Data from: Too much of a good thing? Supplementing current species observations with fossil data to assess climate change vulnerability via ecological niche models
Data files
Jun 05, 2024 version files 3.19 GB
Abstract
Ecological niche models (ENMs) are a powerful tool in ecological research and conservation planning. Since ENMs provide probability maps of suitable areas under environmental change, they may assist in designing conservation actions and addressing conservation priorities. However, ENMs are usually implemented by learning the species climatic preferences from their current geographic distribution, which leaves them vulnerable to the issue of niche truncation issues, as if comes with non-climatic limits to the current species distribution posed by e.g. anthropic activities and settlements, and is bound to assume that species are at equilibrium with their environments. These problems might be alleviated by the inclusion of fossil occurrences, which refer to moments during species evolution when such limits were absent, and a larger fraction of the species fundamental niche was probably explored. Here, we combined current and fossil occurrence data for 38 medium-large mammal species of conservation concern to assess the influence of the fossil record on ENM predictions under future climate change scenarios. We found that ignoring or including fossil data yields consistent trends in terms of predicted range increase/decrease. Yet, although adding fossil data invariably results in increased niche width, estimates of range change magnitude improved for just one half only of the species. These results suggest that most species might be in non-equilibrium with their environment, and that the inclusion of fossil data may be crucial to the better understanding of species climatic requirements, hence for designing effective conservation strategies.
README: Data from: Too much of a good thing? Supplementing current species observations with fossil data to assess climate change vulnerability via ecological niche models
Description of the data and file structure
Data folder contains:
- Geopackages
- Geopackage_BEYER_CHELSA: In this folder are the geopackages for the 28 species achieving AUC > 0.7 in both modern and full ENMs. In each geopackage are coordinates and filtered climatic variable values (once VIF < 5 was applied) for occurrence and background points. The geopackages are loaded in all the scripts.
- Variables
- CHELSA_10km: These are the variables used for present and 2080 climates. They are loaded in following scripts:
- 1_Modern_ENM_training
- 1b_Modern_ENMs_temporal_block
- 2_Full_ENM_training
- 5_RANDOM_FOREST
- Krapp_change: These are the variables used for past climates. They are loaded in following scripts:
- 3_NICHE_OVERLAP
- 5_RANDOM_FOREST
- "var_abbr.xlsx": This file is used in the script "5_RANDOM_FOREST" to generate FIGURE 5
- CHELSA_10km: These are the variables used for present and 2080 climates. They are loaded in following scripts:
- "final.name_bay.ch.txt": This file is used in the scripts to generate names of species where necessary.
- Ecoregions: This folder contains the "wwf_terr_ecos.shp" file needed to identify the ecoregions used in the study. Specifically, the file of interest is ‘wwf_terr_ecos.shp’, the others are accessory files to the shapefile. Thus described:
- wwf_terr_ecos.dbf: a file is one of the three files required for a valid ESRI Shapefile. In addition to a file containing the dBASE table, instances of the ESRI Shapefile format must include a main file and an index file, and may include several others. The dBASE table file contains feature attributes with one record per feature.
- wwf_terr_ecos.htm: a Hypertext Markup Language file that contains metadata information.
- wwf_terr_ecos.lyr: a file that gives the shapefile its graphic appearance when opened in a GIS programme.
- wwf_terr_ecos.prj: it is an optional file that contains the metadata associated with the shapefiles coordinate and projection system.
- wwf_terr_ecos.sbn: this is a binary spatial index file, which is used only by Esri software.
- wwf_terr_ecos.sbx: the files that store the spatial index of the features.
- wwf_terr_ecos.shp: the main file that stores the feature geometry
- wwf_terr_ecos.xml: metadata for ArcGIS—stores information about the shapefile.
- wwf_terr_ecos.shx: the index file that stores the index of the feature geometry.
Script folder contains:
- 1_Modern_ENM_training: In this script, ENMs are generated with modern data only
- 1b_Modern_ENMs_temporal_block: In this script, modern ENMs are evaluated under a temporal block cross-validation scheme
- 2_Full_ENM_training: In this script, ENMs are generated pooling modern and fossil data
- 3_NICHE_OVERLAP: This script describes the niche overlap analysis, which is used to calculate Shoners'D metric as well as the percentage of increase in niche environmental space granted by fossil niche. In addition, the script contains the code to generate the Figure S1.
- 4_LINEAR_MIXED_MODEL: The script contain the code to run a linear mixed model where the ΔRNC is correlated with the percentage niche increase determined by the fossil data. Figures 1 and 3 are generated in this script.
- 5_RANDOM_FOREST: In this script, two Random Forest classification models are carried out to assess whether differences in climates provided by fossil niches lead to alternative responses of species to climate change. Figure 4 is also generated.
Package folder contains:
- commonFunctions_1.4.6: user-defined package containing ancillary functions for various purposes (e.g., a more user-friendly implementation of the niche overlap calculation and plotting functions provided in the ecospat package)