurrence in drainage basins. Scientific Data, 4, 170141. DOI: https://doi.org/10.1038/sdata.2017.141.