Data and code from: Dispersal-limited birds at high risk from cattle farming deforestation in tropical forests
Data files
Sep 25, 2026 version files 494.75 MB
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Files_to_run_scripts.zip
494.72 MB
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README.md
5.62 KB
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Scripts.zip
21.50 KB
Abstract
We explore the question: how do farming activities affect functional diversity and species traits across different spatial scales in tropical forests? This dataset uses outputs from multispecies occupancy models from Socolar and Mills et al. (2025) to estimate avian communities across 13 different biogeographic units at near-national scales in Colombia. We quantify changes in functional diversity resulting from forest-to-pasture conversion and identify the most impacted functional dimension. Includes computing occupancy community-weighted means, regression modelling of occupancy change across functional dimensions, and cumulative changes in functional metrics at increasing scales. Results indicate that functional diversity metrics are only slightly affected across ecoregions and largely reflect the national scale of loss, driven by a moderate reduction in Functional Richness across scales. particularly affects birds with functional traits related to low dispersal capability.
Dataset DOI: 10.5061/dryad.rbnzs7hqz
Description of the data and file structure
Analyses are based on estimated avian communities in forest and pasture habitats across ecoregions. These communities were estimated using multispecies occupancy models from Socolar and Mills et al. (2025). Functional analyses use estimated communities and functional traits from Tobias et a.l (2022). The dataset includes scripts to compute 4 functional diversity metrics and their change from forest to pasture. Including the process to compute the best functional space and functional dimensions. Additionally, it includes modelling of occupancy changes by functional traits and functional dimensions using phylogenetic generalised linear mixed models.
REFS:
Socolar, J. B., Mills, S. C., et al. (2025). Tropical biodiversity loss from land-use change is severely underestimated by local-scale assessments. Nature Ecology & Evolution, 1–13. https://doi.org/10.1038/s41559-025-02779-4
Tobias, J. A., et al.(2022). AVONET: Morphological, ecological and geographical data for all birds. Ecology Letters, 25(3), 581–597. https://doi.org/10.1111/ele.13898
Files and variables
File: Files_to_run_scripts.zip
Description: Zip file with all necessary objects to run scripts; all objects are RDS R software files
birdtree.rds: Phylogenetic tree trimmed to contain only species included in the research. Phylogeny trimming performed using the Rphytools package (code not shown)
cell_WWF_lookup.rds: Lookup table to match grid ID names to spatial region names. A 2x2 km2 grid was overlaid on top of WWF ecoregions of the world polygon. This file matches each grid to its ecoregion name. (code not shown)
CO_func_space.rds: Curated functional space for species list. The functional space was created using a Principal coordinates analysis as described in the paper main text.
CO_traits.rds: Copy of raw morphological bird traits for the species list. The file was modified to include only the sheet with BirdTree taxonomic nomenclature and filtered to the project species list. Original file is the AVONET dataset from Tobias et al. (2022). Due to licensing considerations the original file is not included here but the original file is available at https://figshare.com/s/b990722d72a26b5bfead
comms_forest.rds: Estimated avian communities (presence/absence) in forest habitat across 13 ecoregions and national scale. This object is created in script 01 but included to avoid re-running a time-consuming task.
comms_pasture.rds: Estimated avian communities (presence/absence) in pasture habitat across 13 ecoregions and national scale. This object is created in script 01 but included to avoid re-running a time-consuming task.
names_lookup_fd.rds: Lookup table to match species names under different taxonomic treatments, includes English names, IUCN redlist categories, and BirdLife forest dependency. Useful to match birdtree phylogenies to AVONET names.
occs. rds: Summarised estimated occupancy probabilities of bird species across ecoregions and habitats. Created in script 04 but included to avoid re-running a time-consuming task.
pd_acc_for.rds: Predicted avian communities at increasing scales (join ecoregions) in forest habitat. This object is created in script 02 but included to avoid re-running a time-consuming task.
pd_acc_pas.rds: Predicted avian communities at increasing scales (join ecoregions) in pasture habitat. This object is created in script 02 but included to avoid re-running a time-consuming task.
species_names_matching.rds: Lookup table to match species names under different taxonomic treatments. Useful to match birdtree phylogenies to AVONET names.
summ_regions.rds: Summary of species presence/absence in habitats and regions combinations. This object is created in script 01 but included to avoid re-running a time-consuming task
Code/software
File: Scripts.zip
Description: Zip file with all scripts, all objects, and R software files
1_FD_metrics.R: Compute functional diversity metrics in forest and pasture across ecoregions and national scale
2_FD_accumulation.R: Compute functional diversity metrics in forest and pasture at increasing spatial scales (joining ecoregions)
3_FD_plots.R: Code to replicate all figures and functional diversity change comparisons
4_CWM_funspace_regression.R: Code to compute occupancy community weighted means of traits, functional space changes, and regression models of occupancy by functional dimensions.
5_SES_of_diff.R: Computes the standardised effect size of the differences in functional traits in metrics between habitats
Access information
Other publicly accessible locations of the data:
- https://github.com/gapz01/PhD_year_3 (scripts only)
Data was derived from the following sources:
- Socolar, J. B., Mills, S. C., et al. (2025). Tropical biodiversity loss from land-use change is severely underestimated by local-scale assessments. Nature Ecology & Evolution, 1–13. https://doi.org/10.1038/s41559-025-02779-4
- Tobias, J. A., et al.(2022). AVONET: Morphological, ecological and geographical data for all birds. Ecology Letters, 25(3), 581–597. https://doi.org/10.1111/ele.13898