DOI: 10.5281/zenodo.17506015
title: Repository containing field data, Excel files, and R scripts for the analyses in "Thicket Formation and Light Limitation Drive Patch-Scale Vegetation Transitions in a Semi-Arid Savanna."

description: This repository contains field-collected vegetation and environmental data, Excel spreadsheets, R scripts, and output figures used in the analyses for the manuscript “Thicket Formation and Light Limitation Drive Patch-Scale Vegetation Transitions in a Semi-Arid Savanna.” The dataset includes woody and herbaceous species composition, canopy cover, light transmittance, and leaf area index (LAI) data collected from 51 sites along a woody encroachment gradient at Endwell Farm, Eastern Cape Province, South Africa. Historical aerial imagery from 1949–2021 was used to assess woody cover changes, complemented by cluster analysis, indicator species analysis, and quantile regression. The repository also includes README files describing data structure and instructions for running the R scripts.

Each dataset includes a dedicated README Word document explaining variable definitions and data structure:




File
Description




Readme_CoverLightTrees.docx
Describes columns and variables in CoverLightTrees.xlsx.


Readme_Env.docx
Describes variables in Env.xlsx.


Readme_indicator_values(all).docx
Explains outputs from the IndVal (Indicator Species) analysis.


Readme_Matrices.docx
Describes structure and variable coding of species abundance matrices (MatrixHerb, MatrixTree, and MatrixTreeHerb).




 

R Scripts (used to generate figures in the manuscript)

Each R file corresponds to a figure or analysis step described in the paper:




R Script
Description




Figure_3_woody_cover_changes.R
Analysis and visualization of woody cover changes over time (1949–2021).


Figure_4_Table1_indiciespecies.R
Indicator species analysis (IndVal) and cluster characterization.


Figure_5_herb_sankey_and_tree_sankey.R
Sankey diagrams visualizing connections between herbaceous and tree communities across encroachment stages (does not require Excel input; uses IndVal output).


Figure_6_Herbaceous_basal_cover.R
Quantile regression and visualization of basal cover responses to woody cover and transmittance.




 

Excel Spreadsheets (raw and processed data)




File
Description




CoverLightTrees.csv
Field measurements of tree cover, light transmittance, and leaf area index (LAI).


Env.csv
Environmental variables (e.g., light transmittance, LAI, site metadata).


MatrixHerb.csv
Species abundance matrix for herbaceous vegetation across 51 sites.


MatrixTree.csv
Species abundance matrix for woody species across 51 sites.


MatrixTreeHerb.csv
Combined abundance matrix of tree and herbaceous species used for cluster analysis.


Tree_cover_changes.csv
Long-term changes in woody cover derived from aerial imagery (1949–2021).




 

 

 

 

 

 

 
description: This study was conducted on Endwell Farm in the Eastern Cape Province of South Africa, a semi-arid landscape supporting both livestock farming and wildlife conservation. The area lies within a mosaic of grassland, savanna, and subtropical thicket vegetation, underlain by shallow, stony Glenrosa and Mispah soils derived from shale and sandstone, and experiences a warm, wet summer and cool, dry winter climate with a mean annual rainfall of 722 mm. We examined woody encroachment and its effects on light transmittance and herbaceous composition across 51 sites representing a gradient from open savanna to dense thicket. Historical aerial photographs (1949–2021) were analysed to quantify long-term changes in woody cover, while field sampling between 2019 and 2021 captured contemporary tree, shrub, and herbaceous species composition, canopy structure, and understory light availability. Tree cover and composition were measured within 15 × 6 m plots using canopy area estimates derived from individual crown measurements, and hemispherical photographs were used to quantify leaf area index (LAI) and light transmittance. Herbaceous cover and composition were recorded using subplot-based aerial cover scores and pin-drop basal cover estimates. To identify vegetation thresholds and community shifts along the encroachment gradient, we combined cluster and indicator species analyses with piecewise quantile regression. These analyses revealed how increasing woody cover alters light penetration, species composition, and herbaceous cover, providing insight into the patch-scale mechanisms driving savanna–thicket transitions in semi-arid systems.