DOI: 10.16904/envidat.291
title: Simulating population divergence of Northern chamois in the Alps based on habitat dynamics

description: General description
Genomic data, habitat suitability raster files and scripts to run gen3sis to simulate cumulative divergence over time as approximation for genetic differentiation. Scripts for basic analysis of the simulations (e.g., create distance matrix from sampling locations) are provided, too. See original publication (doi link will be provided after publication) for details. The study area are the European Alps.
All data is uploaded as zipped file. Unzip them after the download and put all data in one folder.
See linked publications for correct citation of the data used, use of the data without correct citation is not allowed.
Corresponding author: Flurin Leugger, email: flurin.leugger@gmail.com
 Description of the data (content of the different zip folders)
 Abiotic data
 Glaciers
Folders with raster stacks with glaciated areas at 0.05° resolution in WGS84 projection from Seguinot et al. (2018).
Seguinot, J., Ivy-Ochs, S., Jouvet, G., Huss, M., Funk, M., & Preusser, F. (2018). Modelling last glacial cycle ice dynamics in the Alps. _The Cryosphere, 12(10)_, 3265–3285. https://doi.org/10.5194/tc-12-3265-2018
 Rivers
* river_raster_elevation_class.tif: raster file (.tif) at 0.05° resolution and WGS84 projection with large rivers (scenario 2 from publication). The rivers (each cell) is classified according to the elevation of the cell.
Natural Earth. (2018). Rivers + lake centerlines version 4.1.0. Retrieved January 22, 2020, from https://www.naturalearthdata.com/downloads/50m-physical-vectors/50m-rivers-lake-centerlines
* river_raster_strahler_class_5km.tif: raster file at 0.05° resolution and WGS84 projection with medium rivers. The rivers are classified according to their Strahler order.
Food and Agriculture Organization of the United Nations. (2014). Rivers in Europe (Derived from HydroSHEDS). Retrieved January 29, 2020, from http://www.fao.org/geonetwork/srv/fr/google.kml?uuid=e0243940-e5d9-487c-8102-45180cf1a99f&layers=AQUAMAPS:37253_rivers_europe
 Fossil records
* chamois_fossil_combined_public.xlsx: list with fossil records until 20,000 years BP from Central Europe, see linked references for citation. 
 Chamois occurrences
* chamois_occurrence.csv: Chamois presences from all sources used for the publication (see Suppl. mat. Table S1 for detailed information and correct citations of the data) aggregated at 0.05° resolution (~5km).
 Gen3sis
* config: folders with all configuration files used to run the simulations for the publication (different dispersal divergence parameters).
* scripts: scripts (and helper functions) to run the gen3sis simulations including scripts for the beginning of the subsequent analysis.
 Genetic
* populations.snps.light.vcf: vcf file of the sampled Northern chamois _(Rupicapra rupicapra)_ . The genomic data encompasses 20k SNPs (from ddRAD sequencing).
* Sequencing_final_without_slovakia.txt: sampling locations of Northern chamois _(Rupicapra rupicapra)_
 HSM
* habitat_suitability_hindcasting: Aggregated habitat suitability raster files (stacks, .grd files) at 0.05° resolution and WGS84 projection from 20,000 years BP until today in 100 year time steps. There are separate folders for each environmental variable scenario used (different terrain slope variables) an the different occurrence/pseudo-absence sampling strategy used.
* ODMAP_LeuggerEtAl2021-10-25.csv: ODMAP protocol
description: Resource Title: Genetic data Northern chamois across Alps
 Size: 29467114 bytes
 Format: application/x-zip-compressed
 URL: https://www.envidat.ch/dataset/880eb4ab-2150-44a9-a52a-985ba444a4ac/resource/f8447807-22a7-4219-a585-4b514421f2cb/download/genetic.zip
 Description: ddRADseq data (vcf file and sampling locations) of 449 Northern chamois (Rupicapra rupicapra) sampled across the European Alps
description: Resource Title: Metadata
 Size: 3868 bytes
 Format: text/plain
 URL: https://www.envidat.ch/dataset/880eb4ab-2150-44a9-a52a-985ba444a4ac/resource/53239b17-86ec-411a-9909-9072d437aa64/download/metadata.txt
 Description: Metadata
description: Resource Title: Rivers and glaciers
 Size: 143478 bytes
 Format: application/x-zip-compressed
 URL: https://www.envidat.ch/dataset/880eb4ab-2150-44a9-a52a-985ba444a4ac/resource/c90c16c5-21ae-494e-b1bf-a367ab38e648/download/abiotic.zip
 Description: Input rasters required to set up gen3sis simulations
description: Resource Title: Fossil records
 Size: 34185 bytes
 Format: application/x-zip-compressed
 URL: https://www.envidat.ch/dataset/880eb4ab-2150-44a9-a52a-985ba444a4ac/resource/801413db-9f0f-4147-99c2-8b36dd664e44/download/fossil_records.zip
 Description: Chamois fossil records with estimated time span and coordinates. Please see the sheet "references_data_sets" for the references and read the read_me.txt file prior to using the data.
description: Resource Title: Chamois occurrences
 Size: 136158 bytes
 Format: application/vnd.ms-excel
 URL: https://www.envidat.ch/dataset/880eb4ab-2150-44a9-a52a-985ba444a4ac/resource/26583b50-5222-4e9c-a69d-062f60965a92/download/chamois_occurrence.csv
 Description: Coordinates (0.05° resolution) of chamois occurrences across the Alps. See Suppl. mat. Table S1 for more information and citation of the data sets used.
description: Resource Title: gen3sis simulations
 Size: 81389 bytes
 Format: application/x-zip-compressed
 URL: https://www.envidat.ch/dataset/880eb4ab-2150-44a9-a52a-985ba444a4ac/resource/599ce7b4-0994-42e4-a374-639012aa6c38/download/gen3sis.zip
 Description: Scripts to run gen3sis simulations, including configs used for the publication.

__1.2_gen3sis_input_generation.R__ creates the input files required for __2.2_gen3sis_simulation_chamois.R__, which is running the gen3sis simulations.
__ 3_gen3sis_track_simulation_over_time.R__ and __4_gen3sis_divergence_sampling_locations.R__ can be used to start the analysis.
description: Resource Title: Habitat suitability raster
 Size: 1908747503 bytes
 Format: application/x-zip-compressed
 URL: https://www.envidat.ch/dataset/880eb4ab-2150-44a9-a52a-985ba444a4ac/resource/ff87fdf4-c8d6-47d0-936a-b455c77c26d2/download/hsm.zip
 Description: Habitat suitability raster stacks (.grd) files for different terrain slope scenarios use (see main publication its supporting information for details) for Northern chamois until 20,000 years BP in 100 year time steps.

### Description of layer names:
* __prob__: habitat suitability ranging continuously from 0 (unsuitable) to 1 (very well suitable).
*__bin__: binary classification of habitat suitability based on TSS threshold optimization (see main publication and supporting information for details).
*__glm__: generalized linear model (to model and predict habitat suitability)
*__gam__: generalized additive model
*__gbm__: generalized boosted regression model
*__rf__: random forest
*__ensemble__: average of all 4 model types