DOI: 10.5281/zenodo.17344464
title: Data from: Sampling bias obscures biodiversity patterns, reveals data gaps in priority conservation areas: a call for improved documentation

description: Description of the data and file structure

The “Dataset_Taxa.csv” file is a manually curated dataset used for spatial mapping of observed amphibian and squamate reptile diversity in the Philippines. Occurrence records were downloaded from the Global Biodiversity Information Facility (GBIF) and subsequently verified for geospatial accuracy. The “PA_dataset_1” and “KBA_dataset_2” files were used to model observed species diversity and sampling effort as a function of several predictor variables, including Pleistocene Aggregate Island Complexes (PAICs), Occurrence_Count, Occurrence_Density, Unique_Species, Total Area (km²), and Topographic Relief (m).

Files and variables

1. Dataset_Taxa

This dataset is provided as a single comma-separated values (CSV) file containing 4 columns and 76,453 rows. The first row lists the column headers, followed by subsequent rows containing species occurrence data.

Columns:





Longitude (numeric) – Longitude coordinate of the occurrence point.




Latitude (numeric) – Latitude coordinate of the occurrence point.




Taxa (text) – Indicates the higher taxonomic group (Amphibian, Lizard, or Snake) associated with each occurrence point. Species names are redacted for our follow-up analyses.




BasisOfRecord (text) – Indicates the source type of each record following GBIF classifications (e.g., Preserved Specimen, Material Citation, Human Observation). The same categories were applied to manually added records.



2. PA_Dataset and KBA_Dataset

These datasets are also formatted as CSV files.





PA_Dataset contains 7 columns and 206 rows (one per Protected Area).




KBA_Dataset contains 7 columns and 110 rows (one per Key Biodiversity Area).



The first row lists the column headers, followed by rows containing values for each conserved area.

Columns:





PA_NAME / KBA_NAME (text) – The name of the Protected Area (PA) or Key Biodiversity Area (KBA), collectively referred to as Conserved Areas (CAs) in the manuscript.




PAIC (text) – The Pleistocene Aggregate Island Complex (PAIC) in which the CA is located, representing a major biogeographic subdivision in the Philippines that explains vertebrate distribution patterns across the archipelago.




Occurrence_Count (integer) – The total number of occurrence records located within the CA polygon.




Occurrence_Density (numeric) – The number of occurrence records per unit area (records/km²) of the CA.




Unique_Species (integer) – The number of distinct nominal and candidate species recorded within each CA polygon.




Area_km2 (numeric) – The total area (in km²) of each CA polygon, calculated using the expanse() function from the terra package in R.




Topo_Relief (numeric) – The difference between the maximum and minimum elevation within each CA polygon.



Code/software

All data processing, spatial analyses, and figure generation were conducted in R Statistical Software (Version 4.2.2). The full analysis pipeline, including scripts used to generate the results presented in the associated manuscript, is provided in the file “11062025_RMarkdown.Rmd.”