Data and code from: Rising plant extinction rates on European mountain summits
Data files
Sep 08, 2026 version files 2.44 MB
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climate_data_GLORIA_europe.csv
52.13 KB
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data_GLORIA_europe.csv
2.20 MB
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extinction_paper_submit_fin_revision.R
174.63 KB
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README.md
6.82 KB
Abstract
Climate change increases plant species richness in alpine ecosystems. However, to what extent this diversity enrichment masks extinction dynamics of resident species remains elusive. Here, we use floristic resurvey data from 896 permanent vegetation plots across 62 European mountain summits to show that local extinctions have increased over the past 21 years. Extinction rates rose with the magnitude of warming, and species were more likely to go extinct towards their low-elevation range margins and in communities undergoing stronger thermophilization. Moreover, local extinctions were significantly related to preceding abundance declines, which can hence serve as an early warning signal. These findings suggest that despite increasing plant species richness, plant assemblages above the treeline face an accelerating, but so far neglected, loss of their most characteristic species.
Dataset DOI: 10.5061/dryad.vmcvdnd6v
Description of the data and file structure
Data from 16 regions consisting of 4 summits containing up to 16 permanent plots across Europe. For each plot (896 plots) four times all vascular plants and their cover was recorded.
Additionally a file containing climate data for all summits consisting of change of temperature and precipitation compared to a baseline of 1900-1950.
Files and variables
File: extinction_paper_submit_fin_revision.R
Description: R script containing complete analysis including shuffling the data and producing all plots for the manuscript.
File: climate_data_GLORIA_europe.csv
Variables
- region: abbreviation for the regions, "ADO" = S-Alps / Dolomites, "CAI" = Cairngorms (Scotland), "CAK" = Central Caucasus / Kazbegi region, "CAM" = Central Apennines / Majella, "CPY" = Central Pyrenees / Ordesa, "CRO" = E-Carpathians / Rodnei Mts., "CTA" = W-Carpathians / High Tatra, "DOV" = Dovrefjell (S-Scandes), "HSW" = NE-Alps / Hochschwab, "LEO" = Crete / Lefka Ori, "MAV" = W-Alps / Mont Avic, "NAP" = Northern Apennines, "SN1" = Central Alps / Swiss National Park - carbonatic, "SN2" = Central Alps / Swiss National Park - siliceous, "SNE" = Sierra Nevada - West, "VAL" = W-Alps / Alps of Valais-Entremont
- summit: abbreviation for the summits, "ACU" = Punta Acuta, "BOV" = Pointe de Boveire, "BRU" = Mont Brûlé, "BUH" = BUHAIESCU, "CAM" = Camp Cairn, "CAS" = Monte Casarola, "CHO" = Chorafas, "CP1" = Cross Pass 1, "CP2" = Cross Pass 2, "CP4" = Cross Pass 4 - Kudebi, "CUP" = Cúpula, "CUS" = Punta Custodia, "FEM" = Femmina Morta, "FOG" = Cima di Foce a Giovo, "GHK" = G´hacktkogel, "GOL" = GOLGOTA, "GRM" = Grasmugl, "GRO" = GROPILE, "KOL" = Kolla, "KRA" = Krátka, "KRI" = Krížna, "LAL" = La Ly, "LOW" = low summit, "MAC" = Cerro de los Machos (in region SNE)/Monte Macellaro (in region CAM), "MAM" = Monte Mammoccio, "MBU" = Munt Buffalora, "MCH" = Munt Chavagl, "MCS" = Mot sper Chamana Sesvenna, "MDG" = Mot dal Gajer, "MIG" = Creag Mhigeachaidh, "MIN" = Minschuns, "MOM" = Alpe di Mommio, "MTS" = Monte Schutto, "OLA" = Punta de las Olas, "PAR" = Pointe du Parc, "PCA" = Cima di Pian Cavallaro, "PFO" = Piz Foraz, "PMU" = Piz Murtèr, "PNL" = Do Peniola, "PPL" = Piz Plazer, "PUL" = Pulpitito, "REB" = REBRA, "RNK" = Ragnaroek, "SED" = Sedielková kopa, "SEK" = South-East of Kakovoli, "SGO" = Sgoran Dubh Mor, "SKI" = Storkinn, "STR" = Sternes, "SU1" = Colle Lago Bianco, "SU2" = Lago Balena, "SU3" = Pra Pelat, "SU4" = Cime Bianche, "TCA" = Pico del Tosal Cartujo, "TOB" = Punta Tobacor, "UNK" = Unknown Hillock, "VAR" = Vesle Armodshokollen, "VEK" = Velká kopa, "VKO" = Veslekolla, "WEK" = Weihbrunnkogel, "ZAK" = Zagelkogel-NW-summit, "ZIK" = Zinken-NW-summit
- Survey: factor indicating which local extinctions (e.g., from the first to the second survey) the climatic change relates to. "ext_12", "ext_23", "ext_34" for local extinctions from the first to the second, second to the third and third to the fourth survey, respectively.
- climate: bio1, i.e., mean annual temperature compared to a baseline of 1900 to 1950 (in °C)
- bio12: annual precipitation sum, compared to a baseline of 1900 to 1950 (in mm)
- prec_sum: precipitation sum in summer (June to August) compared to a baseline of 1900 to 1950 (in mm)
- prec_win: precipitation sum in winter (December to March) compared to a baseline of 1900 to 1950 (in mm)
File: data_GLORIA_europe.csv
Variables
- region: abbreviation for the regions
- summit: abbreviation for the summits
- plot: plot ID
- Final_Name: Species name
- alti_rank: Elevational rank of each species. The ranks indicate the elevational belt within which the species has its center of distribution and were coded as: 1 = nival; 2 = subnival, i.e., at the transition between the upper alpine and lower nival belt; 3 = alpine; 4 = alpine to the treeline; 5 = treeline ecotone; and 6 = montane
- survey1: species cover in the first survey
- survey2: species cover in the second survey
- survey3: species cover in the third survey
- survey4: species cover in the fourth survey
- timespan_12: time in years between survey 1 and survey 2
- timespan_23: time in years between survey 2 and survey 3
- timespan_34: time in years between survey 3 and survey 4
- altitude: elevation of the plot (in meters)
- latitude: latitude of the plot. Coordinates were rounded to one digit in order to reduce potential impact on conservation efforts of vulnerable/endangered species. Therefore, statistical results might deviate slightly.
- longitude: longitude of the plot. Coordinates were rounded to one digit in order to reduce potential impact on conservation efforts of vulnerable/endangered species. Therefore, statistical results might deviate slightly.
- Order: elevation of the plots, ordered per region (low to high)
- expo: exposition of the plot (N, E, S, W)
- alti_rank_mean: mean elevational rank of the species community of the plot in the first survey
- alti_rank_rel_num: relative elevational rank of each species compared to the plot community
- fre2022: frequency analysis done in 2022 (logical)
- ID: combined ID of region, summit and plot
- survYear1: Year of the first survey
- survYear2: Year of the second survey
- survYear3: Year of the third survey
- survYear4: Year of the fourth survey
- avchange_13: average annual cover change from survey 1 to survey 3
- avchange_23: average annual cover change from survey 2 to survey 3
Code/software
R code used to analyse the data:
The two CSV files are loaded at the beginning containing species cover in permanent plots over four surveys across Europe.
Subsequently, the data are shuffled and all analyses from the manuscript are derived analysing:
1) species numbers in relation to time on the level of plots, summits and regions.
2) cover sums per plot in relation to time.
3) number of local extinctions in relation to time, climate change and geographical position on the level of plots, summits and regions.
4) probability of local extinction in the last survey in relation to the cover at the beginning as well as the cover change before extinction (over a 7 year and a 14 year time window, respectively).
5) all analysis for local extinctions were furthermore mirrored for local colonisations.
Besides the results of the statistical analysis the script produces figures showing:
1) percentage of local extinctions over time in relation to climate warming (scatterplot with temperature increase used for coloring).
2) Plots of all model coefficient estimates os the statistical analysis.
3) Local extinction probability in relation to previous cover change.