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| "author": "[{\"affiliation\": \"German Centre for Integrative | | "author": "[{\"affiliation\": \"German Centre for Integrative |
| Biodiversity Research Halle\\u2013Jena\\u2013Leipzig\", | | Biodiversity Research Halle\\u2013Jena\\u2013Leipzig\", |
| \"affiliation_02\": \"ETH Zurich\", \"affiliation_03\": \"\", | | \"affiliation_02\": \"ETH Zurich\", \"affiliation_03\": \"\", |
| \"data_credit\": [\"collection\", \"validation\", \"curation\", | | \"data_credit\": [\"collection\", \"validation\", \"curation\", |
| \"software\", \"publication\"], \"email\": \"oskar@hagen.bio\", | | \"software\", \"publication\"], \"email\": \"oskar@hagen.bio\", |
| \"given_name\": \"Oskar\", \"identifier\": \"0000-0002-7931-6571\", | | \"given_name\": \"Oskar\", \"identifier\": \"0000-0002-7931-6571\", |
| \"name\": \"Hagen\"}, {\"affiliation\": \"Swiss Federal Research | | \"name\": \"Hagen\"}, {\"affiliation\": \"Swiss Federal Research |
| Institute for Forest, Snow and Landscape (WSL)\", \"affiliation_02\": | | Institute for Forest, Snow and Landscape (WSL)\", \"affiliation_02\": |
| \"ETH Zurich\", \"affiliation_03\": \"\", \"data_credit\": | | \"ETH Zurich\", \"affiliation_03\": \"\", \"data_credit\": |
| [\"collection\", \"validation\", \"curation\", \"software\", | | [\"collection\", \"validation\", \"curation\", \"software\", |
| \"publication\"], \"email\": \"alexander.skeels@usys.ethz.ch\", | | \"publication\"], \"email\": \"alexander.skeels@usys.ethz.ch\", |
| \"given_name\": \"Alexander\", \"identifier\": \"\", \"name\": | | \"given_name\": \"Alexander\", \"identifier\": \"\", \"name\": |
| \"Skeels\"}, {\"affiliation\": \"German Centre for Integrative | | \"Skeels\"}, {\"affiliation\": \"German Centre for Integrative |
| Biodiversity Research Halle\\u2013Jena\\u2013Leipzig\", | | Biodiversity Research Halle\\u2013Jena\\u2013Leipzig\", |
| \"affiliation_02\": \"\", \"affiliation_03\": \"\", \"data_credit\": | | \"affiliation_02\": \"\", \"affiliation_03\": \"\", \"data_credit\": |
| [\"collection\", \"publication\"], \"email\": | | [\"collection\", \"publication\"], \"email\": |
| \"renske.onstein@idiv.de\", \"given_name\": \"Renske\", | | \"renske.onstein@idiv.de\", \"given_name\": \"Renske\", |
| \"identifier\": \"0000-0002-2295-3510\", \"name\": \"Onstein\"}, | | \"identifier\": \"0000-0002-2295-3510\", \"name\": \"Onstein\"}, |
| {\"affiliation\": \"Department of Ecology and Evolutionary Biology, | | {\"affiliation\": \"Department of Ecology and Evolutionary Biology, |
| Yale University\", \"affiliation_02\": \"\", \"affiliation_03\": \"\", | | Yale University\", \"affiliation_02\": \"\", \"affiliation_03\": \"\", |
| \"data_credit\": [\"collection\", \"validation\", \"publication\"], | | \"data_credit\": [\"collection\", \"validation\", \"publication\"], |
| \"email\": \"walter.jetz@yale.edu\", \"given_name\": \"Walter\", | | \"email\": \"walter.jetz@yale.edu\", \"given_name\": \"Walter\", |
| \"identifier\": \"0000-0002-1971-7277\", \"name\": \"Jetz\"}, | | \"identifier\": \"0000-0002-1971-7277\", \"name\": \"Jetz\"}, |
| {\"affiliation\": \"ETH Zurich\", \"affiliation_02\": \"Swiss Federal | | {\"affiliation\": \"ETH Zurich\", \"affiliation_02\": \"Swiss Federal |
| Research Institute for Forest, Snow and Landscape (WSL)\", | | Research Institute for Forest, Snow and Landscape (WSL)\", |
| \"affiliation_03\": \"\", \"data_credit\": [\"collection\", | | \"affiliation_03\": \"\", \"data_credit\": [\"collection\", |
| \"validation\", \"curation\", \"software\", \"publication\", | | \"validation\", \"curation\", \"software\", \"publication\", |
| \"supervision\"], \"email\": \"loic.pellissier@usys.ethz.ch\", | | \"supervision\"], \"email\": \"loic.pellissier@usys.ethz.ch\", |
| \"given_name\": \"Loic\", \"identifier\": \"\", \"name\": | | \"given_name\": \"Loic\", \"identifier\": \"\", \"name\": |
| \"Pellissier\"}]", | | \"Pellissier\"}]", |
| "author_email": null, | | "author_email": null, |
| "creator_user_id": "93fd6aa4-4bae-4c26-9561-c54eb9142d42", | | "creator_user_id": "93fd6aa4-4bae-4c26-9561-c54eb9142d42", |
| "date": "[{\"date\": \"2020-04-15\", \"date_type\": \"collected\", | | "date": "[{\"date\": \"2020-04-15\", \"date_type\": \"collected\", |
| \"end_date\": \"2021-09-15\"}]", | | \"end_date\": \"2021-09-15\"}]", |
n | "doi": "", | n | "doi": "10.16904/envidat.246", |
| "funding": "[{\"grant_number\": \"310030-188550\", \"institution\": | | "funding": "[{\"grant_number\": \"310030-188550\", \"institution\": |
| \"Schweizerischer Nationalfonds zur F\u00f6rderung der | | \"Schweizerischer Nationalfonds zur F\u00f6rderung der |
| Wissenschaftlichen Forschung\", \"institution_url\": \"\"}]", | | Wissenschaftlichen Forschung\", \"institution_url\": \"\"}]", |
| "groups": [], | | "groups": [], |
| "id": "b7783edd-a5bc-4854-8e7d-1698afc875b9", | | "id": "b7783edd-a5bc-4854-8e7d-1698afc875b9", |
| "isopen": false, | | "isopen": false, |
| "language": "en", | | "language": "en", |
| "license_id": "wsl-data", | | "license_id": "wsl-data", |
| "license_title": "WSL Data Policy", | | "license_title": "WSL Data Policy", |
| "license_url": | | "license_url": |
| ps://www.wsl.ch/en/about-wsl/programmes-and-initiatives/envidat.html", | | ps://www.wsl.ch/en/about-wsl/programmes-and-initiatives/envidat.html", |
| "maintainer": "{\"affiliation\": \"WSL / ETH\", \"email\": | | "maintainer": "{\"affiliation\": \"WSL / ETH\", \"email\": |
| \"loic.pellissier@usys.ethz.ch\", \"given_name\": \"Loic\", | | \"loic.pellissier@usys.ethz.ch\", \"given_name\": \"Loic\", |
| \"identifier\": \"\", \"name\": \"Pellissier\"}", | | \"identifier\": \"\", \"name\": \"Pellissier\"}", |
| "maintainer_email": null, | | "maintainer_email": null, |
| "metadata_created": "2021-09-15T11:44:16.660831", | | "metadata_created": "2021-09-15T11:44:16.660831", |
n | "metadata_modified": "2021-09-15T12:10:33.355501", | n | "metadata_modified": "2021-09-16T13:07:18.835021", |
| "name": "data-from-hagen_skeels_etal_2021_pnas", | | "name": "data-from-hagen-skeels-etal-pnas", |
| "notes": "Datasets and R scripts | | "notes": "Datasets and R scripts |
n | \r\n\r\n~~~~~Datasets\r\n\r\nDataset_S1.csv includes species diversity | n | \r\n\r\n~~~~~Datasets\r\n\r\nDataset_S1.csv: Distribution of species |
| counts for 237 clades in tropical moist forests (TMF) in the | | diversity in plant and vertebrate clades. Total clade level diversity |
| Neotropics (NeotropicalTMF), Indomalaya (IndomalayanTMF), Afrotropics | | and species diversity in tropical moist forests (TMF) across the |
| (AfrotropicalTMF), All three TMF regions together (AllTMF), all | | Neotropics, Indomalaya and Afrotropics. Pantropical clades are found |
| non-TMF regions (NonTMF), and in total (Total). As well as whether the | | in all three TMF regions with at least one-third of the clades\u2019 |
| clade is pantropical (Pantropical_clade) and shows the pantropical | | total diversity spread throughout these regions. Pantropical diversity |
| diversity disparity (PDD_clade). \r\n\r\nDataset_S2.csv: environmental | | disparity (PDD) clades show lower diversity in TMF in the Afrotropics |
| and species richness data. Longitude (x), latitude (y), potential | | than in the Neotropics and Indomalaya.\r\n\r\nDataset_S2.csv: |
| evapotranspiration (PET), mean annual temperature (MAT), mean annual | | Environmental and species richness data across 110 km x 110 km grid |
| precipitation), amphibian, bird, mammal, and reptile species richness, | | cells in Neotropical, Indomalayan and Afrotropical moist forest sites. |
| PC1 and PC2 of environmental PCA and the region. Environmental data | | Variables include x and y coordinates in the Behrmann equal area |
| (from CHELSA and ENVIREM) and species richness summarised from | | coordinate reference system, potential evapotranspiration (PET), mean |
| published data (vertLife, MOL, IUCN, GARD).\r\n\r\nDataset_S3.csv: - | | annual temperature (MAT), mean annual precipitation (MAP), amphibian, |
| Paleoenvironmental reconstructions (details in the associated SI | | mammal, bird and squamate reptile species richness and biogeographic |
| appendix) including latitude (y), longitude (x), and temperature data | | region, as well as the first two principal components of a principal |
| across 200 myrs at 170 kyr intervals.\r\n\r\nDataset_S4.csv: | | component analysis on PET, MAT and MAP (PC1, |
| | | PC2).\r\n\r\nDataset_S3.csv: Global reconstructed paleo-temperature |
| | | estimates and spatial coordinates across 200 million years at 170,000 |
| | | year intervals at 2 degree spatial resolution.\r\n\r\nDataset_S4.csv: |
| simulation model parameters and diversity summary statistics. | | Gen3sis model parameters and biodiversity summary statistics. Summary |
| Including rate of temperature niche evolution (Tev), temperature niche | | statistics include the number of extant species, the number of extinct |
| width (TW), divergence threshold (S), Dispersal probability | | species, the total number of species, the number of species within the |
| distribution shape (WeibullShape) and information on number of extinct | | tropical moist forest biome boundaries in the Neotropics, the |
| species, number of extant species, total species, Spearman correlation | | Afrotropics and Indomalaya, the pantropical index, and the pantropical |
| coefficient between absolute latitude and species richness | | disparity index, as well as the running time-step and diversity of |
| (latitude_richness_cor), and diversity in the Neotropics, Indomalaya, | | unfinished simulations.\r\n\r\nDataset_S5.csv: Net relatedness index |
| Afrotropics. Also, whether the simulation generated pantropical | | (NRI) values for vertebrate clades showing an observed disparity in |
| distribution of species (pantropicality_index), or the pantropical | | pantropical diversity in the Neotropical, Indomalayan and Afrotropical |
| diversity disparity (PDD_index). Finally what time step the simulation | | moist forest regions and associated P-values. Positive values indicate |
| exited at (0 for complete simulations).\r\n\r\nDataset_S5.csv: Net | | phylogenetic clustering, whereas negative values indicate phylogenetic |
| relatedness index (NRI) in three tropical moist forest regions and | | overdispersion.\r\n\r\n~~~~~Scripts\r\n\r\nScript_1 - GLS.R. R script |
| associated p-values for pantropically distributed | | to replicate the linear modelling analyses.\r\n\r\nScript_2 - |
| taxa.\r\n\r\n~~~~~Scripts\r\n\r\nGen3sis_config_creator.R and | | |
| Gen3sis_config_template.R scripts generate the configurations files to | | Gen3sis_config_template.R. R script to generate the configurations |
| run the simulation experiment.\r\n\r\nGLS.R R script to replicate the | | files to run the simulation experiment.\r\n\r\nScript_3 - |
| linear modelling analyses.\r\n\r\n", | | Gen3sis_config_creator.R. R script to generate the configurations |
| | | files to run the simulation experiment.\r\n\r\n\r\n\r\n", |
| "num_resources": 10, | | "num_resources": 8, |
| "num_tags": 5, | | "num_tags": 5, |
| "organization": { | | "organization": { |
| "approval_status": "approved", | | "approval_status": "approved", |
| "created": "2018-12-01T11:42:44.590217", | | "created": "2018-12-01T11:42:44.590217", |
| "description": "Our laboratory aims at understanding and | | "description": "Our laboratory aims at understanding and |
| forecasting the response of biodiversity to landscape changes. We | | forecasting the response of biodiversity to landscape changes. We |
| investigate the historical responses of species to past changes such | | investigate the historical responses of species to past changes such |
| as plate tectonics or the glaciations of the Quaternary and | | as plate tectonics or the glaciations of the Quaternary and |
| contemporary responses to ongoing global changes. We develop spatial | | contemporary responses to ongoing global changes. We develop spatial |
| mechanistic models of biodiversity that account for processes such as | | mechanistic models of biodiversity that account for processes such as |
| dispersal and biotic interactions.", | | dispersal and biotic interactions.", |
| "id": "3b0fde83-e15c-4f8b-a451-9778f5309a84", | | "id": "3b0fde83-e15c-4f8b-a451-9778f5309a84", |
| "image_url": | | "image_url": |
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| "is_organization": true, | | "is_organization": true, |
| "name": "landscape-ecology", | | "name": "landscape-ecology", |
| "state": "active", | | "state": "active", |
| "title": "Landscape Ecology", | | "title": "Landscape Ecology", |
| "type": "organization" | | "type": "organization" |
| }, | | }, |
| "owner_org": "3b0fde83-e15c-4f8b-a451-9778f5309a84", | | "owner_org": "3b0fde83-e15c-4f8b-a451-9778f5309a84", |
| "private": false, | | "private": false, |
| "publication": "{\"publication_year\": \"2021\", \"publisher\": | | "publication": "{\"publication_year\": \"2021\", \"publisher\": |
| \"EnviDat\"}", | | \"EnviDat\"}", |
n | "publication_state": "", | n | "publication_state": "pub_pending", |
| "related_datasets": "", | | "related_datasets": "", |
| "related_publications": "", | | "related_publications": "", |
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| "relationships_as_subject": [], | | "relationships_as_subject": [], |
| "resource_type": "dataset", | | "resource_type": "dataset", |
| "resource_type_general": "dataset", | | "resource_type_general": "dataset", |
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| "description": "Dataset_S1.csv includes species diversity counts | | "description": "Dataset_S1.csv includes species diversity counts |
| for 237 clades in tropical moist forests (TMF) in the Neotropics | | for 237 clades in tropical moist forests (TMF) in the Neotropics |
| (NeotropicalTMF), Indomalaya (IndomalayanTMF), Afrotropics | | (NeotropicalTMF), Indomalaya (IndomalayanTMF), Afrotropics |
| (AfrotropicalTMF), All three TMF regions together (AllTMF), all | | (AfrotropicalTMF), All three TMF regions together (AllTMF), all |
| non-TMF regions (NonTMF), and in total (Total). As well as whether the | | non-TMF regions (NonTMF), and in total (Total). As well as whether the |
| clade is pantropical (Pantropical_clade) and shows the pantropical | | clade is pantropical (Pantropical_clade) and shows the pantropical |
n | diversity disparity (PDD_clade). ", | n | diversity disparity (PDD_clade). Pantropical clades are found in all |
| | | three TMF regions with at least one-third of the clades\u2019 total |
| | | diversity spread throughout these regions. Pantropical diversity |
| | | disparity (PDD) clades show lower diversity in TMF in the Afrotropics |
| | | than in the Neotropics and Indomalaya.", |
| "doi": "", | | "doi": "", |
| "format": ".csv", | | "format": ".csv", |
| "hash": "", | | "hash": "", |
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| "description": "Dataset_S2.csv: environmental and species | | "description": "Dataset_S2.csv: Environmental and species |
| richness data. Longitude (x), latitude (y), potential | | richness data across 110 km x 110 km grid cells in Neotropical, |
| evapotranspiration (PET), mean annual temperature (MAT), mean annual | | Indomalayan and Afrotropical moist forest sites. Variables include x |
| precipitation), amphibian, bird, mammal, and reptile species richness, | | and y coordinates in the Behrmann equal area coordinate reference |
| PC1 and PC2 of environmental PCA and the region. Environmental data | | system, potential evapotranspiration (PET), mean annual temperature |
| (from CHELSA and ENVIREM) and species richness summarised from | | (MAT), mean annual precipitation (MAP), amphibian, mammal, bird and |
| published data (vertLife, MOL, IUCN, GARD).", | | squamate reptile species richness and biogeographic region, as well as |
| | | the first two principal components of a principal component analysis |
| | | on PET, MAT and MAP (PC1, PC2). Environmental data is from CHELSA and |
| | | ENVIREM and species richness summarised from published data (vertLife, |
| | | MOL, IUCN, GARD).", |
| "doi": "", | | "doi": "", |
| "format": ".csv", | | "format": ".csv", |
| "hash": "", | | "hash": "", |
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| "created": "2021-09-15T12:05:05.340288", | | "created": "2021-09-16T12:41:24.073089", |
| "description": "Dataset_S3.csv: - Paleoenvironmental | | "description": "Dataset_S3.csv: - Paleoenvironmental |
| reconstructions (details in the associated SI appendix) including | | reconstructions (details in the associated SI appendix) including |
| latitude (y), longitude (x), and temperature data across 200 myrs at | | latitude (y), longitude (x), and temperature data across 200 myrs at |
| 170 kyr intervals.", | | 170 kyr intervals.", |
| "doi": "", | | "doi": "", |
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| "created": "2021-09-15T12:05:33.383648", | | "created": "2021-09-16T12:42:56.042298", |
| "description": "Dataset_S4.csv: simulation model parameters and | | "description": "Dataset_S4.csv: simulation model parameters and |
| diversity summary statistics. Including rate of temperature niche | | diversity summary statistics. Including rate of temperature niche |
| evolution (Tev), temperature niche width (TW), divergence threshold | | evolution (Tev), temperature niche width (TW), divergence threshold |
n | (S), Dispersal probability distribution shape (WeibullShape) and | n | (S), Dispersal probability distribution shape (WeibullShape), model |
| | | identifier (model), and random seed (seed). Also includes information |
| information on number of extinct species, number of extant species, | | on number of extinct species (n_extinct), number of extant species |
| total species, Spearman correlation coefficient between absolute | | (n_extant), total species (total_diversity), Spearman correlation |
| latitude and species richness (latitude_richness_cor), and diversity | | coefficient between absolute latitude and species richness |
| in the Neotropics, Indomalaya, Afrotropics. Also, whether the | | (latitude_richness_cor), and diversity in the Neotropics |
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| includes species diversity counts for 237 clades in tropical moist | | |
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| (IndomalayanTMF), Afrotropics (AfrotropicalTMF), All three TMF regions | | |
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| (x), latitude (y), potential evapotranspiration (PET), mean annual | | |
| temperature (MAT), mean annual precipitation), amphibian, bird, | | |
| mammal, and reptile species richness, PC1 and PC2 of environmental PCA | | |
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| species richness summarised from published data (vertLife, MOL, IUCN, | | |
| GARD).\r\nDataset_S3.csv: - Paleoenvironmental reconstructions | | |
| (details in the associated SI appendix) including latitude (y), | | |
| longitude (x), and temperature data across 200 myrs at 170 kyr | | |
| intervals.\r\nDataset_S4.csv: simulation model parameters and | | |
| diversity summary statistics. Including rate of temperature niche | | |
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| information on number of extinct species, number of extant species, | | |
| total species, Spearman correlation coefficient between absolute | | |
| latitude and species richness (latitude_richness_cor), and diversity | | |
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| (PDD_index). Finally what time step the simulation exited at (0 for | | |
| complete simulations).\r\nDataset_S5.csv: Net relatedness index (NRI) | | |
| in three tropical moist forest regions and associated p-values for | | |
| pantropically distributed taxa.\r\nGen3sis_config_creator.R and | | |
| Gen3sis_config_template.R scripts generate the configurations files to | | |
| run the simulation experiment.\r\nGLS.R R script to replicate the | | |
| linear modelling analyses.\r\n", | | |
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| "title": "Data from: Earth history events shaped the evolution of | | "title": "Data from: Earth history events shaped the evolution of |
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