DOI: 10.5061/dryad.ns1rn8q2s
title: Range shift and climatic refugia for alpine lichens under climate changes

description: 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.
description: 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.
description: # Range shift and climatic refugia for alpine lichens under climate
 changes Dataset DOI: [10.5061/dryad.ns1rn8q2s](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](mailto: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/](https://chelsa-climate.org/)); - GBIF
 ([https://www.gbif.org/](https://www.gbif.org/)); * Dolichens
 ([https://italic.units.it/dolichens/](https://italic.units.it/dolichens/)); * ITALIC 7.0 ([https://italic.units.it/](https://italic.units.it/)).