Range shift and climatic refugia for alpine lichens under climate changes
Data files
Nov 03, 2025 version files 90.63 MB
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01_download_bioclim.R
1.66 KB
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02_prep_vars_downscaling.R
4.56 KB
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03_downscaling_temp.R
3.25 KB
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04_downscaling_prec.R
1.43 KB
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AlpiBox.dbf
595 B
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AlpiBox.shp
236 B
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AlpiBox.shx
108 B
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README.md
3.46 KB
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sdm_data_table.csv
90.61 MB
Abstract
Mountain biodiversity is highly threatened by climate change, with many species facing habitat reduction and/or local extinction. Poikilohydric organisms like lichens are extremely sensitive to environmental conditions and changes. A comprehensive overview of the impact of climate change on the future distribution of lichens is still missing. Thus, we quantified the range shift, loss in suitable areas, and potential climatic refugia for more than 250 lichens, exploring these trends for each species and grouping them by their ecological needs and functional traits. We performed species distribution models to investigate the range shifts of 272 lichens under different climate change scenarios. Range shift was investigated by modelling gain and loss in suitability score along the elevational gradient, for each species separately, and grouping them based on growth forms and temperature affinities. Based on the "high suitability score stability" index, we developed maps of potential refuge areas. We predicted a huge loss of habitat suitability over time, especially under the SSP5-5.8. Fruticose lichens will exhibit the highest loss, and cryophilous species will be the most impacted. Moreover, contrary to the assumption of an upward range shift, most species showed no significant relationship between altitude and an increase in habitat suitability, suggesting different redistribution patterns for lichens. In the same way, climatic refugia are not only identified at high elevations but also in deep valleys and cold exposure. The response of lichens to climate change is extremely heterogeneous, and an upper-range shift is less common than expected. Spatial redistribution is highly distinct among functional groups. The identified climatic refugia confirm this pattern, underlining the urgent need to improve the conservation effort, especially for fruticose and cryophilic species.
Dataset DOI: 10.5061/dryad.ns1rn8q2s
Description of the data and file structure
The repository contains the data required to repeat the species distribution models performed in Francesconi et al.
For each of the 272 lichen species, we present in sdm_data_table.csv file the 10 sets of generated background points and occurrences for the calibration area from 3 different sources (Dolichens database, ITALIC 7.0, GBIF). Due to copyright restrictions, occurrences from GBIF have been removed from the file, but can be obtained at the following link: https://doi.org/10.15468/dl.f7563s
For each point, we also provide the corresponding value of the 3 CHELSA bioclimatic variables chosen as predictors. We extracted the mean values of the bioclimatic variables within an area with a radius corresponding to the associated uncertainty value.
In addition, four scripts are available for downloading the bioclimatic variables used and downscaling to the chosen resolution (250 m).
Scripts for data cleaning and species distribution modeling are available upon request from the corresponding author: Michele Di Musciano (michele.dimusciano@univaq.it).
Files and variables
File: sdm_data_table.csv
Description:
Variables
- CHELSA_bio_08_1981.2010_V2.1_clipped_250m: extracted mean values of the CHELSA BIO 08 bioclimatic variable
- CHELSA_bio_15_1981.2010_V2.1_clipped_250m: extracted mean values of the CHELSA BIO 15 bioclimatic variable
- CHELSA_bio_17_1981.2010_V2.1_clipped_250m: extracted mean values of the CHELSA BIO 17 bioclimatic variable
- long: longitude E in decimal degrees WGS84
- lat: latitude N in decimal degrees WGS84
- pa: 0 for background point, 1 for presence point
- uncertainty: coordinate uncertainty in meters
- origin: original dataset (dolichens and italic) or "pseudoabsence" for generated background points
- scientificName: lichen scientific names
- PA_set: number of the 10 sets of background points
File: 01_download_bioclim.R
Description: script to download the CHELSA bioclimatic variables and the DEM
File: 02_prep_vars_downscaling.R
Description: script to create the dataframe needed for the downscaling process
File: 03_downscaling_temp.R
Description: script to downscale the variables of temperature
File: 04_downscaling_prec.R
Description: script to downscale the variables of precipitation
File: AlpiBox.dbf
Description: shapefile of the calibration area
File: AlpiBox.shp
Description: shapefile of the calibration area
File: AlpiBox.shx
Description: shapefile of the calibration area
Code/software
Run the following scripts to download and downscale all the CHELSA bioclimatic variables:
- 01_download_bioclim.R
- 02_prep_vars_downscaling.R
- 03_downscaling_temp.R
- 04_downscaling_prec.R
Be warned, script 3, concerning the downscaling of temperature variables, takes several hours to finish.
Access information
Data was derived from the following sources:
- Chelsa (https://chelsa-climate.org/);
- GBIF (https://www.gbif.org/);
- Dolichens (https://italic.units.it/dolichens/);
- ITALIC 7.0 (https://italic.units.it/).
The lichen occurrences were derived from the following sources: Dolichens (https://italic.units.it/dolichens/), ITALIC 7.0 (https://italic.units.it/), GBIF (https://www.gbif.org/). We retained only occurrence data collected after 1975 and with a coordinate uncertainty of 500 m or less. To reduce spatial bias due to pseudo-replication of occurrences, we performed spatial thinning. Then, we retained only the species with at least 25 occurrence records, a limit that has been shown to provide reliable results in modeling studies. The resulting dataset includes 25 to 469 occurrence records of 272 infrageneric taxa, for a total of 23,521 occurrences. For each species, we generated 10 replicate sets of background points, in a 10:1 ratio with the number of presence points, with an exclusion buffer of 500 m from the presence point.