DOI: 10.5281/zenodo.17573406
title: Data and code for "Beyond 'few winners, many losers': land use drives contrasting impacts across the tree of life" — Pinho et al submitted

description: ### Data and R scripts for “Beyond ‘few winners, many losers’: land use drives contrasting impacts across the tree of life” — Pinho et al. (submitted) ###

Description:

This repository contains the data and R scripts used in the analyses for the manuscript cited above. The work is based on data produced by the Synthesis Core Project of the Biodiversity Exploratories program (DFG Priority Program 1374).

The original synthesis datasets were assembled as described at:https://github.com/biodiversity-exploratories-synthesis/Synthesis_dataset_diversity_grassland  https://github.com/biodiversity-exploratories-synthesis/Synthesis_dataset_diversity_forest

These grassland and forest synthesis datasets have been extended in this study through inclusion of recent data, removal of genus-level data (except for Bacteria and Archaea), and additional refinements to group names and trophic group classifications (see '.../Rscripts/data_assembly.R').

The individual datasets used to assemble the synthesis dataset are available via the Biodiversity Exploratories Information System (DOI: 10.17616/R32P9Q). Dataset identifiers are provided in Extended Data Table 1, and corresponding links are listed in the References section of the manuscript.

For peer review, the data assembled with the scripts indicated above are included here to allow reproduction of all analyses reported in the study.

Repository Structure:

.../Data  Contains all data used for niche modelling and output analyses:

- 'Abund_Func.csv' — Abundance of each taxonomic unit (species, genus, or OTU) per sample plot and year, with respective trophic assignments. - 'LUI_default_STD_2023-12-29.txt' — Standardized land-use intensity (LUI) index for grassland plots.  - 'LUI_default_component_2023-12-29.txt' — Unstandardized individual components of the LUI index for grassland plots.  - 'ForMIX.csv' — Land-use intensity metrics (individual components and overall index) for forest plots.  - 'LUI_ForMIX_avg.csv' — Land-use intensity in grassland and forest plots averaged across years (2008–2023).  

.../Rscripts  Contains R scripts used in the analyses and figures presented in the manuscript:

- 'data_assembly.R' — Updates synthesis datasets (requires original individual datasets; the resulting dataset 'Abund_Func.csv' is available in '.../Data' for subsequent analyses).  - 'niche_model_WinnerLoser.R' — Runs niche modelling to estimate species responses to land-use and classify species as winners, losers, mid-specialists, or neutral (this should run first before running the other scripts below).- 'output_analysis.R' — Calculates diversity metrics and performs trait PCA.  - 'diversity_LUI_models&plots.R' — Models and plots for taxon diversity–LUI relationships (Fig. 2).  - 'niche_trait_models&plots.R' — Trait-based analyses (Fig. 3; Extended Data Figs. 7–8).  - 'Thresholds_models&plots.R' — Threshold analyses (Fig. 4; Extended Data Table 2).  - 'plots_WinnerLoser.R' — Additional plots (e.g., Fig. 1 and extended figures).  

.../Functions  Contains custom R functions supporting the main scripts:

- 'functions_diversity_LUI.R' — Functions for diversity–LUI analyses (used in 'diversity_LUI_models&plots.R').  - 'functions_thresholds.R' — Functions for threshold analyses (used in 'Thresholds_models&plots.R').  - 'BEplotZeros.R' — Function to harmonize plot names across datasets.  

All analyses were run in R version 4.5.1.  Required packages are listed within each R script in the library() calls.