DOI: 10.5061/dryad.bg79cnpjw
title: Land-use impacts on plant functional diversity throughout Europe

description: Aim: Global biodiversity loss resulting from anthropogenic land-use
 activities is a pressing concern, requiring precise assessments of impacts
 at large spatial extents. Existing models mainly focus on species richness
 and abundance, lacking insights into ecological mechanisms and
 species' roles in ecosystem functioning. To bridge this gap, we
 conducted an extensive analysis of the impact of human land use on
 vascular plant functional diversity, across diverse land-use classes and
 bioregions in Europe, comparing it to traditional metrics. Location:
 Europe           Time period: 1992-2019                           Major taxa studied: Vascular plants Methods: Integrating extensive databases of vegetation plots with spatial data on land use and land cover, we paired plots from areas actively used and modified by humans with plots from natural habitats under similar environmental conditions. Using species occurrences and traits, in each plot we computed three complementary functional diversity metrics (functional richness, evenness, and divergence), species richness and abundance. We assessed the impact of land use by comparing the metrics in the paired plots. Results: Our findings revealed that, compared to natural habitats, anthropogenic land use exhibits lower functional richness and divergence but higher functional evenness across most land-use classes and bioregions. The response of functional richness was more marked than the other two metrics and especially pronounced in croplands and urban areas and in northern bioregions. Functional richness exhibited a pattern that did not fully overlap with the trend in species richness, providing useful complementary information. Main conclusions: We provide a large-scale precise assessment of anthropogenic land-use impacts on functional diversity across Europe. Our findings indicate that: (i) human disturbance significantly alters plant functional diversity compared to natural habitats; (ii) this alteration goes in the direction of functional homogenization within sites; (iii) functional diversity metrics complement traditional metrics by offering deeper insights into the ecological mechanisms in response to anthropogenic land use.
description: # Land-use impacts on plant functional diversity throughout Europe ##
 Description of the data and file structure **S10.2**
 S10.2_plot_attributes_row_wise.csv .csv file containing the numerical
 values of proportion of species with traits, geographical distance, plot
 size and corresponding relative values for the vegetation plots considered
 in the study. This is an input file for the script main.R. The list of
 columns is available here below. | Name | Description | Original from
 EVA/sPlot (\*) or calculated/derived/ assigned in the study (\*\*) | |
 :------------------------------ |
 :-------------------------------------------------------------------------------- | :------------------------------------------------------------------------------- | | PlotObservationID | ID code of each vegetation plot sampled in anthropogenic land | \* | | Bioregion\_code | Bioregion code | \*\* | | broad\_class | Anthropogenic land-use class to which the vegetation plot belongs | \*\* | | PlotObservationID.c | ID code of the paired vegetation plot sampled in natural habitat (.c = control) | \* | | pot\_nat\_veg | Land cover type of the plot in natural habitat. | \*\* | | PairingID | ID code of each pairing between vegetation plots | \*\* | | Distance.km | Distance between the paired vegetation plots | \*\* | | prop\_species\_traits.t | Proportion of species with trait of plot in anthropogenic land (.t = treatment) | \*\* | | prop\_species\_traits.c | Proportion of species with trait of paired plot in natural habitat (.c = control) | \*\* | | relative\_prop\_species\_traits | Ratio between prop\_species\_traits.t and prop\_species\_traits.c | \*\* | | Releve.area.t | Sampling area of plot in anthropogenic land (.t = treatment) | \* | | Releve.area.c | Sampling area of paired plot in natural habitat (.c = control) | \* | | relative\_plot\_size | Ratio between Releve.area.t and Releve.area.c | \*\* | \********* #### **S12** S12_List_of_datasets.csv List of datasets included in the study. \********* #### **S14** S14_abs_values_FD_SR_TotAb_RNSR_all-columns.csv .csv file containing the numerical results of the functional and species diversity per vegetation plot, see the list of columns here below. This is the input file for the script main.R. | Name | Description | Original from EVA/sPlot (\*) or calculated/derived/ assigned in the study (\*\*) | | :-------------------------------------- | :------------------------------------------------------------------------------------------------------------ | :------------------------------------------------------------------------------- | | PlotObservationID | ID code of each vegetation plot | \* | | FRic | Functional richness | \*\* | | FEve | Functional evenness | \*\* | | FDiv | Functional divergence | \*\* | | SR | Species Richness | \*\* | | TotAb | Total abundance | \*\* | | RNSR | Relative natural species richness | \*\* | | broad\_class | Land-use class or habitat | \*\* | | distancePC | Distance of PC scores between the paired plots (see Pairing ID) | \*\* | | Bioregion\_code | Bioregion code | \*\* | | PairingID | ID code of each pairing between vegetation plots | \*\* | | Treatment | Anthropogenic land-use class (TRUE) or natural habitat (FALSE)? | \*\* | | loc\_uncertainty\_ranking | Ranking of location uncertainty | \*\* | | broad\_class\_PotNatVeg | Class of potential natural vegetation occurring at the coordinates of the plot | \*\* | | Dataset | EVA dataset | \* | | GIVD.ID | EVA GIVD ID | \* | | Latitude | Latitute of the vegetation plot (rounded at 3 digits) | \* | | Longitude | Longitute of the vegetation plot (rounded at 3 digits) | \* | | Country | Country where the vegetation plot was sampled | \* | | Date.of.recording | Date of sampling | \* | | Location.uncertainty.m | Location uncertainty sampling (meters of the raius) | \* | | Releve.area | Sampling area (square meters) | \* | | Naturalness | Naturalness level from sPlot | \* | | Forest | Was the plot sampled in a forest (1 = yes, 0 = no)? | \* | | Shrubland | Was the plot sampled in a shrubland (1 = yes, 0 = no)? | \* | | Grassland | Was the plot sampled in a grassland (1 = yes, 0 = no)? | \* | | Wetland | Was the plot sampled in a wetland (1 = yes, 0 = no)? | \* | | Sparse.vegetation | Was the plot sampled in sparse vegetation (1 = yes, 0 = no)? | \* | | land\_cover\_code\_ESA\_CCI | ESA CCI land cover code extracted at the coordinates of the vegetation plot | \*\* | | land\_cover\_code\_HILDA | HILDA land cover code extracted at the coordinates of the vegetation plot | \*\* | | label\_ESA\_CCI | ESA CCI land-cover category corresponding to the code | \*\* | | label\_HILDA | HILDA land-cover category corresponding to the code | \*\* | | land\_cover\_code\_NatureMap\_PotNatVeg | NatureMap land cover code of potential natural vegetation extracted at the coordinates of the vegetation plot | \*\* | | label\_NatureMap\_PotNatVeg | NatureMap land-cover category corresponding to the code | \*\* | | land\_cover\_code\_GLOBIO | GLOBIO4 land cover code extracted at the coordinates of the vegetation plot | \*\* | | label\_GLOBIO | GLOBIO4 land-cover category corresponding to the code | \*\* | | PC1 to PC23 | Results of the PCA on the soil and bioclimatic variables extracted at the coordinates of the vegetation plot | \*\* |   \********* #### **S15** S15_relative_FD_SR_TotAb_RNSR.csv .csv file containing the numerical results of the relative functional and species diversity per vegetation plot (relative functional richness, relative species richness and relative total abundance are corrected for plot size, sections 2.7 and S10). This is an output file of the script main.R. The list of columns is available here below. | Name | Description | Original from EVA/sPlot (\*) or calculated/derived/ assigned in the study (\*\*) | | :------------------------ | :---------------------------------------------------------------------------------------------------------------------------------------------------------------- | :------------------------------------------------------------------------------- | | PlotObservationID | ID code of each vegetation plot | \* | | FD\_metric | Label of the functional or species diversity metric | \*\* | | values | Value of the metric | \*\* | | broad\_class | Anthropogenic land-use class for which the relative value has been calculated | \*\* | | distancePC | Distance of PC scores between the vegetation plot and its corresponding vegetation plot in the natural habitat | \*\* | | Bioregion\_code | Bioregion code | \*\* | | PairingID | ID code of the pairing between each vegetation plot sampled in an anthropogenic land-use classes and the corresponding vegetation plot sampled in natural habitat | \*\* | | loc\_uncertainty\_ranking | Ranking of location uncertainty | \*\* | | pot\_nat\_veg | Class of potential natural vegetation occurring at the coordinates of the plot | \*\* | | Wt\_pvalue | p-value of BH-corrected Wilcoxon test for the combination of land-use class and bioregion to which the vegetation plot belongs | \*\* | | n | Number of pairings in the combination of land-use class and bioregion to which the vegetation plot belongs | \*\* | | Sign\_Wt | Significance of the BH-corrected Wilcoxon test | \*\* | | Latitude | Latitute of the vegetation plot (rounded at 3 digits) | \* | | Longitude | Longitute of the vegetation plot (rounded at 3 digits) | \* | | Country | Country where the vegetation plot was sampled | \* | | Releve.area | Sampling area (square meters) | \* | | Naturalness | Naturalness level from sPlot | \* | \********* #### **S16** S16_aggr_abs_values_FD_SR_TotAb_RNSR.csv .csv file containing the numerical results of the absolute values of functional and species diversity per anthropogenic land-use class/natural habitat, aggregated at bioregion level. This is an output file of the script main.R. The list of columns is available here below (no original Eva/sPlot information, all derived). | Name | Description | | :-------------- | :------------------------------------------------------------------------------------------------------------------------------- | | broad\_class | Anthropogenic land-use class or natural habitat | | Bioregion\_code | Bioregion code | | FD\_metric | Label of the functional or species diversity metric | | Mean | Mean of the absolute values of functional of species diversity per land-use class or natural habitat and bioregion | | Median | Median of the absolute values of functional of species diversity per land-use class or natural habitat and bioregion | | Stand\_dev | Standard deviation of the absolute values of functional of species diversity per land-use class or natural habitat and bioregion | | n | Number of pairings in the combination of anthropogenic land-use class and bioregion | \********* #### **S17** S17_aggr_relative_FD_SR_TotAb_RNSR.csv .csv file containing the numerical results of the relative values of functional and species diversity per anthropogenic land-use class, aggregated at bioregion level (aggregated relative functional richness, relative species richness and relative total abundance were based on corrected values for plot size, sections 2.7 and S10). This is an output file of the script main.R. The list of columns is available here below (no original Eva/sPlot information, all derived). | Name | Description | | :-------------- | :------------------------------------------------------------------------------------------------------------------------------- | | broad\_class | Anthropogenic land-use class | | Bioregion\_code | Bioregion code | | FD\_metric | Label of the functional or species diversity metric | | Sign\_Wt | Significance of the BH-corrected Wilcoxon test | | Mean | Mean of the relative values of functional of species diversity per land-use class or natural habitat and bioregion | | Median | Median of the relative values of functional of species diversity per land-use class or natural habitat and bioregion | | Stand\_dev | Standard deviation of the relative values of functional of species diversity per land-use class or natural habitat and bioregion | | n | Number of pairings in the combination of anthropogenic land-use class and bioregion | ## Code All analyses were performed in R version 4.0.5 (2021-03-31). **main.R** : Main script, which performs the data analysis starting from  S14 (S14_abs_values_FD_SR_TotAb_RNSR_all-columns.csv). set_directories.R: Define the directory paths where the files are stored. calculate_relative_values.R: Calculate the relative values of functional and species diversity. correct_results_with_plot_size.R: Correct relative functional richness, relative species richness and relative total abundance for relative plot size. perform_Wilcoxon_significance_test_flex.R : Function to perform the BH Wilcoxon test. aggregate.R : Calculate aggregated values per land-use class and bioregion of absolute and relative values of functional and species diversity. plotting.zip : Compressed folder containing the scripts to plot the figures. data_preparation_and_processing.zip : Compressed folder containing the scripts to prepare and process EVA/sPlot data and merge it with the other data sources to obtain S14_abs_values_FD_SR_TotAb_RNSR_all-columns.csv.