cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.16904/envidat.655
title: Modified TypoCH reference list of diagnostic species for the classification of vegetation types in Switzerland

description: The TypoCH scoring system (Eggenberg & Bornand 2023), which is widely used in Switzerland, provides good results as classification method for vegetation types based on Delarze et al. (2015). However, the reference list contained species with no diagnostic value and important character species were missing. We therefore made a first attempt to modify the list based on numerical methods and expert knowledge to improve the classification success, at least for vegetation types of the open land (i.e. grasslands, fens, bogs).
description: Resource Title: How the TypoCH list was modified.pdf
 Size: 77776 bytes
 Format: application/pdf
 URL: https://www.envidat.ch/dataset/bcf50c9d-3b31-4aa7-a774-57a8f6f60ed7/resource/aa2096a9-b20b-4ca8-a586-84fea79930e6/download/how-the-typoch-list-was-modified.pdf
 Description: Describes details on the modification procedure to improve the TypoCH reference list.
description: Resource Title: TypoCH_modified list.csv
 Size: 496727 bytes
 Format: text/csv
 URL: https://www.envidat.ch/dataset/bcf50c9d-3b31-4aa7-a774-57a8f6f60ed7/resource/47adb4a8-f089-4622-b525-6dff0da104d9/download/typoch_modified-list.csv
 Description: The file contains the vegetation types and the modified list of diagnostic species (based on Delarze et al. (2015). The numbers indicate the weight of a species in the particular vegetation type for the calculation of the TypoCH score:
1) accompanying species -&gt; 1 point
2) dominant accompanying species (if &gt;10% cover in the plot) -&gt; 2 points
3) character species -&gt; 4 points
4) dominant character species (if &gt;10% cover in the plot) -&gt; 8 points
DOI: 10.16904/envidat.658
title: Overland and topsoil interflow time series from the Studibach - summer 2022

description: The dataset comprises the time series of overland flow (OF) and topsoil interflow (TIF) discharges from 14 small runoff plots (1 x 3 m) over 27 rainfall events in 2022 across the Studibach in the Alptal, a typical pre-Alpine catchment in Switzerland. 
The runoff plots were installed on different topographic indices and vegetation covers in order to study the spatio-temporal variability of OF and TIF. 
The runoff was collected into self-made "Upwelling Bernoulli Tubes" and the water level inside these tubes was measured by pressure sensors (DCX-22-CTD, Keller Druck, Switzerland) at a 5-min resolution. The discharge was derived from the water level. 
The precipitation was measured with a tipping bucket at the Erlenhöhe meteorological station and has a 10-min resolution.
description: Resource Title: runoff_responses_plots_studibach.csv
 Size: 873319 bytes
 Format: application/vnd.ms-excel
 URL: https://www.envidat.ch/dataset/98df98ae-dd8e-4ff9-ab2b-dfc56d04bdf6/resource/28238cb9-2c67-4bc9-9565-c35721c56f42/download/runoff_responses_plots_studibach.csv
 Description: Time series of overland flow and topsoil interflow discharge at 14 runoff plot locations in the Studibach catchment over 27 rain events in 2022. 
Format: NEAD
Metadata included in the file: latitude, longitude, data units, timezone. 
Source for reading and writing NEAD format: https://www.doi.org/10.16904/envidat.187.
DOI: 10.16904/envidat.662
title: Metabarcoding of urban and forest bird faecal samples

description: We captured birds in urban parks and peri-urban forests in the cities of Lugano, Zurich (Switzerland) and Napoli (Italy). The urban sites were located in urban forests (Lugano, Napoli) and in a cemetery (Zurich). Bird faecal samples were stored in a screw-capped tube (2 ml), which was previously filled with 1 ml ethanol puriss. (Sigma-Aldrich) under sterile conditions. We wore single-use nitrile gloves and used sterile toothpicks to collect solid samples. The tubes were initially stored in the refrigerator during the field campaign and no later than seven days after collection at -20°C until prepared for DNA extraction.
DNA extraction and library preparation was performed at WSL Phytopathology facilites, Sequencing was performed at Lausanne Genomic Technologies Facility (University of Lausanne; https://wp.unil.ch/gtf/) on an AVITI benchtop sequencing system (Element Biosciences). Bioinformatics was performed at the Genetic Diversity Center (ETH Zurich) using a custom pipeline.
description: Resource Title: p1126_run241028_COX_Results.zip
 Size: 2212086849 bytes
 Format: application/x-zip-compressed
 URL: https://www.envidat.ch/dataset/c4d366dc-23db-4666-b153-09a99d04f2e1/resource/efaee256-d129-405a-860e-fd508ba0bb29/download/p1126_run241028_cox_results.zip
 Description: Raw data including fasta files, OTU counts and taxonomic assignments.
description: Resource Title: p1126_run241028_COX_Reports.zip
 Size: 379931 bytes
 Format: application/x-zip-compressed
 URL: https://www.envidat.ch/dataset/c4d366dc-23db-4666-b153-09a99d04f2e1/resource/1a9abe30-411a-499d-b49d-bac5405c601a/download/p1126_run241028_cox_reports.zip
 Description: Bioinformatic report.
DOI: 10.16904/envidat.643
title: Robot-aided measurement of insect diversity on vegetation using environmental DNA

description: Traditional methods of biodiversity monitoring are often logistically challenging, time-consuming, require experienced experts on species identification and sometimes include destruction of the targeted specimens. Here, we investigated a non-invasive approach of combining the use of drones and environmental DNA (eDNA) to monitor insect biodiversity on vegetation.
We aimed to assess the efficiency of this novel method in capturing insect diversity and comparing insect composition across different vegetation types (grassland, shrub, and forest) in Switzerland. A commercial, off-the-shelf drone was equipped with a specialised probe that autonomously swabbed vegetation and collected eDNA. Then, samples were processed using rapid third-generation Oxford Nanopore sequencing. The obtained data were analysed for insect diversity, comparing taxonomic richness, evenness and community composition across the three habitat types using statistical techniques. Sequencing of the samples yielded 76 hexapods taxa, revealing an insect community with notable differences in taxonomic richness but not in evenness across grassland, shrub, and forest habitats.
Our study demonstrates the potential of drone-based sampling integrated with eDNA and nanopore sequencing for biodiversity monitoring, offering a non-destructive method for detecting insect occurrence on plant surfaces. Integrating robotics and eDNA technology provides a promising solution for fast, large-scale, non-invasive biodiversity monitoring, potentially improving conservation efforts and ecosystem management.
description: Resource Title: Data access
 Size: 262144000 bytes
 Format: No Info
 URL: https://envicloud.wsl.ch/#/?bucket=https://envicloud.wsl.ch/edna/&prefix=su_ch/su_ch_birmen_2024
 Description: Please use cyberduck to download
DOI: 10.16904/envidat.666
title: Environmental DNA Freshwater Colombia Magdalena 2022

description: Monitoring of vertebrates of the lower Magdalena river through eDNA metabarcoding
The Magdalena River basin harbors a large biodiversity of vertebrates, with numerous endemic species, many of which are threatened. Here, we used environmental DNA (eDNA) metabarcoding, with two primer sets targeting different regions of the mitochondrial DNA 12S ribosomal RNA gene, to detect vertebrate diversity in the Magdalena River. We detected a total of 159 vertebrate taxa, not only aquatic but also terrestrial, arboreal, and aerial. The diversity of these vertebrates increases in relation to the proximity to the river mouth with a change in the composition of the assemblage of aquatic vertebrates detected. We conclude that eDNA metabarcoding allows characterizing vertebrate assemblages in large rivers, assessing conservation status, and elucidating biodiversity patterns with minimal ecosystem disturbance. Samples were taken at the sides of the river or in the center using a boat. At each station, we performed two filtration replicates using a peristaltic pump to conduct environmental DNA (eDNA) sampling. Each filtration targeted a maximum duration of 1 hours, during which a maximum of 30 liters of water were filtered through each capsule. After filtration, the water inside the capsules was removed, and the capsules were filled with 50 ml of conservation buffer for preservation at room temperature. We followed strict contamination control protocols throughout both the fieldwork and laboratory processes, adhering to the guidelines of Valentini et al. (2016). To prevent contamination, each sample was processed using disposable gloves and single-use filtration equipment. The MiSeq Reagent Kit v3 (2x75 bp) (Illumina, San Diego, CA, USA) was used for paired-end sequencing at a theoretical sequencing depth of 200,000 reads per sample.
Data content: 
 * rawdata/: contains the raw reads for each individual sample. One archive contains the paired-end reads specified by the _R1 or _R2 suffix as well as individually tagged PCR replicates (if available) together with an archive containing all extraction and PCR blank samples of the library. Reads have been demultiplexed using cutadapt but not trimmed, individual demultiplexing tags and primers remain present in the sequences. 
 * taxadata/: contains the table with all detected taxonomy for each sample after bioinformatic processing (see Polanco et al. 2020 for details; https://doi.org/10.1002/edn3.140) and associated field metadata. 
 * metadata/: contains two metadata files, one related to the data collected in the field for each filter, and the second related to the sequencing process in the lab (including the tag sequence, library name, and marker information for each sample)
description: Resource Title: Data access
 Size: 524288000 bytes
 Format: No Info
 URL: https://envicloud.wsl.ch/#/?bucket=https://envicloud.wsl.ch/edna/&prefix=fw_co/fw_co_magdal_2022
 Description: Please cyberduck to download for the moment
DOI: 10.16904/envidat.669
title: Trends in background mortality in unmanaged forests across Europe over the last century

description: These datasets and script document the analyses and the plot generation for the article **“Trends in background mortality in unmanaged forests across Europe over the last century”**.
We used a comprehensive network of permanent plots with repeated censuses spanning from 1936 to 2020 in 299 unmanaged forest reserves across Europe. The database includes 1.5 million tree records over successive censuses covering a total sampled area of 853.7 ha.
It consists of the following files:
- **Mortality_script.Rmd**: R markdown document to reproduce the analysis and the plot generation.
- **plot_level.RDS**: This dataset contains annual mortality rate values for each permanent plot at each census, of plots with at least three censuses. This dataset is used to calculate the weighted mean annual background mortality rates by forest types, and the series of models to study the trends of annual mortality rates, and then to create Figure 1 and Figure 2.
- **tree_level.RDS**: This dataset contains tree census data for each permanent plot at each census, of plots with at least two censuses. This dataset is used to model species-specific size-dependent mortality probabilities of the studied tree species, and then to create Figure 3.
description: Resource Title: plot_level.RDS
 Size: 41149 bytes
 Format: application/octet-stream
 URL: https://www.envidat.ch/dataset/9e684bf2-daf1-4662-8425-1196c5dedfbc/resource/15a70c68-bb5b-4741-b8f1-49e54c0bbfea/download/plot_level.rds
 Description: This dataset contains annual mortality rate values for each permanent plot at each census, of plots with at least three censuses. This dataset is used to calculate the weighted mean annual background mortality rates by forest types, and the series of models to study the trends of annual mortality rates, and then to create Figure 1 and Figure 2.
description: Resource Title: tree_level.RDS
 Size: 2222669 bytes
 Format: application/octet-stream
 URL: https://www.envidat.ch/dataset/9e684bf2-daf1-4662-8425-1196c5dedfbc/resource/4081e017-d05d-47dd-89a4-68a2cd22b4c6/download/tree_level.rds
 Description: This dataset contains tree census data for each permanent plot at each census, of plots with at least two censuses. This dataset is used to model species-specific size-dependent mortality probabilities of the studied tree species, and then to create Figure 3.
description: Resource Title: Mortality_script.Rmd
 Size: 23700 bytes
 Format: application/octet-stream
 URL: https://www.envidat.ch/dataset/9e684bf2-daf1-4662-8425-1196c5dedfbc/resource/d8382129-4275-456c-b062-de2098d676f6/download/mortality_script.rmd
 Description: R markdown document to reproduce the analysis and the plot generation.
DOI: 10.16904/envidat.672
title: Environmental DNA Freshwater Senegal Casamance 2018

description: Monitoring fish diversity through eDNA metabarcoding along the Casamance river
In 2018, water samples were collected in 13 locations along the Casamance in Senegal. Samples were taken either from a boat or by filtering from the side of the river. At each station, two filtration replicates were performed using a peristaltic pump to conduct environmental DNA (eDNA) sampling. Each filtration targeted a maximum duration of 30 min, during which approximately 30 liters of water were filtered through each filtration capsule. After filtration, the water inside the capsules was removed, and the capsules were filled with 50 ml of conservation buffer for preservation at room temperature. We followed strict contamination control protocols throughout both the fieldwork and laboratory processes, adhering to the guidelines of Valentini et al. (2016). To prevent contamination, each sample was processed using disposable gloves and single-use filtration equipment. We use primers for eukaryote and fish. The MiSeq Reagent Kit v3 (2x75 bp) (Illumina, San Diego, CA, USA) was used for paired-end sequencing at a theoretical sequencing depth of 200,000 reads per sample.
Data content: 
 * rawdata/: contains the raw reads for each individual sample. One archive contains the paired-end reads specified by the _R1 or _R2 suffix as well as individually tagged PCR replicates (if available) together with an archive containing all extraction and PCR blank samples of the library. Reads have been demultiplexed using cutadapt but not trimmed, individual demultiplexing tags and primers remain present in the sequences. 
 * taxadata/: contains the table with all detected taxonomy for each sample after bioinformatic processing (see Polanco et al. 2020 for details; https://doi.org/10.1002/edn3.140) and associated field metadata. 
 * metadata/: contains two metadata files, one related to the data collected in the field for each filter, and the second related to the sequencing process in the lab (including the tag sequence, library name, and marker information for each sample)
description: Resource Title: Data access
 Size: 1610612736 bytes
 Format: No Info
 URL: https://envicloud.wsl.ch/#/?bucket=https://envicloud.wsl.ch/edna/&prefix=fw_sn/fw_sn_casama_2018
 Description: Please use cyberduck to download for the moment
DOI: 10.16904/envidat.674
title: Assessing the impacts of climate change on snow avalanche-induced risk in alpine regions

description: By using hazard scenarios based on CH2018 climate projections and the RAMMS avalanche model, we generated large-scale hazard indication maps for future avalanche hazards. By employing the open-source probabilistic risk assessment platform CLIMADA, along with building data and vulnerability functions, we estimated risks for the present time and two future time frames: mid-century (2060) and the end of the century (2085). An uncertainty and sensitivity analysis complemented the study to account for potential fluctuations in model assumptions. The data contains the hazard information and data used for the Climada risk analysis.
description: Resource Title: ATIOCCOSAIRIAR.zip
 Size: 11274289152 bytes
 Format: .zip
 URL: https://os.zhdk.cloud.switch.ch/envicloud/doi/envidat.674/ATIOCCOSAIRIAR.zip
 Description:
DOI: 10.16904/envidat.675
title: A novel approach for bridging the gap between climate change scenarios and avalanche hazard indication mapping

description: To assess the possible consequences of potential changes in snow accumulation and temperature and their impact on avalanche hazard, we introduce a comprehensive multi-step framework. It includes the analysis of climate change scenarios as well as the modeling of future snow covers and the simulation of avalanches in a case study region in central Switzerland.
Using a downscaling and a quantile mapping approach, we considered the high emission RCP8.5 from the CH2018 Swiss climate change scenarios and simulated a potential snow cover of more than 100 future winters with the snow cover model SNOWPACK. Changing snow accumulation and snow cover temperature was taken into account for two future time frames. The changed parameters were used in the RAMMS::EXTENDED avalanche simulation software on large scale.
description: Resource Title: ANAFBTGBCCAAHIM.zip
 Size: 7838315315 bytes
 Format: .zip
 URL: https://os.zhdk.cloud.switch.ch/envicloud/doi/envidat.675/ANAFBTGBCCAAHIM.zip
 Description:
DOI: 10.16904/envidat.682
title: Environmental DNA Freshwater Namibia Namibia 2022

description: Monitoring terrestrial mammals through eDNA in rivers of northern Namibia
In 2022, we collected 20 water samples from 10 stations two rivers of Namibia. Samples were taken from the side of the river. At each station, we performed two filtration replicates using a peristaltic pump to conduct environmental DNA (eDNA) sampling. Each filtration targeted a maximum duration of 30 minutes, during which approximately 30 liters of water were filtered through each capsule. After filtration, the water inside the capsules was removed, and the capsules were filled with 50 ml of conservation buffer for preservation at room temperature. We followed strict contamination control protocols throughout both the fieldwork and laboratory processes, adhering to the guidelines of Valentini et al. (2016). We used eDNA primers targeting bacteria, bivalves, fish, vertebrates (V05) and all Eukaryotes (Euka03). To prevent contamination, each sample was processed using disposable gloves and single-use filtration equipment. The MiSeq Reagent Kit v3 (2x75 bp) (Illumina, San Diego, CA, USA) was used for paired-end sequencing at a theoretical sequencing depth of 200,000 reads per sample.
Data content: 
 * rawdata/: contains the raw reads for each individual sample. One archive contains the paired-end reads specified by the _R1 or _R2 suffix as well as individually tagged PCR replicates (if available) together with an archive containing all extraction and PCR blank samples of the library. Reads have been demultiplexed using cutadapt but not trimmed, individual demultiplexing tags and primers remain present in the sequences. 
 * taxadata/: contains the table with all detected taxonomy for each sample after bioinformatic processing (see Polanco et al. 2020 for details; https://doi.org/10.1002/edn3.140) and associated field metadata. 
 * metadata/: contains two metadata files, one related to the data collected in the field for each filter, and the second related to the sequencing process in the lab (including the tag sequence, library name, and marker information for each sample)
description: Resource Title: Data access
 Size: 2147483648 bytes
 Format: No Info
 URL: https://envicloud.wsl.ch/#/?bucket=https://envicloud.wsl.ch/edna/&prefix=fw_na/fw_na_namibia_2022
 Description: Please use cyberduck to download for now
DOI: 10.16904/envidat.650
title: Priority ranking for the conservation of all European bryophyte species - dataset

description: This dataset provides data on the occurrence of 672 European bryophyte species in European countries or territories. All species which are considered threatened or near threatened according to the European Red List (Hodgetts et al. 2019) are included (553 species). Further, all species evaluated in the European Red List assessed as LC, DD, NE and EX, which at the same time are either endemic, near endemic or globally rare, are included (119 species). Therefore, the list contains not only all European bryophyte species that are threatened or near threatened, but also all species endemic or near endemic to Europe as well as all globally rare species occurring in Europe. For each of the 553 threatened or near threatened species, we provide a conservation a priority score which was calculated based the Red List status and the proportion of the European population of the global population or the global rarity of the species. For details on the prioritisation approach see Bisang et al. (2025).
description: Resource Title: dataset_conservation_priority_european_bryophytes__20250102.xlsx
 Size: 445684 bytes
 Format: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
 URL: https://www.envidat.ch/dataset/979ea1d0-1eda-4ac1-9793-c3734d0da1bb/resource/ad24b591-64d4-4e60-b445-dea5a9f656e8/download/dataset_conservation_priority_european_bryophytes__20250102.xlsx
 Description:
DOI: 10.16904/envidat.685
title: Flow and tracer data for overland flow and topsoil interflow during rainfall simulation experiments in the Studibach catchment - Alptal - Switzerland

description: Description: 
This dataset comprises the time series of overland flow (OF) and topsoil interflow (TIF) discharge, and tracer concentrations during artificial rainfall simulation experiments at two large (-80 m2) trenched runoff plots in the Studibach catchment in the Alptal, a typical pre-Alpine headwater catchment in Switzerland.
One plot is located in a natural clearing in an open mixed forest and the other in a grassland. Together, they represent the dominant land cover types in the region.
We applied streamwater to the surface of the plots using sprinklers and added tracers after OF and TIF had reached steady state. Deuterium enriched water was applied to the surface of the plots via the sprinklers, while Uranine and NaCl were applied as a line tracer at multiple distances from the trench. NaBr was injected into the topsoil at ~20 cm depth. Samples of overland flow and topsoil interflow were collected for several hours after tracer application, while the sprinklers continued to apply water to the surface. The runoff was collected into self-made "Upwelling Bernoulli Tubes" and the water level inside these tubes was measured using pressure sensors (DCX-22-CTD, Keller Druck, Switzerland) at a 1-min resolution during the day and 5-min resolution during the night. Uranine concentrations and electrical conductivity (EC) were recorded at a 1-minute interval. Samples for deuterium and Bromide were analysed in the lab. 
The celerity of overland flow and topsoil interflow was determined during another experiment by temporarily adding more water to the surface of the plots at different distances from the trench after steady state conditions had been reached. The overland flow and topsoil interflow discharge were again measured using the Upwelling Bernoulli Tubes and pressure transducers.
description: Resource Title: plots_runoff_responses_rainfall_experiment.csv
 Size: 67679 bytes
 Format: application/vnd.ms-excel
 URL: https://www.envidat.ch/dataset/66059067-b7b3-494c-b356-01f922afd554/resource/863aef5c-80d7-4e5b-acbd-a8fe538eda3a/download/plots_runoff_responses_rainfall_experiment.csv
 Description:
description: Resource Title: grassland_tracer_experiment_studibach.csv
 Size: 12060 bytes
 Format: application/vnd.ms-excel
 URL: https://www.envidat.ch/dataset/66059067-b7b3-494c-b356-01f922afd554/resource/4e41685f-5a74-45d6-a044-26ca59df33ad/download/grassland_tracer_experiment_studibach.csv
 Description:
description: Resource Title: clearing_tracer_experiment_studibach.csv
 Size: 64438 bytes
 Format: application/vnd.ms-excel
 URL: https://www.envidat.ch/dataset/66059067-b7b3-494c-b356-01f922afd554/resource/01a9c6b2-5159-4e8c-a49a-15bb6416b6cb/download/clearing_tracer_experiment_studibach.csv
 Description: