Data and code from "Mismatch in reindeer resilience to past and future warming signals ongoing declines"
Creators: name: Canteri, Elisabetta
name: Brown, Stuart
name: Post, Eric
name: Schmidt, Niels Martin
name: Nogués-Bravo, David
name: Fordham, Damien
Publisher: name: figshare
Year: 2025
Subjects: classificationCode: 310306
subject: Palaeoecology
classificationCode: 310307
subject: Population ecology

description: "<b>Data S1.xlsx</b>" quality-rated fossil occurrence dataset for <i>Rangifer</i>."<b>Data S2.xlsx</b>" details of mitochondrial ancient DNA sequences."<b>Data S3.xlsx</b>" contemporary occurrence dataset for <i>Rangifer</i><i>.</i>"<b>Data S4.nex</b>" NEXUS file used to estimate trend in effective population size."<b>Reindeer_Code</b>" is a .zip file that contains:R code to reproduce all results in the manuscript.Data called by the R code.Please note that scripts need to run on a High-Performance Computing Server and some steps can take months to process.<b>Description of Reindeer_Code</b>1. "<b>Data</b>" folder that includes:Historical climate data (CRU_corrected.csv) used to pair reindeer occurrences to climatePaleoclimate (rt_paleoclimate.csv and the rasters in the "Paleoclimate" folder) used to pair the fossils to the paleoclimateTable with fossil records (Reindeer_fossils.csv)Table with GBIF occurrences (Reindeer_GBIF.csv)A study region raster that shows the geographic extent of the region used in the manuscript (study_region_mask.tiff)"<b>Paleopop</b>" folder with the data needed to run simulations and analyze the output. Inside there is a "Paleopop_Data" folder and a "Targets" folder. Inside the "Paleopop_Data" folder:ince_inv_prj.RDS (glacial ice)OuterCells_Polygons.RDS (modification of the temporal land-sea mask)prj_ext.RDS (extent of CRS projection of the study region)reindeer_region_prj.RDS (paleoregion used in simulations)rt_humans_mean_prj.RDS (Humans mean Ne - from CISGEM)rt_humans_sd_prj.RDS (Humans SD Ne - from CISGEM)GreenlandPolygon (folder with polygon of Greenland used in the simulations)HS_PRJ (folder with examples of habitat suitability projections. 5 files are provided to show how the simulations work)Regions (folder) with RegionsPoly.csv (region subdivision in .csv format) and RT_Subreg (shapefile and metadata of the subregions)sample_data.csv (input table)Inside the "Targets" folder:rt_tracer.txt (output of Bayesian Skyline Plot analysis using aDNA sequences of reindeer)Wang_independent_validation.csv (occurrences from environmental aDNA from Wang et al. 2021)ExtinctionTime.csv (extinction times in Europe)EuropePolygons (folder with European polygons used to calculate extinction times)colonisationGreenland.csv (colonization times of Greenland)"<b>FutureSims</b>" folder, which contains a "Future_Data" folder: "reindeer_region_future.RDS" (used in the simulations of forecast reindeer abundances)"RT_GBIF_2022.csv" (file containing GBIF reindeer observations since 2022 used to calculate probability of occupancy)"<b>Scripts</b>" folder. This contains all the code that is needed to obtain the results in the manuscripts. Each file name starts with "Step" and the step number, starting at Step1 and ending at Step20. To be able to generate our results, some steps will need to be repeated before continuing to the next steps. It is clearly written in the files when this needs to happen. Some scripts include sourcing functions from external files, which are provided in the "Functions" folder.Step1_PairClimateObservations.RStep2_AddRandomPoints.RStep3_NicheCut.RStep4_NicheStatistics.RStep5_SelectNiches.RStep6_ENMs.RStep7_RescaleENMs.RStep8_Simulations.RmdStep9_ValidationTargets.RStep10_SummaryMetrics.RStep11_POMValidation.RStep12_PosteriorPredictiveChecks.RStep13_InformedPriors.RStep14_Results.RStep15_ExtirpationMap.RStep16_LandUse.RStep17_FutureSimulations.RStep18_FutureResults,RStep19_ProbabilityOfOccupancy.RStep20_ExtinctionRisk.RFig1.RFig2.RFig3.RFig4.RMovie_1.RMovie_2.R