Changes
On April 6, 2022 at 5:41:08 AM UTC, Flurin Leugger:
-
Updated description of Simulating population divergence of Northern chamois in the Alps based on habitat dynamics from
# 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. ## sampling locations .csv file with coordinates of the 449 sampling locations of the chamois used in the study ## 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_LeuggerEtAl__2021-10-25.csv__: ODMAP protocol
to# 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 Occurrence records 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_LeuggerEtAl__2021-10-25.csv__: ODMAP protocol
f | 1 | { | f | 1 | { |
2 | "author": "[{\"affiliation\": \"Landscape Ecology, Institute of | 2 | "author": "[{\"affiliation\": \"Landscape Ecology, Institute of | ||
3 | Terrestrial Ecosystems, ETH Z\\u00fcrich, 8049 Z\\u00fcrich, | 3 | Terrestrial Ecosystems, ETH Z\\u00fcrich, 8049 Z\\u00fcrich, | ||
4 | Switzerland\", \"affiliation_02\": \"Landscape Ecology, Landscape | 4 | Switzerland\", \"affiliation_02\": \"Landscape Ecology, Landscape | ||
5 | Change Science, Swiss Federal Institute for Forest, Snow and Landscape | 5 | Change Science, Swiss Federal Institute for Forest, Snow and Landscape | ||
6 | Research WSL, 8903 Birmensdorf, Switzerland\", \"affiliation_03\": | 6 | Research WSL, 8903 Birmensdorf, Switzerland\", \"affiliation_03\": | ||
7 | \"\", \"data_credit\": [\"collection\", \"software\", | 7 | \"\", \"data_credit\": [\"collection\", \"software\", | ||
8 | \"publication\"], \"email\": \"flurin.leugger@usys.ethz.ch\", | 8 | \"publication\"], \"email\": \"flurin.leugger@usys.ethz.ch\", | ||
9 | \"given_name\": \"Flurin\", \"identifier\": \"0000-0001-9027-6892\", | 9 | \"given_name\": \"Flurin\", \"identifier\": \"0000-0001-9027-6892\", | ||
10 | \"name\": \"Leugger\"}, {\"affiliation\": \"CNRS, Sorbonne | 10 | \"name\": \"Leugger\"}, {\"affiliation\": \"CNRS, Sorbonne | ||
11 | Universit\\u00e9, UMR 7144, Station Biologique de Roscoff\", | 11 | Universit\\u00e9, UMR 7144, Station Biologique de Roscoff\", | ||
12 | \"affiliation_02\": \"\", \"affiliation_03\": \"\", \"data_credit\": | 12 | \"affiliation_02\": \"\", \"affiliation_03\": \"\", \"data_credit\": | ||
13 | [\"collection\", \"validation\", \"publication\"], \"email\": | 13 | [\"collection\", \"validation\", \"publication\"], \"email\": | ||
14 | \"thomas.broquet@sb-roscoff.fr\", \"given_name\": \"Thomas\", | 14 | \"thomas.broquet@sb-roscoff.fr\", \"given_name\": \"Thomas\", | ||
15 | \"identifier\": \"\", \"name\": \"Broquet\"}, {\"affiliation\": | 15 | \"identifier\": \"\", \"name\": \"Broquet\"}, {\"affiliation\": | ||
16 | \"WSL\", \"affiliation_02\": \"\", \"affiliation_03\": \"\", | 16 | \"WSL\", \"affiliation_02\": \"\", \"affiliation_03\": \"\", | ||
17 | \"data_credit\": [\"collection\", \"publication\"], \"email\": | 17 | \"data_credit\": [\"collection\", \"publication\"], \"email\": | ||
18 | \"dirk.karger@wsl.ch\", \"given_name\": \"Dirk Nikolaus\", | 18 | \"dirk.karger@wsl.ch\", \"given_name\": \"Dirk Nikolaus\", | ||
19 | \"identifier\": \"0000-0001-7770-6229\", \"name\": \"Karger\"}, | 19 | \"identifier\": \"0000-0001-7770-6229\", \"name\": \"Karger\"}, | ||
20 | {\"affiliation\": \"Universit\\u00e9 Grenoble Alpes, Universit\\u00e9 | 20 | {\"affiliation\": \"Universit\\u00e9 Grenoble Alpes, Universit\\u00e9 | ||
21 | Savoie Mont Blanc, CNRS, LECA\", \"affiliation_02\": \"\", | 21 | Savoie Mont Blanc, CNRS, LECA\", \"affiliation_02\": \"\", | ||
22 | \"affiliation_03\": \"\", \"data_credit\": [\"collection\", | 22 | \"affiliation_03\": \"\", \"data_credit\": [\"collection\", | ||
23 | \"publication\"], \"email\": | 23 | \"publication\"], \"email\": | ||
24 | \"Delphine.Rioux@univ-grenoble-alpes.fr\", \"given_name\": | 24 | \"Delphine.Rioux@univ-grenoble-alpes.fr\", \"given_name\": | ||
25 | \"Delphine\", \"identifier\": \"\", \"name\": \"Rioux\"}, | 25 | \"Delphine\", \"identifier\": \"\", \"name\": \"Rioux\"}, | ||
26 | {\"affiliation\": \"University of Primorska, Faculty of Mathematics, | 26 | {\"affiliation\": \"University of Primorska, Faculty of Mathematics, | ||
27 | Natural Sciences, and Information Technologies\", \"affiliation_02\": | 27 | Natural Sciences, and Information Technologies\", \"affiliation_02\": | ||
28 | \"Environmental Protection College\", \"affiliation_03\": \"\", | 28 | \"Environmental Protection College\", \"affiliation_03\": \"\", | ||
29 | \"data_credit\": [\"collection\", \"publication\"], \"email\": | 29 | \"data_credit\": [\"collection\", \"publication\"], \"email\": | ||
30 | \"elena.buzan@famnit.upr.si\", \"given_name\": \"Elena\", | 30 | \"elena.buzan@famnit.upr.si\", \"given_name\": \"Elena\", | ||
31 | \"identifier\": \"\", \"name\": \"Buzan\"}, {\"affiliation\": \"Chair | 31 | \"identifier\": \"\", \"name\": \"Buzan\"}, {\"affiliation\": \"Chair | ||
32 | of Wildlife Ecology and Management, University of Freiburg\", | 32 | of Wildlife Ecology and Management, University of Freiburg\", | ||
33 | \"affiliation_02\": \"Stelvio National Park\", \"affiliation_03\": | 33 | \"affiliation_02\": \"Stelvio National Park\", \"affiliation_03\": | ||
34 | \"\", \"data_credit\": [\"collection\", \"publication\"], \"email\": | 34 | \"\", \"data_credit\": [\"collection\", \"publication\"], \"email\": | ||
35 | \"luca.corlatti@wildlife.uni-freiburg.de\", \"given_name\": \"Luca\", | 35 | \"luca.corlatti@wildlife.uni-freiburg.de\", \"given_name\": \"Luca\", | ||
36 | \"identifier\": \"\", \"name\": \"Corlatti\"}, {\"affiliation\": | 36 | \"identifier\": \"\", \"name\": \"Corlatti\"}, {\"affiliation\": | ||
37 | \"Conservation Genomics Research Unit, Fondazione Edmund Mach\", | 37 | \"Conservation Genomics Research Unit, Fondazione Edmund Mach\", | ||
38 | \"affiliation_02\": \"\", \"affiliation_03\": \"\", \"data_credit\": | 38 | \"affiliation_02\": \"\", \"affiliation_03\": \"\", \"data_credit\": | ||
39 | [\"collection\", \"publication\"], \"email\": | 39 | [\"collection\", \"publication\"], \"email\": | ||
40 | \"barbara.crestanello@fmach.it\", \"given_name\": \"Barbara\", | 40 | \"barbara.crestanello@fmach.it\", \"given_name\": \"Barbara\", | ||
41 | \"identifier\": \"\", \"name\": \"Crestanello\"}, {\"affiliation\": | 41 | \"identifier\": \"\", \"name\": \"Crestanello\"}, {\"affiliation\": | ||
42 | \"Universit\\u00e9 Grenoble Alpes, Universit\\u00e9 Savoie Mont Blanc, | 42 | \"Universit\\u00e9 Grenoble Alpes, Universit\\u00e9 Savoie Mont Blanc, | ||
43 | CNRS, LECA\", \"affiliation_02\": \"\", \"affiliation_03\": \"\", | 43 | CNRS, LECA\", \"affiliation_02\": \"\", \"affiliation_03\": \"\", | ||
44 | \"data_credit\": [\"collection\", \"publication\"], \"email\": | 44 | \"data_credit\": [\"collection\", \"publication\"], \"email\": | ||
45 | \"nadine.curt-grand-gaudin@univ-smb.fr\", \"given_name\": \"Nadine \", | 45 | \"nadine.curt-grand-gaudin@univ-smb.fr\", \"given_name\": \"Nadine \", | ||
46 | \"identifier\": \"\", \"name\": \"Curt-Grand-Gaudin\"}, | 46 | \"identifier\": \"\", \"name\": \"Curt-Grand-Gaudin\"}, | ||
47 | {\"affiliation\": \"Conservation Genomics Research Unit, Fondazione | 47 | {\"affiliation\": \"Conservation Genomics Research Unit, Fondazione | ||
48 | Edmund Mach\", \"affiliation_02\": \"\", \"affiliation_03\": \"\", | 48 | Edmund Mach\", \"affiliation_02\": \"\", \"affiliation_03\": \"\", | ||
49 | \"data_credit\": [\"collection\", \"publication\"], \"email\": | 49 | \"data_credit\": [\"collection\", \"publication\"], \"email\": | ||
50 | \"heidi.hauffe@fmach.it\", \"given_name\": \"Heidi Christine\", | 50 | \"heidi.hauffe@fmach.it\", \"given_name\": \"Heidi Christine\", | ||
51 | \"identifier\": \"\", \"name\": \"Hauffe\"}, {\"affiliation\": | 51 | \"identifier\": \"\", \"name\": \"Hauffe\"}, {\"affiliation\": | ||
52 | \"Institute of Vertebrate Biology of the Czech Academy of Sciences\", | 52 | \"Institute of Vertebrate Biology of the Czech Academy of Sciences\", | ||
53 | \"affiliation_02\": \"\", \"affiliation_03\": \"\", \"data_credit\": | 53 | \"affiliation_02\": \"\", \"affiliation_03\": \"\", \"data_credit\": | ||
54 | [\"collection\", \"publication\"], \"email\": \"roleckova@ivb.cz\", | 54 | [\"collection\", \"publication\"], \"email\": \"roleckova@ivb.cz\", | ||
55 | \"given_name\": \"Barbora\", \"identifier\": \"\", \"name\": | 55 | \"given_name\": \"Barbora\", \"identifier\": \"\", \"name\": | ||
56 | \"Role\\u010dkov\\u00e1\"}, {\"affiliation\": \"University of Zagreb, | 56 | \"Role\\u010dkov\\u00e1\"}, {\"affiliation\": \"University of Zagreb, | ||
57 | Faculty of Agriculture, Department of Fisheries, Apiculture, Wildlife | 57 | Faculty of Agriculture, Department of Fisheries, Apiculture, Wildlife | ||
58 | Management and Special Zoology\", \"affiliation_02\": \"\", | 58 | Management and Special Zoology\", \"affiliation_02\": \"\", | ||
59 | \"affiliation_03\": \"\", \"data_credit\": [\"collection\", | 59 | \"affiliation_03\": \"\", \"data_credit\": [\"collection\", | ||
60 | \"publication\"], \"email\": \"nsprem@agr.hr\", \"given_name\": | 60 | \"publication\"], \"email\": \"nsprem@agr.hr\", \"given_name\": | ||
61 | \"Nikica\", \"identifier\": \"\", \"name\": \"\\u0160prem\"}, | 61 | \"Nikica\", \"identifier\": \"\", \"name\": \"\\u0160prem\"}, | ||
62 | {\"affiliation\": \"Universit\\u00e9 Grenoble Alpes, Universit\\u00e9 | 62 | {\"affiliation\": \"Universit\\u00e9 Grenoble Alpes, Universit\\u00e9 | ||
63 | Savoie Mont Blanc, CNRS, LECA\", \"affiliation_02\": \"\", | 63 | Savoie Mont Blanc, CNRS, LECA\", \"affiliation_02\": \"\", | ||
64 | \"affiliation_03\": \"\", \"data_credit\": [\"collection\", | 64 | \"affiliation_03\": \"\", \"data_credit\": [\"collection\", | ||
65 | \"publication\"], \"email\": \"Nathalie.Tissot@univ-smb.fr\", | 65 | \"publication\"], \"email\": \"Nathalie.Tissot@univ-smb.fr\", | ||
66 | \"given_name\": \"Nathalie\", \"identifier\": \"\", \"name\": | 66 | \"given_name\": \"Nathalie\", \"identifier\": \"\", \"name\": | ||
67 | \"Tissot\"}, {\"affiliation\": \"Universit\\u00e9 Grenoble Alpes, | 67 | \"Tissot\"}, {\"affiliation\": \"Universit\\u00e9 Grenoble Alpes, | ||
68 | Universit\\u00e9 Savoie Mont Blanc, CNRS, LECA\", \"affiliation_02\": | 68 | Universit\\u00e9 Savoie Mont Blanc, CNRS, LECA\", \"affiliation_02\": | ||
69 | \"\", \"affiliation_03\": \"\", \"data_credit\": [\"collection\", | 69 | \"\", \"affiliation_03\": \"\", \"data_credit\": [\"collection\", | ||
70 | \"publication\"], \"email\": \"sophie.tissot@etu.umontpellier.fr\", | 70 | \"publication\"], \"email\": \"sophie.tissot@etu.umontpellier.fr\", | ||
71 | \"given_name\": \"Sophie\", \"identifier\": \"\", \"name\": | 71 | \"given_name\": \"Sophie\", \"identifier\": \"\", \"name\": | ||
72 | \"Tissot\"}, {\"affiliation\": \"Institute of Vertebrate Biology of | 72 | \"Tissot\"}, {\"affiliation\": \"Institute of Vertebrate Biology of | ||
73 | the Czech Academy of Sciences\", \"affiliation_02\": \"\", | 73 | the Czech Academy of Sciences\", \"affiliation_02\": \"\", | ||
74 | \"affiliation_03\": \"\", \"data_credit\": [\"collection\", | 74 | \"affiliation_03\": \"\", \"data_credit\": [\"collection\", | ||
75 | \"publication\"], \"email\": \"radkpol@centrum.cz\", \"given_name\": | 75 | \"publication\"], \"email\": \"radkpol@centrum.cz\", \"given_name\": | ||
76 | \"Radka\", \"identifier\": \"\", \"name\": \"Valterov\\u00e1\"}, | 76 | \"Radka\", \"identifier\": \"\", \"name\": \"Valterov\\u00e1\"}, | ||
77 | {\"affiliation\": \"Universit\\u00e9 Grenoble Alpes, Universit\\u00e9 | 77 | {\"affiliation\": \"Universit\\u00e9 Grenoble Alpes, Universit\\u00e9 | ||
78 | Savoie Mont Blanc, CNRS, LECA\", \"affiliation_02\": \"\", | 78 | Savoie Mont Blanc, CNRS, LECA\", \"affiliation_02\": \"\", | ||
79 | \"affiliation_03\": \"\", \"data_credit\": [\"collection\", | 79 | \"affiliation_03\": \"\", \"data_credit\": [\"collection\", | ||
80 | \"validation\", \"publication\", \"supervision\"], \"email\": | 80 | \"validation\", \"publication\", \"supervision\"], \"email\": | ||
81 | \"glenn.yannic@univ-smb.fr\", \"given_name\": \"Glenn\", | 81 | \"glenn.yannic@univ-smb.fr\", \"given_name\": \"Glenn\", | ||
82 | \"identifier\": \"\", \"name\": \"Yannic\"}, {\"affiliation\": | 82 | \"identifier\": \"\", \"name\": \"Yannic\"}, {\"affiliation\": | ||
83 | \"Landscape Ecology, Institute of Terrestrial Ecosystems, ETH | 83 | \"Landscape Ecology, Institute of Terrestrial Ecosystems, ETH | ||
84 | Z\\u00fcrich, 8049 Z\\u00fcrich, Switzerland\", \"affiliation_02\": | 84 | Z\\u00fcrich, 8049 Z\\u00fcrich, Switzerland\", \"affiliation_02\": | ||
85 | \"Landscape Ecology, Landscape Change Science, Swiss Federal Institute | 85 | \"Landscape Ecology, Landscape Change Science, Swiss Federal Institute | ||
86 | for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, | 86 | for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, | ||
87 | Switzerland\", \"affiliation_03\": \"\", \"data_credit\": | 87 | Switzerland\", \"affiliation_03\": \"\", \"data_credit\": | ||
88 | [\"collection\", \"validation\", \"publication\", \"supervision\"], | 88 | [\"collection\", \"validation\", \"publication\", \"supervision\"], | ||
89 | \"email\": \"loic.pellissier@usys.ethz.ch\", \"given_name\": \"Loic\", | 89 | \"email\": \"loic.pellissier@usys.ethz.ch\", \"given_name\": \"Loic\", | ||
90 | \"identifier\": \"0000-0002-2289-8259\", \"name\": \"Pellissier\"}]", | 90 | \"identifier\": \"0000-0002-2289-8259\", \"name\": \"Pellissier\"}]", | ||
91 | "author_email": null, | 91 | "author_email": null, | ||
92 | "creator_user_id": "29b58075-315f-4aa2-bfff-425ea9553e90", | 92 | "creator_user_id": "29b58075-315f-4aa2-bfff-425ea9553e90", | ||
93 | "date": "[{\"date\": \"2021-03-02\", \"date_type\": \"created\", | 93 | "date": "[{\"date\": \"2021-03-02\", \"date_type\": \"created\", | ||
94 | \"end_date\": \"\"}]", | 94 | \"end_date\": \"\"}]", | ||
95 | "doi": "10.16904/envidat.291", | 95 | "doi": "10.16904/envidat.291", | ||
96 | "funding": "[{\"grant_number\": \"\", \"institution\": \"ETH\", | 96 | "funding": "[{\"grant_number\": \"\", \"institution\": \"ETH\", | ||
97 | \"institution_url\": \"\"}, {\"grant_number\": \"310030_188550\", | 97 | \"institution_url\": \"\"}, {\"grant_number\": \"310030_188550\", | ||
98 | \"institution\": \"SNCF\", \"institution_url\": \"\"}]", | 98 | \"institution\": \"SNCF\", \"institution_url\": \"\"}]", | ||
99 | "groups": [], | 99 | "groups": [], | ||
100 | "id": "880eb4ab-2150-44a9-a52a-985ba444a4ac", | 100 | "id": "880eb4ab-2150-44a9-a52a-985ba444a4ac", | ||
101 | "isopen": false, | 101 | "isopen": false, | ||
102 | "language": "en", | 102 | "language": "en", | ||
103 | "license_id": "wsl-data", | 103 | "license_id": "wsl-data", | ||
104 | "license_title": "WSL Data Policy", | 104 | "license_title": "WSL Data Policy", | ||
105 | "license_url": | 105 | "license_url": | ||
106 | ps://www.wsl.ch/en/about-wsl/programmes-and-initiatives/envidat.html", | 106 | ps://www.wsl.ch/en/about-wsl/programmes-and-initiatives/envidat.html", | ||
107 | "maintainer": "{\"affiliation\": \"WSL\", \"email\": | 107 | "maintainer": "{\"affiliation\": \"WSL\", \"email\": | ||
108 | \"flurin.leugger@usys.ethz.ch\", \"given_name\": \"Flurin\", | 108 | \"flurin.leugger@usys.ethz.ch\", \"given_name\": \"Flurin\", | ||
109 | \"identifier\": \"\", \"name\": \"Leugger\"}", | 109 | \"identifier\": \"\", \"name\": \"Leugger\"}", | ||
110 | "maintainer_email": null, | 110 | "maintainer_email": null, | ||
111 | "metadata_created": "2022-02-10T07:32:55.894233", | 111 | "metadata_created": "2022-02-10T07:32:55.894233", | ||
n | 112 | "metadata_modified": "2022-04-05T14:00:48.224347", | n | 112 | "metadata_modified": "2022-04-06T05:41:07.989919", |
113 | "name": "simulating-chamois-populations", | 113 | "name": "simulating-chamois-populations", | ||
114 | "notes": "# General description\r\n\r\nGenomic data, habitat | 114 | "notes": "# General description\r\n\r\nGenomic data, habitat | ||
115 | suitability raster files and scripts to run gen3sis to simulate | 115 | suitability raster files and scripts to run gen3sis to simulate | ||
116 | cumulative divergence over time as approximation for genetic | 116 | cumulative divergence over time as approximation for genetic | ||
117 | differentiation. Scripts for basic analysis of the simulations (e.g., | 117 | differentiation. Scripts for basic analysis of the simulations (e.g., | ||
118 | create distance matrix from sampling locations) are provided, too. See | 118 | create distance matrix from sampling locations) are provided, too. See | ||
119 | original publication (doi link will be provided after publication) for | 119 | original publication (doi link will be provided after publication) for | ||
120 | details. The study area are the European Alps.\r\nAll data is uploaded | 120 | details. The study area are the European Alps.\r\nAll data is uploaded | ||
121 | as zipped file. Unzip them after the download and put all data in one | 121 | as zipped file. Unzip them after the download and put all data in one | ||
122 | folder.\r\nSee linked publications for correct citation of the data | 122 | folder.\r\nSee linked publications for correct citation of the data | ||
123 | used, use of the data without correct citation is not | 123 | used, use of the data without correct citation is not | ||
124 | allowed.\r\n\r\n__Corresponding author__: Flurin Leugger, email: | 124 | allowed.\r\n\r\n__Corresponding author__: Flurin Leugger, email: | ||
125 | flurin.leugger@gmail.com\r\n\r\n\r\n# Description of the data (content | 125 | flurin.leugger@gmail.com\r\n\r\n\r\n# Description of the data (content | ||
126 | of the different zip folders)\r\n\r\n## Abiotic data\r\n\r\n### | 126 | of the different zip folders)\r\n\r\n## Abiotic data\r\n\r\n### | ||
127 | Glaciers\r\nFolders with raster stacks with glaciated areas at | 127 | Glaciers\r\nFolders with raster stacks with glaciated areas at | ||
128 | 0.05\u00b0 resolution in WGS84 projection from Seguinot et al. | 128 | 0.05\u00b0 resolution in WGS84 projection from Seguinot et al. | ||
129 | (2018).\r\nSeguinot, J., Ivy-Ochs, S., Jouvet, G., Huss, M., Funk, M., | 129 | (2018).\r\nSeguinot, J., Ivy-Ochs, S., Jouvet, G., Huss, M., Funk, M., | ||
130 | & Preusser, F. (2018). Modelling last glacial cycle ice dynamics in | 130 | & Preusser, F. (2018). Modelling last glacial cycle ice dynamics in | ||
131 | the Alps. _The Cryosphere, 12(10)_, 3265\u20133285. | 131 | the Alps. _The Cryosphere, 12(10)_, 3265\u20133285. | ||
132 | https://doi.org/10.5194/tc-12-3265-2018\r\n\r\n### Rivers\r\n* | 132 | https://doi.org/10.5194/tc-12-3265-2018\r\n\r\n### Rivers\r\n* | ||
133 | __river_raster_elevation_class.tif__: raster file (.tif) at 0.05\u00b0 | 133 | __river_raster_elevation_class.tif__: raster file (.tif) at 0.05\u00b0 | ||
134 | resolution and WGS84 projection with large rivers (scenario 2 from | 134 | resolution and WGS84 projection with large rivers (scenario 2 from | ||
135 | publication). The rivers (each cell) is classified according to the | 135 | publication). The rivers (each cell) is classified according to the | ||
136 | elevation of the cell.\r\nNatural Earth. (2018). Rivers + lake | 136 | elevation of the cell.\r\nNatural Earth. (2018). Rivers + lake | ||
137 | centerlines version 4.1.0. Retrieved January 22, 2020, from | 137 | centerlines version 4.1.0. Retrieved January 22, 2020, from | ||
138 | ta.com/downloads/50m-physical-vectors/50m-rivers-lake-centerlines\r\n* | 138 | ta.com/downloads/50m-physical-vectors/50m-rivers-lake-centerlines\r\n* | ||
139 | __river_raster_strahler_class_5km.tif__: raster file at 0.05\u00b0 | 139 | __river_raster_strahler_class_5km.tif__: raster file at 0.05\u00b0 | ||
140 | resolution and WGS84 projection with medium rivers. The rivers are | 140 | resolution and WGS84 projection with medium rivers. The rivers are | ||
141 | classified according to their Strahler order.\r\nFood and Agriculture | 141 | classified according to their Strahler order.\r\nFood and Agriculture | ||
142 | Organization of the United Nations. (2014). Rivers in Europe (Derived | 142 | Organization of the United Nations. (2014). Rivers in Europe (Derived | ||
143 | from HydroSHEDS). Retrieved January 29, 2020, from | 143 | from HydroSHEDS). Retrieved January 29, 2020, from | ||
144 | 9-487c-8102-45180cf1a99f&layers=AQUAMAPS:37253_rivers_europe\r\n\r\n## | 144 | 9-487c-8102-45180cf1a99f&layers=AQUAMAPS:37253_rivers_europe\r\n\r\n## | ||
145 | fossil records\r\n* __chamois_fossil_combined_public.xlsx__: list with | 145 | fossil records\r\n* __chamois_fossil_combined_public.xlsx__: list with | ||
146 | fossil records until 20,000 years BP from Central Europe, see linked | 146 | fossil records until 20,000 years BP from Central Europe, see linked | ||
t | 147 | references for citation. \r\n\r\n## sampling locations\r\n.csv file | t | 147 | references for citation. \r\n\r\n## chamois occurrences\r\nOccurrence |
148 | with coordinates of the 449 sampling locations of the chamois used in | 148 | records from all sources used for the publication (see Suppl. mat. | ||
149 | the study\r\n\r\n## gen3sis\r\n* __config__: folders with all | 149 | Table S1 for detailed information and correct citations of the data) | ||
150 | configuration files used to run the simulations for the publication | 150 | aggregated at 0.05\u00b0 resolution (~5km).\r\n\r\n## gen3sis\r\n* | ||
151 | (different dispersal divergence parameters).\r\n* __scripts__: scripts | 151 | __config__: folders with all configuration files used to run the | ||
152 | (and helper functions) to run the gen3sis simulations including | 152 | simulations for the publication (different dispersal divergence | ||
153 | scripts for the beginning of the subsequent analysis.\r\n\r\n## | 153 | parameters).\r\n* __scripts__: scripts (and helper functions) to run | ||
154 | the gen3sis simulations including scripts for the beginning of the | ||||
155 | subsequent analysis.\r\n\r\n## genetic\r\n* | ||||
154 | genetic\r\n* __populations.snps.light.vcf__: vcf file of the sampled | 156 | __populations.snps.light.vcf__: vcf file of the sampled Northern | ||
155 | Northern chamois _(Rupicapra rupicapra)_ . The genomic data | 157 | chamois _(Rupicapra rupicapra)_ . The genomic data encompasses 20k | ||
156 | encompasses 20k SNPs (from ddRAD sequencing).\r\n* | 158 | SNPs (from ddRAD sequencing).\r\n* | ||
157 | __Sequencing_final_without_slovakia.txt__: sampling locations of | 159 | __Sequencing_final_without_slovakia.txt__: sampling locations of | ||
158 | Northern chamois _(Rupicapra rupicapra)_\r\n\r\n## hsm\r\n* | 160 | Northern chamois _(Rupicapra rupicapra)_\r\n\r\n## hsm\r\n* | ||
159 | __habitat_suitability_hindcasting__: Aggregated habitat suitability | 161 | __habitat_suitability_hindcasting__: Aggregated habitat suitability | ||
160 | raster files (stacks, .grd files) at 0.05\u00b0 resolution and WGS84 | 162 | raster files (stacks, .grd files) at 0.05\u00b0 resolution and WGS84 | ||
161 | projection from 20,000 years BP until today in 100 year time steps. | 163 | projection from 20,000 years BP until today in 100 year time steps. | ||
162 | There are separate folders for each environmental variable scenario | 164 | There are separate folders for each environmental variable scenario | ||
163 | used (different terrain slope variables) an the different | 165 | used (different terrain slope variables) an the different | ||
164 | occurrence/pseudo-absence sampling strategy used.\r\n* | 166 | occurrence/pseudo-absence sampling strategy used.\r\n* | ||
165 | __ODMAP_LeuggerEtAl__2021-10-25.csv__: ODMAP protocol", | 167 | __ODMAP_LeuggerEtAl__2021-10-25.csv__: ODMAP protocol", | ||
166 | "num_resources": 7, | 168 | "num_resources": 7, | ||
167 | "num_tags": 6, | 169 | "num_tags": 6, | ||
168 | "organization": { | 170 | "organization": { | ||
169 | "approval_status": "approved", | 171 | "approval_status": "approved", | ||
170 | "created": "2018-12-01T11:42:44.590217", | 172 | "created": "2018-12-01T11:42:44.590217", | ||
171 | "description": "Our laboratory aims at understanding and | 173 | "description": "Our laboratory aims at understanding and | ||
172 | forecasting the response of biodiversity to landscape changes. We | 174 | forecasting the response of biodiversity to landscape changes. We | ||
173 | investigate the historical responses of species to past changes such | 175 | investigate the historical responses of species to past changes such | ||
174 | as plate tectonics or the glaciations of the Quaternary and | 176 | as plate tectonics or the glaciations of the Quaternary and | ||
175 | contemporary responses to ongoing global changes. We develop spatial | 177 | contemporary responses to ongoing global changes. We develop spatial | ||
176 | mechanistic models of biodiversity that account for processes such as | 178 | mechanistic models of biodiversity that account for processes such as | ||
177 | dispersal and biotic interactions.", | 179 | dispersal and biotic interactions.", | ||
178 | "id": "3b0fde83-e15c-4f8b-a451-9778f5309a84", | 180 | "id": "3b0fde83-e15c-4f8b-a451-9778f5309a84", | ||
179 | "image_url": | 181 | "image_url": | ||
180 | ww.ites.ethz.ch/_jcr_content/orgLogo.imageformat.logo.1518520524.jpg", | 182 | ww.ites.ethz.ch/_jcr_content/orgLogo.imageformat.logo.1518520524.jpg", | ||
181 | "is_organization": true, | 183 | "is_organization": true, | ||
182 | "name": "landscape-ecology", | 184 | "name": "landscape-ecology", | ||
183 | "state": "active", | 185 | "state": "active", | ||
184 | "title": "Landscape Ecology", | 186 | "title": "Landscape Ecology", | ||
185 | "type": "organization" | 187 | "type": "organization" | ||
186 | }, | 188 | }, | ||
187 | "owner_org": "3b0fde83-e15c-4f8b-a451-9778f5309a84", | 189 | "owner_org": "3b0fde83-e15c-4f8b-a451-9778f5309a84", | ||
188 | "private": false, | 190 | "private": false, | ||
189 | "publication": "{\"publication_year\": \"2022\", \"publisher\": | 191 | "publication": "{\"publication_year\": \"2022\", \"publisher\": | ||
190 | \"EnviDat\"}", | 192 | \"EnviDat\"}", | ||
191 | "publication_state": "pub_pending", | 193 | "publication_state": "pub_pending", | ||
192 | "related_datasets": "", | 194 | "related_datasets": "", | ||
193 | "related_publications": "* wsl:27918* Hagen, O., Fl\u00fcck, B., | 195 | "related_publications": "* wsl:27918* Hagen, O., Fl\u00fcck, B., | ||
194 | Fopp, F., Cabral, J. S., Hartig, F., Pontarp, M., \u2026 Pellissier, | 196 | Fopp, F., Cabral, J. S., Hartig, F., Pontarp, M., \u2026 Pellissier, | ||
195 | L. (2021). gen3sis: a general engine for eco-evolutionary simulations | 197 | L. (2021). gen3sis: a general engine for eco-evolutionary simulations | ||
196 | of the processes that shape Earth's biodiversity. PLoS Biology, 19(7), | 198 | of the processes that shape Earth's biodiversity. PLoS Biology, 19(7), | ||
197 | e3001340 (31 pp.). https://doi.org/10.1371/journal.pbio.3001340", | 199 | e3001340 (31 pp.). https://doi.org/10.1371/journal.pbio.3001340", | ||
198 | "relationships_as_object": [], | 200 | "relationships_as_object": [], | ||
199 | "relationships_as_subject": [], | 201 | "relationships_as_subject": [], | ||
200 | "resource_type": "dataset", | 202 | "resource_type": "dataset", | ||
201 | "resource_type_general": "dataset", | 203 | "resource_type_general": "dataset", | ||
202 | "resources": [ | 204 | "resources": [ | ||
203 | { | 205 | { | ||
204 | "cache_last_updated": null, | 206 | "cache_last_updated": null, | ||
205 | "cache_url": null, | 207 | "cache_url": null, | ||
206 | "created": "2022-02-11T09:43:57.774121", | 208 | "created": "2022-02-11T09:43:57.774121", | ||
207 | "description": "ddRADseq data (vcf file and sampling locations) | 209 | "description": "ddRADseq data (vcf file and sampling locations) | ||
208 | of 449 Northern chamois (Rupicapra rupicapra) sampled across the | 210 | of 449 Northern chamois (Rupicapra rupicapra) sampled across the | ||
209 | European Alps", | 211 | European Alps", | ||
210 | "doi": "", | 212 | "doi": "", | ||
211 | "format": "vcf", | 213 | "format": "vcf", | ||
212 | "hash": "", | 214 | "hash": "", | ||
213 | "id": "f8447807-22a7-4219-a585-4b514421f2cb", | 215 | "id": "f8447807-22a7-4219-a585-4b514421f2cb", | ||
214 | "last_modified": null, | 216 | "last_modified": null, | ||
215 | "metadata_modified": "2022-02-11T09:43:57.752427", | 217 | "metadata_modified": "2022-02-11T09:43:57.752427", | ||
216 | "mimetype": null, | 218 | "mimetype": null, | ||
217 | "mimetype_inner": null, | 219 | "mimetype_inner": null, | ||
218 | "name": "Genetic data Northern chamois across Alps", | 220 | "name": "Genetic data Northern chamois across Alps", | ||
219 | "package_id": "880eb4ab-2150-44a9-a52a-985ba444a4ac", | 221 | "package_id": "880eb4ab-2150-44a9-a52a-985ba444a4ac", | ||
220 | "position": 0, | 222 | "position": 0, | ||
221 | "publication_state": "", | 223 | "publication_state": "", | ||
222 | "resource_size": "{\"size_value\": \"\", \"size_units\": | 224 | "resource_size": "{\"size_value\": \"\", \"size_units\": | ||
223 | \"kb\"}", | 225 | \"kb\"}", | ||
224 | "resource_type": null, | 226 | "resource_type": null, | ||
225 | "restricted": "{\"level\": \"public\", \"allowed_users\": \"\", | 227 | "restricted": "{\"level\": \"public\", \"allowed_users\": \"\", | ||
226 | \"shared_secret\": \"\"}", | 228 | \"shared_secret\": \"\"}", | ||
227 | "size": 82077, | 229 | "size": 82077, | ||
228 | "state": "active", | 230 | "state": "active", | ||
229 | "url": | 231 | "url": | ||
230 | c/resource/f8447807-22a7-4219-a585-4b514421f2cb/download/gen3sis.zip", | 232 | c/resource/f8447807-22a7-4219-a585-4b514421f2cb/download/gen3sis.zip", | ||
231 | "url_type": "upload" | 233 | "url_type": "upload" | ||
232 | }, | 234 | }, | ||
233 | { | 235 | { | ||
234 | "cache_last_updated": null, | 236 | "cache_last_updated": null, | ||
235 | "cache_url": null, | 237 | "cache_url": null, | ||
236 | "created": "2022-02-11T09:44:42.143222", | 238 | "created": "2022-02-11T09:44:42.143222", | ||
237 | "description": "Metadata", | 239 | "description": "Metadata", | ||
238 | "doi": "", | 240 | "doi": "", | ||
239 | "format": ".txt", | 241 | "format": ".txt", | ||
240 | "hash": "", | 242 | "hash": "", | ||
241 | "id": "53239b17-86ec-411a-9909-9072d437aa64", | 243 | "id": "53239b17-86ec-411a-9909-9072d437aa64", | ||
242 | "last_modified": "2022-02-11T16:48:23.657107", | 244 | "last_modified": "2022-02-11T16:48:23.657107", | ||
243 | "metadata_modified": "2022-02-11T15:48:24.105442", | 245 | "metadata_modified": "2022-02-11T15:48:24.105442", | ||
244 | "mimetype": null, | 246 | "mimetype": null, | ||
245 | "mimetype_inner": null, | 247 | "mimetype_inner": null, | ||
246 | "name": "Metadata", | 248 | "name": "Metadata", | ||
247 | "package_id": "880eb4ab-2150-44a9-a52a-985ba444a4ac", | 249 | "package_id": "880eb4ab-2150-44a9-a52a-985ba444a4ac", | ||
248 | "position": 1, | 250 | "position": 1, | ||
249 | "publication_state": "", | 251 | "publication_state": "", | ||
250 | "resource_size": "{\"size_value\": \"\", \"size_units\": | 252 | "resource_size": "{\"size_value\": \"\", \"size_units\": | ||
251 | \"kb\"}", | 253 | \"kb\"}", | ||
252 | "resource_type": null, | 254 | "resource_type": null, | ||
253 | "restricted": "{\"level\": \"public\", \"allowed_users\": \"\", | 255 | "restricted": "{\"level\": \"public\", \"allowed_users\": \"\", | ||
254 | \"shared_secret\": \"\"}", | 256 | \"shared_secret\": \"\"}", | ||
255 | "size": 3634, | 257 | "size": 3634, | ||
256 | "state": "active", | 258 | "state": "active", | ||
257 | "url": | 259 | "url": | ||
258 | /resource/53239b17-86ec-411a-9909-9072d437aa64/download/metadata.txt", | 260 | /resource/53239b17-86ec-411a-9909-9072d437aa64/download/metadata.txt", | ||
259 | "url_type": "upload" | 261 | "url_type": "upload" | ||
260 | }, | 262 | }, | ||
261 | { | 263 | { | ||
262 | "cache_last_updated": null, | 264 | "cache_last_updated": null, | ||
263 | "cache_url": null, | 265 | "cache_url": null, | ||
264 | "created": "2022-02-11T09:45:55.307471", | 266 | "created": "2022-02-11T09:45:55.307471", | ||
265 | "description": "Input rasters required to set up gen3sis | 267 | "description": "Input rasters required to set up gen3sis | ||
266 | simulations", | 268 | simulations", | ||
267 | "doi": "", | 269 | "doi": "", | ||
268 | "format": ".tif", | 270 | "format": ".tif", | ||
269 | "hash": "", | 271 | "hash": "", | ||
270 | "id": "c90c16c5-21ae-494e-b1bf-a367ab38e648", | 272 | "id": "c90c16c5-21ae-494e-b1bf-a367ab38e648", | ||
271 | "last_modified": null, | 273 | "last_modified": null, | ||
272 | "metadata_modified": "2022-02-11T09:45:55.287444", | 274 | "metadata_modified": "2022-02-11T09:45:55.287444", | ||
273 | "mimetype": null, | 275 | "mimetype": null, | ||
274 | "mimetype_inner": null, | 276 | "mimetype_inner": null, | ||
275 | "name": "Rivers and glaciers", | 277 | "name": "Rivers and glaciers", | ||
276 | "package_id": "880eb4ab-2150-44a9-a52a-985ba444a4ac", | 278 | "package_id": "880eb4ab-2150-44a9-a52a-985ba444a4ac", | ||
277 | "position": 2, | 279 | "position": 2, | ||
278 | "publication_state": "", | 280 | "publication_state": "", | ||
279 | "resource_size": "{\"size_value\": \"\", \"size_units\": | 281 | "resource_size": "{\"size_value\": \"\", \"size_units\": | ||
280 | \"kb\"}", | 282 | \"kb\"}", | ||
281 | "resource_type": null, | 283 | "resource_type": null, | ||
282 | "restricted": "{\"level\": \"public\", \"allowed_users\": \"\", | 284 | "restricted": "{\"level\": \"public\", \"allowed_users\": \"\", | ||
283 | \"shared_secret\": \"\"}", | 285 | \"shared_secret\": \"\"}", | ||
284 | "size": 143478, | 286 | "size": 143478, | ||
285 | "state": "active", | 287 | "state": "active", | ||
286 | "url": | 288 | "url": | ||
287 | c/resource/c90c16c5-21ae-494e-b1bf-a367ab38e648/download/abiotic.zip", | 289 | c/resource/c90c16c5-21ae-494e-b1bf-a367ab38e648/download/abiotic.zip", | ||
288 | "url_type": "upload" | 290 | "url_type": "upload" | ||
289 | }, | 291 | }, | ||
290 | { | 292 | { | ||
291 | "cache_last_updated": null, | 293 | "cache_last_updated": null, | ||
292 | "cache_url": null, | 294 | "cache_url": null, | ||
293 | "created": "2022-04-05T12:17:42.069552", | 295 | "created": "2022-04-05T12:17:42.069552", | ||
294 | "description": "Coordinates of sampled Northern chamois across | 296 | "description": "Coordinates of sampled Northern chamois across | ||
295 | the Alps", | 297 | the Alps", | ||
296 | "doi": "", | 298 | "doi": "", | ||
297 | "format": ".csv", | 299 | "format": ".csv", | ||
298 | "hash": "", | 300 | "hash": "", | ||
299 | "id": "26583b50-5222-4e9c-a69d-062f60965a92", | 301 | "id": "26583b50-5222-4e9c-a69d-062f60965a92", | ||
300 | "last_modified": null, | 302 | "last_modified": null, | ||
301 | "metadata_modified": "2022-04-05T12:17:42.043849", | 303 | "metadata_modified": "2022-04-05T12:17:42.043849", | ||
302 | "mimetype": null, | 304 | "mimetype": null, | ||
303 | "mimetype_inner": null, | 305 | "mimetype_inner": null, | ||
304 | "name": "Chamois sampling locations", | 306 | "name": "Chamois sampling locations", | ||
305 | "package_id": "880eb4ab-2150-44a9-a52a-985ba444a4ac", | 307 | "package_id": "880eb4ab-2150-44a9-a52a-985ba444a4ac", | ||
306 | "position": 3, | 308 | "position": 3, | ||
307 | "publication_state": "", | 309 | "publication_state": "", | ||
308 | "resource_size": "{\"size_value\": \"\", \"size_units\": | 310 | "resource_size": "{\"size_value\": \"\", \"size_units\": | ||
309 | \"kb\"}", | 311 | \"kb\"}", | ||
310 | "resource_type": null, | 312 | "resource_type": null, | ||
311 | "restricted": "{\"level\": \"public\", \"allowed_users\": \"\", | 313 | "restricted": "{\"level\": \"public\", \"allowed_users\": \"\", | ||
312 | \"shared_secret\": \"\"}", | 314 | \"shared_secret\": \"\"}", | ||
313 | "size": 12871, | 315 | "size": 12871, | ||
314 | "state": "active", | 316 | "state": "active", | ||
315 | "url": | 317 | "url": | ||
316 | -5222-4e9c-a69d-062f60965a92/download/chamois_sampling_locations.csv", | 318 | -5222-4e9c-a69d-062f60965a92/download/chamois_sampling_locations.csv", | ||
317 | "url_type": "upload" | 319 | "url_type": "upload" | ||
318 | }, | 320 | }, | ||
319 | { | 321 | { | ||
320 | "cache_last_updated": null, | 322 | "cache_last_updated": null, | ||
321 | "cache_url": null, | 323 | "cache_url": null, | ||
322 | "created": "2022-02-11T09:47:30.882770", | 324 | "created": "2022-02-11T09:47:30.882770", | ||
323 | "description": "Scripts to run gen3sis simulations, including | 325 | "description": "Scripts to run gen3sis simulations, including | ||
324 | configs used for the | 326 | configs used for the | ||
325 | publication.\r\n\r\n__1.2_gen3sis_input_generation.R__ creates the | 327 | publication.\r\n\r\n__1.2_gen3sis_input_generation.R__ creates the | ||
326 | input files required for __2.2_gen3sis_simulation_chamois.R__, which | 328 | input files required for __2.2_gen3sis_simulation_chamois.R__, which | ||
327 | is running the gen3sis simulations.\r\n__ | 329 | is running the gen3sis simulations.\r\n__ | ||
328 | 3_gen3sis_track_simulation_over_time.R__ and | 330 | 3_gen3sis_track_simulation_over_time.R__ and | ||
329 | __4_gen3sis_divergence_sampling_locations.R__ can be used to start the | 331 | __4_gen3sis_divergence_sampling_locations.R__ can be used to start the | ||
330 | analysis.", | 332 | analysis.", | ||
331 | "doi": "", | 333 | "doi": "", | ||
332 | "format": "R", | 334 | "format": "R", | ||
333 | "hash": "", | 335 | "hash": "", | ||
334 | "id": "599ce7b4-0994-42e4-a374-639012aa6c38", | 336 | "id": "599ce7b4-0994-42e4-a374-639012aa6c38", | ||
335 | "last_modified": "2022-02-11T16:47:39.774586", | 337 | "last_modified": "2022-02-11T16:47:39.774586", | ||
336 | "metadata_modified": "2022-02-11T15:47:40.173174", | 338 | "metadata_modified": "2022-02-11T15:47:40.173174", | ||
337 | "mimetype": null, | 339 | "mimetype": null, | ||
338 | "mimetype_inner": null, | 340 | "mimetype_inner": null, | ||
339 | "name": "gen3sis simulations", | 341 | "name": "gen3sis simulations", | ||
340 | "package_id": "880eb4ab-2150-44a9-a52a-985ba444a4ac", | 342 | "package_id": "880eb4ab-2150-44a9-a52a-985ba444a4ac", | ||
341 | "position": 4, | 343 | "position": 4, | ||
342 | "publication_state": "", | 344 | "publication_state": "", | ||
343 | "resource_size": "{\"size_value\": \"\", \"size_units\": | 345 | "resource_size": "{\"size_value\": \"\", \"size_units\": | ||
344 | \"kb\"}", | 346 | \"kb\"}", | ||
345 | "resource_type": null, | 347 | "resource_type": null, | ||
346 | "restricted": "{\"level\": \"public\", \"allowed_users\": \"\", | 348 | "restricted": "{\"level\": \"public\", \"allowed_users\": \"\", | ||
347 | \"shared_secret\": \"\"}", | 349 | \"shared_secret\": \"\"}", | ||
348 | "size": 81389, | 350 | "size": 81389, | ||
349 | "state": "active", | 351 | "state": "active", | ||
350 | "url": | 352 | "url": | ||
351 | c/resource/599ce7b4-0994-42e4-a374-639012aa6c38/download/gen3sis.zip", | 353 | c/resource/599ce7b4-0994-42e4-a374-639012aa6c38/download/gen3sis.zip", | ||
352 | "url_type": "upload" | 354 | "url_type": "upload" | ||
353 | }, | 355 | }, | ||
354 | { | 356 | { | ||
355 | "cache_last_updated": null, | 357 | "cache_last_updated": null, | ||
356 | "cache_url": null, | 358 | "cache_url": null, | ||
357 | "created": "2022-02-11T14:15:16.337216", | 359 | "created": "2022-02-11T14:15:16.337216", | ||
358 | "description": "Habitat suitability raster stacks (.grd) files | 360 | "description": "Habitat suitability raster stacks (.grd) files | ||
359 | for different terrain slope scenarios use (see main publication its | 361 | for different terrain slope scenarios use (see main publication its | ||
360 | supporting information for details) for Northern chamois until 20,000 | 362 | supporting information for details) for Northern chamois until 20,000 | ||
361 | years BP in 100 year time steps.\r\n\r\n### Description of layer | 363 | years BP in 100 year time steps.\r\n\r\n### Description of layer | ||
362 | names:\r\n* __prob__: habitat suitability ranging continuously from 0 | 364 | names:\r\n* __prob__: habitat suitability ranging continuously from 0 | ||
363 | (unsuitable) to 1 (very well suitable).\r\n*__bin__: binary | 365 | (unsuitable) to 1 (very well suitable).\r\n*__bin__: binary | ||
364 | classification of habitat suitability based on TSS threshold | 366 | classification of habitat suitability based on TSS threshold | ||
365 | optimization (see main publication and supporting information for | 367 | optimization (see main publication and supporting information for | ||
366 | details).\r\n*__glm__: generalized linear model (to model and predict | 368 | details).\r\n*__glm__: generalized linear model (to model and predict | ||
367 | habitat suitability)\r\n*__gam__: generalized additive | 369 | habitat suitability)\r\n*__gam__: generalized additive | ||
368 | model\r\n*__gbm__: generalized boosted regression model\r\n*__rf__: | 370 | model\r\n*__gbm__: generalized boosted regression model\r\n*__rf__: | ||
369 | random forest\r\n*__ensemble__: average of all 4 model types\r\n", | 371 | random forest\r\n*__ensemble__: average of all 4 model types\r\n", | ||
370 | "doi": "", | 372 | "doi": "", | ||
371 | "format": ".grd", | 373 | "format": ".grd", | ||
372 | "hash": "", | 374 | "hash": "", | ||
373 | "id": "ff87fdf4-c8d6-47d0-936a-b455c77c26d2", | 375 | "id": "ff87fdf4-c8d6-47d0-936a-b455c77c26d2", | ||
374 | "last_modified": "2022-02-11T17:15:43.572742", | 376 | "last_modified": "2022-02-11T17:15:43.572742", | ||
375 | "metadata_modified": "2022-02-11T16:15:43.965484", | 377 | "metadata_modified": "2022-02-11T16:15:43.965484", | ||
376 | "mimetype": null, | 378 | "mimetype": null, | ||
377 | "mimetype_inner": null, | 379 | "mimetype_inner": null, | ||
378 | "name": "Habitat suitability raster", | 380 | "name": "Habitat suitability raster", | ||
379 | "package_id": "880eb4ab-2150-44a9-a52a-985ba444a4ac", | 381 | "package_id": "880eb4ab-2150-44a9-a52a-985ba444a4ac", | ||
380 | "position": 5, | 382 | "position": 5, | ||
381 | "publication_state": "", | 383 | "publication_state": "", | ||
382 | "resource_size": "{\"size_value\": \"\", \"size_units\": | 384 | "resource_size": "{\"size_value\": \"\", \"size_units\": | ||
383 | \"kb\"}", | 385 | \"kb\"}", | ||
384 | "resource_type": null, | 386 | "resource_type": null, | ||
385 | "restricted": "{\"level\": \"public\", \"allowed_users\": \"\", | 387 | "restricted": "{\"level\": \"public\", \"allowed_users\": \"\", | ||
386 | \"shared_secret\": \"\"}", | 388 | \"shared_secret\": \"\"}", | ||
387 | "size": 1908747503, | 389 | "size": 1908747503, | ||
388 | "state": "active", | 390 | "state": "active", | ||
389 | "url": | 391 | "url": | ||
390 | 4a4ac/resource/ff87fdf4-c8d6-47d0-936a-b455c77c26d2/download/hsm.zip", | 392 | 4a4ac/resource/ff87fdf4-c8d6-47d0-936a-b455c77c26d2/download/hsm.zip", | ||
391 | "url_type": "upload" | 393 | "url_type": "upload" | ||
392 | }, | 394 | }, | ||
393 | { | 395 | { | ||
394 | "cache_last_updated": null, | 396 | "cache_last_updated": null, | ||
395 | "cache_url": null, | 397 | "cache_url": null, | ||
396 | "created": "2022-04-05T06:03:13.197606", | 398 | "created": "2022-04-05T06:03:13.197606", | ||
397 | "description": "Chamois fossil records with estimated time span | 399 | "description": "Chamois fossil records with estimated time span | ||
398 | and coordinates. Please see the sheet \"references_data_sets\" for the | 400 | and coordinates. Please see the sheet \"references_data_sets\" for the | ||
399 | references and read the read_me.txt file prior to using the data.", | 401 | references and read the read_me.txt file prior to using the data.", | ||
400 | "doi": "", | 402 | "doi": "", | ||
401 | "format": "XLSX", | 403 | "format": "XLSX", | ||
402 | "hash": "", | 404 | "hash": "", | ||
403 | "id": "801413db-9f0f-4147-99c2-8b36dd664e44", | 405 | "id": "801413db-9f0f-4147-99c2-8b36dd664e44", | ||
404 | "last_modified": null, | 406 | "last_modified": null, | ||
405 | "metadata_modified": "2022-04-05T06:03:13.175510", | 407 | "metadata_modified": "2022-04-05T06:03:13.175510", | ||
406 | "mimetype": null, | 408 | "mimetype": null, | ||
407 | "mimetype_inner": null, | 409 | "mimetype_inner": null, | ||
408 | "name": "Fossil records", | 410 | "name": "Fossil records", | ||
409 | "package_id": "880eb4ab-2150-44a9-a52a-985ba444a4ac", | 411 | "package_id": "880eb4ab-2150-44a9-a52a-985ba444a4ac", | ||
410 | "position": 6, | 412 | "position": 6, | ||
411 | "publication_state": "", | 413 | "publication_state": "", | ||
412 | "resource_size": "{\"size_value\": \"\", \"size_units\": | 414 | "resource_size": "{\"size_value\": \"\", \"size_units\": | ||
413 | \"kb\"}", | 415 | \"kb\"}", | ||
414 | "resource_type": null, | 416 | "resource_type": null, | ||
415 | "restricted": "{\"level\": \"public\", \"allowed_users\": \"\", | 417 | "restricted": "{\"level\": \"public\", \"allowed_users\": \"\", | ||
416 | \"shared_secret\": \"\"}", | 418 | \"shared_secret\": \"\"}", | ||
417 | "size": 34185, | 419 | "size": 34185, | ||
418 | "state": "active", | 420 | "state": "active", | ||
419 | "url": | 421 | "url": | ||
420 | rce/801413db-9f0f-4147-99c2-8b36dd664e44/download/fossil_records.zip", | 422 | rce/801413db-9f0f-4147-99c2-8b36dd664e44/download/fossil_records.zip", | ||
421 | "url_type": "upload" | 423 | "url_type": "upload" | ||
422 | } | 424 | } | ||
423 | ], | 425 | ], | ||
424 | "spatial": "{\"type\": \"Polygon\", \"coordinates\": [[[4.8, | 426 | "spatial": "{\"type\": \"Polygon\", \"coordinates\": [[[4.8, | ||
425 | 43.5],[4.8, 48.3],[16.3, 48.3],[16.3, 43.5],[4.8, 43.5]]]}", | 427 | 43.5],[4.8, 48.3],[16.3, 48.3],[16.3, 43.5],[4.8, 43.5]]]}", | ||
426 | "spatial_info": "Switzerland", | 428 | "spatial_info": "Switzerland", | ||
427 | "state": "active", | 429 | "state": "active", | ||
428 | "subtitle": "", | 430 | "subtitle": "", | ||
429 | "tags": [ | 431 | "tags": [ | ||
430 | { | 432 | { | ||
431 | "display_name": "GEOGENOMICS", | 433 | "display_name": "GEOGENOMICS", | ||
432 | "id": "1df91b35-d832-4a4e-9dca-6c832448882b", | 434 | "id": "1df91b35-d832-4a4e-9dca-6c832448882b", | ||
433 | "name": "GEOGENOMICS", | 435 | "name": "GEOGENOMICS", | ||
434 | "state": "active", | 436 | "state": "active", | ||
435 | "vocabulary_id": null | 437 | "vocabulary_id": null | ||
436 | }, | 438 | }, | ||
437 | { | 439 | { | ||
438 | "display_name": "LANDSCAPE GENETICS", | 440 | "display_name": "LANDSCAPE GENETICS", | ||
439 | "id": "272b6cd2-8dab-4443-8e3f-33ca7d74ff0d", | 441 | "id": "272b6cd2-8dab-4443-8e3f-33ca7d74ff0d", | ||
440 | "name": "LANDSCAPE GENETICS", | 442 | "name": "LANDSCAPE GENETICS", | ||
441 | "state": "active", | 443 | "state": "active", | ||
442 | "vocabulary_id": null | 444 | "vocabulary_id": null | ||
443 | }, | 445 | }, | ||
444 | { | 446 | { | ||
445 | "display_name": "PALEO-ENVIRONMENTAL MODELING", | 447 | "display_name": "PALEO-ENVIRONMENTAL MODELING", | ||
446 | "id": "592f9e03-8b22-4ef9-890b-cf6315e36140", | 448 | "id": "592f9e03-8b22-4ef9-890b-cf6315e36140", | ||
447 | "name": "PALEO-ENVIRONMENTAL MODELING", | 449 | "name": "PALEO-ENVIRONMENTAL MODELING", | ||
448 | "state": "active", | 450 | "state": "active", | ||
449 | "vocabulary_id": null | 451 | "vocabulary_id": null | ||
450 | }, | 452 | }, | ||
451 | { | 453 | { | ||
452 | "display_name": "POPULATION GENETICS", | 454 | "display_name": "POPULATION GENETICS", | ||
453 | "id": "be6c4eb3-1e68-490e-a95f-313a5121ebd1", | 455 | "id": "be6c4eb3-1e68-490e-a95f-313a5121ebd1", | ||
454 | "name": "POPULATION GENETICS", | 456 | "name": "POPULATION GENETICS", | ||
455 | "state": "active", | 457 | "state": "active", | ||
456 | "vocabulary_id": null | 458 | "vocabulary_id": null | ||
457 | }, | 459 | }, | ||
458 | { | 460 | { | ||
459 | "display_name": "PROCESS-BASED MODELING", | 461 | "display_name": "PROCESS-BASED MODELING", | ||
460 | "id": "fafe5712-03ce-4760-9ed0-9203fccb4b24", | 462 | "id": "fafe5712-03ce-4760-9ed0-9203fccb4b24", | ||
461 | "name": "PROCESS-BASED MODELING", | 463 | "name": "PROCESS-BASED MODELING", | ||
462 | "state": "active", | 464 | "state": "active", | ||
463 | "vocabulary_id": null | 465 | "vocabulary_id": null | ||
464 | }, | 466 | }, | ||
465 | { | 467 | { | ||
466 | "display_name": "RANGE DYNAMICS", | 468 | "display_name": "RANGE DYNAMICS", | ||
467 | "id": "ef04480a-8566-4d8e-937a-8febe60d2c7a", | 469 | "id": "ef04480a-8566-4d8e-937a-8febe60d2c7a", | ||
468 | "name": "RANGE DYNAMICS", | 470 | "name": "RANGE DYNAMICS", | ||
469 | "state": "active", | 471 | "state": "active", | ||
470 | "vocabulary_id": null | 472 | "vocabulary_id": null | ||
471 | } | 473 | } | ||
472 | ], | 474 | ], | ||
473 | "title": "Simulating population divergence of Northern chamois in | 475 | "title": "Simulating population divergence of Northern chamois in | ||
474 | the Alps based on habitat dynamics", | 476 | the Alps based on habitat dynamics", | ||
475 | "type": "dataset", | 477 | "type": "dataset", | ||
476 | "url": null, | 478 | "url": null, | ||
477 | "version": "1.0" | 479 | "version": "1.0" | ||
478 | } | 480 | } |