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.

README: 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	**

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S12

S12_List_of_datasets.csv

List of datasets included in the study.

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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	**

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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	*

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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

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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.

Land-use impacts on plant functional diversity throughout Europe

Data files

Abstract

README: Land-use impacts on plant functional diversity throughout Europe

Description of the data and file structure

S12

S14

S15

S16

S17

Code

Works referencing this dataset