Global Freshwater Fish Knowledge Shortfalls

Global Freshwater Fish Knowledge Shortfalls A reproducible R-based workflow to quantify global Linnaean, Wallacean, and Darwinian knowledge shortfalls in freshwater fishes and to inform strategic biodiversity collection priorities. Code and Data Availability All R scripts used for data acquisition, processing, analysis, and model fitting in this study. - Programming language: R- License: Creative Commons Attribution 4.0 (CC BY 4.0)- GitHub repository: https://github.com/Otoliths/FW_Fish_Shortfall- Zenodo DOI: https://doi.org/10.5281/zenodo.19864169- Figshare data repository: https://doi.org/10.6084/m9.figshare.29262098 Folder Descriptions code/: Contains all R scripts used for data acquisition, preprocessing, statistical analyses, and model fitting. input/: Stores all datasets used in the analyses, including raw input data (raw/), intermediate processed data (processed/), and analysis-ready datasets (data_prep/). output/: Contains analysis outputs, including fitted model objects (model/), summary tables (tables/), and execution logs (logs/). figures/: Includes all figures generated in this study, organized into main-text figures (main/) and supplementary figures (supplement/). report/: Contains R scripts and R Markdown files used to generate all manuscript figures, including Figure_1-4.R and supplementary figure scripts (Figure_S01-S22.R). FW_Fish_Shortfall.Rproj: RStudio project file used to manage the project structure, file paths, and reproducible workflow. This repository is organized as follows: /project_root ├── /code # Core analysis scripts, to be executed sequentially for full reproducibility. │ │ ├── setup_r_packages.R # install main packages │ │ ├── 00_Get_fishtree.R # Retrieve and preprocess the global freshwater fish phylogeny. │ ├── 00_Get_futurestream.R # Download and prepare FutureStreams river network data. │ ├── 00_Get_gbif.R # Query and download occurrence records from GBIF. │ ├── 00_Get_ncbi.R # Retrieve sequence metadata and records from NCBI. │ ├── 00_Get_obis.R # Download aquatic occurrence data from OBIS. │ │ ├── 01_Country_sp.R # Compile country-level species checklists. │ ├── 01_Futurestream_clean.R # Clean and standardize FutureStreams river attributes. │ ├── 01_Occurrence_clean.R # Quality control and harmonization of occurrence records. │ │ ├── 02_Description.R # Quantify taxonomic description coverage. │ ├── 02_Geolocation.R # Assess georeferencing completeness and precision. │ ├── 02_Sequence.R # Summarize molecular sequence availability. │ ├── 02_Seq_summary_phylo_markers.R # Summarize sequencing effort across phylogenetic markers. │ │ ├── 03_Basin_discharge.R # Basin-level mean river discharge. │ ├── 03_Basin_elevation.R # Basin-level elevation statistics. │ ├── 03_Basin_human_density.R # Human population density aggregated by basin. │ ├── 03_Basin_latitude.R # Latitudinal position of drainage basins. │ ├── 03_Basin_range_size.R # Species geographic range size at the basin scale. │ ├── 03_Basin_rarity.R # Basin-level species rarity metrics. │ ├── 03_Basin_sampling_effort.R # Occurrence-based sampling effort per basin. │ ├── 03_Basin_sequence_effort.R # Molecular sequencing effort per basin. │ ├── 03_Basin_watertemp.R # Basin-level water temperature. │ ├── 03_Watershed area.R # Drainage basin area calculations. │ │ ├── 04_Country_discharge.R # Country-level river discharge. │ ├── 04_Country_elevation.R # Country-level elevation. │ ├── 04_Country_human_density.R # Human population density at the country level. │ ├── 04_Country_latitude.R # Country centroid latitude. │ ├── 04_Country_range_size.R # Species range size summarized by country. │ ├── 04_Country_rarity.R # Country-level species rarity. │ ├── 04_Country_sampling_effort.R # Occurrence sampling effort by country. │ ├── 04_Country_sequence_effort.R # Sequencing effort summarized by country. │ ├── 04_Country_watertemp.R # Country-level water temperature. │ │ ├── 05_Body_size.R # Compile and standardize species body size traits. │ ├── 05_Taxonomic_activity.R # Metrics of taxonomic activity effort. │ ├── 05_Taxonomic_effort.R # Metrics of taxonomic research effort. │ │ ├── 06_Basin_linnaean_model.R # Statistical model for basin-level Linnaean shortfalls. │ ├── 06_Basin_wallacean_model.R # Statistical model for basin-level Wallacean shortfalls. │ ├── 06_Basin_darwinian_model.R # Statistical model for basin-level Darwinian shortfalls. │ │ ├── 06_Country_linnaean_model.R # Country-level Linnaean shortfall model. │ ├── 06_Country_wallacean_model.R # Country-level Wallacean shortfall model. │ ├── 06_Country_darwinian_model.R # Country-level Darwinian shortfall model. │ │ ├── 07_Basin_linnaean_shortfall.R # Quantification of basin-level Linnaean shortfalls. │ ├── 07_Basin_wallacean_shortfall.R # Quantification of basin-level Wallacean shortfalls. │ ├── 07_Basin_darwinian_shortfall.R # Quantification of basin-level Darwinian shortfalls. │ │ ├── 07_Country_linnaean_shortfall.R # Country-level Linnaean shortfalls. │ ├── 07_Country_wallacean_shortfall.R # Country-level Wallacean shortfalls. │ ├── 07_Country_darwinian_shortfall.R # Country-level Darwinian shortfalls. │ │ ├── Dawinian_deficits_basin.R # Aggregated Darwinian knowledge deficits at the basin scale. │ ├── Dawinian_deficits_country.R # Aggregated Darwinian knowledge deficits at the country scale. │ │ ├── preserved_specimen.R # Quantification of Preserved specimen. │ │ ├── Cost_Taxonomy.R # Cost estimation for taxonomic research. │ ├── Cost_field_sampling.R # Cost estimation for field sampling campaigns. │ ├── Cost_sequencing.R # Cost estimation for molecular sequencing. │ ├── Cost_all.R # Integrated cost assessment across knowledge gaps. │ ├── Shortfall_reductions.R # Scenario-based evaluation of shortfall reduction strategies. │ │ ├── functions/ # Custom helper functions used throughout the pipeline. │ │ ├── clean_species_occ.R # Species-level occurrence data cleaning functions. │ │ ├── gompertz_family.R # Custom Gompertz distribution. │ │ ├── TAE_function.R # Functions related to Taxonomic Effort. │ │ ├── xxx.R # Additional utility functions. │ │ ├── yyy.R # Additional utility functions. │ │ └── zzz.R # Additional utility functions. │ │ └── exec/ │ ├── wget.exe # External binary used for automated data downloads. │ ├── /input │ ├── raw/ # Raw, unmodified input data. │ ├── processed/ # Intermediate processed datasets. │ ├── data_prep/ # Data prepared for modeling and visualization. │ ├── /output │ ├── model/ # Fitted model objects and predictions. │ ├── logs/ # Execution logs and diagnostics. │ ├── tables/ # Final tables used in the manuscript. │ ├── /figures │ ├── main/ # Figures included in the main text. │ ├── supplement/ # Supplementary figures. │ ├── /report │ ├── Figure_1.R / Figure_1.Rmd # Script and R Markdown for generating Figure 1. │ ├── Figure_2.R / Figure_2.Rmd # Script and R Markdown for generating Figure 2. │ ├── Figure_3.R / Figure_3.Rmd # Script and R Markdown for generating Figure 3. │ ├── Figure_4.R / Figure_4.Rmd # Script and R Markdown for generating Figure 4. │ ├── Figure_1.html # Rendered HTML output for Figure 1. │ ├── Figure_2.html # Rendered HTML output for Figure 2. │ ├── Figure_3.html # Rendered HTML output for Figure 3. │ ├── Figure_4.html # Rendered HTML output for Figure 4. │ ├── Figure_S01-S22.R # Scripts for supplementary figures. │ └── FW_Fish_Shortfall.Rproj # RStudio project file managing paths and workflow. Supporting Information [Figshare] Table_Extended_S1.xlsx: Inventory of 18,821 freshwater fish species included in the analysis (updated 24 November 2024). Table_Extended_S2.xlsx: Body-size data flags distinguishing measured and imputed values. Table_Extended_S3.xlsx: Inventory of freshwater fish knowledge deficiencies units identified in this study. Table_Extended_S4.xlsx: Drainage basins prioritized for future freshwater biodiversity data collection. Figure_Extended_S1.pptx Animated visualization of global first georeferenced freshwater fish records A global geospatial dataset of freshwater fish species at the drainage-basin scale (updated to December 2024) If you use this code or data, please cite: Ding et al., (2026). Global Freshwater Fish Knowledge Shortfalls (Version 2.0). Zenodo. https://doi.org/10.5281/zenodo.18136683