DOI: 10.5061/dryad.02v6wwq96
title: 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: 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. 
description: # 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: 1. **Geopackages** * Geopackage_BEYER_CHELSA: In
 this folder are the geopackages for the 28 species achieving AUC &gt; 0.7
 in both modern and full ENMs. In each geopackage are coordinates and
 filtered climatic variable values (once VIF &lt; 5 was applied) for
 occurrence and background points. The geopackages are loaded in all the
 scripts. 2. **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 3.
 **"final.name_bay.ch.txt"**: This file is used in the scripts to
 generate names of species where necessary. 4. **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)