Data and code from: Drivers of individual plant species contributions to β-diversity are scale-dependent
Data files
May 15, 2026 version files 2.91 MB
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1_trait_data_fractal.R
13.27 KB
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2_scbd_calculation_fractal.R
6.95 KB
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3_csMSPD_fractal.R
4.60 KB
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4_UK_site_GBIF_downloads.R
5.94 KB
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5_UK_sites_trait_data.R
9.86 KB
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6_UK_landscape_scale_SCBD_calculations.R
4.75 KB
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7_UK_landscape_scale_csMSPD.R
13.79 KB
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8_Modelling___figures.R
20.05 KB
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archbold21.xlsx
17.68 KB
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boothby22.xlsx
21.61 KB
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boothby23.csv
36.27 KB
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budworth21.xlsx
11.43 KB
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determinants_of_SCBD_src.r
1.37 KB
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enez21.xlsx
12.01 KB
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knepp22.xlsx
33.30 KB
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knepp23.xlsx
61.37 KB
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ordu21.xlsx
11.38 KB
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processed_fractal.csv
1.85 MB
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README.md
13.45 KB
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reinischkogel21.xlsx
14.30 KB
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rhf_17.csv
42.75 KB
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rhf_18.csv
189.88 KB
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rhf_19.csv
214.54 KB
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rhf_20.csv
124.90 KB
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rhf_21.csv
60.39 KB
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silwood21.xlsx
9.80 KB
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silwood22.xlsx
36.52 KB
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silwood23.csv
18.52 KB
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specieslist.csv
54.92 KB
Abstract
Species introductions and local extinctions of native species are driving biotic homogenisation in plant communities by reducing β-diversity. Individual species vary in their contributions to β-diversity (Species Contribution to β-Diversity; species-β), yet our understanding of how species characteristics shape these contributions remains limited. Additionally, although the ecological processes influencing β-diversity are known to vary with spatial scale, we lack understanding of how species contributions, or their underlying determinants, change across scales. Here, we modelled how plant functional traits, phylogenetic relatedness, and introduction status influence their contributions to β-diversity using plant community data from 429 plots surveyed from 2017 to 2023 across three nested spatial scales (up to 1 km²) in nine sites spanning four countries. We extended the analysis to broader spatial extents (100 km² to the entire UK) using GBIF occurrence data. We found that functional traits associated with competitive ability influenced species-β, but the direction and strength of their effects varied with scale. Likewise, increasing phylogenetic distance increased species-β at small scales but reduced it at larger ones. After accounting for traits and phylogeny, introduced species consistently contributed less to β-diversity than native species—especially at broader spatial extents. These results demonstrate that species’ ecological and evolutionary characteristics shape their contributions to β-diversity, but that these effects are scale-dependent. Our findings highlight the importance of scale-explicit approaches in understanding both the determinants of β-diversity and how we can combat its loss to mitigate biotic homogenisation.
Dataset DOI: 10.5061/dryad.xpnvx0kwm
Description of the data and file structure
Data and code for "Learmonth et al. (2026). Determinants of plant species contributions to β-diversity vary across spatial scales. Oikos."
Data was collected as part of the Ecological Fractal Network according to the protocol described in Simpson & Pearse, 2021 Oikos; Pates et al., 2025, Ecological Solutions & Evidence, and Learmonth et al., 2026 Oikos.
Files and variables
File: archbold21.xlsx
Description: Percentage cover quadrat data for fractal sampling in Archbold, Florida, USA, 2021.
Variables
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Plot: sample site named according to Ecological Fractal Network convention
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Species: plant species Latin name
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Quadrant: portion of the quadrat sampled (1-4)
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Cover: percentage cover in that quadrat portion
Unavailable information (cells containing NA) for fractal data indicate missing values from data transcription.
File: boothby22.xlsx
Description: Percentage cover quadrat data for fractal sampling in Boothby, UK, 2022.
Variables
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Year: year of sampling (2022)
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Plot: sample site named according to Ecological Fractal Network convention
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Quadrant: portion of quadrat sampled (1-4)
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Species: plant species Latin name
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Cover: percentage cover in that quadrant
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Site: site name (Boothby)
Unavailable information (cells containing NA) for fractal data indicate missing values from data transcription.
File: boothby23.csv
Description: Percentage cover quadrat data for fractal sampling in Boothby, UK, 2023.
Variables
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Year: year of sampling (2023)
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Plot: sample site named according to Ecological Fractal Network convention
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Quadrant: portion of quadrat sampled (1-4)
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Species: plant species Latin name
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Cover: percentage cover in that quadrant
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Site: site name (Boothby)
Unavailable information (cells containing NA) for fractal data indicate missing values from data transcription.
File: budworth21.xlsx
Description: Percentage cover quadrat data for fractal sampling in Budworth, UK, 2021.
Variables
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Date: date of sampling
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Site: site name (Boothby)
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Plot: sample site named according to Ecological Fractal Network convention
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Quadrant: portion of quadrat sampled (1-4)
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Species: plant species Latin name
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Cover: percentage cover in that quadrant
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Year: year of sampling (2021)
Unavailable information (cells containing NA) for fractal data indicate missing values from data transcription.
File: enez21.xlsx
Description: Percentage cover quadrat data for fractal sampling in Enez Forest, Türkiye, 2021.
Variables
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Date: date of sampling
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Site: site name (Enez forest)
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Plot: sample site named according to Ecological Fractal Network convention
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Quadrant: portion of quadrat sampled (1-4)
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Species: plant species Latin name
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Cover: percentage cover in that quadrant
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Year: year of sampling (2021)
Unavailable information (cells containing NA) for fractal data indicate missing values from data transcription.
File: knepp22.xlsx
Description: Percentage cover quadrat data for fractal sampling in Knepp Estate, UK, 2022.
Variables
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Year: year of sampling (2022)
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Block: block of repeated fractal design, organised into different zones of Knepp Estate, see Pates et al., 2025 Ecological Solutions and Evidence for full details
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Plot: sample site within each block, named according to Ecological Fractal Network convention
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Quadrant: portion of quadrat sampled (1-4)
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Species: plant species Latin name
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Cover: percentage cover in that quadrant
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Site: site name (Knepp)
Unavailable information (cells containing NA) for fractal data indicate missing values from data transcription.
File: knepp23.xlsx
Description: Percentage cover quadrat data for fractal sampling in Knepp Estate, UK, 2023.
Variables
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Year: year of sampling (2022)
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Block: block of repeated fractal design, organised into different zones of Knepp Estate, see Pates et al., 2025 Ecological Solutions and Evidence for full details
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Plot: sample site within each block, named according to Ecological Fractal Network convention
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Quadrant: portion of quadrat sampled (1-4)
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Species: plant species Latin name
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Cover: percentage cover in that quadrant
-
Site: site name (Knepp)
Unavailable information (cells containing NA) for fractal data indicate missing values from data transcription.
File: ordu21.xlsx
Description: Percentage cover quadrat data for fractal sampling in Ordu, Türkiye, 2021.
Variables
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Date: date of sampling
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Site: site name (Ordu_urban)
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Plot: sample site named according to Ecological Fractal Network convention
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Quadrant: portion of quadrat sampled (1-4)
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Species: plant species Latin name
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Cover: percentage cover in that quadrant
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Year: year of sampling (2021)
Unavailable information (cells containing NA) for fractal data indicate missing values from data transcription.
File: reinischkogel21.xlsx
Description: Percentage cover quadrat data for fractal sampling in Reinischkogel, Austria, 2021.
Variables
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Date: date of sampling
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Site: site name (Reinischkogel)
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Block: here used as proxy for quadrant
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Plot: sample site named according to Ecological Fractal Network convention
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Species: plant species Latin name
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Cover: percentage cover in that block/plot combination
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Year: year of sampling (2021)
Unavailable information (cells containing NA) for fractal data indicate missing values from data transcription.
File: rhf_17.csv
Description: Percentage cover quadrat data for fractal sampling in Right Hand Fork, Utah, USA, 2017.
Variables
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Date: date of sampling
-
Plot: sample site named according to Ecological Fractal Network convention
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Quadrant: portion of quadrat sampled (1-4)
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Species: plant species Latin name
-
Cover: percentage cover in that quadrant
Unavailable information (cells containing NA) for fractal data indicate missing values from data transcription.
File: rhf_18.csv
Description: Percentage cover quadrat data for fractal sampling in Right Hand Fork, Utah, USA, 2018.
Variables
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Date: date of sampling
-
Plot: sample site named according to Ecological Fractal Network convention
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Quadrant: portion of quadrat sampled (1-4)
-
Species: plant species Latin name
-
Cover: percentage cover in that quadrant
Unavailable information (cells containing NA) for fractal data indicate missing values from data transcription.
File: rhf_19.csv
Description: Percentage cover quadrat data for fractal sampling in Right Hand Fork, Utah, USA, 2019.
Variables
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Date: date of sampling
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Plot: sample site named according to Ecological Fractal Network convention
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Quadrant: portion of quadrat sampled (1-4)
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Species: plant species Latin name
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Cover: percentage cover in that quadrant
-
Notes: any additional information recorded
Unavailable information (cells containing NA) for fractal data indicate missing values from data transcription.
File: silwood22.xlsx
Description: Percentage cover quadrat data for fractal sampling in Silwood Park, UK, 2022.
Variables
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Date: date of sampling
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Site: Silwood Park
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Plot: sample site named according to Ecological Fractal Network convention
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Quadrant: portion of quadrat sampled (1-4)
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Species: plant species Latin name
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Cover: percentage cover in that quadrant
-
Year: year of sampling (2022)
Unavailable information (cells containing NA) for fractal data indicate missing values from data transcription.
File: rhf_20.csv
Description: Percentage cover quadrat data for fractal sampling in Right Hand Fork, Utah, USA, 2020.
Variables
-
Date: date of sampling
-
Plot: sample site named according to Ecological Fractal Network convention
-
Quadrant: portion of quadrat sampled (1-4)
-
Species: plant species Latin name
-
Cover: percentage cover in that quadrant
-
Notes: any additional information recorded
Unavailable information (cells containing NA) for fractal data indicate missing values from data transcription.
File: silwood21.xlsx
Description: Percentage cover quadrat data for fractal sampling in Silwood Park, UK, 2021,
Variables
-
Date: date of sampling
-
Plot: sample site named according to Ecological Fractal Network convention
-
Quadrant: portion of quadrat sampled (1-4)
-
Species: plant species Latin name
-
Cover: percentage cover in that quadrant
-
Year: year of sampling (2021)
Unavailable information (cells containing NA) for fractal data indicate missing values from data transcription.
File: rhf_21.csv
Description: Percentage cover quadrat data for fractal sampling in Right Hand Fork, Utah, USA, 2021.
Variables
-
Date: date of sampling
-
Plot: sample site named according to Ecological Fractal Network convention
-
Quadrant: portion of quadrat sampled (1-4)
-
Species: plant species Latin name
-
Cover: percentage cover in that quadrant
-
Notes: any additional information recorded
Unavailable information (cells containing NA) for fractal data indicate missing values from data transcription.
File: silwood23.csv
Description: Percentage cover quadrat data for fractal sampling in Silwood Park, UK, 2023.
Variables
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Year: year of sampling (2021)
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Site: site (Silwood Park)
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Plot: sample site named according to Ecological Fractal Network convention
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Quadrant: portion of quadrat sampled (1-4)
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Species: plant species Latin name
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Cover: percentage cover in that quadrant
Unavailable information (cells containing NA) for fractal data indicate missing values from data transcription.
File: specieslist.csv
Description: Introduction status for all species at each site, based on records from Plants of the World Online (POWO), Kew Gardens.
Variables
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Species: plant Latin name
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Site: one of Boothby, Knepp, Silwood, etc.
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Introduced_status: Introduced or Native, based on POWO classification maps for site
Blank/NA cells specieslist.csv indicate species for which information was unavailable on Plants of the World Online, Kew Gardens
File: processed_fractal.csv
Description: Processed dataset produced from all site data, BIEN trait values, specieslist.csv introduction status, and calculated species-β.
Variables
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Site: one of Boothby, Knepp, Silwood, etc.
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Plot: sample site named according to Ecological Fractal Network convention
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Quadrant: portion of quadrat sampled (1-4)
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Species: plant species Latin name
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Cover: percentage cover in that quadrant
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Year: year of sampling
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SLA: BIEN trait mean specific leaf area (m2 kg-1)
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Height: BIEN trait mean plant height (metres)
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Seed mass: BIEN trait mean plant seed mass (mg)
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Introduced_status: introduction status from Kew Gardens POWO (introduced vs native)
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Majortriad: identifier for major triad (medium fractal scale)
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Minortriad: identifier for minor triad (small fractal scale)
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Beta_contrib_major: species-β at large fractal scale
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Beta_contrib_minor: species-β at medium fractal scale
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Beta_contrib_plot: species-β at small fractal scale
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csMSPD: community-standardised mean species pairwise distance
Blank/NA values indicate where data was unavailable, e.g. from Bien trait database, or where beta-diversity could not be calculated because a single species was present.
Code/software
Microsoft excel or similar needed to view data.
R scripts to run analyses should be run on R version 4.3.1 in order 1-8. Figures are produced at the end of script 8.
Script: determinants_of_SCBD_src.r
Description: Load required packages for full analysis, and specify paths for data, models and figures.
Script: 1_trait_data_fractal.R
Description: load and clean fractal data, extract trait values and introduction status.
Script: 2_scbd_calculation_fractal.R
Description: calculate species-β at each fractal scale.
Script: 3_csMSPD_fractal.R
Description: calculate community-standardised mean species pairwise distance from phylogeny
Script: 4_UK_site_GBIF_downloads.R
Description: download GBIF occurrence records for UK and UK sites.
Script: 5_UK_sites_trait_data.R
Description: extract trait data for species from GBIF download.
Script: 6_UK_landscape_scale_SCBD_calculations.R
Description: calculate species-β for landscape and UK scales.
Script: 7_UK_landscape_scale_csMSPD.R
Description: calculate community-standardised mean species pairwise distance from phylogeny for landscape and UK scales.
Script: 8_Modelling___figures.R
Description: Run beta-regression models with multi-model inference for each scale, and produce plots of model predictions. Output files generated by the scripts (e.g. plantdata.csv, fractal_traits_mean.csv) serve as input files for the subsequent code in the workflow.
Access information
Other publicly accessible locations of the data:
