DOI: 10.5061/dryad.6hdr7srcx
title: Data from: Strong variation in land-use change impacts on tropical avian phylogenetic diversity between ecoregions highlights the need to sample large spatial scales

description: Forest conversion for agriculture is a major cause of tropical
 biodiversity loss. Quantifying the biodiversity impacts of forest loss is
 challenging because the severity of outcomes is influenced by spatial
 scale, with the higher rate of species turnover in forests than in
 farmland increasing the severity of losses at larger relative to smaller
 scales. Conservation efforts increasingly prioritise phylogenetic
 diversity to preserve unique evolutionary history under global change, but
 how deforestation-driven changes in phylogenetic diversity vary across
 large spatial scales remains a key question. We compiled a large field
 database from across 13 biogeographically diverse regions affected by
 deforestation for cattle farming, covering most of Colombia, a megadiverse
 tropical country. We use occupancy models to estimate bird communities for
 1,614 species across 13 ecoregions and nationally in both forest and
 pasture habitats. This dataset includes base information and scripts to
 quantify six different phylogenetic diversity metrics in forest and
 pasture habitats. and the process to compare changes between habitats and
 the differences from regional to national scales. It also includes data to
 estimate and plot changes in phylogenetic trees for bird communities
 across ecoregions and to replicate the study area map. We found that
 although single regional-scale loss of phylogenetic diversity was, on
 averag,e comparable to broader scales, there was high variability between
 regional units. Such underestimation of national-scale impacts highlights
 the importance of sampling across multiple regions. 
description: # Data from: Strong variation in land-use change impacts on tropical avian
 phylogenetic diversity between ecoregions highlights the need to sample
 large spatial scales Dataset DOI:
 [10.5061/dryad.6hdr7srcx](10.5061/dryad.6hdr7srcx) ## Description of the
 data and file structure All data and scripts are provided in a zip folder.
 Dataset includes field detections of birds, model outputs and spatial data
 from Socolar and Mills et al (2025), but adapted for the aims of this
 research (i.e not identical to their datasets) Scripts follow the
 procedures to take occupancy probability of each bird species in forest
 and pasture habitats and obtain avian communities across ecoregions and
 national scale in Colombia, then use them along with phylogenetic tress to
 six compute metrics of phylogenetic diversity at each ecoregions and then
 by combining ecoregions to reach a national scale. finally it assesed
 misestimation of phylogenetic diversity change from ecoregion compared to
 national levels. ### Files and variables #### File:
 Files_to_run_scripts.zip **Description:** Zip file containing all datasets
 * Birds_rds_link.txt: link to Zenodo storage were raw field data is stored
 ([https://doi.org/10.5281/zenodo.15318727](https://doi.org/10.5281/zenodo.15318727)) - Birdtree_COL_taxonomy.csv: curated list of species and taxonomic categories. Columns: *TipLabel*: Bird species names following birdtree taxonomy, *Clade*: species clade classification, *Family*: species taxonomic family classification, *Order*: species taxonomic order classification, *OscSubOsc*: species subclade classification. * cell_WWF_lookup.rds: R software object, lookup table to match id cells to ecoregion names. Columns: *label_id*: consecutive numeric identifier for ecoregions, *id_cell*: numeric identifier for individual cells within ecoregions, *label*: ecoregion names. - CO_birds_Hacket_ALL.rds: R software object,10000 Phylogenetic trees of all Colombian birds included in the research * ED_values. rds: R software object containing average values of evolutionary distinctiveness and rarity computed across 10000 phylogenetic trees for each species. Columns: *species*: Bird species names following birdtree taxonomy, *ED_mean*: average evolutionary distinctiveness, *EDR_mean*: average evolutionary distinctiveness rarity values, *EDGE_median*: evolutionary distinct and globally endangered median values, *RL.cat*: IUCN redlist category. - lpo_and_coefs.rds: R software object, linear predictors and coeficients (400 draws) from model in Socolar and Mills et al., (2025), modified to this research aims. Variables: *species*: Bird species names following birdtree taxonomy, *lpo_forest*: linear predictor for forest habitat, *lpo_pasture*: linear predictor for pasture habitat. * regions_sequences.rds: R software object, contains random sequences of agregating regions (for reproducibility) - species_names_matching.rds: R software object, lookup table to match species names across different taxonomic treatments and old/new names. Columns: *model*: Bird species names following ebird taxonomy, *phylogeny*: Bird species names following birdtree taxonomy * WWF_lookup.rds:  R software object, lookup table to match ecoregion names (spatial). Columns: *label*: ecoregions full names, *label_id*: consecutive numeric identifier for ecoregions. - WWF_terrestrial_ecoregions.rds: R software objetc, shapefiles for sampled ecoregions * xy_lookup.rds:  R software object, lookup table to match id cells to model id. Columns: *id_cell*: numeric identifier for individual cells within ecoregions, *id_x*:  model cell location in x, *id_y*: model cell location in y. ## Code/software All analyses were conducted in R studio and R version 4.4.1 #### File: Scripts.zip **Description:** Zip file containing all R software scripts 1_compute_predicted_occupancy.R: Spatially explicit predict occupancy probability in forest and pasture at 2x2 km2 cells across study area. 2_Phylogeny_plots.R: Plot phylogenies across ecoregions 3_PD_metrics.R: compute phylogenetic diversity metrics in habitats across ecoregions 4_PD_Accumulation.R: compute cummulative phylogenetic diversity metrics in habitats at increasing scale 5_study_area.R: replicate study area figures and sampling points  ## Access information Other publicly accessible locations of the data: * [https://github.com/gapz01/PhD_year_two](https://github.com/gapz01/PhD_year_two) (only scripts) Data was derived from the following sources: * [https://zenodo.org/records/15318728](https://zenodo.org/records/15318728) (Creative Commons Attribution 4.0 International)