The global geography of threats to freshwater biodiversity
Data files
Sep 14, 2026 version files 232.09 KB
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AreaRichnessCorrections.R
38.80 KB
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ExtinctionAnalyses.R
44.62 KB
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IBTComparison.R
9.46 KB
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ImpactModel.R
8.95 KB
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LPIPreparationAnalysis.R
8.53 KB
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MainThreat.R
18.08 KB
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Metrics.R
21.80 KB
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README.md
4.76 KB
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README.txt
3.71 KB
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RedListPreparation.R
50.82 KB
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TerrestrialComparison.R
22.56 KB
Abstract
Human activities are eroding biodiversity, especially in freshwater systems. Despite major advances in quantifying species vulnerability and threats, we still lack a crucial understanding of where threats are impacting freshwater species globally. Here, we produce a species-centered spatial assessment of threats, mapping the impact of 45 threats across 21,490 freshwater species of amphibians, fish, mammals, odonates, and reptiles. We find that species in highly developed and water-managed regions are strongly impacted by multiple overlapping threats. Although threats vary across taxa and regions, increasing threat probabilities elevate extinction risk and population declines, with freshwater species experiencing greater threat intensity and distinct spatial patterns compared to terrestrial species. Our findings establish a spatially explicit baseline for targeting the most urgently needed freshwater conservation and management interventions.
Authors: Christophe Brabant, Laura Pollock, Jonas Geldmann, Mette Bendixen, Lise Comte, Harith Farooq, Katherine Hébert, Bernhard Lehner, Catherine Sayer, Lars Lønsmann Iversen
Code is available from Dryad repository, see below. Dataset DOI: 10.5061/dryad.02v6wwqh0
Data is available from Zenodo repository under a CC-BY-NC license, see below. Dataset DOI: 10.5281/zenodo.18507964
Data availability (Zenodo)
Zenodo Dataset DOI: 10.5281/zenodo.18507964
This dataset will be made public upon publication of the manuscript. For any additional questions, please contact christophe.brabant@mail.mcgill.ca
All raw data are freely available from the original sources.
The Zenodo repository contains presence data, threat code, and range size needed to reproduce the study. Appropriate citations to original sources are required.
All newly created materials (225 threat maps) are available for download under a CC-BY-NC license.
Files
1) FWThreatMaps.RDS: contains all threat maps for all 45 threats and all 5 freshwater taxonomic groups, with species richness of each group, the geometry of sub-watersheds spatial units, and the uncertainty (scaled and quantiles, see methods and Fig. S1).
2) CumulativeMaps.RDS: contains cumulative threat maps from the manuscript (Fig. 1A & Fig. S2)
Code availability (Dryad)
Dryad Dataset DOI: 10.5061/dryad.02v6wwqh0
All code used for the analysis and visualisation presented in the manuscript is available in the following R scripts:
Files
File: LPIPreparationAnalysis.R
Description: Contains code to obtain LPI data, calculate growth rates and perform analyses.
File: AreaRichnessCorrections.R
Description: Framework to (1) control for richness in the comparison of threat impact to freshwater vs terrestrial species, (2) account for freshwater availability in the cumulative threat pattern, and (3) account for the freshwater species richness in the cumulative threat pattern.
File: IBTComparison.R
Description: Contains code to extract IBT index in sub-watersheds and compare it to an adapted cumulative impact index.
File: TerrestrialComparison.R
Description: Contains code to rerun terrestrial threat maps (without freshwater species) from Farooq et al., 2024, and to compare the impact of threats to freshwater vs terrestrial groups (reptiles and mammals).
File: MainThreat.R
Description: Creates maps of the main threat in each watershed, the intensity of the main threat, and taxonomic variation.
File: ExtinctionAnalyses.R
Description: Contains code for (1) the logistic regression models calculating extinction risk in each sub-watershed, (2) code to compare the impact of threats in high extinction risk areas to their global average, (3) a sensitivity analysis for the cutoff of high-risk areas, and (4) identification of main threats in high-risk areas.
File: RedListPreparation.R
Description: Contains (1) code to clean range maps obtained from the IUCN and intersect the range polygons with sub-watershed polygons (level 8 resolution from HydroBASINS, freely available at: https://www.hydrosheds.org/products/hydrobasins), (2) code to obtain threat assessment for all 45 IUCN threats for each species included in the study (alternatively can be downloaded using the Red List API https://api.iucnredlist.org/), and (3) code to prepare the input format for the impact probability model.
File: ImpactModel.R
Description: Runs logistic regression models for each sub-watershed and for all threats with separate models for each taxonomic group.
File: Metrics.R
Description: Contains code to create the cumulative impact index for all taxonomic groups (together and separate) and rank threats in order of their mean impact globally, as well as other index formulations.
File: README.txt
Description: Code description
Access information
Data was derived from the following sources:
- Data on range maps are freely available at https://www.iucnredlist.org/resources/spatial-data-download and https://www.iucnredlist.org/search. IUCN threat classification assessment data can be downloaded using the Red List API (https://api.iucnredlist.org/) or on request from IUCN’s Global Species Programme Red List Unit (redlist@iucn.org). Other data are freely available using citations in the manuscript.