Data from: The effects of land-use dynamics on avian phylogenetic diversity across island ecosystems
Data files
Jul 14, 2026 version files 1.10 MB
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Datasets___Phylo_tree.zip
1.08 MB
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R_scripts.zip
5.32 KB
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README.md
5.38 KB
Abstract
To test whether forest extent and recent forest‐cover change are associated with avian phylogenetic diversity and community-level evolutionary value across islands. This study took place on seven islands spanning Borneo and Wallacea in the Malay Archipelago. The taxonomic focus was terrestrial birds. We sampled 1,410 sites (2010–2022). We calculated phylogenetic diversity (PD), mean phylogenetic distance (MPD), mean nearest taxon distance (MNTD), and their standardised effect sizes (SES), as well as community-level EDGE (Evolutionarily Distinct and Globally Endangered). Responses to (i) average forest proportion (250-m radius) and (ii) recent forest-cover change were analysed with spatial linear mixed-effects. Observed PD showed a negative visual trend with increasing forest proportion, whereas SES PD declined. MPD showed only a weak positive visual trend with forest proportion, whereas SES MPD showed no clear response. Although observed MNTD appeared to increase in the binned visual summaries, both observed MNTD and SES MNTD showed significant negative associations with forest cover in the spatial models, indicating stronger nearest-neighbour phylogenetic clustering in more forested sites. Effects of recent forest loss (2010–2022) on SES metrics were generally weak and inconsistent. Although PD also declined with decreasing rates of forest change, community-level EDGE was higher where forest cover was greater, indicating higher average evolutionary distinctiveness and extinction risk. In this archipelagic system, forest amount is a key correlate of phylogenetic structure and the retention of evolutionarily distinctive, high-risk lineages. By contrast, recent forest-cover change showed weaker and more context-dependent associations. Conserving intact forests remains crucial for safeguarding the evolutionary legacy of island bird communities.
This repository contains the data and R scripts required to reproduce the analyses presented in the manuscript. The repository is organised into two folders:
R_scripts.zip
Datasets___Phylo_tree.zip
R scripts
The R scripts in this repository reproduce:
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Calculation of phylogenetic diversity metrics (PD, MPD, MNTD)
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Calculation of standard effect size (SES)
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Calculation of community-level EDGE metrics
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All linear mixed-effects models
Please run the scripts in the order indicated in the script headers.
Dataset01_binary_presence_absence.xlsx
This Excel workbook contains two sheets. Sheet 1 contains the binary bird community matrix used in this study. This community matrix is a harmonised analytical compilation derived from the sources listed below and is not a reproduction of any source dataset in its original form. The original source datasets differed in structure and content, including abundance-based records, common-name usage, and site coverage. For the present study, these data were standardised to scientific names and converted to binary presence–absence format (presence = 1, absence = 0), and additional sampling points from more recent surveys were incorporated. Raw source data remain available from the original repositories. Sheet 2 contains the metadata, including descriptions of all columns in Sheet 1. Sources used in compiling this dataset:
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https://catalogue.ceh.ac.uk/documents/87f36a61-ca79-40c6-b781-8936ead162cc
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This file contains:
Rows = sampling sites
Columns = bird species (presence = 1, absence = 0).This dataset is used to compute all phylogenetic diversity metrics (PD, MPD, MNTD and SES metrics). Before running the scripts, this file must be converted to CSV format.
Dataset02_Species_list.xlsx
This Excel workbook contains two sheets. Sheet 1 contains the species-level metadata used to calculate community-level conservation and phylogenetic metrics. The species list in this file was compiled from the community matrix in Dataset01, but the remaining fields were generated by the author for the present study, including species-level analytical and conservation-related variables. Sheet 2 contains the metadata, including descriptions of all columns in Sheet 1. It includes:
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Scientific species names (as used in the community matrix and phylogenetic tree)
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Harmonised taxonomy
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IUCN Red List status
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Population trend categories
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Information used to derive species-level EDGE scores
This dataset is used to compute community-level mean IUCN status, mean population trend, and community EDGE metrics.
Before running the scripts, this file must be converted to CSV format.
Dataset03_EDGE_PD_forest_matrices.xlsx
This Excel workbook contains two sheets. Sheet 1 contains the main site-level analytical dataset used for all statistical analyses and figures in the manuscript. The columnsSite,x,y, andIslandrepresent the original sampling-point information used in the study. All other columns were generated by the author for the present study, including phylogenetic metrics, community-level conservation metrics, forest-cover variables, and forest-change variables. Sheet 2 contains the metadata, including descriptions of all columns in Sheet 1. It includes:
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Site identifiers and island identity
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Forest-cover proportion (250 m radius)
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Forest-cover change (annual slope, 2010–2022)
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Community-level phylogenetic metrics:
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Phylogenetic diversity (PD)
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Mean pairwise distance (MPD)
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Mean nearest taxon distance (MNTD)
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Standardised effect sizes (SES-PD, SES-MPD, SES-MNTD)
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Community-level conservation metrics:
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Mean EDGE score
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Mean IUCN status
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Mean population trend
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Species richness
This dataset represents the final analytical dataset used in all spatial linear mixed-effects models and figures in the main text.
Before running the scripts, this file must be converted to CSV format.
Bird_phylogeny_422.newick
This file contains the phylogenetic tree used to compute all phylogenetic diversity metrics.
prepared_phylo_data.RData
This R workspace file contains pre-processed objects used for the phylogenetic diversity and SES analyses, including:
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The filtered and harmonised community matrix (presence–absence)
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The filtered phylogenetic tree with matched species
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The filtered species list
This file is loaded by the SES analysis scripts to avoid repeating computationally intensive data preparation steps (e.g. matching species names between the community matrix and the phylogenetic tree). It is generated from the original data files provided in this repository.
