Data and code for case study bridging macroecology and temporal dynamics to better attribute global change impacts on biodiversity
Data files
Nov 28, 2025 version files 75.88 MB
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MacroEcoDynamics_repo.tar
75.87 MB
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README.md
7.90 KB
Abstract
The ongoing biodiversity crisis presents a complex challenge for ecological science. Despite a consensus on general biodiversity decline, identifying clear trends remains difficult due to variability in data, methodologies, and scales of analysis. To enhance our understanding of ongoing biodiversity changes and address discrepancies in biodiversity trend detection, we propose integrating macroecological theory with temporal and trait-based perspectives.
- First, analyzing temporal changes in diversity scaling relationships, such as species accumulation curves or distance decay, can reconcile and synthesize conflicting observations of biodiversity change, enabling quantification of diversity shifts from local to regional spatial scales.
- Second, diversity patterns across scales are linked to three proximate components: abundance, evenness, and spatial aggregation of species. Investigating temporal changes in these components provides deeper insights into how human activities directly influence biodiversity trends.
- Third, incorporating species traits into the analysis of these macroecological patterns improves our understanding of human impacts on biodiversity by elucidating the links between species characteristics and their responses to environmental changes.
We illustrate this integration in a case study of forest and farmland birds in France, highlighting how studying diversity changes across scale, and decomposing temporal change in different components, can help to elucidate the mechanisms driving diversity change.
We discuss the limitations and challenges of this integrative approach and highlight how it offers a comprehensive framework for understanding the drivers of biodiversity change across scales. This framework facilitates a more nuanced understanding of how human activities impact biodiversity, ultimately paving the way for more informed actions to mitigate biodiversity loss across spatial and temporal scales.
https://doi.org/10.5061/dryad.cnp5hqcg9
Author: Gazre Pierre (2025)
Overview
This repository, archived in "MacroEcoDynamics_repo.tar," contains data and code to replicate all analyses (simulations and case study) presented in the paper. The repository has folders :
- figures, an empty folder where figures created will be stored
- code_outputs, an empty folder where intermediate. The R data files created will be stored
- code, which contains R scripts detailed below
- data, which contains the following data files
Data file inventory (data folder)
| file name | format | key content |
|---|---|---|
Habitat_class_PECBMS.csv |
CSV (semicolon delimiter) | Mapping of each PECBMS species to one of three habitat classes (Forest, Farmland, Other). |
div_sites.Rdata |
R binary workspace (.Rdata) |
Data frame div_sites with four habitat diversity indices (2000, 2006, 2012, 2018) and plot coordinates. |
div_sites_clc.Rdata |
R binary workspace | Data frame div_sites_clc; same as div_sites plus dominant CORINE class of each plot. |
cover_sites.Rdata |
R binary workspace | Longformat cover_sites listing proportional cover of four aggregated landcover categories for each plot and year. |
clim_sites.Rdata |
R binary workspace | Annual time series clim with temperature and precipitation (plus oneyear lags) for each plot. |
sites_coord.Rdata |
R binary workspace | Data frame sites_coord providing plot identifiers and coordinates. |
Detailed data descriptions
1Habitat_class_PECBMS.csv
- observations: one row per species
- variables
speciesscientific name following PECBMS taxonomy (character)habitat_classForest,FarmlandorOther(character)
2div_sites.Rdata object div_sites
| variable | type | description |
|---|---|---|
site |
factor | unique 5digit plot code |
x_etrs89, y_etrs89 |
numeric | coordinates in ETRS89LAEA Europe (m) |
x_wgs84, y_wgs84 |
numeric | longitude / latitude (; EPSG4326) |
div_2000, div_2006, div_2012, div_2018 |
numeric | habitat diversity (Simpson index) for four CORINE snapshots |
3div_sites_clc.Rdata object div_sites_clc
Same variables as div_sites, plus clc_class (factor): dominant CLC2018 level3 code (e.g. 211=nonirrigated arable land).
4cover_sites.Rdata object cover_sites
Long format with one row per site cover category.
| variable | description |
|---|---|
site |
plot identifier |
my_code |
landcover category (Agricultural, Artificial, Forest, Open) |
cover_2000``cover_2018 |
percentage cover for four inventory years |
| duplicated coordinate columns | convenience fields |
5clim_sites.Rdata object clim
Annual time series (20012022) with:
| variable | unit | description |
|---|---|---|
tempK |
0.1K | mean temperature 10 |
temp |
C | mean temperature |
precip |
mm | total precipitation |
temp_1, precip_1 |
lagged values (year1) |
6sites_coord.Rdata object sites_coord
Site identifiers and coordinates (see table above).
STOC_2001_2019_noComma.txt : This dataset lists bird observations from 2007 in a single STOC-EPS survey square in department 01. It contains species list and individuals observed. All observations share the same location, altitude, and coordinates.
Spatial reference
All coordinates follow WGS84 (EPSG4326). Cartesian operations used ETRS89LAEA Europe (EPSG3035).
Temporal coverage
- Land cover snapshots: 2000, 2006, 2012, 2018 (CORINE).
- Climate: 20012022 (annual).
- Habitat diversity: same four CORINE snapshots.
File formats and software
All .Rdata files were saved with R4.4.0 using compress = "xz".
load("div_sites.Rdata") # loads object 'div_sites'
CSV file import example:
habitat <- read.csv2("Habitat_class_PECBMS.csv", stringsAsFactors = FALSE)
Analysis scripts (code folder)
Two commented R scripts accompany the dataset and reproduce all analyses in the manuscript. They are optional for reusing the raw data but ensure methodological transparency.
case_study_mob_STOC.Rannotated workflow that- harmonises 20022013 STOCEPS bird counts and environmental covariates;
- constructs mobr community objects for farmland and forest assemblages;
- decomposes richness change into samplingdensity, SAD and spatial aggregation components (deltastats);
- visualises multiscale richness trends and attributes environmental drivers;
- caches intermediate results in
code_outputs/.
simulations.Rsimulation study showing how changes in total abundance, evenness and spatial clumping modify biodiversity patterns. It- creates four artificial landscapes with mobsim;
- samples them with identical quadrats;
- fits Lomolino speciesaccumulation models, speciesarea curves and distancedecay relationships;
- computes directional rarefaction metrics;
- exports SVG figures used for conceptual illustrations.
Both scripts were developed under R4.2 with CRAN packages listed at their top. Random seeds are not fixed; reruns produce slightly different simulations but identical qualitative patterns.
function_accumulate_environment_multi. R: This function calculates environmental accumulation curves for different groups, variables, and methods.- It checks inputs, splits the dataset by a grouping variable, and for each group it builds site-ordering sequences (spatial or random).
- Then it repeatedly (nrep times) accumulates environmental values according to these orders and averages the results.
Finally, it returns a long-format data frame containing cumulative values for each group, method, variable, and sampling effort.
Usage rights
Creative Commons Zero (CC0). Please cite this dataset and the original sources (PECBMS, CopernicusCLC, EOBS) in derivative works.
Acknowledgements
We thank the PECBMS volunteers, the European Environment Agency for CORINE Land Cover, and the EOBS consortium for open climate data.
Access information
Other publicly accessible locations of the data:
Bird community data were from the French Breeding Bird Survey. The French breeding bird survey was designed to monitor population dynamics of common passerine bird species in France. In this survey, skilled volunteer ornithologists count birds at a given site, following a standardized protocol, at the same site, year after year (Jiguet et al. 2012). Species abundances are recorded across 2792 sites, each covering a 4km² area. Volunteers provide their home locality to the national coordinator, and a 2×2 km site is randomly selected from within a 10 km radius (out of 80 possible sites) by the coordinator. Each spring, volunteers carry out 10 point counts separated by at least 300 m within the selected site, for a fixed period of five minutes. Two sampling sessions are carried out from 1 April to 8 May, and then from 9 May to the end of June, to detect both early and late breeders, with a gap of 4–6 weeks between sessions. Counts are repeated annually on approximately the same date (±7 days) and at dawn (1–4 h after sunrise) by the same observer, in the same order. The highest count from these two sessions is used as the measure of point-level species abundance. We sub-selected sites that were monitored between 2002 and 2013, in order to avoid the first year of the restructured monitoring scheme (i.e 2001), and to limit our analyses to linear trends, more likely to characterize decadal dynamics. We used the latest PECBMS classification (https://pecbms.info/) to classify farmland and forest species according to their pre- dominant habitat.
Climatic data were extracted from CHELSA (https://chelsa-climate.org/, v.2.1) for each site and each sampling year. We computed the average daily temperature and precipitation during the bird breeding season (April - August). Land cover data were extracted from CORINE Land Cover (European Environment Agency 2010). Percentage land covers within FBBS site were computed by taking the habitat class area (in square meters) and dividing it by the total area of the site. Because CLC data were available only for 2000, 2006, 2012 and 2018, some FBBS site-year combinations were not covered by the dataset. In this case, we attributed site land cover for the uncovered year to the last year for which we had CLC data available (for example, sites monitored in 2001 were attributed land cover from CLC 2000). More specifically, we focused on two aggregated CLC classes, agricultural areas and forests.
