DOI: 10.6084/m9.figshare.28373567
title: Datasets and R codes of the manuscript "Contrasted effects of human pressure on biodiversity in the UK: a multi-taxonomic assessment using airborne environmental DNA"

description: <br><b>DATA TABLES FOR RUNNING THE SCRIPTS</b><b>"Dataset.csv" </b>: this file contains the ASV table refined from the dataset generated by Tournayre et al. 2025. The refinement process involved retaining 1) only the 2022 data, and 2) only birds (excluding exotic caged birds such as budgerigars, cockatiels, and grey parrots), mammals (including domestic ones), insects, non-algal plants, and fungi (except for two phyla represented by three ASVs that were rarely detected). The columns "Supergroup", "group", "phylum", "class", "Order", "Family", "Genus", and "species" provide the detailed taxonomy of each ASV. The column "FINAL_ID" indicates the final ASV identification at the most precise taxonomic level, using the following prefixes: "c:" for class, "p:" for phylum, "o:" for order, "f:" for family, "g:" for genus, and "s:" for species. Sample names are coded as follows: the first four letters represent the site, followed by the sampling year and month. For example, "AUCH_2022_apr" corresponds to a sample collected at Auchencorth Moss in April 2022.<br><b>"Dataset_no-domestic-mammals.csv" </b>: Same dataset as <b>"Dataset.csv"</b> described above, minus the domestic mammals: rabbit, sheep, horse, donkey, cat, dog, goat and pig.<br><b>"CorineMetal.csv"</b>: this dataset contains CORINE Land Cover 2018 surface data (Cole et al., 2021, add reference) and heavy metal pollutant concentrations (© Crown 2025) used to perform the land cover – pollution PCA. Land cover categories were aggregated into five main types based on the CORINE land cover classification: Artificial surfaces (codes: 111, 112, 121–124, 131–133, 141, 142), Agricultural areas (codes: 211, 222, 231, 242, 243), Forest and semi-natural areas (codes: 311–313, 321–324, 331, 333), Wetlands (codes: 411, 412, 421, 423), Water bodies (codes: 511, 512, 522, 523). Pollutant data for 2022 were obtained from the DEFRA UK AIR Information Resource (https://uk-air.defra.gov.uk/data/) (© Crown 2025). These include the average concentrations (ng/m³) of metals primarily emitted from fossil fuel combustion and industrial processes: arsenic (As), cadmium (Cd), cobalt (Co), copper (Cu), iron (Fe), manganese (Mn), nickel (Ni), lead (Pb), selenium (Se), vanadium (V), and zinc (Zn). The dataset provides site-averaged values for each metal. The "Environment_type" column specifies the environment type of UK Heavy Metal air quality monitoring sites, as defined on the UK AIR website (https://uk-air.defra.gov.uk/networks/site-types).<br><b>"hfp2013_merisINT.tif"</b> : a raster file used to extract average values from the 2013 Human Footprint maps (Williams et al., 2020).<br><b>"BetaComp_output_nodomestic.csv"</b> : a dataset containing beta diversity component outputs (total beta diversity "BDTotal", turnover, and nestedness) calculated for each site and urban vs. rural environments using the beta.div.comp function (coeff = "BJ", Baselga Jaccard-based) from the adespatial R package (Dray et al., 2024). This dataset is used to generate <b>Figure S3</b>. Note that it excludes domestic mammal species.<br><b>"Site_coordinates_info.csv"</b> : a table providing site details, including: Full site name ("Site"), Site code ("SITE_ID"), UK-AIR Station ID ("UK-AIR ID"), Geographic coordinates ("Latitude", "Longitude"), Label position adjustments for visualization ("nudge_x", "nudge_y"), Environment type (Urban vs. Rural) based on the UK AIR Information Resource.<b>R SCRIPTS TO RUN THE ANALYSES</b><b>"Analyses.R"</b> : this script performs the alpha and beta diversity analyses. Note that plots for different taxonomic groups were generated separately and later manually combined into the final figures.<br><b>"Make_The_Map.R"</b> : this script generates the map used in the top panel of Figure 1.<br>